From bac2fa921a4790787d2804967276f43c23af7495 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 25 Jun 2015 17:44:36 +0200 Subject: [PATCH 001/566] NLopt easyconfig --- .../n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..abf5bbc277 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'NLopt' +version = '2.4.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://ab-initio.mit.edu/nlopt/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/libnlopt.a", "include/nlopt.h"], + 'dirs': [""], +} + +moduleclass = 'numlib' -- GitLab From a8328c3b2e010c31888b1edcf6076d413a5cb3d4 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Fri, 10 Jun 2016 15:21:38 +0200 Subject: [PATCH 002/566] Create NAMD-2.11-intel-2016a-mpi.eb --- .../n/NAMD/NAMD-2.11-intel-2016a-mpi.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb new file mode 100644 index 0000000000..bd27d52f00 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb @@ -0,0 +1,28 @@ +name = 'NAMD' +version = '2.11' +versionsuffix = '-mpi' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +runtest = False + +parallel = 12 + +sources = ['NAMD_%(version)s_Source.tar.gz'] + +dependencies = [ + ('Tcl', '8.6.4'), + ('FFTW', '3.3.4'), +] + +charm_arch = 'mpi-linux-x86_64' + +namd_cfg_opts = " --with-tcl --tcl-prefix $EBROOTTCL " + +prebuildopts = 'echo "TCLLIB=-L\$(TCLDIR)/lib -ltcl8.6 -ldl -lpthread" >> Make.config && ' + +moduleclass = 'chem' -- GitLab From 46c9e87b624824295e678071def0de1b2f262ee3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2016 18:53:26 +0200 Subject: [PATCH 003/566] style fixes for NAMD 2.11 easyconfig --- .../easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb index bd27d52f00..8e28254ee8 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb @@ -3,14 +3,11 @@ version = '2.11' versionsuffix = '-mpi' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'opt': True, 'pic': True, 'usempi': True} - -runtest = False - -parallel = 12 +toolchainopts = {'pic': True, 'usempi': True} sources = ['NAMD_%(version)s_Source.tar.gz'] @@ -19,6 +16,8 @@ dependencies = [ ('FFTW', '3.3.4'), ] +runtest = False + charm_arch = 'mpi-linux-x86_64' namd_cfg_opts = " --with-tcl --tcl-prefix $EBROOTTCL " -- GitLab From a5b2984c569ffdebc1a7d7cb886b439631334e46 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:25:38 +0200 Subject: [PATCH 004/566] add easyconfig MultiQC-0.7-goolf-1.7.20.eb --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb new file mode 100644 index 0000000000..1d864fa9f0 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -0,0 +1,79 @@ +# 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 = 'Bundle' + +name = 'MultiQC' +version = '0.7' + +homepage = 'http://multiqc.info/' +description = """Aggregate results from bioinformatics analyses across many samples into a single report""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': False, 'pic': False} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s'), + ('numpy', '1.10.1', '-Python-%(pyver)s'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('pyparsing', '2.1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('pytz', '2016.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + }), + ('python-dateutil', '2.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + }), + ('PyYAML', '3.12', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', + }), + ('simplejson', '3.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('multiqc', version, { + #'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], + 'LD_LIBRARY_PATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_paths = { + 'files': [], + #'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] + 'dirs': ['.'] +} + +moduleclass = 'bio' -- GitLab From 4d84d1c074fd1ce8e38af2ffb9df37698abb7bd2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:34:56 +0200 Subject: [PATCH 005/566] added missing deps --- ...lotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb | 45 +++++++++++++++++++ ...numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb | 23 ++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..506dad104c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.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': 'goolf', 'version': '1.7.20'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.5.5'), + ('libpng', '1.6.18'), +] + +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/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..b4a5ec30e9 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +#patches = ['numpy-1.8.0-mkl.patch'] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' -- GitLab From 1692d120c89603830a89dac9eb2348d6d1d0f2bf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:43:45 +0200 Subject: [PATCH 006/566] added sanity checking --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 1d864fa9f0..7c5179be13 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -71,9 +71,8 @@ modextrapaths = { } sanity_check_paths = { - 'files': [], - #'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] - 'dirs': ['.'] + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/multiqc-%(version)s-py%(pyshortver)s.egg'] } moduleclass = 'bio' -- GitLab From ad9690f939d7cb1df29891addb2e6ab2bd943116 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:57:10 +0200 Subject: [PATCH 007/566] added missing deps --- .../f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.18-goolf-1.7.20.eb | 19 +++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb new file mode 100644 index 0000000000..c3aab419f3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.18')] + +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-1.6.18-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb new file mode 100644 index 0000000000..a083925f91 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.18' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From 8ade81939c72f037ae59f9f4e7f1f2d16d478740 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 08:58:56 +0200 Subject: [PATCH 008/566] remove toolchainopts --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 7c5179be13..3c54d448e9 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -12,7 +12,6 @@ homepage = 'http://multiqc.info/' description = """Aggregate results from bioinformatics analyses across many samples into a single report""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': False, 'pic': False} parallel = 1 -- GitLab From 516ee8e6c960b2723c9dbb4d86465de772ce7c52 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:00:14 +0200 Subject: [PATCH 009/566] remove numpy dep --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 3c54d448e9..f2c87048d9 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -18,7 +18,7 @@ parallel = 1 dependencies = [ ('Python', '2.7.11'), ('matplotlib', '1.5.1', '-Python-%(pyver)s'), - ('numpy', '1.10.1', '-Python-%(pyver)s'), + # numpy dependency provided by python module ] # this is a bundle of Python packages -- GitLab From 7680debb5c3e01b70ca6fe8e1fd8bfc2572248c8 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:00:43 +0200 Subject: [PATCH 010/566] added version suffix --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index f2c87048d9..14c2e7f378 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -7,6 +7,7 @@ easyblock = 'Bundle' name = 'MultiQC' version = '0.7' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://multiqc.info/' description = """Aggregate results from bioinformatics analyses across many samples into a single report""" -- GitLab From 264450f3c354dc0d322b16b8e4eaa1348b3288ce Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:23:45 +0200 Subject: [PATCH 011/566] file renamed to add suffix --- ...-goolf-1.7.20.eb => MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MultiQC/{MultiQC-0.7-goolf-1.7.20.eb => MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb rename to easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb -- GitLab From 7c1c632123eea66191c8bb8a4a75218f8621dadf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 15:24:30 +0200 Subject: [PATCH 012/566] updated dependencies --- .../f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.21-goolf-1.7.20.eb | 19 +++++++++++++++++ ...lotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb | 4 ++-- 3 files changed, 42 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..76cd412cf3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +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-1.6.21-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb new file mode 100644 index 0000000000..cb4fbebab2 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb index 506dad104c..697a58300b 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb @@ -16,8 +16,8 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.11'), - ('freetype', '2.5.5'), - ('libpng', '1.6.18'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), ] exts_list = [ -- GitLab From 95a8a8ebeb6e358b8ce4ce24a8e6903e5f2421d7 Mon Sep 17 00:00:00 2001 From: edo Date: Thu, 22 Dec 2016 12:58:28 +0100 Subject: [PATCH 013/566] adding easyconfigs: libpciaccess-0.13.4-foss-2016a.eb --- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb index c39482e40c..0baaea5ccf 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'foss', 'version': '2016a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], -- GitLab From 175e23dc49bf0d75743200410f8d726937f306ad Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:27:23 +0100 Subject: [PATCH 014/566] adding easyconfigs: OpenFOAM-4.0-foss-2016b.eb --- .../o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb new file mode 100644 index 0000000000..bf8451bef3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '4.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['294b520811aae87241f3a78423f05952'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + #('METIS', '5.1.0', '-32bitIDX'), + ('SCOTCH', '6.0.4'), + #('Boost', '1.61.0'), + ('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 f45bd6199b3798c3e71822f0dd8a39f9fc37bcc9 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:41:04 +0100 Subject: [PATCH 015/566] Missing dep. --- .../c/CGAL/CGAL-4.8.1-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb new file mode 100644 index 0000000000..20c45dda38 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb @@ -0,0 +1,34 @@ +name = 'CGAL' +version = '4.8.1' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Boost', '1.61.0'), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Eigen', '3.2.9'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' -- GitLab From ffd9e45bc0efcbb849de538cfec749b3bc9979c1 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:50:57 +0100 Subject: [PATCH 016/566] Missing dep. --- .../m/MPFR/MPFR-3.1.4-foss-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb new file mode 100644 index 0000000000..d0abf27110 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.1')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 8ecbcdc8d31f3058a3dca8daa4122933479d7696 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:53:02 +0100 Subject: [PATCH 017/566] Missing dep. --- .../easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb new file mode 100644 index 0000000000..66c30f53b8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From a1158ee3b38aaa61221ad610324a0b35a60831c1 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:54:24 +0100 Subject: [PATCH 018/566] Missing dep. --- .../easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb new file mode 100644 index 0000000000..2e997dc434 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.9' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 15166547d968dd415bcd4ee7ff3afd3c4c87801b Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:34:02 +0100 Subject: [PATCH 019/566] Update Eigen-3.2.9-foss-2016b.eb --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb index 2e997dc434..ce9863f2a8 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb @@ -10,4 +10,4 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -moduleclass = 'math' +moduleclass = 'math' -- GitLab From dc32386174c298a197a322b054861cc680465e9b Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:34:36 +0100 Subject: [PATCH 020/566] Update MPFR-3.1.4-foss-2016b.eb --- easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb index d0abf27110..d9a98da483 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb @@ -23,4 +23,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'math' +moduleclass = 'math' -- GitLab From 8f00294c539073d806560da454b5c50866c9bd0e Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:35:05 +0100 Subject: [PATCH 021/566] Update Qt5-5.7.0-foss-2016b.eb --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb index 66c30f53b8..22b14d640f 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -30,4 +30,4 @@ dependencies = [ ('libGLU', '9.0.0'), ] -moduleclass = 'devel' +moduleclass = 'devel' -- GitLab From 335d827a10dea245843c2417a102742267739caa Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:35:49 +0100 Subject: [PATCH 022/566] Update OpenFOAM-4.0-foss-2016b.eb --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb index bf8451bef3..4f9d282dad 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -1,7 +1,7 @@ name = 'OpenFOAM' version = '4.0' -homepage = 'http://www.openfoam.com/' +homepage = 'http://www.openfoam.org/' 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, @@ -24,7 +24,6 @@ dependencies = [ ('METIS', '5.1.0'), #('METIS', '5.1.0', '-32bitIDX'), ('SCOTCH', '6.0.4'), - #('Boost', '1.61.0'), ('CGAL', '4.8.1'), ('ParaView', '5.1.2', '-mpi'), ] -- GitLab From 9c776b363b36183ecb03badc02d0237d47b49bc0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:37:20 +0100 Subject: [PATCH 023/566] Update CGAL-4.8.1-foss-2016b.eb --- easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb index 20c45dda38..44d057e3a2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb @@ -17,7 +17,7 @@ dependencies = [ ('MPFR', '3.1.4'), ('GMP', '6.1.1'), ('libGLU', '9.0.0'), - ('Qt5', '5.7.0'), + ('Qt', '4.8.7'), ] builddependencies = [ -- GitLab From 4229c6053dfea2329c61f5e83c035753155de94d Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:50:19 +0100 Subject: [PATCH 024/566] Update Qt5-5.7.0-foss-2016b.eb --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb index 22b14d640f..aed1d16c64 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -14,8 +14,6 @@ source_urls = [ ] sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] -patches = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] - builddependencies = [ ('pkg-config', '0.29.1'), ] -- GitLab From 1932c3467cfc0b1758decc73685ce2643f69ce3c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 13 Feb 2017 13:42:55 +0100 Subject: [PATCH 025/566] adding easyconfigs: disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb --- ...iguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..08032c986d --- /dev/null +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,40 @@ +# 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 = "PythonPackage" + +name = 'disambiguate' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/AstraZeneca-NGS/disambiguate" +description = "Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["https://github.com/AstraZeneca-NGS/disambiguate/archive/"] +sources = ["v%(version)s.tar.gz"] + +dependencies = [ + ('Python', '2.7.11'), + ('BamTools', '2.4.0'), + ('zlib', '1.2.8'), + ('Pysam', '0.9.0', versionsuffix), +] + +# this application provides a python implementation and a C++ implementation +# in the postinstallcmds we compile the C++ version +postinstallcmds = ['$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + 'cp disambiguate %(installdir)s/bin/'] + +# workaround to avoid the import sanity check +options = {'modulename': 'os'} + +sanity_check_paths = { + 'files': ['bin/disambiguate.py', 'bin/disambiguate'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 1c7a87a90015a6afb50d6e963021d0888f8661eb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 13 Feb 2017 14:49:40 +0100 Subject: [PATCH 026/566] added bamtools dependency --- .../b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..d0e6af59d8 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb @@ -0,0 +1,16 @@ +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': 'goolf', 'version': '1.7.20'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '2.8.12')] + +files_to_copy = ["bin", "lib", "include", "docs", "LICENSE", "README"] + +moduleclass = 'bio' -- GitLab From 1f87bce8231854d3f77defafd5c9b76e51af0cc6 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 23 Feb 2017 16:32:27 +0000 Subject: [PATCH 027/566] Added an easyconfig with PETSc 3.7.5 and download options rather than relying on existing modules. --- .../PETSc/PETSc-3.7.5-intel-2016a-download.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb new file mode 100644 index 0000000000..a59522d52f --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb @@ -0,0 +1,41 @@ +name = 'PETSc' +version = '3.7.5' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] + +shared_libs = 1 +pic = 1 + +downloadinstall = True + +dependencies = [('HDF5','1.8.18')] + +configopts = "" +# compiles PETSc shared +configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " +configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +# external packages that are downloaded +external_packages = ['mumps', 'ptscotch', 'superlu', 'superlu_dist', 'parmetis', 'metis', 'ml', 'suitesparse', 'hypre', 'prometheus'] +# compiles the external dependencies non-shared +external_packages_shared = "no" +for p in external_packages: + configopts += "--download-%s=yes --download-%s-shared=%s " % (p,p,external_packages_shared) +configopts += "--download-triangle=yes" # download-triangle-shared is not supported + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'numlib' + +modluafooter = """ +family("petsc") +""" + -- GitLab From 32a7e256f1753eb22ef21a3eebe466a03106e429 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 2 Mar 2017 14:04:48 +0800 Subject: [PATCH 028/566] prepare release notes for eb311 --- RELEASE_NOTES | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a240d6d9d8..aa222f795f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,55 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,488 easyconfig files, for 1,152 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.1.1 (March 3rd 2017) +----------------------- + +bugfix release +- added example easyconfig files for 15 new software packages: + - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), + meshio (#4178), miRDeep2 (#4229), OOMPA (#4211), PBSuite (#4230), randfold (#4217), Smoldyn (#4110), + SpiecEasi (#4215), stress (#4180) +- added additional easyconfigs for various supported software packages, including: + - ATK 2.22.0, Armadillo 7.600.2 + 7.800.0, arpack-ng 3.4.0, BLASR 2.2, Bazel 0.4.4, BioPerl 1.7.1, CFITSIO 3.41, + CGAL 4.9, CMake 3.7.2, Cantera 2.3.0, cURL 7.52.1, DMTCP 2.5.0, Eigen 3.2.10 + 3.3.2 + 3.3.3, Emacs 25.1, + ea-utils 1.04.807, freetype 2.7.1, GMP 6.1.2, Graphviz 2.38.0, gettext 0.19.8.1, IPython 5.2.2, JasPer 2.0.10, + Java 1.8.0_121, Lmod 7.3, libQGLViewer 2.6.4, libpng 1.6.27 + 1.6.28, likwid 4.2.0, MCL 02.063 + 14.137, + MCR R2013b + 2014b + R2015b + R2016b, matplotlib 2.0.0, networkx 1.1, OpenSSL 1.1.0e, OrthoMCL 1.4 + 2.0.9, + PCRE 8.40, PyTables 3.2.3.1, Pysam 0.10.0, path.py 10.1, prompt-toolkit 1.0.13, Qt5 5.8.0, ROOT 6.06.02, + SCons 2.5.1, Stacks 1.44, StringTie 1.3.3, sickle 1.33, VTK 7.1.0, ViennaRNA 2.2.3, Vim 8.0, XZ 5.2.3, + Yade 2017.01a +- added easyconfigs for new 'iomkl/2017a' and 'iompi/2017a' toolchains (#4216) +- various enhancements, including: + - clean up dependencies in libdrm (#4113) + - update X11 bundle and dependencies for GCCcore-6.3.0 (#4147) + - fix style in several easyconfigs (#4174, #4176, #4190) +- various bug fixes, including: + - allow intel 2017 to compile (#4102) + - work around build failure with GCC 6 in pkg-config (#4109) + - add Bison and gettext as build deps for X11 (#4111) + - fix ippicv source download and library install in OpenCV (#4126) + - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4135) + - get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146) + - remove duplicate sources specification in OpenMPI (#4150) + - fix definition of buildopts/installopts in Cantera easyconfig (#4164) + - use http rather than ftp source URLs in CFITSIO easyconfigs (#4167) + - fix broken test in Cantera 2.3.0 rather than skipping it (#4177) + - add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179) + - update $PATH in OrthoMCL 1.4 easyconfig (#4182) + - bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a (#4188) + - add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192) + - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) + - set CMAKE_PREFIX_PATH to ncurses install directory (#4196) + - switch to lowopt=True for libxc v2.2.* and v3.* (#4199) + - remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200) + - fix version (& homepage) in ea-utils easyconfigs (#4205) + - remove --with-threads configure option in OpenMPI-2.* (#4213) + - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) + - fix check for Szip library in configure script for netCDF 4.1.3 (#4226) +- fix source_urls in several easyconfigs, including: + - bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227) + + v3.1.0 (February 3rd 2017) -------------------------- -- GitLab From 05ffcaa5c995fd346fa6b373b604412834c14637 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 2 Mar 2017 11:47:37 +0100 Subject: [PATCH 029/566] fix missing PYTHONPATH --- .../r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb index 81755cd856..6bb0455477 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb @@ -42,4 +42,6 @@ configopts += '-Doracle=OFF -Dpgsql=OFF -Dqt=OFF -Dsqlite=OFF ' configopts += '-Dcxx14=ON ' configopts += '-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON ' +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 97c578af87d9a9e16dd112cb980d70451d127f0a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 2 Mar 2017 13:35:05 +0100 Subject: [PATCH 030/566] rootpy-foss-2016a-python-2.7.11 --- .../rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a81bc6e8ba --- /dev/null +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'rootpy' +version = '0.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.rootpy.org/' + +description = """The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with +ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to +improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a +multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface +between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate +your data and to take advantage of these alternatives if needed.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/rootpy/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), + ('ROOT','v6.08.02','-Python-%(pyver)s'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s') +] + +options = {'modulename': 'os'} + +#sanity_check_paths = { +# 'files': ['bin/quast.py'], +# 'dirs': [''], +#} + +moduleclass = 'bio' -- GitLab From 0853a413d724c2ae3d24353a42abaf97d635f6f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Thu, 2 Mar 2017 16:30:31 +0100 Subject: [PATCH 031/566] add tmux-2.3 --- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 26 ++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-2.3.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb new file mode 100644 index 0000000000..d9aa356199 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '2.3' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily +between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.1.8'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 66e53395be9c6c3a6e823fa9066ae6f810fff67c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Thu, 2 Mar 2017 16:40:48 +0100 Subject: [PATCH 032/566] add libevent-2.1.8.eb --- .../easyconfigs/l/libevent/libevent-2.1.8.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb new file mode 100644 index 0000000000..964ec6943d --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.8' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://github.com/downloads/%(name)s/%(name)s/', + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +moduleclass = 'lib' -- GitLab From 051a170864a0a07b45d308ce35ef14a1dcb31137 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 3 Mar 2017 11:00:50 +0100 Subject: [PATCH 033/566] sanity check fix --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index a81bc6e8ba..d40917cf4c 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -24,11 +24,9 @@ dependencies = [ ('matplotlib', '1.5.1', '-Python-%(pyver)s') ] -options = {'modulename': 'os'} - -#sanity_check_paths = { -# 'files': ['bin/quast.py'], -# 'dirs': [''], -#} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} moduleclass = 'bio' -- GitLab From ce387d60825aa0b2ff37fe5c1b7e1a110a0a9a7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 11:40:22 +0100 Subject: [PATCH 034/566] @boegel change too long line into tmux, fix sources libevent and added sanity_check_paths to libevent --- easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb | 13 +++++++++++-- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 3 ++- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb index 964ec6943d..369e68366a 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -11,9 +11,18 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'https://github.com/downloads/%(name)s/%(name)s/', - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', + 'https://downloads.sourceforge.net/project/levent/release-%(version)s-stable/', ] + sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['f3eeaed018542963b7d2416ef1135ecc'] + +sanity_check_paths = { + 'files': ["bin/event_rpcgen.py"] + + ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]] + + ['include/event2/%s' % x for x in ['buffer_compat.h', 'bufferevent.h', 'bufferevent_struct.h', 'dns_compat.h', 'dns_struct.h', 'event-config.h', 'event_struct.h', 'http.h', 'keyvalq_struct.h', 'rpc_compat.h', 'rpc_struct.h', 'tag.h', 'util.h', 'bufferevent_compat.h', 'bufferevent_ssl.h', 'buffer.h', 'dns.h', 'event_compat.h', 'event.h', 'http_compat.h', 'http_struct.h', 'listener.h', 'rpc.h', 'tag_compat.h', 'thread.h', 'visibility.h']], + 'dirs': ["lib"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb index d9aa356199..d8ea21b236 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -5,7 +5,8 @@ version = '2.3' homepage = 'http://tmux.sourceforge.net/' description = """tmux is a terminal multiplexer. It lets you switch easily -between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" +between several programs in one terminal, detach them (they keep +running in the background) and reattach them to a different terminal.""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'optarch': True} -- GitLab From 1ad34056480aec11dbfb1667b72b1e37fc15e4dc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 12:40:44 +0200 Subject: [PATCH 035/566] adding easyconfigs: GROMACS-2016.2-foss-2017a.eb --- .../g/GROMACS/GROMACS-2016.2-foss-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb new file mode 100644 index 0000000000..5a3fc10eef --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -0,0 +1,36 @@ +## +# 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 +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.2' + +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. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.6.2'), +] + +moduleclass = 'bio' -- GitLab From 3fb14327fb696d1717d7cde894e720db5dbd2de3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:28:54 +0100 Subject: [PATCH 036/566] add eb Singularity-2.2.1-GCC-6.3.0-2.27.eb next step chown root:root /apps/all/Singularity/*/etc/singularity/singularity.conf chown root:root /apps/all/Singularity/*/libexec/singularity/sexec-suid chmod +s /apps/all/Singularity/*/libexec/singularity/sexec-suid --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..e11fd1f16c --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '2.2.1' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], + 'dirs': ['etc', '', 'libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From 68865c34f791fa80abd0ba566daed7de531c3761 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:35:36 +0100 Subject: [PATCH 037/566] move sanity_check_paths - files -> dirs ... libevents --- easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb index 369e68366a..41eaa5ab15 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -21,8 +21,8 @@ checksums = ['f3eeaed018542963b7d2416ef1135ecc'] sanity_check_paths = { 'files': ["bin/event_rpcgen.py"] + - ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]] + - ['include/event2/%s' % x for x in ['buffer_compat.h', 'bufferevent.h', 'bufferevent_struct.h', 'dns_compat.h', 'dns_struct.h', 'event-config.h', 'event_struct.h', 'http.h', 'keyvalq_struct.h', 'rpc_compat.h', 'rpc_struct.h', 'tag.h', 'util.h', 'bufferevent_compat.h', 'bufferevent_ssl.h', 'buffer.h', 'dns.h', 'event_compat.h', 'event.h', 'http_compat.h', 'http_struct.h', 'listener.h', 'rpc.h', 'tag_compat.h', 'thread.h', 'visibility.h']], - 'dirs': ["lib"] + ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]], + 'dirs': ["lib", "include/event2"] +} moduleclass = 'lib' -- GitLab From 2d1a8eba2da61b56a08904c302d3279ddeeb3408 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:55:21 +0100 Subject: [PATCH 038/566] remove '', --- .../s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb index e11fd1f16c..e1e43de48b 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -17,7 +17,7 @@ preconfigopts = './autogen.sh && ' sanity_check_paths = { 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], - 'dirs': ['etc', '', 'libexec/singularity'], + 'dirs': ['etc', 'libexec/singularity'], } moduleclass = 'tools' -- GitLab From b025dbb557c46605389c3ff16f68b965d5ec6c79 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 14:18:57 +0200 Subject: [PATCH 039/566] Forgot to add dependency, CMake 3.6.2. --- .../c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f496787852 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +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': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.27'), +] + + +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', '1.1.0c'), +] + +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 c5582a708e0fdffca7f963810101a93be63047f4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 17:31:17 +0200 Subject: [PATCH 040/566] Updated dependency for Gromacs to CMake 3.7.2. Fixed missing parts in CMake 3.6.2 config. --- easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb index f496787852..50e2df64aa 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), @@ -29,7 +29,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb index 5a3fc10eef..8ad8f765c7 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -30,7 +30,7 @@ source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('CMake', '3.6.2'), + ('CMake', '3.7.2'), ] moduleclass = 'bio' -- GitLab From ee8d9018a1381e77be204e32195d29de9268fc3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Mar 2017 11:40:34 +0100 Subject: [PATCH 041/566] complete release notes for v3.1.1 & bump version --- RELEASE_NOTES | 46 ++++++++++++++++++---------------------------- setup.py | 2 +- 2 files changed, 19 insertions(+), 29 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index aa222f795f..060a0725f1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,53 +3,43 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,488 easyconfig files, for 1,152 different software packages, +The latest version of easybuild-easyconfig provides 6,643 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.1 (March 3rd 2017) +v3.1.1 (March 6th 2017) ----------------------- bugfix release -- added example easyconfig files for 15 new software packages: +- added example easyconfig files for 16 new software packages: - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), - meshio (#4178), miRDeep2 (#4229), OOMPA (#4211), PBSuite (#4230), randfold (#4217), Smoldyn (#4110), - SpiecEasi (#4215), stress (#4180) + meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246), + Smoldyn (#4110), SpiecEasi (#4215), stress (#4180) - added additional easyconfigs for various supported software packages, including: - - ATK 2.22.0, Armadillo 7.600.2 + 7.800.0, arpack-ng 3.4.0, BLASR 2.2, Bazel 0.4.4, BioPerl 1.7.1, CFITSIO 3.41, - CGAL 4.9, CMake 3.7.2, Cantera 2.3.0, cURL 7.52.1, DMTCP 2.5.0, Eigen 3.2.10 + 3.3.2 + 3.3.3, Emacs 25.1, - ea-utils 1.04.807, freetype 2.7.1, GMP 6.1.2, Graphviz 2.38.0, gettext 0.19.8.1, IPython 5.2.2, JasPer 2.0.10, - Java 1.8.0_121, Lmod 7.3, libQGLViewer 2.6.4, libpng 1.6.27 + 1.6.28, likwid 4.2.0, MCL 02.063 + 14.137, - MCR R2013b + 2014b + R2015b + R2016b, matplotlib 2.0.0, networkx 1.1, OpenSSL 1.1.0e, OrthoMCL 1.4 + 2.0.9, - PCRE 8.40, PyTables 3.2.3.1, Pysam 0.10.0, path.py 10.1, prompt-toolkit 1.0.13, Qt5 5.8.0, ROOT 6.06.02, - SCons 2.5.1, Stacks 1.44, StringTie 1.3.3, sickle 1.33, VTK 7.1.0, ViennaRNA 2.2.3, Vim 8.0, XZ 5.2.3, - Yade 2017.01a -- added easyconfigs for new 'iomkl/2017a' and 'iompi/2017a' toolchains (#4216) + - binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0, + PCRE 8.40, Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 2017.01a +- added new easyconfigs for existing toolchains: + - iomkl/2017a (#4216), intel/2017.02 (#4248) - various enhancements, including: - - clean up dependencies in libdrm (#4113) - - update X11 bundle and dependencies for GCCcore-6.3.0 (#4147) - - fix style in several easyconfigs (#4174, #4176, #4190) + - fix style in several easyconfigs (#4174, #4176, #4190, #4233) + - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) + - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) - various bug fixes, including: - - allow intel 2017 to compile (#4102) - - work around build failure with GCC 6 in pkg-config (#4109) - add Bison and gettext as build deps for X11 (#4111) - - fix ippicv source download and library install in OpenCV (#4126) - - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4135) + - clean up dependencies in libdrm (#4113) + - make sure Ghostscript picks up external libraries (#4118) + - fix ippicv source download and library install for OpenCV v3.1.0 (#4126) + - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4134, #4135) - get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146) - remove duplicate sources specification in OpenMPI (#4150) - - fix definition of buildopts/installopts in Cantera easyconfig (#4164) + - fix definition of buildopts/installopts in Cantera easyconfig (#4133, #4164, #4177) - use http rather than ftp source URLs in CFITSIO easyconfigs (#4167) - - fix broken test in Cantera 2.3.0 rather than skipping it (#4177) - add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179) - - update $PATH in OrthoMCL 1.4 easyconfig (#4182) - - bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a (#4188) - add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192) - - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) - - set CMAKE_PREFIX_PATH to ncurses install directory (#4196) + - set CMAKE_PREFIX_PATH to ncurses install directory in CMake easyconfigs (#4196) - switch to lowopt=True for libxc v2.2.* and v3.* (#4199) - remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200) - fix version (& homepage) in ea-utils easyconfigs (#4205) - remove --with-threads configure option in OpenMPI-2.* (#4213) - - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) - fix check for Szip library in configure script for netCDF 4.1.3 (#4226) - fix source_urls in several easyconfigs, including: - bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227) diff --git a/setup.py b/setup.py index a3f5efb8ac..2cd1801e1b 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 = '3.1.0' +VERSION = '3.1.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 7b15ed20fa7b321bb2ef12657e381d1a1c57bc8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 6 Mar 2017 08:00:12 +0100 Subject: [PATCH 042/566] 'dummy' -> '' --- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb index d8ea21b236..0423702965 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -8,7 +8,7 @@ description = """tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -- GitLab From bb62863e09d4935fe68e96b4055e023014bd2e5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 11:39:09 +0100 Subject: [PATCH 043/566] adding easyconfigs: SPAdes-3.10.1-foss-2016b.eb --- .../s/SPAdes/SPAdes-3.10.1-foss-2016b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb new file mode 100644 index 0000000000..c4ecdeaede --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -0,0 +1,47 @@ +# 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 = '3.10.1' + +homepage = 'http://cab.spbu.ru/software/spades/' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Boost', '1.63.0', '-Python-2.7.12'), +] + +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 08689b0d378055ebfe07de920e6a08974761792f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 13:25:09 +0100 Subject: [PATCH 044/566] add easyconfig for missing CMake dep --- .../c/CMake/CMake-3.7.2-foss-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb new file mode 100644 index 0000000000..1d41f93b9b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +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 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +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 ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ff49dc26d982489ed1ade8b1e5fd821c2dc239d6 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 6 Mar 2017 14:28:40 +0100 Subject: [PATCH 045/566] add sanity check python module --- .../r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb index 6bb0455477..902a9ecafd 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb @@ -42,6 +42,8 @@ configopts += '-Doracle=OFF -Dpgsql=OFF -Dqt=OFF -Dsqlite=OFF ' configopts += '-Dcxx14=ON ' configopts += '-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON ' +sanity_check_commands = ["python -c 'import ROOT'"] + modextrapaths = {'PYTHONPATH': 'lib/'} moduleclass = 'data' -- GitLab From de7e657c88579abd4e19329524edce969ff8dce6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 6 Mar 2017 18:47:52 +0100 Subject: [PATCH 046/566] adding easyconfigs: awscli-1.11.56-foss-2016b-Python-2.7.12.eb --- ...awscli-1.11.56-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..729a10008f --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'awscli' +version = '1.11.56' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'foss', '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 adfd421614f445e8fb39495272de39760de504d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 18:57:47 +0100 Subject: [PATCH 047/566] {lang}[intel/2017a] Python v2.7.13 --- .../g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb | 31 ++++ .../libreadline-7.0-GCCcore-6.3.0.eb | 33 +++++ .../p/Python/Python-2.7.13-intel-2017a.eb | 133 ++++++++++++++++++ .../p/Python/numpy-1.12.0-mkl.patch | 55 ++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb | 30 ++++ 5 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..046f2d1718 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +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': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('binutils', '2.27'), + ('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/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a64400af8e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '7.0' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +builddependencies = [('binutils', '2.27')] +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/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb new file mode 100644 index 0000000000..31e0d3d932 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -0,0 +1,133 @@ +name = 'Python' +version = '2.7.13' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated March 6th 2017 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('Cython', '0.25.2', { + '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', '2.6.0', { + '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', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch new file mode 100644 index 0000000000..3d09924f96 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch @@ -0,0 +1,55 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py +--- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 +@@ -675,7 +675,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -756,6 +756,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py +--- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 +@@ -123,3 +123,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9dca9f6e5c --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From cf160c44110226e8f37de1d8e3e235af08a0a369 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 08:55:17 +0100 Subject: [PATCH 048/566] bump easyconfig files count in release notes --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 060a0725f1..1c930d74fe 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,643 easyconfig files, for 1,168 different software packages, +The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.1.1 (March 6th 2017) -- GitLab From 36877ded32473a03edb33e9d27e99a7f498fc7e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 08:57:52 +0100 Subject: [PATCH 049/566] fix release date for EasyBuild v3.1.1 --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1c930d74fe..96a76caa5a 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.1 (March 6th 2017) +v3.1.1 (March 7th 2017) ----------------------- bugfix release -- GitLab From 533a573a1c8455697a72bd8883503a86c13bf7c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 15:21:30 +0100 Subject: [PATCH 050/566] bump version to 3.2.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 2cd1801e1b..0683e432c9 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 = '3.1.1' +VERSION = '3.2.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From fde809e0021a1eb648084501f5b8c547cdd255f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 16:24:48 +0100 Subject: [PATCH 051/566] adding easyconfigs: EasyBuild-3.1.1.eb --- .../e/EasyBuild/EasyBuild-3.1.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb new file mode 100644 index 0000000000..2dbc7fa9ba --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.1.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/ef/c7/640c6d791ba452321c0d1371b6626486bb495e0645bb896d33c78a09f810', + # vsc-base + 'https://pypi.python.org/packages/da/90/ee40b1a6a5bfed24139042c737500a9b45db0373a6735e76481fc860fe37', + # easybuild-framework + 'https://pypi.python.org/packages/f2/19/1c79b1ad24f0004e9507f12d4222367611f42ac479abd6315a50a23c52f5', + # easybuild-easyblocks + 'https://pypi.python.org/packages/87/aa/2a19f05c78dd2550f7bd42ef0964b9c51c5626c1e715c2ee0a4f778780b8', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/e6/68/5e977f549bf04b8cd87cdc5179d8b36c1eb971cfe3c43f98053f2dbe9c64', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.25.tar.gz', + 'vsc-base-2.5.7.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 65002095722c407e0105a5f67bb6950a788793c4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 11:08:55 +0800 Subject: [PATCH 052/566] yet another batch of minor style fixes --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb | 3 ++- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb | 3 ++- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb | 3 ++- .../a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb | 3 +-- easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb | 3 +-- ...-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb | 2 +- .../Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb | 2 +- ...6.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb | 5 ++++- .../easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb | 5 +++-- 23 files changed, 57 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb index 094f648512..1b2933e3ca 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.12.1' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb index f899ce8f01..e7d7f8108e 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.13.5' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb index 2063066a88..77fcbc5c08 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.14.1' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb index bde2863301..6fb42921f6 100644 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb index 0e9c615ba9..70205ebf3a 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb @@ -15,7 +15,6 @@ sources = ['advisor_xe_%(version)s.tar.gz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb index 22d5bebaad..6e2edca0dc 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -17,7 +17,6 @@ checksums = ['af87b381394be3100507827a3461b3bc'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' 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 4e451954c3..4e75833d6e 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 @@ -3,7 +3,7 @@ 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]) +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 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 f910ba5400..b2fcc5fada 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 @@ -3,7 +3,7 @@ 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]) +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 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 1b29f57d52..8895c479d8 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 @@ -3,7 +3,7 @@ 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]) +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 diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb index 3d86e53a57..552c3eb907 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb @@ -4,7 +4,10 @@ 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.""" +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': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb index 1e344106ca..612bf18994 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb @@ -4,7 +4,10 @@ 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.""" +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': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb index 69f6af4aa8..ffe0aa3aaf 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.8.4' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb index ed48c65191..f37d535fe6 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.8.4' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb index 4e4944c69e..7a79bafbc3 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.0' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb index b01a6297fc..ab777254e9 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.0' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb index ad986bd576..03ba48168e 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.3' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb index e1662e8bf2..986e3e5a6f 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.3' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb index 7da7aa32db..6036bb0be8 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.6' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb index 3ee7c5b406..d51a118fba 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb index d93ecdb14e..0e7df6fdf1 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb index b048fcd097..33aa30131b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.6' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb index 407fa7e1c0..0f10c1689b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb index 08bcaf86cf..f22f0e01b7 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} -- GitLab From 645b2a7dc2bad09463a04674595d23417da5a78c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 11:30:46 +0800 Subject: [PATCH 053/566] yet another batch of minor style fixes --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 2 +- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 2 +- .../easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb | 5 +++-- .../b/BCFtools/BCFtools-1.2-intel-2015a.eb | 3 ++- .../easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 3 ++- .../b/BCFtools/BCFtools-1.3-intel-2016a.eb | 3 ++- .../easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb | 6 +++--- easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb | 3 ++- .../b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb | 3 ++- easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb | 3 ++- .../easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 3 ++- .../b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb | 1 - .../easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb | 11 +++++------ .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 6 ++---- easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb | 2 +- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- .../BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 1 - .../Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Biopython-1.65-foss-2016a-Python-2.7.11.eb | 3 ++- .../Biopython-1.68-foss-2016b-Python-2.7.12.eb | 3 ++- .../Biopython-1.68-intel-2016b-Python-2.7.12.eb | 3 ++- .../Biopython-1.68-intel-2016b-Python-3.5.2.eb | 3 ++- .../Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb | 2 +- .../easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb | 4 ++-- .../easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb | 4 ++-- .../b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 9 +++------ .../b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb | 9 +++------ 30 files changed, 56 insertions(+), 53 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 76e04042bc..938cb4bc7e 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'foss', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_66' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index d1646b7dbe..83c91ab617 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'foss', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_74' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index 7e9be8c9b6..52eabb1bfe 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -10,7 +10,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] dependencies = [('Java', '1.8.0_112', '', True)] diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb index 2ee4f62216..3ef62f1ae2 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb @@ -4,8 +4,9 @@ name = 'BCFtools' version = '1.2' homepage = 'http://www.htslib.org/' -description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index f9319eca14..41baab6d42 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -5,7 +5,8 @@ version = '1.2' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index 6d469bdd3b..a0b589e82c 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -5,7 +5,8 @@ version = '1.3' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb index bd1b04228a..af2dc1fef7 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb @@ -5,7 +5,8 @@ version = '1.3' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb index 47aaf73fa3..4ed43caefd 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb @@ -27,9 +27,9 @@ parallel = 1 files_to_copy = ["bin"] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed", - "starchcat", "vcf2bed", "wig2bed", - "gtf2bed", "bedops", "wig2bed"]], + 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed", "sort-bed", + "starchcat", "vcf2bed", "wig2bed", + "gtf2bed", "bedops", "wig2bed"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb index afbf2938b8..eb88b061dd 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb index e2d58bafb6..0222da1546 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb index 5f6044dcec..955ee61e30 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 9cbb01f191..2dbdeeb980 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA -# Authors:: George Tsouloupas , Fotis Georgatos , Daniel Navarro +# Authors:: George Tsouloupas , Fotis Georgatos , +# Daniel Navarro # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb index 9cd875e7c6..c0802f9ddd 100644 --- a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb +++ b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb index e948c06e11..65f14b74d8 100644 --- a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb @@ -25,12 +25,11 @@ start_dir = 'sources' parallel = 1 -files_to_copy = [(['sources/g_baypass'], 'bin/'), - 'BayPass_manual_2.1.pdf', - 'examples', - 'Licence_CeCILL-B_V1-en.txt', - 'utils' -] +files_to_copy = [(['sources/g_baypass'], 'bin/'), + 'BayPass_manual_2.1.pdf', + 'examples', + 'Licence_CeCILL-B_V1-en.txt', + 'utils'] sanity_check_paths = { 'files': ['bin/g_baypass'], diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 20f57806c7..0d36886635 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -4,9 +4,7 @@ name = 'BayesAss' version = '3.0.4' homepage = 'http://www.rannala.org/?page_id=245' -description = """ -BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes -""" +description = "BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes" toolchain = {'name': 'foss', 'version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] @@ -21,7 +19,7 @@ runtest = 'check' sanity_check_paths = { 'files': ['bin/BA3'], - 'dirs' : ['bin', 'include'] + 'dirs': ['bin', 'include'] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index 972161d135..283940594d 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -18,7 +18,7 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o toolchain = {'name': 'dummy', 'version': ''} -source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] +source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] sources = ['BEASTv%(version)s.tgz'] dependencies = [ diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 5afb842c80..ff35b3fe93 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2 installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+prog+'.'+flavor+'.x' + 'files': ['bin/' + prog + '.' + flavor + '.x' for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 9d064dae20..0f2dfc0807 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2 installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+prog+'.'+flavor+'.x' + 'files': ['bin/' + prog + '.' + flavor + '.x' for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 2661f0fe38..c32f54aa1d 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -37,4 +37,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb index a3dca17749..26ff0e4f6a 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb index 5efa64f0e0..462ab92f17 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index a42f248efe..c5aa94f58c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb index 1c5fd3f356..f5a410bf23 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## 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 index 953304846e..762f84f558 100644 --- 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 @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## 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 index b22f51705c..36d03b946c 100644 --- 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 @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb index b906f81abf..24c748d95f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb @@ -18,7 +18,7 @@ pythonversion = '2.7.11' versionsuffix = '-Python-%s' % pythonversion dependencies = [ - ('bzip2', '1.0.6' ), + ('bzip2', '1.0.6'), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb index 95d2b2fb64..bcb89c1b4e 100644 --- a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb @@ -19,8 +19,8 @@ builddependencies = [('CMake', '3.5.2')] configopts = "-DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] - + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x, SHLIB_EXT) for x in ['Collision', 'Dynamics']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb index d23fa88f57..dce0112a41 100644 --- a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb @@ -19,8 +19,8 @@ builddependencies = [('CMake', '3.5.2')] configopts = "-DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] - + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x, SHLIB_EXT) for x in ['Collision', 'Dynamics']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb index 29785ed5e6..49900e2203 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -2,12 +2,9 @@ easyblock = 'ConfigureMake' name = 'beagle-lib' version = '2.1.2' -homepage= 'https://github.com/beagle-dev/beagle-lib' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb index ba27dc855d..eb31afb551 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -3,12 +3,9 @@ easyblock = 'ConfigureMake' name = 'beagle-lib' version = '2.1.2' -homepage= 'https://github.com/beagle-dev/beagle-lib' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From cb34f841946cc8f5be8a95031e763e7c2ddc4c9d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 14:41:26 +0800 Subject: [PATCH 054/566] yet another batch of minor style fixes --- .../easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb | 14 +++++++------- easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb | 3 ++- .../easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb | 3 ++- .../CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb | 5 +++-- .../CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb | 9 ++++----- .../Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 3 ++- .../Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb | 3 ++- .../Cython-0.24.1-foss-2016a-Python-2.7.11.eb | 3 ++- 14 files changed, 37 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb index fbd1e0f85d..137bbb1603 100644 --- a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb @@ -4,13 +4,13 @@ name = 'CLooG' version = '0.18.1' homepage = 'http://www.bastoul.net/cloog/index.php' -description = """CLooG is a free software and library to generate code for scanning Z-polyhedra. -That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. -CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. -Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best -polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user -has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code. -""" +description = """CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a + code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. CLooG has been + originally written to solve the code generation problem for optimizing compilers based on the polytope model. + Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the + best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While + the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a + very effective code.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb index 299410b70c..8997152413 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb @@ -36,7 +36,8 @@ elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION else: - print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % (OS_NAME, OS_VERSION) + OS = (OS_NAME, OS_VERSION) + print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % OS system = 'ubuntu11.10' elif OS_NAME == "opensuse": system = 'suse12.1' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb index 9b2a072f8b..194a2991a9 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb @@ -36,7 +36,8 @@ elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION else: - print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % (OS_NAME, OS_VERSION) + OS = (OS_NAME, OS_VERSION) + print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % OS system = 'ubuntu11.10' elif OS_NAME == "opensuse": system = 'suse12.1' diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb index 071eb0169f..e06141ece5 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb @@ -5,8 +5,9 @@ version = '1.1.5' homepage = 'http://abel.ee.ucla.edu/cvxopt/' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. -Its main purpose is to make the development of software for convex optimization applications straightforward -by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.""" + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb index 3e32468f92..795f2f0360 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb @@ -5,8 +5,9 @@ version = '1.1.5' homepage = 'http://abel.ee.ucla.edu/cvxopt/' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. - Its main purpose is to make the development of software for convex optimization applications straightforward - by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.""" + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb index 112a9312bc..8f554a1eb2 100644 --- a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -9,11 +9,10 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-pgi module. toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version - ('PrgEnv-pgi', EXTERNAL_MODULE), - ('pgi/16.3.0' , EXTERNAL_MODULE), - ('cray-mpich/7.3.2', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-pgi', EXTERNAL_MODULE), + ('pgi/16.3.0', EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb index fa53744e7c..e22250c990 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.16' 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.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb index f2fb277465..33b4c1bc5b 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.16' 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.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb index 0e8ac631d0..ec51d696a0 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.19.1' 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.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb index 6ba8ee3375..1cdbf2c1fc 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.19.1' 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.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb index 80955e4cc6..8494b353e5 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb @@ -5,7 +5,8 @@ version = '0.19.2' 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.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 1a87b1c99c..769f55ce72 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.22' 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.""" +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb index 426fedf887..dd9fc1ad56 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb @@ -6,7 +6,8 @@ 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.""" +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} 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 index a2db0bddbe..0dfcb1056b 100644 --- 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 @@ -6,7 +6,8 @@ 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.""" + 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'} -- GitLab From b2c06bc2d82e3c1e666cff29ade846e11e5eade3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 14:59:09 +0800 Subject: [PATCH 055/566] yet another batch of minor style fixes --- easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb | 2 +- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 1 - easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 3 ++- easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb | 3 ++- easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 3 ++- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 3 ++- easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb | 1 - easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb | 1 - easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 2 +- 10 files changed, 11 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb index fcf1bd7696..b1a5625761 100644 --- a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb @@ -15,4 +15,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 8c069fec94..03f4831ace 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'data' - 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 index 7071afdb2c..c041d6e2aa 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -16,7 +16,8 @@ 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']] + + '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'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index 0940c66fb5..e933c1af39 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -16,7 +16,8 @@ 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']] + + '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'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index f322881382..74d90eb777 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -16,7 +16,8 @@ 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']] + + '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'] } diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 99e680c26d..389f7d8425 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -4,7 +4,8 @@ name = 'DFT-D3' version = '3.1.1' homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' -description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb index 597de0792e..04e4fd7a51 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb index 3f64420e2e..1687e9b44d 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index ed4f3f692d..3d7e8e50d6 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -23,7 +23,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] +files_to_copy = [(['drfast'], 'bin'), "README.txt"] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 3f01a8dfb9..33794a918d 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -23,7 +23,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] +files_to_copy = [(['drfast'], 'bin'), "README.txt"] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], -- GitLab From 7573dd7036cbb7fd602b4a4c786a4b6c924b0413 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 15:06:39 +0800 Subject: [PATCH 056/566] yet another batch of minor style fixes --- .../e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb | 12 ++++++------ .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 3 ++- .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 3 ++- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb index 6b962c6687..a429626ec5 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb @@ -11,12 +11,12 @@ name = 'EIGENSOFT' version = '6.1.1' homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' -description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) - and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components - analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; - the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, - minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in - plotting script and supports multiple file formats and quantitative phenotypes.""" +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. + 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal + components analysis to explicitly model ancestry differences between cases and controls along continuous axes of + variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral + populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT + package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index 89cd537fc7..5d29ad3201 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -23,7 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +configopts += 'LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index bbbc8c56b4..b5d3e358e9 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -23,7 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +configopts += 'LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' -- GitLab From b9e4dd100da43895e59db82f464b1e4c11a84ce8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 08:43:10 +0100 Subject: [PATCH 057/566] adding easyconfigs: PGI-17.1-GCC-6.3.0-2.27.eb --- .../p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..6502b349fb --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '17.1' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['836f536ad8b0aac0234f7528fbd56b62'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From ebd527a224dce1fa117b30a94a8f5fd5ab75a0fc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 16:15:51 +0800 Subject: [PATCH 058/566] yet another batch of minor style fixes --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 2 +- easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb | 6 +++--- .../easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb | 3 ++- easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb | 3 ++- .../f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb | 3 ++- 25 files changed, 50 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb index c1501d5c82..cb997fa593 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb index 6b9a39e112..31a89c0085 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb @@ -2,7 +2,8 @@ # 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 +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb index d7d711211d..aee9c310da 100644 --- a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), ('HDF5', '1.8.16'), -# ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile + # ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile ] # define hardware platform to be 'parallel intel compiler, 64 bit, use scalapack') diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb index 59de3272db..1788c8a21a 100644 --- a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb @@ -9,9 +9,9 @@ name = 'Firefox' version = '44.0.2' homepage = 'https://www.mozilla.org/en-US/firefox/new/' -description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code - base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy - and security measures, smart searching, and RSS live bookmarks.""" +description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the + Mozilla code base and offers customization options and features such as its capability to block pop-up windows, + tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb index 09e345ac68..7e51dd88f4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb @@ -13,7 +13,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb index f0c8e977f8..bcf6608413 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb @@ -12,7 +12,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb index dafae024b0..916f1302f2 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb @@ -13,7 +13,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb index 93ed64ef31..26eaffc5f6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb @@ -12,7 +12,8 @@ source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb index c7a87aa9ac..cbbe1daafc 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb index 5fa7fbc89e..a5e70027fa 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb index 6af71f85ba..8fa382b0ca 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb index 7424371c29..0571a145ad 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.9')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb index 1840f18b99..cea107f292 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb index cf4ca6186c..9b0aae30b7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb index 68312d108d..45d6dc8e93 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb index e9f0fd7c95..c9b6e770b4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb index 5eb7f91b58..07f4f8160c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb index ca24a618dc..44080cb0f8 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb index 8978812458..7cfa18b2f4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb index af7228f4f5..78c7fb98d6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb index 316e040e08..4cf88e23a7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb index 32b12425a8..8405a0ec93 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb @@ -16,7 +16,8 @@ versionsuffix = '-libpng-%s' % libpngver dependencies = [('libpng', libpngver)] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb index 0913227caf..9c9d2b2e08 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.18')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb index 32c4b9ab5c..bbfd2a2508 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.20')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb index 54449d2405..912f826139 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } -- GitLab From 16127fff4d6a6db5774b196d529850bdf34fc427 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 09:21:20 +0100 Subject: [PATCH 059/566] revert back to using shipped Boost for SPAdes 3.10.1, since Boost version difference is too big --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb index c4ecdeaede..6e5c9aeb32 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -20,10 +20,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://cab.spbu.ru/files/release%(version)s'] sources = [SOURCE_TAR_GZ] -builddependencies = [ - ('CMake', '3.7.2'), - ('Boost', '1.63.0', '-Python-2.7.12'), -] +builddependencies = [('CMake', '3.7.2')] dependencies = [ ('zlib', '1.2.8'), -- GitLab From fc7300777ea6b8d9938c626e0f3642a3f7e4119b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 16:45:11 +0800 Subject: [PATCH 060/566] yet another batch of minor style fixes --- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb | 3 ++- easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb | 1 - .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb | 4 ++-- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb | 4 ++-- .../g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb | 4 ++-- .../easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb | 4 ++-- .../easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb | 3 ++- .../easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb | 3 ++- easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb | 3 ++- .../g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb | 4 ++-- easybuild/easyconfigs/g/gompi/gompi-2016.07.eb | 4 ++-- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 3 ++- 27 files changed, 51 insertions(+), 33 deletions(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index 69dadef3c7..bae4a90d91 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index c8e83f1af6..88a772e2f8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index e60f317150..d0d5a239b6 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index 47af207c6f..b6d45b10ea 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb index 9faee44d8b..935f73ec90 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb index fa068137af..6ed0f40863 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb index 9d0b198d0f..afc148cb14 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 4cfb618383..e5810437c4 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 70eb5b0a10..0a33e2b925 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 477760c3c0..49772e1a73 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index d952c14671..98f0d96369 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb index 73ce1be6d6..fecad61365 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index 918c5aec06..b29b2e7ddf 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb index 3e8dd8b2df..ffe44a8cda 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb index cabfe78d32..ba98f92742 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb index ab0d6b9ba8..e822e11f35 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb index 7fae7e2b3f..adf36de398 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb index 83b2732fb5..f52ab6e342 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb index 350a3d6cfa..3f046b2129 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb index f8d1e53e32..5f20cd92b4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb @@ -28,8 +28,8 @@ source_urls = [ sources = [ SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', + # seems to have disappeared? + # 'regressiontests-5.0.2.tar.gz', ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb index fa06ee75b2..dd5cd622b8 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb @@ -10,7 +10,8 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_subdir = 'gs%(version_major)s%(version_minor)s' +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb index 8612f2848b..59430c9acb 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -10,7 +10,8 @@ description = """Ghostscript is a versatile processor for PostScript data with t 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/"] +source_subdir = 'gs%(version_major)s%(version_minor)s' +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ 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 index 43c5a459fa..af08c394ee 100644 --- 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 @@ -4,7 +4,8 @@ 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.""" +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'} diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb index 991e6da6fa..fe0e24229f 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -46,4 +46,4 @@ sanity_check_paths = { modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb index bd4f6deeb9..c16d2b51eb 100755 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -25,8 +25,8 @@ sanity_check_paths = { # add the installation dir to PATH modextrapaths = { - 'PATH': '', - } + 'PATH': '', +} # remove exec permission for the provided installation script postinstallcmds = ["chmod og-x %(installdir)s/install.sh"] diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb index 5eca4152c8..eec2b277ee 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb @@ -15,8 +15,8 @@ gccbinver = '%s-%s' % (gccver, binutilsver) # compiler toolchain dependencies dependencies = [ - ('GCC', gccbinver), # includes both GCC and binutils - ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), + ('GCC', gccbinver), # includes both GCC and binutils + ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index a0f2ba3078..2f14396e13 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -21,7 +21,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, + 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', + 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, 'lib/libgtkglext-x11-1.0.a', 'lib/libgtkglext-x11-1.0.%s' % SHLIB_EXT], 'dirs': ['include/gtkglext-1.0/gdk', 'include/gtkglext-1.0/gtk', 'lib/pkgconfig'], } -- GitLab From 068f2709b301b502210412079179f44b4f9865b5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:02:26 +0800 Subject: [PATCH 061/566] yet another style fix --- easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 index c041d6e2aa..2a15cb846c 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -16,8 +16,8 @@ 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']] + + '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'] } -- GitLab From c3c6264ef9172d1aab091bb2ba6c0bd42b16ac07 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:12:07 +0800 Subject: [PATCH 062/566] yet another style fix --- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index 5d29ad3201..c9a900612f 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -23,8 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -configopts += 'LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index b5d3e358e9..9783862078 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -23,8 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -configopts += 'LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' -- GitLab From f0ad795a7ccf37af9a466968552f3feee9e98dcb Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Wed, 8 Mar 2017 10:26:58 +0100 Subject: [PATCH 063/566] Correction: EBROOTLIGJPEGTURBO -> EBROOTLIBJPEGMINTURBO --- .../easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb index 63e63419b2..5eee841793 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb @@ -37,7 +37,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb index 6355e7d5d7..6e30f9da8c 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb @@ -32,7 +32,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb index 9e5b8f7b62..d2c01232d3 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb @@ -34,7 +34,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment -- GitLab From f2188cf1ad91631353221a858924aae5cbf26719 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:32:58 +0800 Subject: [PATCH 064/566] yet another style fix --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 7 ++----- easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb | 4 ++-- .../g/Ghostscript/Ghostscript-9.19-intel-2016a.eb | 2 +- .../g/Ghostscript/Ghostscript-9.19-intel-2016b.eb | 2 +- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 4 ++-- 11 files changed, 20 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index e5810437c4..a4b668c8cb 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 0a33e2b925..ec6e1d4b8c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 49772e1a73..33b05c7f1c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 98f0d96369..3d36571118 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb index fecad61365..02f569f33b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index b29b2e7ddf..08fc164519 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb index ffe44a8cda..8ed215628a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb index ba98f92742..0cfae7ee91 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb index dd5cd622b8..9a3a3ea548 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} source_subdir = 'gs%(version_major)s%(version_minor)s' -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/" + source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb index 59430c9acb..0d5843bdd6 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} source_subdir = 'gs%(version_major)s%(version_minor)s' -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/" + source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index 2f14396e13..8dc32d3aad 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -21,8 +21,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', - 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, + 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', + 'lib/libgdkglext-x11-1.0.a', 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, 'lib/libgtkglext-x11-1.0.a', 'lib/libgtkglext-x11-1.0.%s' % SHLIB_EXT], 'dirs': ['include/gtkglext-1.0/gdk', 'include/gtkglext-1.0/gtk', 'lib/pkgconfig'], } -- GitLab From 52d921264b76ac2563135e32a93f5df07a4b0be6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:37:23 +0800 Subject: [PATCH 065/566] yet another batch of minor style fixes --- easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb | 3 ++- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb | 6 +++--- .../h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 6 +++--- .../h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb | 6 +++--- .../easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb | 7 ++++--- .../easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb | 7 ++++--- .../easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb | 9 +++++---- .../easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb | 7 ++++--- easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb | 2 +- .../h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 2 +- .../easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb | 7 ++++--- .../h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- 84 files changed, 245 insertions(+), 232 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index 28e5e6ad36..e115932f8e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -4,7 +4,8 @@ name = 'HDF' version = '4.2.11' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index fa2a08d015..16556a59b7 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -4,7 +4,8 @@ name = 'HDF' version = '4.2.8' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index b1098f85e1..7250d32fe5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -24,4 +24,4 @@ dependencies = [ ('libxml2', '2.9.3') ] -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 76836f3aed..259d3f70b6 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -16,7 +16,8 @@ name = 'HPCBIOS_Debuggers' version = '20130829' homepage = 'http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-05.html' -description = """Common Set of Debuggers includes a set of debuggers that can assist HPC users for managing parallel codes.""" +description = """Common Set of Debuggers includes a set of debuggers that can assist HPC users for managing parallel + codes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb index 576cc9a699..5feb085a79 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb index cf3bd5fd41..0715af27f9 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb index d327bfbbab..cd888a1b77 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.5.16'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb index fa3e730343..96f1d5781a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb index 91a1cadef9..e3f05fd328 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb index 934cc8d3eb..4edf03da45 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayCCE', 'version': '2015.06'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb index 7a8e5a0800..76ee40d652 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayCCE', 'version': '2015.11'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb index 4f4dbfc813..2c9f0ea5ba 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb index 455f495e6e..bff436a5d6 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb index f64bec348b..b1fe7ccd3c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb index 57414cfc79..c7a116c4f3 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb index b59f7317b1..b9880180b4 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb index 00ee4facc9..4749294d9f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb index 651ae824ba..32ea90665e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2015.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb index 9ab9de3734..ab2e745599 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb index 6e7b16eb21..c750f970fb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015.05'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb index 225cb3be6a..97e132a043 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb index 728ad9cf2e..fe7bda0c23 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb index e65fa73eda..6c486063ce 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb index e44a4ac54d..416d5bc913 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb index e43e4270dd..df93eaf60f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb index 5634e6bd4f..c40112704f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb index 50fef4fac6..5d0475520c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True, 'usempi': True, 'openmp': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb index ae8a971cbf..7513b5c69c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': 'gmpolf', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb index dda08f35b9..7a3660c3cf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': 'gmvolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb index d581afc6f7..b99e6ef61e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': 'gmvolf', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb index fd109a8fed..51de797385 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb index 92f6036e1c..036b47fd97 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb index 55ab924d7d..7fd7fc7bf8 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb index 38c3e337e3..595430c600 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb index 4c3646267b..095ac318fe 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.10'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb index 4e8b437981..271e44e3ae 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb index 07ff11637e..1740a95776 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2014b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb index 7597cf43f8..bfca06cd24 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2015.02'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb index 4e727e3fcd..0be6dec3cf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2015.08'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb index 97b6ceedd3..774ed3383d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2015a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb index fa34ec665e..ecdaa77a80 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2015b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb index 406d3ae039..3f8d9be6d0 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.00'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb index 27b235374a..7fa2f28990 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.01'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb index 977c7d487d..21af879c00 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.02-GCC-4.9'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb index ffa453cdb4..d6bd01277c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.02-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb index f2d54cf671..2c8b3ccfcc 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.03-GCC-4.9'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb index 7eaca67c16..eb86100453 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.03-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb index 660c68898c..3aa6c8de88 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.03-GCC-5.4'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb index a3af786ca9..2349780aef 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb index 226f45477c..f4cc398833 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb index e2c8df3cc6..8cc92060d3 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2015.01'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb index 28511646d6..645f1e333c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2015.02'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb index 59e1705669..2247657f83 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2015.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb index 42249afb29..ac09c4d824 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +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': '2016.07'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb index 9552b4d653..2f6f29630a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb index 4d48990b54..9b006fcd88 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb index 112d6aa634..23e9cfc7a8 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.09'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb index c44018425b..09db015192 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb @@ -2,9 +2,9 @@ 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.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.07'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb index be4db4593e..0766c10887 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb @@ -2,9 +2,9 @@ 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.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.09'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb index e59ac471b9..95e36ebf95 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb @@ -2,9 +2,9 @@ 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.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} 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 index d1430d0e3a..c13e143bbf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb @@ -2,9 +2,9 @@ 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.""" +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} 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 index fff961832d..069cc730f1 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb @@ -2,9 +2,9 @@ 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.""" +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} 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 index 48447ddb28..d09d150a57 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb @@ -2,9 +2,9 @@ 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.""" +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} 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 index 64700f3b27..0db9bffabb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb @@ -2,9 +2,9 @@ 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.""" +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} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb index 976ad59fb7..f53793fe5b 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb @@ -2,9 +2,9 @@ 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.""" +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': '2017.02'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb index 80e701d1a6..6caac90930 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb @@ -2,9 +2,9 @@ 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.""" +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': '2017a'} toolchainopts = {'usempi': True} 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 index 05f316bde4..b6258c055e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb @@ -2,9 +2,9 @@ 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.""" +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} 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 index 22cd32989a..579a293142 100644 --- 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 @@ -2,9 +2,9 @@ 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.""" +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} 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 index efda5a282c..ed855cdf2a 100644 --- 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 @@ -2,9 +2,9 @@ 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.""" +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} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb index d890354a7b..37c0a37f5d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb @@ -2,9 +2,9 @@ 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.""" +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': '2017.01'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb index 77dc4ed21f..77467edaf2 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb @@ -2,9 +2,9 @@ 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.""" +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': '2017a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb index 005a57564c..3ef2663a61 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb @@ -2,9 +2,9 @@ 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.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.09'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb index d46bdf7367..3b8e366300 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.3.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given -a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) -in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb index 44e47d185b..c2eb89d992 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.3.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb index 783b534519..f62ed07a47 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.4' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} @@ -16,4 +17,4 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb index 8b0afc7b1f..cf92cc3c69 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.4' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} diff --git a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb index 80e0503ba7..5ab80c6f39 100644 --- a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb @@ -4,7 +4,7 @@ name = 'Hoard' version = '3.10' homepage = 'http://www.hoard.org/' -description = """Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications.""" +description = "Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 17626346c5..1807b63953 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'h5py' version = '2.0.1' homepage = 'http://code.google.com/p/h5py/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. - HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of + enormous amounts of data.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index 12d6705dfa..d7449726a8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (2 * (pythonshortver, ))], 'dirs': [], } diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb index 09424f6b1b..b789858736 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb @@ -4,9 +4,10 @@ name = 'h5utils' version = '1.12.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/H5utils' -description = """h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable - HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes programs to - convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK).""" +description = """h5utils is a set of utilities for visualization and conversion of scientific data in the free, + portable HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes + programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, + Vis5d, and VTK).""" source_urls = ['http://ab-initio.mit.edu/h5utils/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb index 944bc27a5e..4ab8e8fc9a 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 778a209cab..401ada28ea 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb index 3f0df333bf..067d4ce450 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb index d1f6974e2a..786bdb4f54 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], -- GitLab From 8dba00cbe75ceb7740ef6134c488fba62efc5b7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:45:35 +0800 Subject: [PATCH 066/566] yet another style fix --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index a4b668c8cb..8e387e8194 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index ec6e1d4b8c..3a8e68733e 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 33b05c7f1c..b9b142b82c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 3d36571118..12435392e5 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] -- GitLab From e67ec58c9ff764e522fd00ff67a5fcecfb2ca8e9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:51:04 +0800 Subject: [PATCH 067/566] yet another style fix --- easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index e933c1af39..7dab289eff 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -16,8 +16,8 @@ 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']] + + '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'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index 74d90eb777..e221d7bbc5 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -16,8 +16,8 @@ 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']] + + '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'] } -- GitLab From 64e7a3722e4418e57d89348f065681af55ab9f9b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 8 Mar 2017 11:00:24 +0100 Subject: [PATCH 068/566] fix to be sure the HDF5 provided by easybuild is used --- easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb index 7b47764f47..1461dc4f22 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb @@ -23,6 +23,9 @@ dependencies = [('HDF5', '1.8.11')] skipsteps = ['configure'] +prebuildopts = 'export HDF5LIBDIR=$EBROOTHDF5/lib &&' +prebuildopts += 'export HDF5INCLUDEDIR=$EBROOTHDF5/include &&' + # the STATIC= option is a workaround. Check details here: # https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 buildopts = ' STATIC= ' diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb index ea4423904f..d31c4ec289 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb @@ -23,6 +23,9 @@ dependencies = [('HDF5', '1.8.18')] skipsteps = ['configure'] +prebuildopts = 'export HDF5LIBDIR=$EBROOTHDF5/lib &&' +prebuildopts += 'export HDF5INCLUDEDIR=$EBROOTHDF5/include &&' + # the STATIC= option is a workaround. Check details here: # https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 buildopts = ' STATIC= ' -- GitLab From 515b3bd20aba2f214e9f33d37475e64c53b907ef Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 18:24:06 +0800 Subject: [PATCH 069/566] yet another style fix --- .../h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 1807b63953..72344ad38b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ @@ -27,7 +26,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index d7449726a8..56c251d6fa 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s-serial' % (python, pythonver) prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' @@ -29,8 +28,8 @@ dependencies = [ builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (2 * (pythonshortver, ))], - 'dirs': [], + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'data' -- GitLab From 2968917cdbfbd864ae1b92aed11f2321f3e049b3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 18:26:07 +0800 Subject: [PATCH 070/566] yet another batch of minor style fixes --- .../easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb | 2 +- .../easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb | 2 +- .../easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb | 11 +++++------ .../IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 6 +++--- easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb | 2 +- .../easyconfigs/i/Inspector/Inspector-2013_update6.eb | 3 ++- .../Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 4 +++- .../Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb | 2 +- .../i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-11.1.073.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-11.1.075.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.10.319.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.13.367.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.3.174.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.6.233.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.1.117.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.2.146.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.3.163.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.4.183.eb | 3 +-- .../easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.0.090.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.1.133.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb | 3 +-- .../i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 3 +-- .../i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- .../i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 3 +-- .../i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/iccifort/iccifort-2015.0.090.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2015.1.133.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2015.3.187.eb | 3 ++- .../i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2016.0.109.eb | 3 ++- .../i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 3 ++- .../i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 3 ++- .../i/iccifortcuda/iccifortcuda-2016.10.eb | 3 ++- .../easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb | 3 ++- easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb | 3 +-- .../i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb | 3 +-- .../i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- .../i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 3 +-- .../i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb | 6 +++--- easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb | 3 ++- easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb | 3 ++- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb | 3 +-- .../i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb | 7 +++---- .../i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-iompi-2015.01.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb | 3 +-- .../i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb | 3 +-- .../i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb | 3 +-- .../i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb | 3 +-- .../i/imkl/imkl-11.2.2.164-iompi-2015.02.eb | 3 +-- .../i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb | 3 +-- .../imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb | 3 +-- .../i/imkl/imkl-11.2.3.187-iompi-2015.03.eb | 7 +++---- .../imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 3 +-- .../impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 3 +-- .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 3 +-- .../impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 3 +-- .../impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 3 +-- .../i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 3 +-- .../impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 3 +-- .../easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 3 +-- .../impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 3 +-- ...pi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- .../i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 3 +-- .../i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 3 +-- ...pi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- ...pi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- ...pi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/intel/intel-2014.06.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014.10.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014.11.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015.02.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015.08.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015a.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016.00.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016.01.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016a.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.00.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.01.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.02.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017a.eb | 3 ++- .../intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb | 2 +- .../intltool-0.51.0-intel-2016a-Perl-5.20.3.eb | 2 +- .../easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb | 3 ++- .../i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 ++- .../i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb | 3 ++- .../i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb | 1 - .../i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb | 1 - easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb | 3 +-- easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb | 3 +-- easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb | 3 +-- 210 files changed, 286 insertions(+), 363 deletions(-) diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb index 54799f31a3..bfcfa298dc 100644 --- a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name ='IMa2p' +name = 'IMa2p' version = '20151123' commit = '66e7ac7bc5e4c5bbadbd7de943465afeb4641770' diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb index 28cdb8a360..6621f7655d 100644 --- a/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name ='IMa2p' +name = 'IMa2p' version = '20160804' commit = '1ebe5777ed96b878cc81109bede84dc3f7bb5e3b' diff --git a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb index 9e03233c20..6af67462a3 100644 --- a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb @@ -4,10 +4,8 @@ name = 'IOzone' version = '3.434' homepage = 'http://www.iozone.org/' -description = """ -IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported - to many machines and runs under many operating systems. -""" +description = """IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file + operations. Iozone has been ported to many machines and runs under many operating systems.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -22,8 +20,9 @@ files_to_copy = [ (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'report.pl', 'Changes.txt']], 'share/doc'), (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'Generate_Graphs', 'gnu3d.dem']], 'share'), (['docs/iozone.1'], 'share/man/man1'), - (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', 'Run_rules.doc']], - 'share/doc'), + (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', + 'Run_rules.doc']], + 'share/doc'), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb index bc8f42751d..89001fc17a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('testpath', '0.3', versionsuffix), # required by 'nbconvert', but causes problems w.r.t. 'backports' module... # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('entrypoints', '0.2.2', versionsuffix), + # ('entrypoints', '0.2.2', versionsuffix), ('path.py', '10.1', versionsuffix), ('prompt-toolkit', '1.0.13', versionsuffix), ] @@ -113,9 +113,9 @@ exts_list = [ }), # disabled because entrypoints on which this depends pull in configparser, which causes problems # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('nbconvert', '5.1.1', { + # ('nbconvert', '5.1.1', { # '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/'], }), diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index a303238f9b..6e5acb74b1 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.14' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb index e711a7699f..00012d332d 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb index 5ae9fcabbc..a5f0f5cc5f 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb index bd7c2f7f2a..6fbb191c8b 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb index 6b38a91f39..e6211fab28 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.16' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb index a7b67d3ddf..23ff5b76f6 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.17' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index 59aa3e7414..ab3458b6cb 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -2,7 +2,8 @@ name = 'Inspector' version = '2013_update6' homepage = 'http://software.intel.com/en-us/intel-inspector-xe' -description = "Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications" +description = """Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and + parallel applications""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 6966353326..5ec986a817 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,9 @@ version = '1.0.0' homepage = 'https://launchpad.net/instant' description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. -It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://fenicsproject.org).""" + It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project + (http://fenicsproject.org).""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} majorversion = "%s.x" % ".".join(version.split('.')[:-1]) diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb index 4e88df4047..06af631540 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'Instant' version = '1.0.0' homepage = 'https://launchpad.net/instant' -description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. - It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://fenicsproject.org).""" +description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. + It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project + (http://fenicsproject.org).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb index a0ac2c0885..6b3017a194 100644 --- a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name ='i-PI' +name = 'i-PI' version = '1.0-20160213' commit = '2a09a6d' versionsuffix = '-Python-%(pyver)s' 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 efeb188af2..e0c5f7e40e 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 @@ -14,7 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} exts_defaultclass = 'PythonPackage' exts_list = [ - # airspeed requires this specific version of cachetools + # airspeed requires this specific version of cachetools ('cachetools', '0.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/c/cachetools/'], }), diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb index 25d906e87f..6db65c8a2e 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb @@ -15,8 +15,7 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb index 270e177a0c..426c8d4726 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb index 005adc34f3..367d02cc42 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb index e8019bf5f8..df976c997d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb index 17d0cd2bbe..0e9f729010 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb index cf51e4e41b..69a166ec56 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb index 4079daa6ca..5c240e5c11 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb index 818ade63f2..f259138a7e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb index 086b7132e2..c135115579 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb index 08d3496656..b9b8d9d6de 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb index 8c5cfaeab5..db58351c1b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb index 446396ee03..a1fab236a7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb index 3be64f6a79..e42dd9678e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb index be5072e46d..ace7d02238 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb index 2e5244fe91..b62448cecd 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb index b742c2c7e4..939c072363 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb index e4c5184bc0..3ebed03a03 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb index 5850a5593b..26892de20b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb @@ -15,5 +15,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb index d02dca7d22..e290c96aa6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb index dba6123fdb..352973960c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb index 368b594177..13ebafc260 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb index 08a6748331..326875c307 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index 8439c044f4..dbb4b84039 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index 37331a1488..ae1d56e8a6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -17,7 +17,6 @@ dependencies = [(gnu, gnuver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb index 55dec91be5..833da3c0c7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb index 1ca6568cb7..b9a332e3a0 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb @@ -20,7 +20,6 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 32978c0fbe..f15a97cd30 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -29,7 +29,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index e56edba4db..18895dbe61 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -20,7 +20,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 9d56289dfc..d375c69cbb 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -29,7 +29,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb index 51b0376b09..ebdf9f10ca 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.0.090' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb index cb21cd2b6c..06b3d4cc94 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.1.133' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb index 8387432380..7029a01c14 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb index f1a5e6d54b..d51e11b541 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.0.109' versionsuffix = '-GCC-4.9.3-2.25' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb index a66481f29c..f03bb37944 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb @@ -5,7 +5,8 @@ name = 'iccifort' version = '2016.0.109' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 618d381f6e..8bf45db5e6 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.1.150' versionsuffix = '-GCC-4.9.3-2.25' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 871fae395a..7fc5fd1e8f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.2.181' versionsuffix = '-GCC-4.9.3-2.25' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb index e07e4371a2..0b2036c9e0 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.2.181' versionsuffix = '-GCC-5.3.0-2.26' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 73f4eda01f..f961d74a1f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-4.9.3-2.25' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb index a1f40c75ae..f89991b41e 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-5.3.0-2.26' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 944d7a23b2..52e91145c6 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.3.210' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 3ed3f947b9..e2ed764a7b 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2017.0.098' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} 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 index 8034a2a1e1..6e347be3a2 100644 --- 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 @@ -6,7 +6,8 @@ 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 11f7aab8ea..ea60f74334 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,8 @@ version = '2017.1.132' versionsuffix = '-GCC-6.3.0-2.27' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb index a3141d5631..d622580adc 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,8 @@ version = '2017.2.174' versionsuffix = '-GCC-6.3.0-2.27' 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""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb index 1eeb749c6e..2e8347c1be 100644 --- a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb @@ -4,7 +4,8 @@ name = 'iccifortcuda' 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""" +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'} diff --git a/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb index ed01c4e744..ecd5b0b755 100644 --- a/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb +++ b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb @@ -4,8 +4,8 @@ name = 'icmake' version = '7.23.02' homepage = 'http://icmake.sourceforge.net/' -description = """Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written to - provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.""" +description = """Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written + to provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True} @@ -18,8 +18,8 @@ install_cmd += './icm_bootstrap %(installdir)s && ./icm_install strip all /' sanity_check_paths = { 'files': [ - 'bin/icmake', 'bin/icmbuild', 'bin/icmstart', 'bin/icmun', - 'lib/icmake/icm-comp', 'lib/icmake/icm-exec', 'lib/icmake/icm-pp' + 'bin/icmake', 'bin/icmbuild', 'bin/icmstart', 'bin/icmun', + 'lib/icmake/icm-comp', 'lib/icmake/icm-exec', 'lib/icmake/icm-pp' ], 'dirs': [] } diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb index fc33afb1ef..7f60c5dadb 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.2.0' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb index a6b070f713..0cd535b843 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.3.0' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb index aeb15217ff..feae6d3047 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.4.0' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb index 55b4f558df..7d3a7fe132 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.5.0' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb index e5194b8648..72271c8f07 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '6.1.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb index 41d6ceb53e..fca7778a45 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '6.2.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb index b3dda3d539..d54f7d5724 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '7.1.2' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb index 6190ed2906..e482585790 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '7.3.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb index c4b7144887..640705e6d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb @@ -15,8 +15,7 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb index da0e19e8a7..ee69dc8e33 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb index f8534d1717..1372125c7c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb index c0ab005da2..222eeaca4e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb index 8d6eeaafb4..ef3f60866f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb index 65ff75aa5c..5b08216822 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb index 0749ed0e0c..ad4923d074 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb index 99bf3863c6..43b7969dc4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb index 54b49ddcaf..018ac9b87d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb index 4efd890d23..d84bb054d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb index 05c638d451..e1ae8632f1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb index 901fc019cc..0b6f0c22ab 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb index 32705da10f..7b9de4dea5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb index dc69a4da5e..6402e2f9ac 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb index 8d50c3c460..c762cdb26a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb index 058b29e416..f987a0ac44 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb index 6a206056e1..a605451b28 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb index 4e061aba7c..104d8f2770 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb @@ -15,5 +15,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb index a94df9884b..420984ed94 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb index 62bde3a68e..b312c804d8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb index 419e0257c0..a775af60a0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb index 02137b7498..c2c4c3e7d1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb index 5767d1400f..6478030728 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb index 0f54df3a82..4a9762b2d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -17,7 +17,6 @@ dependencies = [(gnu, gnuver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb index 8253a3390b..6e0324f9b5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb index 2fd9b5a946..446656fb7a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -20,7 +20,6 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' 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 9599d68348..a32fd8278a 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 @@ -32,7 +32,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index 657a607db3..b40428eab7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -23,7 +23,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' 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 9afeb8bcc9..fdfcf853b6 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 @@ -32,7 +32,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index ddf779e0e0..b0f9d10dbb 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -17,9 +17,9 @@ source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] builddependencies = [('Autotools', '20150215')] patches = [ - 'igraph-%(version)s-no-lapack-no-blas.patch', - 'igraph-%(version)s-fix-aclocal-version.patch' - ] + 'igraph-%(version)s-no-lapack-no-blas.patch', + 'igraph-%(version)s-fix-aclocal-version.patch' +] # link against MKL rather than blas/lapack preconfigopts = "env LDFLAGS='-lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm'" diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb index d62bc1e82f..8ea51a816a 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb @@ -4,7 +4,8 @@ name = 'iimpi' version = '7.1.2' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb index b0fe67cb26..7f36db9539 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -4,7 +4,8 @@ name = 'iimpi' version = '7.3.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 39b3d7cf7b..f12c8b0a4a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -29,7 +29,6 @@ interfaces = True m32 = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb index b1eb6ee6e3..16e7150410 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb @@ -24,7 +24,6 @@ dependencies = [ interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb index 91c64cfa0d..c3482af83f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb @@ -24,7 +24,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index b8769ef805..b9464f9703 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb index b5b58cc188..23c4595c45 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb @@ -23,7 +23,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb index 8adf971a63..11b669be47 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb index c1e7124884..cf9de7a5fc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb index ccd95b2a7a..beeabe2d96 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb index 74e9065d7c..36091633a7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb index 8b97b3ff26..cfa4fa1e11 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb index 471f7e9aa6..ce891766f7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb index 98e5ffd25f..d8ef766bc1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb index e04b151136..5c4db1885b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb index 0d09ac1d4b..dbddd3cc86 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb index 0fe1b14e46..66e98d5997 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb index 7b7f159547..3c52f96be0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb index e37a375b7a..5ffe362a58 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb index cc9f1d89b5..581df89fa9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb index 3b9cb14613..1381ccc44e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb @@ -27,7 +27,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb index 4843fd2442..b0b43aa3b0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb @@ -26,7 +26,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb index 3ad520461a..7a0a1e5352 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb @@ -3,8 +3,8 @@ version = '11.1.2.144' 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.""" + 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': ''} @@ -29,7 +29,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb index 2114374474..846edaec6c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb index 8854a89598..82e9db5fed 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb index 2559891bcc..6bbcefb5d7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb index 47e59ba9fc..ddbbf90fd9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb index bd599cfe0d..4b1c8e4141 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb index dcb2085bf3..7028d56135 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb index 3ce046efac..c0c59f1570 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb index a249ac518b..2ee043da29 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb index aadf66c552..490c88a422 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb index 82eec3eecb..e1fa90b6ca 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb index ccc021a957..4573f18614 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb index b76de536ee..8c6606cc65 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb index 807b5f2004..1b7dda307a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb index 0772c5ff65..5af833e7d6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb @@ -3,8 +3,8 @@ version = '11.2.3.187' homepage = 'http://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines -for science, engineering, and financial applications that require maximum performance. Core math functions include -BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + 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': '2015.03'} @@ -13,7 +13,6 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index f295b50925..a928de1ca4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -17,8 +17,7 @@ checksums = ['47567e38801efe273b36b5250c759af7'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index e40fb8448a..49c3e5d75b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -17,8 +17,7 @@ checksums = ['b57ff502b5f97f2f783e4bbda7ce42b3'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb index 53b6037e3f..a1225d2d74 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb index de96c38b15..c807d796b6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 6a204cb330..f95dd72e44 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 4c78a146fe..028fa649be 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -14,8 +14,7 @@ sources = ['l_mpi_pu_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index c44ccfe556..e460a1a60c 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_pu_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 001ee2403f..7828e8ee3d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -15,8 +15,7 @@ patches = ['impi_4.x_productsdb.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 6178aa2f65..209842e727 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 99cabee972..c4e43d9fa9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index c4adbe0ae3..9b5a71ce36 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 2121a1a6d9..36a86386a0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 92c9a61b43..3f28cb9676 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 3cd6a18055..ee1796488d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 22f0699649..97573c0075 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 922aa79344..5524846083 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index b7639d24d1..5301684735 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 21ed19633f..3eef4c39b6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index da5a2ab9be..de266ab029 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 9e61812d8f..81b707143d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index 9a3879ee53..91e7ec80d3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 5e4968df60..3b51024f12 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index 43cd007ba4..7b345a78e7 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 28ece27457..154d705ccf 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 6f2bcda1cb..952a3f2313 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index a9d198b99f..62a9caf2ee 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index 25f7950bae..46722880e7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index df72fa53c0..452ab3ddd5 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 4b32c5dbb2..7de5ce16aa 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index c247bd8cc6..51baff5e35 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index 362bb90b08..51936e972d 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -14,8 +14,7 @@ sources = ['l_mpi_p_5.1.0.038.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index aafd77aff0..8d146fd342 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -16,7 +16,6 @@ checksums = ['aa4aaec41526aa5b244e531811877b01'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb index 9e343efe2e..af79fd7190 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index da4a993780..6042d117f6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -16,8 +16,7 @@ checksums = ['ec4db8f718c34f09fccf9d1c89454f0a'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "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' diff --git a/easybuild/easyconfigs/i/intel/intel-2014.06.eb b/easybuild/easyconfigs/i/intel/intel-2014.06.eb index 57c2903c57..37318d6737 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.06.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.06.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.06' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014.10.eb b/easybuild/easyconfigs/i/intel/intel-2014.10.eb index d89452f540..42ecc0b6a8 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.10.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.10.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.10' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014.11.eb b/easybuild/easyconfigs/i/intel/intel-2014.11.eb index 1bdbdfe846..82213850c0 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.11.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.11.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.11' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014b.eb b/easybuild/easyconfigs/i/intel/intel-2014b.eb index 9d433db3c4..2cc20c2772 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014b' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015.02.eb b/easybuild/easyconfigs/i/intel/intel-2015.02.eb index ab8507944b..a5c22d20a4 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.02.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015.02' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015.08.eb b/easybuild/easyconfigs/i/intel/intel-2015.08.eb index f154fb6c65..fc731e26ee 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.08.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.08.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015.08' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015a.eb b/easybuild/easyconfigs/i/intel/intel-2015a.eb index 2cb7f99ce4..702e767c23 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015a' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015b.eb b/easybuild/easyconfigs/i/intel/intel-2015b.eb index e0b4b71ab1..dcc37ce659 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015b' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.00.eb b/easybuild/easyconfigs/i/intel/intel-2016.00.eb index 241463337a..2f03a7cc46 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.00.eb @@ -5,7 +5,8 @@ name = 'intel' version = '2016.00' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.01.eb b/easybuild/easyconfigs/i/intel/intel-2016.01.eb index 37f96fa014..7c51ee2938 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.01.eb @@ -5,7 +5,8 @@ name = 'intel' version = '2016.01' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb index 41552f25a9..535ba2e732 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -6,7 +6,8 @@ gcc_maj_min = '4.9' versionsuffix = '-GCC-%s' % gcc_maj_min 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb index 4d1e0dddac..904f548c97 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.3' versionsuffix = '-GCC-%s' % gcc_maj_min 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb index aa6be8f54d..c7bc45badd 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb @@ -6,7 +6,8 @@ gcc_maj_min = '4.9' versionsuffix = '-GCC-%s' % gcc_maj_min 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb index 3de185ca63..04c3682224 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.3' versionsuffix = '-GCC-%s' % gcc_maj_min 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb index 1de4297cce..fd9c783f53 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.4' versionsuffix = '-GCC-%s' % gcc_maj_min 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016a.eb b/easybuild/easyconfigs/i/intel/intel-2016a.eb index c858c20f53..5b6fecfd23 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2016a' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016b.eb b/easybuild/easyconfigs/i/intel/intel-2016b.eb index 92aacd886c..5866da643e 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2016b' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.00.eb b/easybuild/easyconfigs/i/intel/intel-2017.00.eb index ad8be63148..a3c48fa4ca 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.00.eb @@ -4,7 +4,8 @@ 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.01.eb b/easybuild/easyconfigs/i/intel/intel-2017.01.eb index 9993bc8e47..10392160f1 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.01.eb @@ -4,7 +4,8 @@ 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.02.eb b/easybuild/easyconfigs/i/intel/intel-2017.02.eb index 941245b3e6..e39d8da948 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.02.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017.02' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017a.eb b/easybuild/easyconfigs/i/intel/intel-2017a.eb index 4e98f5a7f2..f1760e4271 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017a' 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.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb index 0acb163cda..4d7b443901 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'GCCcore', 'version': '4.9.3'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb index 8fd4cb48f8..4d3f41da10 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb index 9d67e52066..74d4ba917e 100644 --- a/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb +++ b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb @@ -4,10 +4,10 @@ name = 'io_lib' version = '1.14.8' homepage = 'http://sourceforge.net/projects/staden/files/io_lib/' -description = """Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment - File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded - into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. -""" +description = """Io_lib is a library of file reading and writing code to provide a general purpose trace file (and + Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure + with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS + Windows.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb index aa85e82a98..a9a545eec7 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.01' 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.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb index 544ad6da2e..e17fa43dd2 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.02' 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.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb index f9059cff3e..93dbfc98f8 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.03' 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.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb index 54ed73649a..5d1d743242 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2016.07' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} 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 cf9954cf88..ced0e87585 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 @@ -4,7 +4,8 @@ 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.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} 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 index 6b0377e8e3..f0219ff350 100644 --- 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 @@ -4,7 +4,8 @@ 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.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb index 6039ebaad3..9d9e8846e6 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2017.01' 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.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb index 032f6eb6a2..4d75373f4f 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2017a' 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.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} 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 3c9854b3e1..9580ff5296 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 @@ -17,4 +17,3 @@ dependencies = [ ] 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 index 6ab1a7b7d5..db8c7fb2af 100644 --- 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 @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb index 1497f12bc7..af01ee3ccc 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb @@ -18,5 +18,4 @@ moduleclass = 'perf' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb index dce7087021..2df68edb57 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb @@ -14,7 +14,6 @@ sources = ['l_ipp_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb index c5381d564c..c7f19f61c1 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb @@ -14,7 +14,6 @@ sources = ['l_ipp_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb index b8febc89fc..5e7c707582 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi4' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb index 67482320a6..546ec40361 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi4' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb index 42551d67c6..8922806632 100644 --- a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi5' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' -- GitLab From 30861069b7bb9df66f8c347f7ec1010ddcbbf8fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 14:26:59 +0100 Subject: [PATCH 071/566] adding easyconfigs: fqtrim-0.9.4-intel-2016b.eb --- .../f/fqtrim/fqtrim-0.9.4-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb new file mode 100644 index 0000000000..f57e94703f --- /dev/null +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'fqtrim' +version = '0.9.4' + +homepage = 'http://ccb.jhu.edu/software/fqtrim/' +description = """fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, + terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing + machines.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] +sources = [SOURCE_TAR_GZ] + +buildopts = 'release CC="$CXX" LINKER="$CXX" LDFLAGS="$LDFLAGS $CXXFLAGS"' + +files_to_copy = [(['fqtrim'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fqtrim'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ff7cd40c2f0a8da36dee04fb0661c1a3deb211b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:17:27 +0100 Subject: [PATCH 072/566] no need to include $CXXFLAGS into LDFLAGS, thanks @wpoely86 --- easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb index f57e94703f..4e2183f308 100644 --- a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] sources = [SOURCE_TAR_GZ] -buildopts = 'release CC="$CXX" LINKER="$CXX" LDFLAGS="$LDFLAGS $CXXFLAGS"' +buildopts = 'release CC="$CXX" LINKER="$CXX"' files_to_copy = [(['fqtrim'], 'bin')] -- GitLab From 2fa39e0e47203bebce534d5f36f30a5298d5e0f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:18:18 +0100 Subject: [PATCH 073/566] adding easyconfigs: DBG2OLC-20170208-intel-2016b.eb --- .../d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb new file mode 100644 index 0000000000..0f90c41b2a --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20170208' +commit = 'b452286' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] + +cmds_map = [('.*', "$CXX $CXXFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a3c162e9306d788f99d59fd3cfe93c4fee0a4929 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:40:56 +0100 Subject: [PATCH 074/566] adding easyconfigs: L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb --- ...folder-20141124-intel-2016b-Perl-5.24.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..dd21d5b9af --- /dev/null +++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'L_RNA_scaffolder' +version = '20141124' +versionsuffix = '-Perl-5.24.0' + +homepage = 'http://www.fishbrowser.org/software/L_RNA_scaffolder/' +description = "L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.fishbrowser.org/software/L_RNA_scaffolder/downloads/'] +sources = ['L_RNA_scaffolder.tar.gz'] +checksums = ['3cc401886c452b1000d434dea776970e'] + +dependencies = [('BioPerl', '1.7.1', versionsuffix)] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency', + 'delete_block', 'delete_linker', 'delete_same_fragment', 'exon_length', 'filter_scaffold.pl', + 'find_end_node', 'find_reliable_connection', 'find_start_node', 'form_block', 'form_initial_path.pl', + 'form_path.pl', 'generate_scaffold.pl', 'generate_unscaffold.pl', 'L_RNA_scaffolder.sh', 'link_block', + 'order', 'overlap', 'route.pl', 'search_guider', 'select', 'select_nodes'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From d789421eeaf1847ca641fdd45ae509c85c2a4b82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:49:35 +0100 Subject: [PATCH 075/566] also include $LDFLAGS in compilation command --- easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb index 0f90c41b2a..82d644aaff 100644 --- a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] sources = ['%s.tar.gz' % commit] -cmds_map = [('.*', "$CXX $CXXFLAGS -o DBG2OLC *.cpp")] +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] files_to_copy = [(['DBG2OLC'], 'bin')] -- GitLab From a9d2e2ae16a0f109e81838f40bc98e395798b2a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 16:02:14 +0100 Subject: [PATCH 076/566] adding easyconfigs: BLAT-3.5-intel-2016b.eb --- .../b/BLAT/BLAT-3.5-intel-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb new file mode 100644 index 0000000000..48a47daaa1 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.5' + +homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' +description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +source_urls = ['http://users.soe.ucsc.edu/~kent/src'] + +dependencies = [('libpng', '1.6.23')] + +buildopts = 'CC="$CC" COPT= L="$LIBS"' + +files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', + 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 2f20fd4e1aa1e702281a703d7bc114752e1d9b4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 18:07:11 +0100 Subject: [PATCH 077/566] adding easyconfigs: STAR-2.5.2b-intel-2016b.eb --- .../s/STAR/STAR-2.5.2b-intel-2016b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb new file mode 100644 index 0000000000..05c3e56c2f --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb @@ -0,0 +1,43 @@ +# 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 +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.2b' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ["bin/STAR", "bin/STARlong"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 1dbcd246623116c0cde17cb04e85f87b6cba548d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:07:23 +0800 Subject: [PATCH 078/566] yet another batch of minor style fixes --- .../j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb | 2 +- .../jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index 07eff74434..4dba96087d 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -10,7 +10,7 @@ version = '2.1.10r20160303' versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" +description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index ecf1089f64..37a4b9dd9a 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -9,7 +9,7 @@ name = 'jModelTest' version = '2.1.9r20160115' homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" +description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 86c6bb0e2a0d992ba77efcc6a0577127d18a7b11 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:25:41 +0800 Subject: [PATCH 079/566] yet another batch of minor style fixes --- easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb | 4 ++-- .../easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb | 8 +++----- .../easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 3 ++- .../l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb | 2 +- .../l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb | 2 +- .../easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb | 2 +- .../l/libreadline/libreadline-6.2-goolf-1.7.20.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-5.4.0.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb | 8 ++++---- .../easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb | 5 +++-- .../l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-foss-2015b.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-foss-2016a.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-intel-2015b.eb | 8 ++++---- 22 files changed, 58 insertions(+), 55 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb index 4228c8e824..59f694676c 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb @@ -29,8 +29,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb index c5eee2ec3d..daaaa15ecd 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb @@ -4,10 +4,8 @@ name = 'LevelDB' version = '1.18' homepage = 'https://github.com/google/leveldb' -description = """ -LevelDB is a fast key-value storage library written at Google that provides an -ordered mapping from string keys to string values. -""" +description = """LevelDB is a fast key-value storage library written at Google that provides an + ordered mapping from string keys to string values.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -19,7 +17,7 @@ files_to_copy = [ (['include/leveldb/*.h'], 'include/leveldb') ] -postinstallcmds=[ +postinstallcmds = [ 'cd %(installdir)s/lib; ln -s libleveldb.so.%(version)s libleveldb.so.%(version_major)s', 'cd %%(installdir)s/lib; ln -s libleveldb.so.%%(version)s libleveldb.%s' % SHLIB_EXT, ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb index 56cf148c48..593afa9ec4 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb @@ -16,7 +16,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb index 08a7cf496f..928179dc39 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb @@ -20,7 +20,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index accf89b9e8..785074f0f9 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -20,7 +20,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb index 8b0e336093..b4b7228f14 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb index 0f71868663..bc42f60686 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 68589245d1..0e45004907 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 60cd626d31..2316d70175 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb index ea33d4f180..e34d4affc3 100644 --- a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/xf86vmode.h']+ + 'files': ['include/X11/extensions/xf86vmode.h'] + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb index 873ae3da80..1fb8f730cc 100644 --- a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/xf86vmode.h']+ + 'files': ['include/X11/extensions/xf86vmode.h'] + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb index b76c98f402..7caa32f2db 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb @@ -19,7 +19,7 @@ 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)], + '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'], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb index be707f2f9d..6d2b145e5d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "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' : [], + '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/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb index 12e011a8ed..ade9c01fee 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] 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' : [], + '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/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 1710b5c8bc..8708402541 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '5.9')] 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' : [], + '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/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb index a4fb8619cb..7bfc1d634c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '5.9')] 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' : [], + '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/libreadline/libreadline-6.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb index c434630db4..33e6e24615 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '6.0')] 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' : [], + '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/libsmm/libsmm-20111205-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb index d7907d8655..ca93b0d47a 100644 --- a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb @@ -2,8 +2,9 @@ name = 'libsmm' version = '20111205' homepage = 'http://cp2k.berlios.de/index.html' -description = """libsmm is part of CP2K. It is a library tuned for small size matrix multiplication, - an area where regular BLAS is not so well-tuned. The source can be found in the tools/build_libssm directory of CP2K code.""" +description = """libsmm is part of CP2K. It is a library tuned for small size matrix multiplication, an area where + regular BLAS is not so well-tuned. The source can be found in the tools/build_libssm directory of CP2K code.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['CP2K-%s.tar.gz' % version] diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb index 6d7bea7d3d..5c7a628aaf 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb index 3c6b226b5a..57b9a33b63 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb index 052063704a..25d25c5148 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb index 19e0b26c92..bf35428b39 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb @@ -17,10 +17,10 @@ patches = ['libunistring_icc_builtin_nan-inf.patch'] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' -- GitLab From 204a49a722c80e724b395046c744d92ea1076f6b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:27:35 +0800 Subject: [PATCH 080/566] yet another batch of minor style fixes --- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 3 ++- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb | 3 ++- easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb | 7 +++---- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 7 ++++--- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 4 ++-- .../m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb | 9 +++------ .../easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb | 1 - .../m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb | 6 ++++-- .../easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 4 ++-- .../m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb | 2 +- .../m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb | 2 +- .../m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb | 2 +- .../m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb | 2 +- .../m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb | 8 ++++---- .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb | 2 +- .../m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb | 2 +- 22 files changed, 39 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index f289c8d654..c29dfc7a1a 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -2,7 +2,8 @@ name = 'MVAPICH2' version = '1.8.1' homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' -description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. It is based on MPICH2 and MVICH." +description = """This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. + It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb index 372dd0b722..777e5a69e1 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb @@ -2,7 +2,8 @@ name = 'MVAPICH2' version = '1.9a2' homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' -description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. It is based on MPICH2 and MVICH." +description = """This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. + It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb index b78da99d83..8357cd6199 100644 --- a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -8,16 +8,15 @@ name = 'Maq' version = '0.7.0' homepage = 'http://maq.sourceforge.net/maq-man.shtml' -description = """ Maq is a software that builds mapping -assemblies from short reads generated by the -next-generation sequencing machines. """ +description = """Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing + machines.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://sourceforge.net/projects/maq/files/maq/%(version)s/'] sources = ['maq-%(version)s_x86_64-linux.tar.bz2'] -checksums= ["65edff1529c84783d0a4b9208a91efa9"] +checksums = ["65edff1529c84783d0a4b9208a91efa9"] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index 57483e1d4f..ea99e518c2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '7.11.2' homepage = 'http://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - -a system for rendering interactive 3D graphics.""" + a system for rendering interactive 3D graphics.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} @@ -37,8 +38,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index ac83c1243a..55c990890f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -39,8 +39,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 810e10d3bb..4b5ad07db8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -39,8 +39,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb index 04f7962ec3..8c234a753f 100644 --- a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb @@ -4,11 +4,8 @@ name = 'Metal' version = '2011-03-25' homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' -description = """ -Metal - Meta Analysis Helper -The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a - convenient, rapid and memory efficient manner. -""" +description = """Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large + datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.""" sources = ['generic-%(namelower)s-%(version)s.tar.gz'] source_urls = ['http://csg.sph.umich.edu/abecasis/Metal/download/'] @@ -18,7 +15,7 @@ toolchainopts = {'pic': True} patches = ['Metal-%(version)s_Makefile.patch'] -skipsteps=['configure'] +skipsteps = ['configure'] buildopts = 'all' diff --git a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb index 8523144221..947de950b4 100644 --- a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb @@ -28,4 +28,3 @@ sanity_check_paths = { } moduleclass = 'bio' - 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 index 50e766c0ce..c6a015a815 100644 --- 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 @@ -24,8 +24,10 @@ 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 + # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), + ] # firt move to folder libStatGen to run make clean && make diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb index ba77602cd4..4c07b64293 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -5,7 +5,7 @@ version = '2.0.0' homepage = 'http://icl.cs.utk.edu/magma/' description = """The MAGMA project aims to develop a dense linear algebra library similar to -LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} @@ -15,7 +15,7 @@ source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] patches = [('magma-2.0.0.patch')] -builddependencies = [ ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE) ] +builddependencies = [('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb index 08d2e9759c..73545656c9 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb index 221229e3a6..763ccba836 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb index 5d19338ab3..dab01e8798 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb index b6703cee30..4aa55f0033 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index ee1c589750..eb46a80abe 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb index 1673c64e60..62f71cc876 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb index 23fd809bd7..1b74bd9124 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb index 3a9a7c7e64..91ed160613 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb @@ -4,9 +4,9 @@ name = 'motif' version = '2.3.5' homepage = 'http://motif.ics.com/' -description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building - applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. - It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for + building applications that follow that specification under the X Window System on Unix and other POSIX-compliant + systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" toolchain = {'name': 'foss', 'version': '2016a'} # use -O1 to dance around icc segfaulting @@ -42,4 +42,4 @@ sanity_check_paths = { 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], } -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb index 2b7c9b71bd..fb05915a84 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -21,7 +21,7 @@ parallel = 1 buildopts = ' CC="$CC"' -files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] +files_to_copy = [(['mrfast'], 'bin'), "LICENSE"] sanity_check_paths = { 'files': ["bin/mrfast"], diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb index 086efed6cd..1bc0838af6 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -21,7 +21,7 @@ parallel = 1 buildopts = ' CC="$CC"' -files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] +files_to_copy = [(['mrfast'], 'bin'), "LICENSE"] sanity_check_paths = { 'files': ["bin/mrfast"], diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb index 7da0c48dde..e58c648eee 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -24,7 +24,7 @@ patches = ['mrsFAST-%(version)s-intel-compiler.patch'] parallel = 1 -files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] +files_to_copy = [(['mrsfast'], 'bin'), "Changelog"] sanity_check_paths = { 'files': ["bin/mrsfast"], diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb index fda1eaa51f..933177a5af 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -24,7 +24,7 @@ patches = ['mrsFAST-%(version)s-intel-compiler.patch'] parallel = 1 -files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] +files_to_copy = [(['mrsfast'], 'bin'), "Changelog"] sanity_check_paths = { 'files': ["bin/mrsfast"], -- GitLab From 78a9d5a38696a3871b1c9a30cc838f5a3a6a2274 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 9 Mar 2017 17:42:47 +1030 Subject: [PATCH 081/566] PileOMeth added --- .../p/PileOMeth/PileOMeth-0.1.11.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb new file mode 100644 index 0000000000..af4dcdba98 --- /dev/null +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +### + +easyblock = 'MakeCp' + +name = 'PileOMeth' +version = '0.1.11' + +homepage = 'https://github.com/dpryan79/PileOMeth' +description = """PileOMeth processes a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments. +PileOMeth extracts per-base methylation metrics from them. +PileOMeth requires an indexed fasta file containing the reference genome as well. +""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(version)s.zip'] +source_urls = ['https://github.com/dpryan79/PileOMeth/archive/'] + +dependencies = [ + ('HTSlib', '1.2.1', '', ('foss', '2017a')) +] + +files_to_copy = [ + (["PileOMeth"], "bin"), "*.c", "*.h" +] + +sanity_check_paths = { + 'files': ["bin/PileOMeth"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e1b83120c8d9ac9a9753f21956a8e66d731a0242 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 09:40:33 +0100 Subject: [PATCH 082/566] miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 8a8e1422a7..7f489ba651 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -20,10 +20,13 @@ dependencies = [ ('randfold', '2.0.1'), # also provides SQUID ] -install_cmd = "chmod a+x mirdeep*/src/*.pl && cp -a mirdeep*/src %(installdir)s/bin" +install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " + +# scripts include a hard check for a file called 'install_successful' in the install directory... +install_cmd += "touch %(installdir)s/install_successful" sanity_check_paths = { - 'files': ['bin/make_html.pl'], + 'files': ['bin/mapper.pl', 'bin/miRDeep2.pl'], 'dirs': [], } -- GitLab From a2c62538a6049740584c8c668082799db24e404f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 9 Mar 2017 10:45:09 +0100 Subject: [PATCH 083/566] added GFOLD easyconfig for goolf and intel --- .../g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb | 34 +++++++++++++++++++ .../g/GFOLD/GFOLD-1.1.4-intel-2016a.eb | 34 +++++++++++++++++++ .../g/GFOLD/gfold-1.1.4-makefile.patch | 18 ++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..8d11408e6b --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.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 = 'MakeCp' + +name = 'GFOLD' +version = '1.1.4' + +homepage = 'http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html' +description = 'Generalized fold change for ranking differentially expressed genes from RNA-seq data' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://bitbucket.org/feeldead/gfold/downloads/'] +sources = ['%(namelower)s.V%(version)s.tar.gz'] + +patches = ['gfold-%(version)s-makefile.patch'] + +dependencies = [ + ('GSL', '1.16'), +] + +files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..3b289b47ea --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.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 = 'MakeCp' + +name = 'GFOLD' +version = '1.1.4' + +homepage = 'http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html' +description = 'Generalized fold change for ranking differentially expressed genes from RNA-seq data' + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/feeldead/gfold/downloads/'] +sources = ['%(namelower)s.V%(version)s.tar.gz'] + +patches = ['gfold-%(version)s-makefile.patch'] + +dependencies = [ + ('GSL', '1.16'), +] + +files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch new file mode 100644 index 0000000000..15699d96ba --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -0,0 +1,18 @@ +fix the hardcoded compiler + +diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile +--- gfold.V1.1.4.orig/Makefile 2015-05-24 01:47:13.000000000 +0200 ++++ gfold.V1.1.4/Makefile 2017-03-09 10:32:23.919031000 +0100 +@@ -5,10 +5,10 @@ + all: program + + debug: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc +- g++ -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} -Wall -g main.cc -o gfold -lgsl -lgslcblas + + program: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc +- g++ -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas + + docu: doc/gfold.pod + pod2man doc/gfold.pod > doc/gfold.man -- GitLab From 4f92b9fa68fb297f350a600d382f67e09cb723f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:04:34 +0100 Subject: [PATCH 084/566] adding easyconfigs: GDAL-2.1.3-foss-2016b-Python-2.7.12.eb --- .../GDAL-2.1.3-foss-2016b-Python-2.7.12.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0f954c1b05 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +#patches = ['GDAL-2.1.2_fix-vrtsources.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +# there is a bug in the build system causing the build with libtool to fail for the moment +# (static library is also missing because of this) +#configopts += ' --without-libtool' + +#buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' -- GitLab From b7eee70912a1b3dc6722c933b62449e870a44ffa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:04:52 +0100 Subject: [PATCH 085/566] adding easyconfigs: PROJ-4.9.3-foss-2016b.eb --- .../p/PROJ/PROJ-4.9.3-foss-2016b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb new file mode 100644 index 0000000000..7c6ed61f58 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -0,0 +1,57 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-55-44 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 94.84, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", 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"system_python_path": "/usr/bin/python", + "timestamp": 1488891344, + "total_memory": 64303, +}] -- GitLab From 6e355d309317b055b0623b27a22b1a1ff72f6f2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:07:54 +0100 Subject: [PATCH 086/566] adding easyconfigs: GEOS-3.6.1-foss-2016b-Python-2.7.12.eb, SWIG-3.0.11-foss-2016b-Python-2.7.12.eb --- .../GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 55 +++++++++++++++++++ .../SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 47 ++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ff17f25dff --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,55 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_14-08-23 +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.12')] + +builddependencies = [('SWIG', '3.0.11', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' + +# Build statistics +buildstats = [{ + "build_time": 431.44, + "command_line": 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b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bd7c62c123 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,47 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_14-01-11 +name = 'SWIG' +version = '3.0.11' +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': 'foss', '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' + +# Build statistics +buildstats = [{ + "build_time": 62.35, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", 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2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 5103738, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmpn3FMec/gcc", + "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", + "timestamp": 1488891671, + "total_memory": 64303, +}] -- GitLab From 222de2e3bcc8228b30cb935fa60a8e9e27fa2b9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:08:12 +0100 Subject: [PATCH 087/566] adding easyconfigs: libspatialindex-1.8.5-foss-2016b.eb --- .../libspatialindex-1.8.5-foss-2016b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb new file mode 100644 index 0000000000..33443350fb --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -0,0 +1,46 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-58-08 +easyblock = 'ConfigureMake' + +name = 'libspatialindex' +version = '1.8.5' + +homepage = 'http://libspatialindex.github.io' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/libspatialindex/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.a', 'lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 143.61, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 5693279, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmp07Ujmt/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1488891488, + "total_memory": 64303, +}] -- GitLab From 6191d257e6b77b205173a2ef627a9a8f8b81a01d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:08:50 +0100 Subject: [PATCH 088/566] adding easyconfigs: FreeXL-1.0.2-foss-2016b.eb --- .../f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb new file mode 100644 index 0000000000..1e91b6e6f0 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -0,0 +1,49 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-59-03 +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.2' + +homepage = "https://www.gaia-gis.it/fossil/freexl/index" +description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.7.1')] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] + } + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 55.18, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 205319, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmp6qSQU6/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1488891543, + "total_memory": 64303, +}] -- GitLab From 67d6b752d1bfb4e6abe3a7596f966e6a62de5e45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:12:37 +0100 Subject: [PATCH 089/566] remove buildstats --- .../p/PROJ/PROJ-4.9.3-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb index 7c6ed61f58..bd62ff7fdd 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -29,29 +29,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 94.84, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 4259625, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpNuI7H2/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891344, - "total_memory": 64303, -}] -- GitLab From 8367087c08ef9ae7372e516dc3c7952708051cfa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:13:40 +0100 Subject: [PATCH 090/566] remove buildstats --- .../GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 26 ------------------- .../SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 26 ------------------- 2 files changed, 52 deletions(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb index ff17f25dff..95a33702aa 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -27,29 +27,3 @@ sanity_check_paths = { } moduleclass = 'math' - -# Build statistics -buildstats = [{ - "build_time": 431.44, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 13415865, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpb49pQv/gcc", - "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", - "timestamp": 1488892103, - "total_memory": 64303, -}] diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb index bd7c62c123..ef67967e6e 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -19,29 +19,3 @@ dependencies = [ ] moduleclass = 'devel' - -# Build statistics -buildstats = [{ - "build_time": 62.35, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 5103738, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpn3FMec/gcc", - "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", - "timestamp": 1488891671, - "total_memory": 64303, -}] -- GitLab From b5c23e38fc28cceee226e97635e52133ab9ecc3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:13:40 +0100 Subject: [PATCH 091/566] remove buildstats --- .../libspatialindex-1.8.5-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb index 33443350fb..6393dbd967 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -18,29 +18,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 143.61, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 5693279, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmp07Ujmt/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891488, - "total_memory": 64303, -}] -- GitLab From 1cf8d4ec36e74b4eedd969376ccce569e18fd13f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:14:58 +0100 Subject: [PATCH 092/566] remove buildstats --- .../f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index 1e91b6e6f0..f20ffb2db6 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -21,29 +21,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 55.18, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 205319, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmp6qSQU6/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891543, - "total_memory": 64303, -}] -- GitLab From eb3e66959e2ab315db0c3819b436b186463b65a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:22:06 +0100 Subject: [PATCH 093/566] remove commented out lines --- .../g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb index 0f954c1b05..bc2162b8fb 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb @@ -16,8 +16,6 @@ toolchainopts = {'usempi': True} source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] -#patches = ['GDAL-2.1.2_fix-vrtsources.patch'] - dependencies = [ ('Python', '2.7.12'), ('netCDF', '4.4.1.1'), @@ -38,11 +36,6 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -# there is a bug in the build system causing the build with libtool to fail for the moment -# (static library is also missing because of this) -#configopts += ' --without-libtool' - -#buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -- GitLab From 9795a9c4c7c3d4ba24cbd1f0ace84bb7b426f937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:00:51 +0100 Subject: [PATCH 094/566] remove 'Built with' comments --- .../easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 1 - easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb | 1 - .../easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 1 - 3 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb index 95a33702aa..02e7eb0e40 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_14-08-23 easyblock = 'ConfigureMake' name = 'GEOS' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb index bd62ff7fdd..7b1bb021f3 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-55-44 ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb index ef67967e6e..645b771837 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_14-01-11 name = 'SWIG' version = '3.0.11' versionsuffix = '-Python-%(pyver)s' -- GitLab From 85ee43bb91417d48bb753d3e85f0427c50f03069 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:01:56 +0100 Subject: [PATCH 095/566] remove 'Built with' comment --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index f20ffb2db6..2775a19a49 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-59-03 easyblock = 'ConfigureMake' name = 'FreeXL' -- GitLab From 62fc9ea965433cb32529fb9b5e058a6fe5805367 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:03:24 +0100 Subject: [PATCH 096/566] remove 'Built with' comment --- .../l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb index 6393dbd967..5ff79fa5a7 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-58-08 easyblock = 'ConfigureMake' name = 'libspatialindex' -- GitLab From 7206a55c12c3eb2b748b83b94957030601c762b5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 13:22:27 +0100 Subject: [PATCH 097/566] add ${CXXFLAGS} to the patch file --- easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch index 15699d96ba..08f6097072 100644 --- a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -8,11 +8,11 @@ diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile debug: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc - g++ -Wall -g main.cc -o gfold -lgsl -lgslcblas -+ ${CXX} -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} ${CXXFLAGS} -Wall -g main.cc -o gfold -lgsl -lgslcblas program: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc - g++ -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas -+ ${CXX} -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} ${CXXFLAGS} -Wall -g main.cc -o gfold -lgsl -lgslcblas docu: doc/gfold.pod pod2man doc/gfold.pod > doc/gfold.man -- GitLab From 6efe46cb2ad1f6a29fb5a8268ff27a9fb7dd9c5e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 13:22:50 +0100 Subject: [PATCH 098/566] update the patch comment --- easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch index 08f6097072..23ba52ac63 100644 --- a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -1,4 +1,4 @@ -fix the hardcoded compiler +fix the hardcoded compiler and use ${CXXFLAGS} diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile --- gfold.V1.1.4.orig/Makefile 2015-05-24 01:47:13.000000000 +0200 -- GitLab From ff1bba6485cfb033f60e7a58f5442b49ff854d0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:49:40 +0100 Subject: [PATCH 099/566] fix minor style issue --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index 2775a19a49..b7981e18c5 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.7.1')] sanity_check_paths = { 'files': ['lib/libfreexl.a'], 'dirs': [] - } +} moduleclass = 'lib' -- GitLab From 76eec10c26deba272148df8e3229eab11166444c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:09:46 +0100 Subject: [PATCH 100/566] fix shebang in miRDeep2 Perl scripts --- easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 7f489ba651..de73467658 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -21,6 +21,7 @@ dependencies = [ ] install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " +install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From 31b0580e2f82fe48ac5901484363f8d60bcf4fdc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:34:50 +0100 Subject: [PATCH 101/566] adding easyconfigs: flex-2.6.3-GCCcore-5.4.0.eb, M4-1.4.18-GCCcore-5.4.0.eb, help2man-1.47.4-GCCcore-5.4.0.eb --- .../f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 23 +++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 19 ++++++++++++++ .../m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 25 +++++++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..5044907def --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -0,0 +1,23 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('binutils', '2.26'), + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..7b53bd8797 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.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': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..345402c605 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '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 = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b35c28b493af2a252f41971c1d3b492a7000460c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:36:09 +0100 Subject: [PATCH 102/566] adding easyconfigs: GDAL-2.1.3-intel-2016b-Python-2.7.12.eb --- .../GDAL-2.1.3-intel-2016b-Python-2.7.12.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..015f10d595 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' -- GitLab From 59df1b140f4267a1b1abfac49143a39edf87063c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:38:46 +0100 Subject: [PATCH 103/566] adding easyconfigs: QCA-2.1.3-intel-2016b.eb --- .../q/QCA/QCA-2.1.3-intel-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb new file mode 100644 index 0000000000..2b7816fd3c --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.1.3' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/src/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.7.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From f4c13b9569fe8b33ab8a8ebb5a38f51846cad3a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:39:12 +0100 Subject: [PATCH 104/566] adding easyconfigs: QJson-0.9.0-intel-2016b.eb --- .../q/QJson/QJson-0.9.0-intel-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb new file mode 100644 index 0000000000..44efa4db59 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7'), +] +builddependencies = [ + ('CMake', '3.7.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson.%s' % SHLIB_EXT], + 'dirs': ['include/qjson', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From 8c335a1b251205d9c90948cbdff9deca9386b26a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:39:36 +0100 Subject: [PATCH 105/566] adding easyconfigs: QScintilla2-2.10-intel-2016b-Python-2.7.12.eb --- ...intilla2-2.10-intel-2016b-Python-2.7.12.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..be392c7b0b --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'QScintilla2' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla2-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +start_dir = 'Qt4Qt5' + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@\$\$\[QT_INSTALL_LIBS\]@%(installdir)s/lib@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_HEADERS\]@%(installdir)s/include@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_TRANSLATIONS\]@%(installdir)s/trans@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_DATA\]@%(installdir)s/data@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_HOST_DATA\]@%(installdir)s/data@g' qscintilla.pro && " +prebuildopts += "qmake qscintilla.pro && " + +buildopts = 'CXXFLAGS="$CXXFLAGS \$(DEFINES)"' + +python_bindings_install_cmd = "cd ../Python && mkdir -p %(installdir)s/share/sip/PyQt4 && " +python_bindings_install_cmd += "python configure.py --destdir %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 --qsci-sipdir %(installdir)s/share/sip/PyQt4 --qsci-incdir %(installdir)s/include --qsci-libdir %(installdir)s/lib --pyqt-sipdir $EBROOTPYQT/share/sip/PyQt4 --apidir %(installdir)s/qsci/api/python --no-stubs && " +python_bindings_install_cmd += "make && make install && cd %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 && " +python_bindings_install_cmd += "for x in $(ls $EBROOTPYQT/lib/python2.7/site-packages/PyQt4); do ln -s $EBROOTPYQT/lib/python2.7/site-packages/PyQt4/$x; done && " +python_bindings_install_cmd += "rm __init__.py* && touch __init__.py" +postinstallcmds = [python_bindings_install_cmd] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libqscintilla2_qt4.so'], + 'dirs': ['include/Qsci', 'lib/python%(pyshortver)s/site-packages/PyQt4', 'qsci/api/python', 'share/sip/PyQt4', 'trans'], +} + +sanity_check_commands = ["python -c 'import PyQt4.Qsci'"] + +moduleclass = 'vis' -- GitLab From 8a542052a3ba44588900ab6efbc20a18a457e8a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:42:02 +0100 Subject: [PATCH 106/566] adding easyconfigs: QGIS-2.14.12-intel-2016b-Python-2.7.12.eb --- .../QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..abd1b36a0c --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '2.14.12' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['QGIS-2.14.12.patch'] + +dependencies = [ + ('Qt', '4.8.7'), + ('PROJ', '4.9.3'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), # stick to this version for compatibility with Python 2.7.12 + ('libspatialite', '4.3.0a'), + ('libspatialindex', '1.8.5'), + ('GDAL', '2.1.3', versionsuffix), + ('Qwt', '6.1.3'), + ('QwtPolar', '1.1.1'), + ('expat', '2.2.0'), + ('QCA', '2.1.3'), + ('PyQt', '4.12', versionsuffix), + # QScintilla2 must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla2', '2.10', versionsuffix), + ('GSL', '2.3'), + ('QJson', '0.9.0'), +] +builddependencies = [ + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +separate_build_dir = True + +configopts = '-DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson -DCMAKE_PREFIX_PATH=$EBROOTQT -DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so -DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4' + +buildopts = "VERBOSE=1 V=1" + +sanity_check_paths = { + 'files': ['bin/qgis'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From bb02a546f8c3ed7ac96345ed57cb7ccf8cdfc9d5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 14:52:18 +0100 Subject: [PATCH 107/566] style fixes --- .../disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 08032c986d..816f774c49 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -26,8 +26,10 @@ dependencies = [ # this application provides a python implementation and a C++ implementation # in the postinstallcmds we compile the C++ version -postinstallcmds = ['$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', - 'cp disambiguate %(installdir)s/bin/'] +postinstallcmds = [ + '$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + 'cp disambiguate %(installdir)s/bin/' +] # workaround to avoid the import sanity check options = {'modulename': 'os'} -- GitLab From 7101d3a09bda45ed7591d2231f16a6e72148ec07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 16:42:59 +0100 Subject: [PATCH 108/566] update QScintilla easyconfig to use QScintilla easyblock, add easyconfig for QScintilla 2.9.4 --- ...cintilla-2.10-intel-2016b-Python-2.7.12.eb | 21 ++++++++ ...ntilla-2.10_fix-link-python-bindings.patch | 14 +++++ ...intilla-2.9.4-intel-2016b-Python-2.7.12.eb | 21 ++++++++ ...tilla-2.9.4_fix-link-python-bindings.patch | 14 +++++ ...intilla2-2.10-intel-2016b-Python-2.7.12.eb | 52 ------------------- 5 files changed, 70 insertions(+), 52 deletions(-) create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch delete mode 100644 easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a974a1c6ac --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch new file mode 100644 index 0000000000..cca6cde624 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch @@ -0,0 +1,14 @@ +add missing link to QScintilla library to correctly build Python bindings + +author: Kenneth Hoste (HPC-UGent) +--- QScintilla_gpl-2.10/Python/configure.py.orig 2017-03-08 14:29:36.344465661 +0100 ++++ QScintilla_gpl-2.10/Python/configure.py 2017-03-08 14:36:00.439001287 +0100 +@@ -1510,7 +1510,7 @@ + + libs = qmake_config.get('LIBS') + if libs: +- pro.write('LIBS += %s\n' % libs) ++ pro.write('LIBS += %s -lqscintilla2_qt4\n' % libs) + + if not opts.static: + pro.write(''' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..e3f0cde600 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch new file mode 100644 index 0000000000..3abd6f5965 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch @@ -0,0 +1,14 @@ +add missing link to QScintilla library to correctly build Python bindings + +author: Kenneth Hoste (HPC-UGent) +--- QScintilla_gpl-2.9.4/Python/configure.py.orig 2017-03-08 14:29:36.344465661 +0100 ++++ QScintilla_gpl-2.9.4/Python/configure.py 2017-03-08 14:36:00.439001287 +0100 +@@ -1510,7 +1510,7 @@ + + libs = qmake_config.get('LIBS') + if libs: +- pro.write('LIBS += %s\n' % libs) ++ pro.write('LIBS += %s -lqscintilla2\n' % libs) + + if not opts.static: + pro.write(''' diff --git a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb deleted file mode 100644 index be392c7b0b..0000000000 --- a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'QScintilla2' -version = '2.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.riverbankcomputing.com/software/qscintilla' -description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" - -toolchain = {'name': 'intel', 'version': '2016b'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s/QScintilla-%(version)s/'] -sources = ['QScintilla_gpl-%(version)s.tar.gz'] - -patches = ['QScintilla2-%(version)s_fix-link-python-bindings.patch'] - -dependencies = [ - ('Python', '2.7.12'), - ('PyQt', '4.12', versionsuffix), -] - -start_dir = 'Qt4Qt5' - -skipsteps = ['configure'] - -prebuildopts = "sed -i 's@\$\$\[QT_INSTALL_LIBS\]@%(installdir)s/lib@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_HEADERS\]@%(installdir)s/include@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_TRANSLATIONS\]@%(installdir)s/trans@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_DATA\]@%(installdir)s/data@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_HOST_DATA\]@%(installdir)s/data@g' qscintilla.pro && " -prebuildopts += "qmake qscintilla.pro && " - -buildopts = 'CXXFLAGS="$CXXFLAGS \$(DEFINES)"' - -python_bindings_install_cmd = "cd ../Python && mkdir -p %(installdir)s/share/sip/PyQt4 && " -python_bindings_install_cmd += "python configure.py --destdir %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 --qsci-sipdir %(installdir)s/share/sip/PyQt4 --qsci-incdir %(installdir)s/include --qsci-libdir %(installdir)s/lib --pyqt-sipdir $EBROOTPYQT/share/sip/PyQt4 --apidir %(installdir)s/qsci/api/python --no-stubs && " -python_bindings_install_cmd += "make && make install && cd %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 && " -python_bindings_install_cmd += "for x in $(ls $EBROOTPYQT/lib/python2.7/site-packages/PyQt4); do ln -s $EBROOTPYQT/lib/python2.7/site-packages/PyQt4/$x; done && " -python_bindings_install_cmd += "rm __init__.py* && touch __init__.py" -postinstallcmds = [python_bindings_install_cmd] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_paths = { - 'files': ['lib/libqscintilla2_qt4.so'], - 'dirs': ['include/Qsci', 'lib/python%(pyshortver)s/site-packages/PyQt4', 'qsci/api/python', 'share/sip/PyQt4', 'trans'], -} - -sanity_check_commands = ["python -c 'import PyQt4.Qsci'"] - -moduleclass = 'vis' -- GitLab From 058dd65ade21434c77d9b72656ae5863f2eaf3c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 16:53:26 +0100 Subject: [PATCH 109/566] QScintilla2 -> QScintilla, clean up configopts, enhance sanity check for QGIS --- .../QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index abd1b36a0c..d97a872052 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -28,8 +28,8 @@ dependencies = [ ('expat', '2.2.0'), ('QCA', '2.1.3'), ('PyQt', '4.12', versionsuffix), - # QScintilla2 must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 - ('QScintilla2', '2.10', versionsuffix), + # QScintilla must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), ] @@ -41,13 +41,16 @@ builddependencies = [ separate_build_dir = True -configopts = '-DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson -DCMAKE_PREFIX_PATH=$EBROOTQT -DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so -DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4' - -buildopts = "VERBOSE=1 V=1" +# specify locations that CMake can't figure out correctly +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4" sanity_check_paths = { - 'files': ['bin/qgis'], - 'dirs': [], + 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_networkanalysis.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], } moduleclass = 'geo' -- GitLab From 358985ef2ee5d86074951462c0d8a6c3a3533eb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 17:00:42 +0100 Subject: [PATCH 110/566] add patch for QGIS 2.14.12 --- .../QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 2 +- .../q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index d97a872052..9b31165cdc 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True, 'cstd': 'gnu++11'} source_urls = ['http://qgis.org/downloads/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['QGIS-2.14.12.patch'] +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] dependencies = [ ('Qt', '4.8.7'), diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch new file mode 100644 index 0000000000..2eb3299a7d --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch @@ -0,0 +1,14 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +--- qgis-2.14.12/cmake/SIPMacros.cmake.orig 2017-03-09 12:57:14.037320233 +0100 ++++ qgis-2.14.12/cmake/SIPMacros.cmake 2017-03-09 13:05:55.739057294 +0100 +@@ -102,7 +102,7 @@ + ENDIF(PEDANTIC) + + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_abs_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} -I$ENV{EBROOTPYQT}/share/sip/PyQt4 ${_abs_module_sip}) + SET(SUPPRESS_SIP_WARNINGS FALSE CACHE BOOL "Hide SIP warnings") + MARK_AS_ADVANCED(SUPPRESS_SIP_WARNINGS) + IF(SUPPRESS_SIP_WARNINGS) -- GitLab From 616fe782803b18052ff11d6a1fc6eba545cb57e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 17:37:13 +0100 Subject: [PATCH 111/566] fix $EBROOT for QScintilla --- .../q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index 9b31165cdc..43245eb873 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -43,8 +43,8 @@ separate_build_dir = True # specify locations that CMake can't figure out correctly configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " -configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so " -configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4" +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt4" sanity_check_paths = { 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, -- GitLab From c326a3be445d0ad2f149747707daf4addd88ff7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:41:37 +0100 Subject: [PATCH 112/566] adding easyconfigs: libspatialite-4.3.0a-foss-2016b.eb --- .../libspatialite-4.3.0a-foss-2016b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb new file mode 100644 index 0000000000..c87d185cc1 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL', '1.0.2'), + ('GEOS', '3.6.1', '-Python-2.7.12'), + ('SQLite', '3.13.0'), + ('PROJ', '4.9.3'), +] + +builddependencies = [('CMake', '3.7.1')] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} + +moduleclass = 'lib' -- GitLab From de1032dfcb6d247eb98e23a8f63146c82dc6f57d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:56:54 +0100 Subject: [PATCH 113/566] adding easyconfigs: PyQt-4.12-foss-2016b-Python-2.7.12.eb, SIP-4.19-foss-2016b-Python-2.7.12.eb --- .../PyQt-4.12-foss-2016b-Python-2.7.12.eb | 37 +++++++++++++++++++ .../SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb | 30 +++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f8e50daad2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] +sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('SIP', '4.19', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..be020214d2 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.12')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From fccbb78c76415fc8bafa07811b51c091e3bcf9a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:57:53 +0100 Subject: [PATCH 114/566] also enable installation of SIP files in PyQt 4.12 easyconfig used intel/2016b --- .../easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb index 9ea42178d7..8afd4b1225 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ dependencies = [ configopts = "configure-ng.py --confirm-license" configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " -configopts += " --no-sip-files" +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" options = {'modulename': '%(name)s%(version_major)s'} -- GitLab From f1dba5919c4d1a1081412e33b37fa8d863b53904 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:00:15 +0100 Subject: [PATCH 115/566] include binutils as build dep in flex/help2man/M4 easyconfigs using GCCcore/5.4.0 --- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 3 ++- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 5 +++++ easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 3 +++ 3 files changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb index 5044907def..fea2687908 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -15,9 +15,10 @@ checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] dependencies = [('M4', '1.4.18')] builddependencies = [ - ('binutils', '2.26'), ('Bison', '3.0.4'), ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb index 7b53bd8797..0d730043fb 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -11,6 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), +] + sanity_check_paths = { 'files': ['bin/help2man'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 345402c605..c1c1439bf3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -13,6 +13,9 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] 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" -- GitLab From dfb169134cb268f9ae36f937ba2e650e605ef173 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:05:28 +0100 Subject: [PATCH 116/566] adding easyconfigs: QwtPolar-1.1.1-foss-2016b.eb, Qwt-6.1.3-foss-2016b.eb --- .../easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb | 29 +++++++++++++++++++ .../q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb new file mode 100644 index 0000000000..f2b00bf192 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.3' + +homepage = 'http://qwt.sourceforge.net/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qt', '4.8.7'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@QWT_INSTALL_PREFIX[ ]*=.*@QWT_INSTALL_PREFIX = %(installdir)s@g' qwtconfig.pri && " +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb new file mode 100644 index 0000000000..bf12b1ad5e --- /dev/null +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'QwtPolar' +version = '1.1.1' + +homepage = 'http://qwtpolar.sourceforge.net/' +description = "The QwtPolar library contains classes for displaying values on a polar coordinate system." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qwt', '6.1.3'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@INSTALL_PREFIX[ ]*=.*@INSTALL_PREFIX = %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " +prebuildopts += "qmake qwtpolar.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwtpolar.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' -- GitLab From cf4446f582499934c66770414128fd17c3b1f804 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:17:17 +0100 Subject: [PATCH 117/566] adding easyconfigs: QJson-0.9.0-foss-2016b.eb --- .../q/QJson/QJson-0.9.0-foss-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb new file mode 100644 index 0000000000..32b2329111 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7'), +] +builddependencies = [ + ('CMake', '3.7.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson.%s' % SHLIB_EXT], + 'dirs': ['include/qjson', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From b280b34714182becf501f1b79cb4f7c83d335a63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:17:47 +0100 Subject: [PATCH 118/566] adding easyconfigs: QCA-2.1.3-foss-2016b.eb --- .../easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb new file mode 100644 index 0000000000..4a94646890 --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.1.3' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/src/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.7.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From c21818052a0b1ca09202778fa7b6cb5361cb15aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:13:51 +0100 Subject: [PATCH 119/566] adding easyconfigs: QScintilla-2.10-foss-2016b-Python-2.7.12.eb, QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb --- ...Scintilla-2.10-foss-2016b-Python-2.7.12.eb | 21 +++++++++++++++++++ ...cintilla-2.9.4-foss-2016b-Python-2.7.12.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..13dd45e489 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f6edee2ee2 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' -- GitLab From 6b206c39bf1a05d066bf894be6ff0838dbe84ee8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:19:58 +0100 Subject: [PATCH 120/566] {geo}[foss/2016b] QGIS v2.18.4 --- .../QGIS-2.18.4-foss-2016b-Python-2.7.12.eb | 56 +++++++++++++++++++ .../q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch | 14 +++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f6d58e7bf7 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '2.18.4' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] + +dependencies = [ + ('Qt', '4.8.7'), + ('PROJ', '4.9.3'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), # stick to this version for compatibility with Python 2.7.12 + ('libspatialite', '4.3.0a'), + ('libspatialindex', '1.8.5'), + ('GDAL', '2.1.3', versionsuffix), + ('Qwt', '6.1.3'), + ('QwtPolar', '1.1.1'), + ('expat', '2.2.0'), + ('QCA', '2.1.3'), + ('PyQt', '4.12', versionsuffix), + # QScintilla must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla', '2.10', versionsuffix), + ('GSL', '2.3'), + ('QJson', '0.9.0'), +] +builddependencies = [ + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +separate_build_dir = True + +# specify locations that CMake can't figure out correctly +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt4" + +sanity_check_paths = { + 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_networkanalysis.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch new file mode 100644 index 0000000000..5d04066fb1 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch @@ -0,0 +1,14 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +--- qgis-2.18.4/cmake/SIPMacros.cmake.orig 2017-03-08 17:44:20.698576501 +0100 ++++ qgis-2.18.4/cmake/SIPMacros.cmake 2017-03-08 17:46:39.110172584 +0100 +@@ -96,7 +96,7 @@ + ADD_DEFINITIONS( /bigobj ) + ENDIF(MSVC) + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_abs_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} -I$ENV{EBROOTPYQT}/share/sip/PyQt4 ${_abs_module_sip}) + SET(SUPPRESS_SIP_WARNINGS FALSE CACHE BOOL "Hide SIP warnings") + MARK_AS_ADVANCED(SUPPRESS_SIP_WARNINGS) + IF(SUPPRESS_SIP_WARNINGS) -- GitLab From ad89278bbc144ca83fef7955ceb5580c69721100 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:37:17 +0100 Subject: [PATCH 121/566] also check with Tcl module syntax, Lua is the default in EasyBuild v3.x --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 13ca5c0612..07cebed738 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,11 +4,11 @@ env: matrix: - 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=5.8 EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=6.6.3 - - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=7.0 - - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Tcl matrix: # mark build as finished as soon as job has failed fast_finish: true -- GitLab From 64f3c1865cccb676751b50727b46261ffe3b92e5 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 12:25:14 +1030 Subject: [PATCH 122/566] Style fixed --- .../{PileOMeth-0.1.11.eb => PileOMeth-0.1.11-foss-2016b.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PileOMeth/{PileOMeth-0.1.11.eb => PileOMeth-0.1.11-foss-2016b.eb} (87%) diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb similarity index 87% rename from easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb rename to easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb index af4dcdba98..edf4ca1f37 100644 --- a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb @@ -19,17 +19,17 @@ description = """PileOMeth processes a coordinate-sorted and indexed BAM or CRAM PileOMeth extracts per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'foss', 'version': '2016b'} sources = ['%(version)s.zip'] source_urls = ['https://github.com/dpryan79/PileOMeth/archive/'] dependencies = [ - ('HTSlib', '1.2.1', '', ('foss', '2017a')) + ('HTSlib', '1.2.1') ] files_to_copy = [ - (["PileOMeth"], "bin"), "*.c", "*.h" + (["PileOMeth"], "bin"), ] sanity_check_paths = { -- GitLab From c0d6c2c7a08c93059ce58bcb0970daac4738744d Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 12:27:59 +1030 Subject: [PATCH 123/566] HTSlib added --- .../h/HTSlib/HTSlib-1.2.1-foss-2016b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb new file mode 100644 index 0000000000..66babc415c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb @@ -0,0 +1,39 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Acknowledgement:: +# Original Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +## + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.2.1' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 94d3b3ff4ea86240bfbb2b4a06361d80410076f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:27:41 +0100 Subject: [PATCH 124/566] also copy Rfam_for_miRDeep.fa to mirDeep2 bin directory --- easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index de73467658..466cd04f4d 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -22,6 +22,7 @@ dependencies = [ install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' +install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s/bin/ && " # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From e5f020956911d15e337bfa2f7a0fd140843d84f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:36:31 +0100 Subject: [PATCH 125/566] adding easyconfigs: requests-2.13.0-foss-2016b-Python-2.7.12.eb, requests-2.13.0-intel-2016b-Python-2.7.12.eb --- ...equests-2.13.0-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ ...quests-2.13.0-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2546a92787 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans""" + +toolchain = {'name': 'foss', '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-2.13.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3d08d7d724 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +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' -- GitLab From bdee396c0c108c92a0ea57f8540ed45571e7aa4f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:46:42 +0100 Subject: [PATCH 126/566] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb index a2bf4ab035..b3d257608f 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -33,4 +33,8 @@ configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_ configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 398343a8cdb5277b46ab50061bb26bf009c7126e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:47:44 +0100 Subject: [PATCH 127/566] fix PostgreSQL homepage + minor style fixes --- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 15 +++++++-------- .../PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 10 ++++++---- .../PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 10 ++++++---- .../PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb | 8 ++++---- 4 files changed, 23 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index b694510474..8b0668a68f 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PostgreSQL' version = '9.3.5' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' 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). @@ -18,18 +18,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] - -java = 'Java' -javaver = '1.7.0_60' - dependencies = [ - (java, javaver, '', True), + ('Java', '1.7.0_60', '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # 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', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.2'), ('flex', '2.5.39'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index a7d2b6c4a0..6302a94b89 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.4.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' 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). @@ -19,15 +19,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # 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', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.4'), ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index 46e78c9224..c49c4abba6 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' 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). @@ -19,15 +19,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # 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', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.4'), ('flex', '2.6.0'), 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 index 8f8750717c..67556bd516 100644 --- 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 @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.6.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' 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). @@ -19,13 +19,13 @@ 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 + # 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', '1.0.1i'), ] builddependencies = [ -- GitLab From 51bbcc9046b2b2825a455be134d694e4bb7ba615 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:48:03 +0100 Subject: [PATCH 128/566] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb index f56b457e0d..99a4b3d8d6 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb @@ -33,4 +33,8 @@ configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-x configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 526cbfca04174161d69fd149e9e407c9e313cc56 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:50:15 +0100 Subject: [PATCH 129/566] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index a263fbc4af..c111bdfea0 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -38,4 +38,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 7c1a1484d29b05d06349acaa11a8829e87a1caf0 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:51:16 +0100 Subject: [PATCH 130/566] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb index 4f55d64d72..a90994c1ab 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -38,4 +38,8 @@ configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdi configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From eaa6b52cb1d25ecd15bb5ac553cbc3771b02b9fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:53:30 +0100 Subject: [PATCH 131/566] adding easyconfigs: psycopg2-2.7-intel-2016b-Python-2.7.12.eb, psycopg2-2.7-foss-2016b-Python-2.7.12.eb, PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb, PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb --- ...stgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb | 46 +++++++++++++++++++ ...tgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb | 46 +++++++++++++++++++ .../psycopg2-2.7-foss-2016b-Python-2.7.12.eb | 25 ++++++++++ .../psycopg2-2.7-intel-2016b-Python-2.7.12.eb | 25 ++++++++++ 4 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..537ebb2758 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.postgresql.org/' +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.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +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' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9d98aaa673 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.postgresql.org/' +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +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' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..948a2bd8f6 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://initd.org/psycopg/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PostgreSQL', '9.6.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3ac0511ce1 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://initd.org/psycopg/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PostgreSQL', '9.6.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From ba956899575eb5c51c8ef37229213151fdcafad1 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:54:43 +0100 Subject: [PATCH 132/566] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb index 81b811dc89..80a084ac4d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb @@ -36,4 +36,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 412ba617c5167ddb3593007a38cb0820f7c1702a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:56:02 +0100 Subject: [PATCH 133/566] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index 9dd615415d..718fb2f36d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -54,4 +54,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 83e7f94a3fea698444e22140da2fc3b7eb97f119 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:56:58 +0100 Subject: [PATCH 134/566] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index b51c955db4..d8466b4858 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -54,4 +54,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From e80f2a6d6aa67ace904af25a62af8efe2646b08a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:57:41 +0100 Subject: [PATCH 135/566] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb index 2ddf7531c8..6d3d2000b8 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb @@ -52,4 +52,8 @@ configopts += ' --with-x11-libdir=$EBROOTX11/lib --with-xext-libdir=$EBROOTLIBX1 configopts += ' --with-xft-libdir=$EBROOTX11/lib' configopts += ' --with-xpm-incdir=$EBROOTX11/include --with-xpm-libdir=$EBROOTX11/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 17e252c4b0b1c3fcb5830d97cb42bcd636e394f8 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 11:09:37 +0100 Subject: [PATCH 136/566] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index a8ab1f540d..f662b0deda 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -42,4 +42,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From e0b7bd52bbfda4bec6fca382313bd6b7825276ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 11:11:42 +0100 Subject: [PATCH 137/566] fix location for Rfam_for_miRDeep.fa --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 466cd04f4d..83e5129dff 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -22,7 +22,7 @@ dependencies = [ install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' -install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s/bin/ && " +install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s && " # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From f2326dc17da8f931f34c89935d2c5572dd788645 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 11:16:20 +0100 Subject: [PATCH 138/566] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 5801dbe265..6073d0e56c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -56,4 +56,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 7487ef4bd7ec0e279be25ab423ec2b9be38f1e38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 11:21:12 +0100 Subject: [PATCH 139/566] detect use of '$root', which is not compatible with module files in Lua syntax --- test/easyconfigs/easyconfigs.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 551695c259..993e9395ba 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -235,6 +235,11 @@ def template_easyconfig_test(self, spec): self.assertTrue(name, app.name) self.assertTrue(ec['version'], app.version) + # make sure that $root is not used, since it is not compatible with module files in Lua syntax + res = re.findall('.*\$root.*', ec.rawtxt, re.M) + error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" + self.assertFalse(res, error_msg % res) + # make sure all patch files are available specdir = os.path.dirname(spec) specfn = os.path.basename(spec) -- GitLab From 667725596613b792b086d6356b7e6cdc7c22326a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 10 Mar 2017 11:57:26 +0100 Subject: [PATCH 140/566] added $CXXFLAGS --- .../disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 816f774c49..7de0a8ea92 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -27,7 +27,7 @@ dependencies = [ # this application provides a python implementation and a C++ implementation # in the postinstallcmds we compile the C++ version postinstallcmds = [ - '$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + '$CXX $CXXFLAGS -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', 'cp disambiguate %(installdir)s/bin/' ] -- GitLab From 75998c8fd4ad81ef8b43d41152800e059a3adc88 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 21:55:20 +1030 Subject: [PATCH 141/566] style fixed --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb index 66babc415c..a58dae978a 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], 'dirs': [], } -- GitLab From d1132ead52ea73d356501e39a3b9b603dffb4c0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 13:12:07 +0100 Subject: [PATCH 142/566] add requests and psycopg2 as dependencies for QGIS --- .../q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index 43245eb873..4878b7d629 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -32,6 +32,8 @@ dependencies = [ ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), ] builddependencies = [ ('CMake', '3.7.2'), -- GitLab From 3d0c4aa8ab68e2d7fed93ce83b3f9652a7ad03f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 13:47:15 +0100 Subject: [PATCH 143/566] add requests and psycopg2 as dependencies for QGIS --- .../easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb index f6d58e7bf7..837899aa93 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb @@ -32,6 +32,8 @@ dependencies = [ ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), ] builddependencies = [ ('CMake', '3.7.2'), -- GitLab From 674ce7782bb9b25ee3721dbe0017218df74cd31b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 14:01:42 +0100 Subject: [PATCH 144/566] avoid use of '$root', replace with '%(installdir)s' --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 10 +++------- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 10 +++------- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 11 +++-------- .../MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 11 +++-------- .../m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb | 4 +--- .../easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 4 +--- .../easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 4 +--- 7 files changed, 15 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 56456bbd62..4c41ac6ece 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -25,16 +25,12 @@ dependencies = [ separate_build_dir = True -modextravars = { - 'ALPS_ROOT': '$root', -} -modextrapaths = { - 'PYTHONPATH': ['lib/'] -} - sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } +modextravars = {'ALPS_ROOT': '%(installdir)s'} +modextrapaths = {'PYTHONPATH': ['lib/']} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index f21285e25b..3d3e67389f 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -25,16 +25,12 @@ dependencies = [ separate_build_dir = True -modextravars = { - 'ALPS_ROOT': '$root', -} -modextrapaths = { - 'PYTHONPATH': ['lib/'] -} - sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } +modextravars = {'ALPS_ROOT': '%(installdir)s'} +modextrapaths = {'PYTHONPATH': ['lib']} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 21ae128381..6e3b23ba3c 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -31,17 +31,12 @@ postinstallcmds = [ "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s", ] -modextrapaths = { - 'CLASSPATH': 'lib', -} - -modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory -} - sanity_check_paths = { 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], 'dirs': [] } +modextravars = {'MPJ_HOME': '%(installdir)s'} +modextrapaths = {'CLASSPATH': 'lib'} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 41195e5042..8577e3deb4 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -34,17 +34,12 @@ postinstallcmds = [ "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s", ] -modextrapaths = { - 'CLASSPATH': 'lib', -} - -modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory -} - sanity_check_paths = { 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], 'dirs': [] } +modextravars = {'MPJ_HOME': '%(installdir)s'} +modextrapaths = {'CLASSPATH': 'lib'} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb index 44efa704ef..973e13d894 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -25,8 +25,6 @@ sanity_check_paths = { 'dirs': ["lib"], } -modextravars = { - 'PERL5LIB': '$root/lib' -} +modextrapaths = {'PERL5LIB': 'lib'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index 77fe169073..c6a5e3fa14 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -31,9 +31,7 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index 70198200d8..96ac9d6530 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -31,9 +31,7 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" -- GitLab From 7b5bab1965fb311d42f87d63078aa80dad41820f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Mar 2017 15:25:56 +0200 Subject: [PATCH 145/566] adding easyconfigs: Yasm-1.3.0-foss-2017a.eb, Yasm-1.3.0-intel-2017a.eb --- .../y/Yasm/Yasm-1.3.0-foss-2017a.eb | 31 +++++++++++++++++++ .../y/Yasm/Yasm-1.3.0-intel-2017a.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb new file mode 100644 index 0000000000..bae739cbfa --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb new file mode 100644 index 0000000000..f0db7e8256 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 7ab680ea704aa1db04f7db38635b33a760437b9a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Mar 2017 16:56:47 +0200 Subject: [PATCH 146/566] The patch is the result of applying the upstream patch and running the maintainer scripts to regenerate the interface files. --- .../f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch | 1527 +++++++++++++++++ .../f/FFTW/FFTW-3.3.6-gompi-2017a.eb | 4 + .../f/FFTW/FFTW-3.3.6-intel-2017a.eb | 29 + 3 files changed, 1560 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch new file mode 100644 index 0000000000..70d5168fbf --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch @@ -0,0 +1,1527 @@ +# The scrips that generate the MPI F03 interface was broken in 3.3.6-pl1 +# The scripts were using fftw3.h from /usr/include, not ../api, and were +# failing silently if fftw3.h was not installed. This bug led to a +# fftw-3.3.6pl1 release with incomplete mpi/f03 header files. +# See commit 83092f8efbf872aefe7cfc6ee8fa43412f8e167a in FFTW upstream +# git. +# +# This patch is the result of applying that commit and running the +# maintainer mode scripts. +# +# Åke Sandgrem 2017-03-07 +diff -ru fftw-3.3.6-pl1.orig/mpi/f03api.sh fftw-3.3.6-pl1/mpi/f03api.sh +--- fftw-3.3.6-pl1.orig/mpi/f03api.sh 2017-01-15 13:03:24.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03api.sh 2017-03-08 15:46:56.000000002 +0100 +@@ -37,7 +37,7 @@ + + echo + echo " interface" +- grep -v 'mpi.h' fftw3-mpi.h | gcc -D__GNUC__=5 -D__i386__ -E - |grep "fftw${p}_mpi_init" |tr ';' '\n' | perl ../api/genf03.pl ++ grep -v 'mpi.h' fftw3-mpi.h | gcc -I../api -D__GNUC__=5 -D__i386__ -E - |grep "fftw${p}_mpi_init" |tr ';' '\n' | perl ../api/genf03.pl + echo " end interface" + + done +diff -ru fftw-3.3.6-pl1.orig/mpi/f03-wrap.c fftw-3.3.6-pl1/mpi/f03-wrap.c +--- fftw-3.3.6-pl1.orig/mpi/f03-wrap.c 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03-wrap.c 2017-03-08 16:20:11.000000002 +0100 +@@ -3,3 +3,282 @@ + #include "fftw3-mpi.h" + #include "ifftw-mpi.h" + ++FFTW_EXTERN ptrdiff_t XM(local_size_many_transposed_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_many_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_transposed_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_many_1d_f03)(ptrdiff_t n0, ptrdiff_t howmany, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_1d_f03)(ptrdiff_t n0, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_2d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_3d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN X(plan) XM(plan_many_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, R * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block, ptrdiff_t tblock, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_1d_f03)(ptrdiff_t n0, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_r2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_f03)(int rnk, const ptrdiff_t * n, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, X(r2r_kind) kind2, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_r2c_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_f03)(int rnk, const ptrdiff_t * n, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_c2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN void XM(gather_wisdom_f03)(MPI_Fint f_comm_); ++FFTW_EXTERN void XM(broadcast_wisdom_f03)(MPI_Fint f_comm_); ++ ++ptrdiff_t XM(local_size_many_transposed_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many_transposed)(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_many_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many)(rnk,n,howmany,block0,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_transposed_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_transposed)(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size)(rnk,n,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_many_1d_f03)(ptrdiff_t n0, ptrdiff_t howmany, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many_1d)(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start); ++} ++ ++ptrdiff_t XM(local_size_1d_f03)(ptrdiff_t n0, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_1d)(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start); ++} ++ ++ptrdiff_t XM(local_size_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_2d)(n0,n1,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_2d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_2d_transposed)(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_3d)(n0,n1,n2,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_3d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_3d_transposed)(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++X(plan) XM(plan_many_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, R * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_transpose)(n0,n1,howmany,block0,block1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_transpose)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_many_dft_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block, ptrdiff_t tblock, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft)(rnk,n,howmany,block,tblock,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft)(rnk,n,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_1d_f03)(ptrdiff_t n0, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_1d)(n0,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_2d)(n0,n1,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_3d)(n0,n1,n2,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_many_r2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_r2r)(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags); ++} ++ ++X(plan) XM(plan_r2r_f03)(int rnk, const ptrdiff_t * n, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r)(rnk,n,in,out,comm,kind,flags); ++} ++ ++X(plan) XM(plan_r2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r_2d)(n0,n1,in,out,comm,kind0,kind1,flags); ++} ++ ++X(plan) XM(plan_r2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, X(r2r_kind) kind2, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r_3d)(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags); ++} ++ ++X(plan) XM(plan_many_dft_r2c_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft_r2c)(rnk,n,howmany,iblock,oblock,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_f03)(int rnk, const ptrdiff_t * n, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c)(rnk,n,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c_2d)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c_3d)(n0,n1,n2,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_many_dft_c2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft_c2r)(rnk,n,howmany,iblock,oblock,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r)(rnk,n,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r_2d)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r_3d)(n0,n1,n2,in,out,comm,flags); ++} ++ ++void XM(gather_wisdom_f03)(MPI_Fint f_comm_) ++{ ++ MPI_Comm comm_; ++ ++ comm_ = MPI_Comm_f2c(f_comm_); ++ XM(gather_wisdom)(comm_); ++} ++ ++void XM(broadcast_wisdom_f03)(MPI_Fint f_comm_) ++{ ++ MPI_Comm comm_; ++ ++ comm_ = MPI_Comm_f2c(f_comm_); ++ XM(broadcast_wisdom)(comm_); ++} +diff -ru fftw-3.3.6-pl1.orig/mpi/f03-wrap.sh fftw-3.3.6-pl1/mpi/f03-wrap.sh +--- fftw-3.3.6-pl1.orig/mpi/f03-wrap.sh 2017-01-15 13:03:24.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03-wrap.sh 2017-03-08 15:46:56.000000002 +0100 +@@ -15,8 +15,8 @@ + echo + + # Declare prototypes using FFTW_EXTERN, important for Windows DLLs +-grep -v 'mpi.h' fftw3-mpi.h | gcc -E - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl | grep "MPI_Fint" | sed 's/^/FFTW_EXTERN /;s/$/;/' ++grep -v 'mpi.h' fftw3-mpi.h | gcc -E -I../api - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl | grep "MPI_Fint" | sed 's/^/FFTW_EXTERN /;s/$/;/' + +-grep -v 'mpi.h' fftw3-mpi.h | gcc -E - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl ++grep -v 'mpi.h' fftw3-mpi.h | gcc -E -I../api - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl + + +diff -ru fftw-3.3.6-pl1.orig/mpi/fftw3l-mpi.f03.in fftw-3.3.6-pl1/mpi/fftw3l-mpi.f03.in +--- fftw-3.3.6-pl1.orig/mpi/fftw3l-mpi.f03.in 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/fftw3l-mpi.f03.in 2017-03-08 16:20:11.000000002 +0100 +@@ -8,4 +8,398 @@ + end type fftwl_mpi_ddim + + interface ++ subroutine fftwl_mpi_init() bind(C, name='fftwl_mpi_init') ++ import ++ end subroutine fftwl_mpi_init ++ ++ subroutine fftwl_mpi_cleanup() bind(C, name='fftwl_mpi_cleanup') ++ import ++ end subroutine fftwl_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftwl_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftwl_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwl_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftwl_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwl_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftwl_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftwl_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_transpose ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft ++ ++ type(C_PTR) function fftwl_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftwl_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftwl_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftwl_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) & ++ bind(C, name='fftwl_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r_3d ++ ++ subroutine fftwl_mpi_gather_wisdom(comm_) bind(C, name='fftwl_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwl_mpi_gather_wisdom ++ ++ subroutine fftwl_mpi_broadcast_wisdom(comm_) bind(C, name='fftwl_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwl_mpi_broadcast_wisdom ++ ++ subroutine fftwl_mpi_execute_dft(p,in,out) bind(C, name='fftwl_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft ++ ++ subroutine fftwl_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftwl_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_LONG_DOUBLE), dimension(*), intent(inout) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft_r2c ++ ++ subroutine fftwl_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftwl_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft_c2r ++ ++ subroutine fftwl_mpi_execute_r2r(p,in,out) bind(C, name='fftwl_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_LONG_DOUBLE), dimension(*), intent(inout) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_r2r ++ + end interface +diff -ru fftw-3.3.6-pl1.orig/mpi/fftw3-mpi.f03.in fftw-3.3.6-pl1/mpi/fftw3-mpi.f03.in +--- fftw-3.3.6-pl1.orig/mpi/fftw3-mpi.f03.in 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/fftw3-mpi.f03.in 2017-03-08 16:20:11.000000002 +0100 +@@ -13,6 +13,399 @@ + end type fftw_mpi_ddim + + interface ++ subroutine fftw_mpi_init() bind(C, name='fftw_mpi_init') ++ import ++ end subroutine fftw_mpi_init ++ ++ subroutine fftw_mpi_cleanup() bind(C, name='fftw_mpi_cleanup') ++ import ++ end subroutine fftw_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftw_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftw_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftw_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftw_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftw_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftw_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftw_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_transpose ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft ++ ++ type(C_PTR) function fftw_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft ++ ++ type(C_PTR) function fftw_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftw_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftw_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftw_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r ++ ++ type(C_PTR) function fftw_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftw_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftw_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) bind(C, name='fftw_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r_3d ++ ++ subroutine fftw_mpi_gather_wisdom(comm_) bind(C, name='fftw_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftw_mpi_gather_wisdom ++ ++ subroutine fftw_mpi_broadcast_wisdom(comm_) bind(C, name='fftw_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftw_mpi_broadcast_wisdom ++ ++ subroutine fftw_mpi_execute_dft(p,in,out) bind(C, name='fftw_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft ++ ++ subroutine fftw_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftw_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_DOUBLE), dimension(*), intent(inout) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft_r2c ++ ++ subroutine fftw_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftw_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft_c2r ++ ++ subroutine fftw_mpi_execute_r2r(p,in,out) bind(C, name='fftw_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_DOUBLE), dimension(*), intent(inout) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_r2r ++ + end interface + + type, bind(C) :: fftwf_mpi_ddim +@@ -20,4 +413,398 @@ + end type fftwf_mpi_ddim + + interface ++ subroutine fftwf_mpi_init() bind(C, name='fftwf_mpi_init') ++ import ++ end subroutine fftwf_mpi_init ++ ++ subroutine fftwf_mpi_cleanup() bind(C, name='fftwf_mpi_cleanup') ++ import ++ end subroutine fftwf_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftwf_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftwf_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwf_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftwf_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwf_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftwf_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftwf_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_transpose ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft ++ ++ type(C_PTR) function fftwf_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftwf_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftwf_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftwf_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) & ++ bind(C, name='fftwf_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r_3d ++ ++ subroutine fftwf_mpi_gather_wisdom(comm_) bind(C, name='fftwf_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwf_mpi_gather_wisdom ++ ++ subroutine fftwf_mpi_broadcast_wisdom(comm_) bind(C, name='fftwf_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwf_mpi_broadcast_wisdom ++ ++ subroutine fftwf_mpi_execute_dft(p,in,out) bind(C, name='fftwf_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft ++ ++ subroutine fftwf_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftwf_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_FLOAT), dimension(*), intent(inout) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft_r2c ++ ++ subroutine fftwf_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftwf_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft_c2r ++ ++ subroutine fftwf_mpi_execute_r2r(p,in,out) bind(C, name='fftwf_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_FLOAT), dimension(*), intent(inout) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_r2r ++ + end interface diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb index 039c1bb824..4325e0c729 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -12,6 +12,10 @@ source_urls = [homepage] sources = ['fftw-%(version)s-pl1.tar.gz'] checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + runtest = 'check' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb new file mode 100644 index 0000000000..07c5fa9224 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -0,0 +1,29 @@ +name = 'FFTW' +version = '3.3.6' + +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': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] + +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma +use_fma = False + +runtest = 'check' + +moduleclass = 'numlib' -- GitLab From 6f719a74f5ac27d67427c5cc6a1063745ced50ff Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 09:08:33 +0200 Subject: [PATCH 147/566] Updated the patch with the URL to the upstream commit from fftw git. --- .../easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch index 70d5168fbf..f09a971da7 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch @@ -2,13 +2,15 @@ # The scripts were using fftw3.h from /usr/include, not ../api, and were # failing silently if fftw3.h was not installed. This bug led to a # fftw-3.3.6pl1 release with incomplete mpi/f03 header files. -# See commit 83092f8efbf872aefe7cfc6ee8fa43412f8e167a in FFTW upstream -# git. +# +# See commit +# https://github.com/FFTW/fftw3/commit/83092f8efbf872aefe7cfc6ee8fa43412f8e167a +# in FFTW upstream git. # # This patch is the result of applying that commit and running the # maintainer mode scripts. # -# Åke Sandgrem 2017-03-07 +# Åke Sandgren, 2017-03-07 diff -ru fftw-3.3.6-pl1.orig/mpi/f03api.sh fftw-3.3.6-pl1/mpi/f03api.sh --- fftw-3.3.6-pl1.orig/mpi/f03api.sh 2017-01-15 13:03:24.000000002 +0100 +++ fftw-3.3.6-pl1/mpi/f03api.sh 2017-03-08 15:46:56.000000002 +0100 -- GitLab From 4a0b7275c165adf41ab75b4d3fc1082f51388bb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:05:20 +0100 Subject: [PATCH 148/566] {tools}LSMS-3_rev237 --- easybuild/easyconfigs/l/LSMS-3_rev237.eb | 31 ++++++ easybuild/easyconfigs/l/LSMS-Makefiles.patch | 106 +++++++++++++++++++ 2 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSMS-3_rev237.eb create mode 100644 easybuild/easyconfigs/l/LSMS-Makefiles.patch diff --git a/easybuild/easyconfigs/l/LSMS-3_rev237.eb b/easybuild/easyconfigs/l/LSMS-3_rev237.eb new file mode 100644 index 0000000000..014f9beea4 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS-3_rev237.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'LSMS' +version = '3_rev237' + +homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' +description = "LSMS benchmark, part of CORAL suite" + +toolchain = {'name': 'foss', 'version': '2015g' } + +source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] +sources = ['%(name)s_%(version)s.tar.bz2'] + +checksums = ['8c864c9223b93488663815557e61cd0b'] + +patches = ['LSMS-Makefiles.patch'] + +files_to_copy = ['bin/lsms', 'bin/wl-lsms'] + +buildopts = '-j 1' + +dependencies = [ + ('HDF5', '1.8.16'), +] + +sanity_check_paths = { + 'files': ['lsms', 'wl-lsms'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS-Makefiles.patch new file mode 100644 index 0000000000..5c1f5e5908 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS-Makefiles.patch @@ -0,0 +1,106 @@ +--- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 ++++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 +@@ -1,6 +1,29 @@ + dlvl = ./. + include $(dlvl)/Makefile.in +-include ../architecture.h ++ ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + all: alllib alltst + +--- LSMS_3_rev237/src/Test/buildKKRMatrixTest/Makefile 2012-02-15 19:41:17.000000000 +0100 ++++ LSMS_3_rev237_working/src/Test/buildKKRMatrixTest/Makefile 2017-03-09 15:47:04.088863802 +0100 +@@ -3,7 +3,29 @@ + export INC_PATH = + export LIBS := + +-include $(TOP_DIR)/architecture.h ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + export INC_PATH += -I $(TOP_DIR)/include -I $(TOP_DIR)/src + export MISC = $(TOP_DIR)/src/Misc +--- LSMS_3_rev237/Makefile 2017-03-09 15:47:50.699882415 +0100 ++++ LSMS_3_rev237_working/Makefile 2017-03-09 14:58:44.845436772 +0100 +@@ -1,10 +1,35 @@ + + export TOP_DIR = $(shell pwd) +-export INC_PATH = + # export LIBS := -L$(TOP_DIR)/lua/lib -llua $(TOP_DIR)/mjson/mjson.a + export LIBS := $(TOP_DIR)/lua/lib/liblua.a $(TOP_DIR)/mjson/mjson.a + +-include architecture.h ++export CC = gcc ++export CXX = g++ ++export F77 = gfortran ++ ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + + all: liblua $(ADDITIONAL_TARGETS) libmjson LSMS -- GitLab From bc135bc82da4d927fa86526d64fac52b273fd338 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:15:58 +0100 Subject: [PATCH 149/566] change directory and added toolchain to name --- .../l/{LSMS-3_rev237.eb => LSMS/LSMS-3_rev237-foss-2015g.eb} | 0 easybuild/easyconfigs/l/{ => LSMS}/LSMS-Makefiles.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/{LSMS-3_rev237.eb => LSMS/LSMS-3_rev237-foss-2015g.eb} (100%) rename easybuild/easyconfigs/l/{ => LSMS}/LSMS-Makefiles.patch (100%) diff --git a/easybuild/easyconfigs/l/LSMS-3_rev237.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb similarity index 100% rename from easybuild/easyconfigs/l/LSMS-3_rev237.eb rename to easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb diff --git a/easybuild/easyconfigs/l/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch similarity index 100% rename from easybuild/easyconfigs/l/LSMS-Makefiles.patch rename to easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch -- GitLab From 12a958880fea5a3840959fada778f82ab132238f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:33:54 +0100 Subject: [PATCH 150/566] change $root to $root/bin --- .../easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb index 014f9beea4..c708bb19a4 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb @@ -15,17 +15,18 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +files_to_copy = ['bin'] buildopts = '-j 1' -dependencies = [ - ('HDF5', '1.8.16'), +dependencies = [ + ('HDF5', '1.8.16'), ] sanity_check_paths = { - 'files': ['lsms', 'wl-lsms'], + 'files': ['bin/lsms', 'bin/wl-lsms'], 'dirs': [], } - + moduleclass = 'tools' -- GitLab From 8fe97272f49beba4d341c2b087eac159294f9606 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:45:25 +0100 Subject: [PATCH 151/566] remove singularity --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb deleted file mode 100644 index e1e43de48b..0000000000 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Singularity' -version = '2.2.1' - -homepage = 'http://gmkurtzer.github.io/singularity' -description = """Singularity is a portable application stack packaging and runtime utility.""" - -toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} - -source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] -sources = ['%(version)s.tar.gz'] - -builddependencies = [('Autotools', '20150215')] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], - 'dirs': ['etc', 'libexec/singularity'], -} - -moduleclass = 'tools' -- GitLab From c4732f5b681ee9ec959c2bf50470ff9c6b24704a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:09:46 +0100 Subject: [PATCH 152/566] add LSMS-3_rev237-foss-2016a --- .../l/LSMS/LSMS-3_rev237-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb new file mode 100644 index 0000000000..ff6c8b7de3 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'LSMS' +version = '3_rev237' + +homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' +description = "LSMS benchmark, part of CORAL suite" + +toolchain = {'name': 'foss', 'version': '2016a' } + +source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] +sources = ['%(name)s_%(version)s.tar.bz2'] + +checksums = ['8c864c9223b93488663815557e61cd0b'] + +patches = ['LSMS-Makefiles.patch'] + +#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +files_to_copy = ['bin'] + +buildopts = '-j 1' + +dependencies = [ + ('HDF5', '1.8.16'), +] + +sanity_check_paths = { + 'files': ['bin/lsms', 'bin/wl-lsms'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a05f85ff643946fe8058d7a839a979093f2b7239 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 11:31:59 +0200 Subject: [PATCH 153/566] adding easyconfigs: arpack-ng-3.4.0-foss-2017a.eb, arpack-ng-3.4.0-intel-2017a.eb --- .../a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb | 25 +++++++++++++++++++ .../arpack-ng/arpack-ng-3.4.0-intel-2017a.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb new file mode 100644 index 0000000000..12081625ca --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.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': 'foss', 'version': '2017a'} +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="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb new file mode 100644 index 0000000000..f92abdeafa --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 587c000e0c2e3dfc7f6e6c6f03713a725841813f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:35:36 +0100 Subject: [PATCH 154/566] remove #... comment --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb | 1 - easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb index c708bb19a4..34bdeac5c9 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb @@ -15,7 +15,6 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] files_to_copy = ['bin'] buildopts = '-j 1' diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index ff6c8b7de3..fa65d19eb5 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -15,7 +15,6 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] files_to_copy = ['bin'] buildopts = '-j 1' -- GitLab From 91015b03a8a9dd192e46e16e20c22a47a8d55c00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:46:11 +0100 Subject: [PATCH 155/566] remove eb for LSMS-3_rev237-foss-2015g.eb --- .../l/LSMS/LSMS-3_rev237-foss-2015g.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb deleted file mode 100644 index 34bdeac5c9..0000000000 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'MakeCp' - -name = 'LSMS' -version = '3_rev237' - -homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' -description = "LSMS benchmark, part of CORAL suite" - -toolchain = {'name': 'foss', 'version': '2015g' } - -source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] -sources = ['%(name)s_%(version)s.tar.bz2'] - -checksums = ['8c864c9223b93488663815557e61cd0b'] - -patches = ['LSMS-Makefiles.patch'] - -files_to_copy = ['bin'] - -buildopts = '-j 1' - -dependencies = [ - ('HDF5', '1.8.16'), -] - -sanity_check_paths = { - 'files': ['bin/lsms', 'bin/wl-lsms'], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From 8b8979ea29dd134984613cb79ebbb6e54216e1f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 10:50:16 +0100 Subject: [PATCH 156/566] adding easyconfigs: SWASH-4.01-intel-2017a-mpi.eb --- .../s/SWASH/SWASH-4.01-intel-2017a-mpi.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb new file mode 100644 index 0000000000..57c47cdddd --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '4.01' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' -- GitLab From 5129611740578748995df814108c604e645b9f98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 10:56:56 +0100 Subject: [PATCH 157/566] fixed homepage and source_urls --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 759ecb7840..3da591ce62 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.0.7' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index f0b4020253..d13e7d8912 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.0.7' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] patches = ['ViennaRNA_ictce-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 106d2f71e3..3e54d3ed83 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.1.6' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_1_x/'] patches = ['ViennaRNA-2.1.6_ictce.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 714f3edc9e..1988a82b1e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.2.3' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_2_x/'] patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] -- GitLab From 773a85389fae914ab1520ec122b738c621bc8cd0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 10:57:22 +0100 Subject: [PATCH 158/566] added ViennaRNA-2.3.4-foss-2016b --- .../v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb new file mode 100644 index 0000000000..5b2bac1762 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.3.4' + +homepage = 'http://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/'] + +checksums = ['c77bff267606d22557a4f867df635822'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a3afeb3f7dcda784d5a8e79ebb8a7365edf912f9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 12:22:05 +0200 Subject: [PATCH 159/566] Use SHLIB_EXT instead of hardcoded ".so" --- easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb index 12081625ca..f7c3095a50 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb @@ -18,7 +18,7 @@ preconfigopts = "sh bootstrap && " configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb index f92abdeafa..17c7254907 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb @@ -18,7 +18,7 @@ preconfigopts = "sh bootstrap && " configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT], 'dirs': [] } -- GitLab From 6760a85f0f6e38d783af94b074b4c2d684bf579b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:22:55 +0100 Subject: [PATCH 160/566] pass $FFLAGS to $FLAGS_OPT for SWASH --- easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb index 57c47cdddd..58632f03e4 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "unset FC && make config && " -buildopts = 'mpi' +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' parallel = 1 -- GitLab From 7ed9150a0c5b3a194039f14ba74a46484abe55dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:57:00 +0100 Subject: [PATCH 161/566] {lib}[intel/2016b] Tensorflow v1.0.1 w/ Python 2.7.12 + 3.5.2 --- ...sorflow-1.0.1-intel-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ ...nsorflow-1.0.1-intel-2016b-Python-3.5.2.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..f1c3f15e89 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/7e/7c/f398393beab1647be0a5e6974b8a34e4ea2d3cb7bd9e38bd43a657ed27d1/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['5c88e656fcd34cd89d4cf48d3ec7dd67'] + +dependencies = [ + ('Python', '%s.%s.12' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..2d9a2afe66 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '3' +pymin = '5' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['bccff4d9b87331d4dcecafa43c970b89'] + +dependencies = [ + ('Python', '%s.%s.2' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From fe7e8ddf7a2583411547d522ce9b297a07bc9cb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:59:35 +0100 Subject: [PATCH 162/566] fix sources spec for Tensorflow 1.0.1 w/ Python 3.5.2 --- .../t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb index 2d9a2afe66..42b703619c 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -15,7 +15,7 @@ pymajmin = pymaj + pymin source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/'] sources = [ - 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] checksums = ['bccff4d9b87331d4dcecafa43c970b89'] -- GitLab From 689d70e53f565ae1b0a6a5917182b633f72be48a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 13:24:33 +0100 Subject: [PATCH 163/566] pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs --- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb | 2 +- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb | 2 +- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb index 767e04327d..c01885134c 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "unset FC && make config && " -buildopts = 'mpi' +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' parallel = 1 diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb index a9d434ebd1..b19bb39b27 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'omp' +buildopts = 'omp FLAGS_OPT="$FFLAGS"' parallel = 1 diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb index ad04f26f31..1ff3f68105 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb @@ -14,7 +14,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'ser' +buildopts = 'ser FLAGS_OPT="$FFLAGS"' parallel = 1 -- GitLab From d12d27667f6a522666539d2d5a0e44993c18b7d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 13:47:47 +0100 Subject: [PATCH 164/566] adding easyconfigs: ImageJ-1.51k.eb --- .../easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb new file mode 100644 index 0000000000..ec975dfc22 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -0,0 +1,40 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.51k' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'https://imagej.nih.gov/ij/download/src/', + 'http://www.mecourse.com/landinig/software/', +] +sources = [ + 'ij%(version_major)s%(version_minor)s-src.zip', + 'morphology.zip', +] +checksums = [ + 'e7b634bd1d46cec7694a6990180c5cd9', # ij151k-src.zip + '21491b55bbef5cc50ebff495a4d2b420', # morphology.zip +] + +dependencies = [ + ('Java', '1.8.0_121'), +] + +builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] + +install_cmd = "cd source && ant build && cp ij.jar %(installdir)s && " +install_cmd += "mkdir -p %(installdir)s/plugins && cp -a %(builddir)s/Morphology/* %(installdir)s/plugins/" + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': ['plugins'], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dplugins.dir=$EBROOTIMAGE/plugins'\n" + +moduleclass = 'tools' -- GitLab From a57f5ac9fda2e860342fcd32051027934120b5a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 14:04:35 +0100 Subject: [PATCH 165/566] correctly specify location of plugins for ImageJ --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb index ec975dfc22..9875b136f1 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -35,6 +35,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dplugins.dir=$EBROOTIMAGE/plugins'\n" +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGE/plugins'\n" moduleclass = 'tools' -- GitLab From 50d330cc3ae39f3ef14a287c0e92ffa9d7782cd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 14:09:10 +0100 Subject: [PATCH 166/566] add easyconfigs for ant/JUnit build deps for ImageJ 1.51k --- .../a/ant/ant-1.10.1-Java-1.8.0_121.eb | 26 +++++++++++++++++++ .../j/JUnit/JUnit-4.12-Java-1.8.0_121.eb | 22 ++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb new file mode 100644 index 0000000000..42ed3e6196 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb @@ -0,0 +1,26 @@ +name = 'ant' +version = '1.10.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.8.0_121')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb new file mode 100644 index 0000000000..43aa70ed7b --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.8.0_121')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a22fd2b0ff22c524c032bbe7974ef910699cb6bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:02:55 +0100 Subject: [PATCH 167/566] @boegel LSMS-3_rev237-foss-2016a.eb - buildopts = '-j 1' -> parallel = 1 && move dependencies, below patches --- .../easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index fa65d19eb5..3ca77887d0 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -15,13 +15,13 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -files_to_copy = ['bin'] +dependencies = [ + ('HDF5', '1.8.16'), +] -buildopts = '-j 1' +files_to_copy = ['bin'] -dependencies = [ - ('HDF5', '1.8.16'), -] +parallel = 1 sanity_check_paths = { 'files': ['bin/lsms', 'bin/wl-lsms'], -- GitLab From 9c29e8517e77273ba61625703c06025da2dcb73b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:06:38 +0100 Subject: [PATCH 168/566] {tools}LSMS-3_rev237 renamed LSMS-Makefiles.patch -> LSMS-3_rev237_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 2 +- .../{LSMS-Makefiles.patch => LSMS-3_rev237_fix-Makefiles.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/LSMS/{LSMS-Makefiles.patch => LSMS-3_rev237_fix-Makefiles.patch} (100%) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index 3ca77887d0..198945fde4 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -13,7 +13,7 @@ sources = ['%(name)s_%(version)s.tar.bz2'] checksums = ['8c864c9223b93488663815557e61cd0b'] -patches = ['LSMS-Makefiles.patch'] +patches = ['LSMS-3_rev237_fix-Makefiles.patch'] dependencies = [ ('HDF5', '1.8.16'), diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch similarity index 100% rename from easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch rename to easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch -- GitLab From d3026219c7e50a7fa5e18488b33dd77711ffb30f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:18:43 +0100 Subject: [PATCH 169/566] {tools}LSMS-3_rev237 add head LSMS-3_rev237_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch index 5c1f5e5908..e650269d91 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch @@ -1,3 +1,5 @@ +#change PATH and exports +#Golasowski Martin, martin.golasowski@vsb.cz, 2016 IT4Innovations --- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 +++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 @@ -1,6 +1,29 @@ -- GitLab From 31b9523262215334f596cde4ac75aae9242e2798 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:25:21 +0100 Subject: [PATCH 170/566] {tools}LSMS-3_rev237 2016 -> 2017 --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch index e650269d91..191092dc63 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch @@ -1,5 +1,5 @@ #change PATH and exports -#Golasowski Martin, martin.golasowski@vsb.cz, 2016 IT4Innovations +#Golasowski Martin, martin.golasowski@vsb.cz, 2017 IT4Innovations --- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 +++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 @@ -1,6 +1,29 @@ -- GitLab From a1bc03948dde0ab43e356d72a91f8d543f6c4202 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 15:32:02 +0100 Subject: [PATCH 171/566] changed source_urls to use templates --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 3da591ce62..45a8cbb1a5 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index d13e7d8912..fafae9335e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA_ictce-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 3e54d3ed83..29c51c1030 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_1_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA-2.1.6_ictce.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 1988a82b1e..3214395e25 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_2_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb index 5b2bac1762..ec625ff6c6 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] checksums = ['c77bff267606d22557a4f867df635822'] -- GitLab From 7a01868d8490d06d2ef9786713232c44550a0cb6 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 13 Mar 2017 17:19:43 +0100 Subject: [PATCH 172/566] HDF5 1.10.0 patch1 for golfs incl. dependencies This is a simple port from foss/2016b - same gcc compiler --- .../HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb | 22 ++++++++++++++++++ .../s/Szip/Szip-2.1-goolfc-2016.10.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb new file mode 100644 index 0000000000..a728a33f56 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolfc', 'version': '2016.10'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb new file mode 100644 index 0000000000..c2c5a38e56 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.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': 'goolfc', 'version': '2016.10'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 774f17a8c7232229bdf1d3520a30a1608c94fda3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Tue, 14 Mar 2017 07:33:04 +0100 Subject: [PATCH 173/566] {tools}LSMS-3_rev237 change LSMS-3_rev237_fix-Makefiles.patch -> LSMS-%(version)s_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index 198945fde4..b39dd8a48b 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -13,7 +13,7 @@ sources = ['%(name)s_%(version)s.tar.bz2'] checksums = ['8c864c9223b93488663815557e61cd0b'] -patches = ['LSMS-3_rev237_fix-Makefiles.patch'] +patches = ['LSMS-%(version)s_fix-Makefiles.patch'] dependencies = [ ('HDF5', '1.8.16'), -- GitLab From 152c3f7593cef4db3a1197f42adef4734a8c12a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Mar 2017 15:20:50 +0100 Subject: [PATCH 174/566] remove unneeded CMake easyconfig --- .../c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb deleted file mode 100644 index 50e2df64aa..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -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': 'GCCcore', 'version': '6.3.0'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - -builddependencies = [ - ('binutils', '2.27'), -] - - -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', '1.1.0c'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From 40f76e4b2f7d9e80850d6b94f5dfdec20bf15c99 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Mar 2017 16:21:25 +0200 Subject: [PATCH 175/566] adding easyconfigs: GROMACS-2016.3-foss-2017a.eb --- .../g/GROMACS/GROMACS-2016.3-foss-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb new file mode 100644 index 0000000000..c3f26a2915 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb @@ -0,0 +1,36 @@ +## +# 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 +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' + +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. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +moduleclass = 'bio' -- GitLab From 3d561c8d11759dda93628cbd5ddea9f294e1537c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Mar 2017 16:30:25 +0100 Subject: [PATCH 176/566] adding easyconfigs: GROMACS-2016.3-intel-2017a.eb --- .../g/GROMACS/GROMACS-2016.3-intel-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb new file mode 100644 index 0000000000..edcd456df0 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb @@ -0,0 +1,36 @@ +## +# 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 +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' + +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. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +moduleclass = 'bio' -- GitLab From 13d0854b39af72736c182706b19fb7ee83ddcec8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 14 Mar 2017 18:32:41 +0000 Subject: [PATCH 177/566] Updated PETSc recipe to the modified version of the download install feature. --- .../PETSc/PETSc-3.7.5-intel-2016a-download.eb | 34 ++++++++++--------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb index a59522d52f..111a8d2edd 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb @@ -1,5 +1,6 @@ name = 'PETSc' version = '3.7.5' +versionsuffix = '-downloaded_deps' homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -11,31 +12,32 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [('CMake', '3.5.2')] shared_libs = 1 pic = 1 downloadinstall = True +# For these dependencies, we do not download them dependencies = [('HDF5','1.8.18')] - configopts = "" -# compiles PETSc shared configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" -# external packages that are downloaded -external_packages = ['mumps', 'ptscotch', 'superlu', 'superlu_dist', 'parmetis', 'metis', 'ml', 'suitesparse', 'hypre', 'prometheus'] -# compiles the external dependencies non-shared -external_packages_shared = "no" -for p in external_packages: - configopts += "--download-%s=yes --download-%s-shared=%s " % (p,p,external_packages_shared) -configopts += "--download-triangle=yes" # download-triangle-shared is not supported - -builddependencies = [('CMake', '3.5.2')] +# external packages that are downloaded with --download-=1 and --download--static=1 +download_deps_static = [ + 'hypre', + 'metis', + 'ml', + 'mumps', + 'parmetis', + 'prometheus', + 'ptscotch', + 'suitesparse', + 'superlu', + 'superlu_dist' +] +# triangle cannot be downloaded with --download-triangle-static because it fails +download_deps = ['triangle'] moduleclass = 'numlib' - -modluafooter = """ -family("petsc") -""" - -- GitLab From 11c424082a6f064552f34bc0e74a766cebbbd695 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:25:33 +0100 Subject: [PATCH 178/566] Add kaiju/1.5.0 --- .../k/Kaiju/kaiju-1.5.0-intel-2016b.eb | 27 ++++++++++++++++ .../k/Kaiju/kaiju-1.5.0-makefile.patch | 31 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb new file mode 100644 index 0000000000..1a3e1acaed --- /dev/null +++ b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'Kaiju' +version = '1.5.0' + +homepage = 'http://kaiju.binf.ku.dk/' +description = """Kaiju is a program for sensitive taxonomic classification of high-throughput +sequencing reads from metagenomic whole genome sequencing experiments""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/bioinformatics-centre/kaiju/archive/'] + +patches = ['kaiju-%(version)s-makefile.patch'] + +start_dir = 'src' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['kaiju', 'kaiju2krona', 'kaijup', 'kaijuReport', 'kaijux']], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch new file mode 100644 index 0000000000..3ae20a25b6 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch @@ -0,0 +1,31 @@ +diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile +--- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 ++++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 +@@ -1,7 +1,7 @@ +-CC = gcc ++CC ?= gcc + #CFLAGS = -g +-CFLAGS = -O3 -g -Wno-unused-result +-LDLIBS = -lpthread -lm ++CFLAGS ?= -O3 -g -Wno-unused-result ++LDLIBS ?= -lpthread -lm + + all: mkbwt mkfmi Makefile + +diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +--- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 ++++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 +@@ -1,8 +1,8 @@ +-CC = gcc +-CXX = g++ +-CFLAGS = -g -O3 -DNDEBUG -Wall -Wno-uninitialized +-CXXFLAGS = -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +-LDLIBS = -lpthread ++CC ?= gcc ++CXX ?= g++ ++CFLAGS ?= -g -O3 -DNDEBUG -Wall -Wno-uninitialized ++CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function ++LDLIBS ?= -lpthread + INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ + + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From 1042b8e7ef4cf2bd8866e1ab43a2d8b3ecd918f4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:35:58 +0100 Subject: [PATCH 179/566] Use capitals for easyconfig file --- .../{kaiju-1.5.0-intel-2016b.eb => Kaiju-1.5.0-intel-2016b.eb} | 0 .../{kaiju-1.5.0-makefile.patch => Kaiju-1.5.0-makefile.patch} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/k/Kaiju/{kaiju-1.5.0-intel-2016b.eb => Kaiju-1.5.0-intel-2016b.eb} (100%) rename easybuild/easyconfigs/k/Kaiju/{kaiju-1.5.0-makefile.patch => Kaiju-1.5.0-makefile.patch} (100%) diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb similarity index 100% rename from easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb rename to easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch similarity index 100% rename from easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch rename to easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch -- GitLab From 868ea7d2d5d5be6bdef3d33e8a91b89e1c230127 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:45:23 +0100 Subject: [PATCH 180/566] Fix name of patch --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb index 1a3e1acaed..7f4e002400 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb @@ -13,7 +13,7 @@ toolchainopts = {'cstd': 'c++11'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/bioinformatics-centre/kaiju/archive/'] -patches = ['kaiju-%(version)s-makefile.patch'] +patches = ['%(name)s-%(version)s-makefile.patch'] start_dir = 'src' -- GitLab From fd9d12a31ff48581a75fe834c0c6bff21e99f62b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Wed, 15 Mar 2017 15:14:09 +0100 Subject: [PATCH 181/566] {tools}Singularity-2.2.1-GCC-6.3.0 added --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..e1e43de48b --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '2.2.1' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], + 'dirs': ['etc', 'libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From d388e8264a2f10668639379434435e81beb41709 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Wed, 15 Mar 2017 15:20:01 +0100 Subject: [PATCH 182/566] {tools}Singularity-2.2.1-GCC-6.3.0 added comment `next steps after instalations` --- .../s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb index e1e43de48b..8c36b33253 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -20,4 +20,10 @@ sanity_check_paths = { 'dirs': ['etc', 'libexec/singularity'], } +# next steps after instalations +# INSTALATION_PATH=your_instalation_path +# chown root:root $INSTALATION_PATH/Singularity/*/etc/singularity/singularity.conf +# chown root:root $INSTALATION_PATH/Singularity/*/libexec/singularity/sexec-suid +# chmod +s $INSTALATION_PATH/Singularity/*/libexec/singularity/sexec-suid + moduleclass = 'tools' -- GitLab From 765acc339dc67081c2630070b3f5c726609a375f Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 16 Mar 2017 09:32:27 +0100 Subject: [PATCH 183/566] Fixed wrong sanity check in Mesa --- .../m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 5 ++--- .../m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 5 ++--- .../m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 7 +++---- .../m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 7 +++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 10 ++++++---- 14 files changed, 79 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 41d6a64d37..d8ac10c171 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -64,9 +64,8 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%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/GL/wmesa.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 8b03ae9140..d3f8230305 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -64,9 +64,8 @@ sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%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/GL/wmesa.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 5224023e11..7d75f18d6f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -64,10 +64,9 @@ sanity_check_paths = { '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'], + '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': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index ec21cce29c..346166fe00 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -64,10 +64,9 @@ sanity_check_paths = { 'lib/libGLESv1_CM.so', 'lib/libGLESv2.so', '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'], + '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': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index 81337fce92..9b02d2b02b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 84db881b8b..45545e7c83 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 9a2892bda4..92703769fd 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index 8fe85b43fb..61b180d1ef 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index c0ae4f1fc2..6660454e4c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' 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'], + '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/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } 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 index b8a0ae2d3f..8376070490 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -49,10 +49,13 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --di 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'], + '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/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index d9578ef42b..2ac60cb5d0 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -49,10 +49,13 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --di 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'], + '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/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index ea99e518c2..a2555dbfc0 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -47,10 +47,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', - 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'include/GL/wmesa.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 55c990890f..1ef5829725 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -48,10 +48,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', - 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'include/GL/wmesa.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 4b5ad07db8..6f68f37b53 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -48,10 +48,12 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], 'dirs': [] } -- GitLab From 2234ef0dd76e1809483f978a790f39731dc593c7 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 16 Mar 2017 10:02:28 +0100 Subject: [PATCH 184/566] Fixed a character introduced by mistake --- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index d8ac10c171..8757076334 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -65,7 +65,7 @@ sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], + 'include/GL/glx_mangle.h', 'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index d3f8230305..ffc67154d8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -65,7 +65,7 @@ sanity_check_paths = { 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], + 'include/GL/glx_mangle.h', 'include/GL/wmesa.h'], 'dirs': [] } -- GitLab From e782dc8c1ec30ea348a225a9fa1dc9ce8d7651f5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 16 Mar 2017 11:35:45 +0100 Subject: [PATCH 185/566] Explain what patch does --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch index 3ae20a25b6..94fd3d70c6 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch @@ -1,3 +1,5 @@ +# Let the makefiles use EB provides values if they are set +# wpoely86@gmail.com diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile --- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 @@ -9,9 +11,9 @@ diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile -LDLIBS = -lpthread -lm +CFLAGS ?= -O3 -g -Wno-unused-result +LDLIBS ?= -lpthread -lm - + all: mkbwt mkfmi Makefile - + diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile --- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 @@ -27,5 +29,5 @@ diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +LDLIBS ?= -lpthread INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ - + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From aa621c0d62036c47acd1ef0843033cc6e8f532f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 16 Mar 2017 11:44:38 +0100 Subject: [PATCH 186/566] Fix patch again (dropped whitespace) --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch index 94fd3d70c6..3ae20a25b6 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch @@ -1,5 +1,3 @@ -# Let the makefiles use EB provides values if they are set -# wpoely86@gmail.com diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile --- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 @@ -11,9 +9,9 @@ diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile -LDLIBS = -lpthread -lm +CFLAGS ?= -O3 -g -Wno-unused-result +LDLIBS ?= -lpthread -lm - + all: mkbwt mkfmi Makefile - + diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile --- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 @@ -29,5 +27,5 @@ diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +LDLIBS ?= -lpthread INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ - + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From 7db1bd4556ffbe3ed7aa2e128be29cb1016da9b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Mar 2017 12:26:50 +0100 Subject: [PATCH 187/566] adding easyconfigs: MyMediaLite-3.12-intel-2017a.eb, Mono-4.8.0.495-intel-2017a.eb --- .../m/Mono/Mono-4.8.0.495-intel-2017a.eb | 21 +++++++++++++++++++ .../MyMediaLite-3.12-intel-2017a.eb | 14 +++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb create mode 100644 easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb b/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb new file mode 100644 index 0000000000..7b8956bcd6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'Mono' +version = '4.8.0.495' + +homepage = 'http://www.mono-project.com/' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [ + ('Autotools', '20150215'), + ('CMake', '3.7.2'), + ('gettext', '0.19.8.1'), +] + +configopts = "--with-large-heap=yes --without-x" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb new file mode 100644 index 0000000000..63966d2c9c --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.12' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/zenogantner/MyMediaLite/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('Mono', '4.8.0.495')] + +moduleclass = 'lib' -- GitLab From 1c713b31d319cec1b07ac27b14befb58054f2b04 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Thu, 16 Mar 2017 16:39:42 +0100 Subject: [PATCH 188/566] SAMtools 1.4 - 2 additional dependencies (additional compression algorithms), but also needs a modified easyblock as errmod.h and kprobaln.h are no loger provided nor needed. --- .../s/SAMtools/SAMtools-1.4-intel-2016b.eb | 40 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.4_Makefile.patch | 21 ++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb new file mode 100644 index 0000000000..28fabf7d41 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-%(version)s_Makefile.patch'] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch new file mode 100644 index 0000000000..321f1c822c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch @@ -0,0 +1,21 @@ +# Use EB modules for zlib and ncurses +# Author: Kurt Lust, UAntwerpen +# Developed from the 1.3.1 patch by Adam Huffman of The Francis Crick Institute +--- samtools-1.4-orig/Makefile 2017-03-16 15:11:35.236460000 +0100 ++++ samtools-1.4/Makefile 2017-03-16 15:14:45.964895969 +0100 +@@ -86,13 +86,13 @@ + + ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz $(LIBS) ++ALL_LIBS = -L$(EBROOTZLIB) -lz $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ -- GitLab From bb9402e3934ef52a1cfa253c9eddae1cbff90600 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 17 Mar 2017 08:41:47 +0100 Subject: [PATCH 189/566] {lang}[foss/2016b] R/3.3.3 w/ X11-20160819 (REVIEW) --- easybuild/easyconfigs/r/R/Cairo-1.5-9.patch | 33 ++ .../r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 509 ++++++++++++++++++ 2 files changed, 542 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/Cairo-1.5-9.patch create mode 100644 easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb diff --git a/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch b/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch new file mode 100644 index 0000000000..e88f9455e6 --- /dev/null +++ b/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch @@ -0,0 +1,33 @@ +# pkg-config --libs cairo-pdf +# and +# pkg-config --libs cairo-ps +# should return zlib library location, otherwise configure would use system zlib for cairo compilation tests +# (but not for the builds) +# in the cairo-{ps,pdf} +# Requires: cairo +# sould be +# Reuires: cairo zlib +# So It might be a cairo/pkg-config issue +# March 16th 2017 by B. Hajgato (Free Univeristy Brussels - VUB) +--- Cairo/MD5.org 2015-09-26 09:05:40.000000000 +0200 ++++ Cairo/MD5 2017-03-16 20:28:51.181957519 +0100 +@@ -4,7 +4,7 @@ + 652a130cdb89035bd21add505f09ff6c *R/Cairo.R + 45f780dde83799bfd5ec2d67659fded4 *R/imgtools.R + a9008f9a9abd726e834484d834008b47 *R/zzz.R +-c5196eb2ad5615b9198965124fbbc2f7 *configure ++0eb0d0ae1f7558f449dc797d3e37677d *configure + 938f465e81a73126bac6eabfdfce8ea0 *configure.ac + 9ab259fe324885b6524858aa98ab51ef *configure.win + 9b9c0bd04bd4f6444182d8a4b8e209b5 *man/Cairo.Rd +--- Cairo/configure.org 2015-09-25 19:49:11.000000000 +0200 ++++ Cairo/configure 2017-03-16 20:25:42.687704125 +0100 +@@ -3479,7 +3479,7 @@ + { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${modlist}" >&5 + $as_echo "${modlist}" >&6; } + CAIRO_CFLAGS=`"${PKGCONF}" --cflags ${modlist}` +- CAIRO_LIBS=`"${PKGCONF}" --libs ${modlist}` ++ CAIRO_LIBS="-L$EBROOTZLIB/lib `"${PKGCONF}" --libs ${modlist}`" + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "no" >&6; } diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb new file mode 100644 index 0000000000..2584758870 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -0,0 +1,509 @@ +name = 'R' +version = '3.3.3' +x11ver = '20160819' +versionsuffix = '-X11-%s' % x11ver + +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" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.6'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), + ('PCRE', '8.39'), + ('libpng', '1.6.24'), # for plotting in R + ('libjpeg-turbo', '1.5.0'), # for plottting in R + ('LibTIFF', '4.0.6'), + ('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 + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +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 March 7th 2017 +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', '0.6-6', 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ext_options), + ('adephylo', '1.1-10', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.19', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-8', ext_options), + ('dismo', '1.1-4', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.4', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.10', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-5', ext_options), + ('rgl', '0.98.1', ext_options), + ('labdsv', '1.8-0', ext_options), + ('stabs', '0.6-2', ext_options), + ('modeltools', '0.2-21', ext_options), + ('strucchange', '1.5-1', ext_options), + ('TH.data', '1.0-8', ext_options), + ('multcomp', '1.4-6', ext_options), + ('coin', '1.1-3', ext_options), + ('party', '1.2-2', ext_options), + ('mboost', '2.7-0', ext_options), + ('msm', '1.6.4', ext_options), + ('nor1mix', '1.2-2', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-9', ext_options), + ('polspline', '1.1.12', ext_options), + ('rms', '5.1-0', ext_options), + ('RWekajars', '3.9.1-1', ext_options), + ('RWeka', '0.4-31', ext_options), + ('slam', '0.1-40', ext_options), + ('tm', '0.7-1', ext_options), + ('TraMineR', '1.8-13', ext_options), + ('chemometrics', '1.4.1', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-6', ext_options), + ('statmod', '1.4.29', ext_options), + ('miscTools', '0.6-22', 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', '1.3.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.51.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '3.0', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-12', ext_options), + ('pbkrtest', '0.4-6', ext_options), + ('car', '2.1-4', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.35', 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', '2.10', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '2.0', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '3.2', ext_options), + ('RGCCA', '2.1', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '4.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.2.0', ext_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('VennDiagram', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '8.0', ext_options), + ('fma', '2.3', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.9-1', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.5-6', ext_options), + ('goftest', '1.0-4', ext_options), + ('spatstat', '1.49-0', ext_options), + ('rgdal', '1.2-5', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.9.9', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.3-1', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-21', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('ModelMetrics', '1.1.0', ext_options), + ('caret', '6.0-73', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.10', ext_options), + ('ggvis', '0.4.3', ext_options), + ('mlr', '2.10', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-9', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.14', 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', '0.6', ext_options), + ('commonmark', '1.2', ext_options), + ('desc', '1.1.0', ext_options), + ('roxygen2', '6.0.1', ext_options), + ('git2r', '0.18.0', ext_options), + ('rversions', '1.0.3', ext_options), + ('withr', '1.0.2', ext_options), + ('devtools', '1.12.0', ext_options), + ('Rook', '1.1-1', ext_options), + ('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.2-3', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-8', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-10', ext_options), + ('ks', '1.10.5', ext_options), + ('logcondens', '2.1.5', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-50', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.4.2', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.6.12', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-23.1097', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.9-3', ext_options), + ('mi', '1.0', ext_options), + ('visNetwork', '1.0.3', ext_options), + ('rgexf', '0.15.3', ext_options), + ('influenceR', '0.1.0', ext_options), + ('DiagrammeR', '0.9.0', ext_options), + ('sem', '3.1-8', ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', 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', '1.4.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.1.1', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('imager', '0.31', ext_options), +] + +moduleclass = 'lang' + -- GitLab From 80146673bc89daf3861e7df57114c0aa32a68f23 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Fri, 17 Mar 2017 10:03:41 +0100 Subject: [PATCH 190/566] Removed unnecessary patch from SAMtools 1.4 and 1.3.1 for intel/2016b and removed the 1.4 patch file from the repository. --- .../s/SAMtools/SAMtools-1.3.1-intel-2016b.eb | 3 --- .../s/SAMtools/SAMtools-1.4-intel-2016b.eb | 3 --- .../s/SAMtools/SAMtools-1.4_Makefile.patch | 21 ------------------- 3 files changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb index 068f81d41a..ad73efb9d9 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb @@ -22,9 +22,6 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -# Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-%(version)s_Makefile.patch'] - dependencies = [ ('ncurses', '6.0'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb index 28fabf7d41..3167310f24 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -25,9 +25,6 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -# Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-%(version)s_Makefile.patch'] - # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. dependencies = [ diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch deleted file mode 100644 index 321f1c822c..0000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch +++ /dev/null @@ -1,21 +0,0 @@ -# Use EB modules for zlib and ncurses -# Author: Kurt Lust, UAntwerpen -# Developed from the 1.3.1 patch by Adam Huffman of The Francis Crick Institute ---- samtools-1.4-orig/Makefile 2017-03-16 15:11:35.236460000 +0100 -+++ samtools-1.4/Makefile 2017-03-16 15:14:45.964895969 +0100 -@@ -86,13 +86,13 @@ - - ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz $(LIBS) -+ALL_LIBS = -L$(EBROOTZLIB) -lz $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. - - config.mk: -- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ -+ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ - - config.h: - echo '/* Basic config.h generated by Makefile */' > $@ -- GitLab From e96b2fbf0f49b0f448e32e7029def139d9143e3a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 17 Mar 2017 17:38:10 +0800 Subject: [PATCH 191/566] prepare release notes for eb312 --- RELEASE_NOTES | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 96a76caa5a..a515a07590 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,36 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.1.2 (March 17th 2017) +------------------------ + +bugfix release +- added example easyconfig files for 12 new software packages: + - DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335), + L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307), QJson (#4305), + QScintilla (#4306, #4313) +- added additional easyconfigs for various supported software packages, including: + - BLAT v3.5, FFTW v3.3.6, flex v2.6.3, FreeXL v1.0.2, GDAL v2.1.3, GEOS v3.6.1, GROMACS v2016.2 + v2016.3, + HDF5 1.10.0-patch1, help2man v1.47.4, ImageJ v1.51k, libspatialindex v1.8.5, libspatialite v4.3.0a, M4 v1.4.18, + Mono v4.8.0.495, MyMediaLite v3.12, PGI v17.1, PROJ v4.9.3, PyQt v4.12, QCA v2.1.3, QwtPolar v1.1.1, Qwt v6.1.3, + requests v2.13.0, SIP v4.19, SPAdes v3.10.1, STAR v2.5.2b, SWASH v4.01, SWIG v3.0.11, Tensorflow v1.0.1, + ViennaRNA 2.3.4, Yasm v1.3.0 +- various enhancements, including: + - fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318) + - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) +- various bug fixes, including: + - fix missing PYTHONPATH in ROOT v6.08.02 easyconfig (#4239) + - correct libjpeg turbo references in GDAL (#4276) + - fix to be sure the HDF5 provided by easybuild is used in BLASR (#4278) + - miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... (#4291) + - fix shebang in miRDeep2 Perl scripts (#4301) + - also check with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) + - also copy Rfam_for_miRDeep.fa to mirDeep2 directory (#4316) + - detect use of '$root', which is not compatible with module files in Lua syntax (#4330) + - correctly set $PYTHONPATH in ROOT easyconfigs (#4331) + - add requests and psycopg2 as dependencies for QGIS (#4332) + + v3.1.1 (March 7th 2017) ----------------------- -- GitLab From e3cb8e7f412614e49f061056d460adc144640bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 13:28:43 +0100 Subject: [PATCH 192/566] adding easyconfigs: sketchmap-20170130-intel-2016b.eb --- .../sketchmap-20170130-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb b/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb new file mode 100644 index 0000000000..6caab74f6e --- /dev/null +++ b/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'sketchmap' +version = '20170130' +commit = '7e059bd' + +homepage = 'http://sketchmap.org/' +description = """Sketch-map is a dimensionality reduction algorithm that is particularly well suited to examining + the high-dimensionality data that is routinely produced in atomistic simulations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/cosmo-epfl/sketchmap/archive/'] +sources = ['%s.tar.gz' % commit] + +buildopts = 'CXX="$CXX" MAKEDEPEND="$CXX -M \$(CXXFLAGS)" LLAPACK="$LIBLAPACK_MT"' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/dimdist', 'bin/dimlandmark', 'bin/dimproj', 'bin/dimred'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From b886e0f5e7426e7fdb73dc73aa4eba4d96d134b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:25:31 +0100 Subject: [PATCH 193/566] adding easyconfigs: snaphu-1.4.2-intel-2016b.eb --- .../s/snaphu/snaphu-1.4.2-intel-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb new file mode 100644 index 0000000000..8397d4ea59 --- /dev/null +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'snaphu' +version = '1.4.2' + +homepage = 'https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/' +description = """SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping + proposed by Chen and Zebker""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/'] +sources = ['snaphu-v%(version)s.tar.gz'] + +start_dir = 'src' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' -- GitLab From 5f80281a8224f78bc2f8b8544cb8fcb596f9b9ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:25:51 +0100 Subject: [PATCH 194/566] adding easyconfigs: Triangle-1.6-intel-2016b.eb --- .../t/Triangle/Triangle-1.6-intel-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb new file mode 100644 index 0000000000..f3df6e7173 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +dependencies = [ + ('X11', '20160819'), +] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 89a2a4661e0639138aef33016134925343aedb1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:32:46 +0100 Subject: [PATCH 195/566] remove unneeded X11 dep in Triangle easyconfig since 'showme' binary isn't being built --- easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb index f3df6e7173..77785bc785 100644 --- a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb @@ -18,10 +18,6 @@ checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] patches = ['%(name)s-%(version)s_makefile.patch'] -dependencies = [ - ('X11', '20160819'), -] - buildopts = 'triangle trilibrary' files_to_copy = [ -- GitLab From a10c62c9e46d52fa47d1eae69f094c52307c559b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 18 Mar 2017 09:33:54 +0100 Subject: [PATCH 196/566] adding easyconfigs: SAMtools-1.4-foss-2016b.eb --- .../s/SAMtools/SAMtools-1.4-foss-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb new file mode 100644 index 0000000000..340f9547b8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 491b626efb646f6115990fb080b7267d23737efe Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 18 Mar 2017 10:06:18 +0100 Subject: [PATCH 197/566] adding easyconfigs: HTSlib-1.4-foss-2016b.eb, HTSlib-1.4-intel-2016b.eb --- .../h/HTSlib/HTSlib-1.4-foss-2016b.eb | 36 +++++++++++++++++++ .../h/HTSlib/HTSlib-1.4-intel-2016b.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb new file mode 100644 index 0000000000..9bdb215d4c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('cURL', '7.49.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb new file mode 100644 index 0000000000..5c5a91710c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('cURL', '7.49.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3e057c110297155dcb957faa7a10335bdc21613b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2017 11:07:56 +0100 Subject: [PATCH 198/566] complete release notes for EasyBuild v3.1.2 & bump version --- RELEASE_NOTES | 40 ++++++++++++++++++---------------------- setup.py | 2 +- 2 files changed, 19 insertions(+), 23 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a515a07590..1faff06d0d 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,43 +3,39 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, +The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.2 (March 17th 2017) +v3.1.2 (March 20th 2017) ------------------------ -bugfix release -- added example easyconfig files for 12 new software packages: +bugfix/update release +- add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface (#4334) + - note that this warrants rebuilding FFTW that is a part of foss/2017a +- added example easyconfig files for 14 new software packages: - DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335), - L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307), QJson (#4305), - QScintilla (#4306, #4313) -- added additional easyconfigs for various supported software packages, including: - - BLAT v3.5, FFTW v3.3.6, flex v2.6.3, FreeXL v1.0.2, GDAL v2.1.3, GEOS v3.6.1, GROMACS v2016.2 + v2016.3, - HDF5 1.10.0-patch1, help2man v1.47.4, ImageJ v1.51k, libspatialindex v1.8.5, libspatialite v4.3.0a, M4 v1.4.18, - Mono v4.8.0.495, MyMediaLite v3.12, PGI v17.1, PROJ v4.9.3, PyQt v4.12, QCA v2.1.3, QwtPolar v1.1.1, Qwt v6.1.3, - requests v2.13.0, SIP v4.19, SPAdes v3.10.1, STAR v2.5.2b, SWASH v4.01, SWIG v3.0.11, Tensorflow v1.0.1, - ViennaRNA 2.3.4, Yasm v1.3.0 + L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307, #4332), QJson (#4305), + QScintilla (#4306, #4313), sketchmap (#4360), snaphu (#4362) +- added additional easyconfigs for various supported software packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4 - various enhancements, including: - fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318) - - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) - various bug fixes, including: - - fix missing PYTHONPATH in ROOT v6.08.02 easyconfig (#4239) + - correctly set $PYTHONPATH in ROOT easyconfigs (#4239, #4331) - correct libjpeg turbo references in GDAL (#4276) - - fix to be sure the HDF5 provided by easybuild is used in BLASR (#4278) - - miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... (#4291) - - fix shebang in miRDeep2 Perl scripts (#4301) - - also check with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) - - also copy Rfam_for_miRDeep.fa to mirDeep2 directory (#4316) + - make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (#4278) + - fix issues with miRDeep2 installation (#4291, #4301, #4316) + - also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) + - fix PostgreSQL homepage + minor style fixes (#4318) - detect use of '$root', which is not compatible with module files in Lua syntax (#4330) - - correctly set $PYTHONPATH in ROOT easyconfigs (#4331) - - add requests and psycopg2 as dependencies for QGIS (#4332) + - fix homepage/source_urls for ViennaRNA (#4338) + - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) + - remove include/GL/wglext.h from Mesa sanity check (#4354) v3.1.1 (March 7th 2017) ----------------------- -bugfix release +bugfix/update release - added example easyconfig files for 16 new software packages: - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246), diff --git a/setup.py b/setup.py index 0683e432c9..0512590286 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 = '3.2.0.dev0' +VERSION = '3.1.2' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 4b402eaee4aa4427376aa3ab0871650e6e87758e Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:24:22 +0000 Subject: [PATCH 199/566] cannot have directories with trailing dot in windows --- .../s/{S.A.G.E. => SAGE}/S.A.G.E.-6.3.eb | 4 +-- easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb | 25 +++++++++++++++++++ 2 files changed, 27 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/{S.A.G.E. => SAGE}/S.A.G.E.-6.3.eb (79%) create mode 100644 easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb diff --git a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb similarity index 79% rename from easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb rename to easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb index 28ef2c7ef6..52a2bd4d13 100644 --- a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb @@ -7,14 +7,14 @@ easyblock = "Tarball" name = 'S.A.G.E.' version = '6.3' -homepage = 'https://code.google.com/archive/p/opensage/' +homepage = 'http://darwin.cwru.edu/sage/' description = """ S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/opensage/'] +source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb new file mode 100644 index 0000000000..7935579b22 --- /dev/null +++ b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'S.A.G.E.' +version = '6.4' + +homepage = 'http://darwin.cwru.edu/sage/' +description = """ S.A.G.E. (Statistical Analysis for Genetic +Epidemiology) is free software package containing programs for +use in the genetic analysis of family, pedigree and individual data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://darwin.cwru.edu/sage/files/'] +sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/freq", "bin/ageon", "bin/segreg"], + 'dirs': ["data_files", "documentaion"] +} + +moduleclass = 'bio' -- GitLab From 13f84a024104777d4ef6d6aa90f158b1d37a6589 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:31:51 +0000 Subject: [PATCH 200/566] rename so everything uses the non-dot names --- easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.3.eb => SAGE-6.3.eb} | 4 ++-- easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.4.eb => SAGE-6.4.eb} | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.3.eb => SAGE-6.3.eb} (90%) rename easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.4.eb => SAGE-6.4.eb} (90%) diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb similarity index 90% rename from easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb rename to easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 52a2bd4d13..3ff2689829 100644 --- a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -4,7 +4,7 @@ easyblock = "Tarball" -name = 'S.A.G.E.' +name = 'SAGE' version = '6.3' homepage = 'http://darwin.cwru.edu/sage/' @@ -15,7 +15,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] -sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] +sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb similarity index 90% rename from easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb rename to easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index 7935579b22..fa85d69211 100644 --- a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -4,7 +4,7 @@ easyblock = "Tarball" -name = 'S.A.G.E.' +name = 'SAGE' version = '6.4' homepage = 'http://darwin.cwru.edu/sage/' @@ -15,7 +15,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://darwin.cwru.edu/sage/files/'] -sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] +sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], -- GitLab From 56f97bf6c0649519fd493ee0861496d065da3209 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:43:24 +0000 Subject: [PATCH 201/566] updating with checksums --- easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb | 1 + easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 3ff2689829..603afb8db8 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] +checksums = ['c94a0b9af656212251ce452f7b2f99ec'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index fa85d69211..f518617128 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://darwin.cwru.edu/sage/files/'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] +checksums = ['da3b135389df1ab9a21288cb041ac0c3'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], -- GitLab From d6dc1c333d65c9336a6f0ccd622a6c05d0e0bbbe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2017 16:40:08 +0100 Subject: [PATCH 202/566] include #4368 in v3.1.2 release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1faff06d0d..a56c5c3afe 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -30,6 +30,7 @@ bugfix/update release - fix homepage/source_urls for ViennaRNA (#4338) - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) - remove include/GL/wglext.h from Mesa sanity check (#4354) + - rename S.A.G.E. to SAGE, can't have directories with trailing dot in Windows (#4368) v3.1.1 (March 7th 2017) -- GitLab From d7ce8c79da296aef4c19d2b976caa770d7552fbc Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 15:43:15 +0000 Subject: [PATCH 203/566] update with version variable --- easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 603afb8db8..3c539b01d1 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -14,7 +14,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] +source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v%(version)s'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] checksums = ['c94a0b9af656212251ce452f7b2f99ec'] -- GitLab From ecc192ceba36db967ebf16ba3ac1131f0f1c1ec4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Mar 2017 18:29:56 +0100 Subject: [PATCH 204/566] add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs --- .../easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb | 10 ++++++++++ .../l/libunwind/libunwind-1.1-foss-2015a.eb | 2 +- .../l/libunwind/libunwind-1.1-foss-2016a.eb | 1 + .../l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 1 + .../l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 1 + .../l/libunwind/libunwind-1.1-intel-2016b.eb | 1 + 6 files changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 6bc89f03e7..43105b8275 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -15,6 +15,16 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index 15053fb3db..fe52e32d1e 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index ac65492ae4..24e009d090 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 6d87f10400..daf551f8aa 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 6e07f18865..aae5a5fed7 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index aea3c64e51..e201bb7758 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } -- GitLab From ccf4d6591d7369bbba30a1af83fa1de8219b39d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Mar 2017 18:57:45 +0100 Subject: [PATCH 205/566] add missing XZ easyconfig --- .../easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb new file mode 100644 index 0000000000..0423282a10 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +patches = ['XZ-%(version)s_compat-libs.patch'] + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', '0.19.8', '', True), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 2311bc03eae3c5cf5562baff913f2b366e778a45 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 20 Mar 2017 10:09:29 +0100 Subject: [PATCH 206/566] fix freetype dependency and moduleclass --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index d40917cf4c..e7e4443ff3 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.11'), ('ROOT','v6.08.02','-Python-%(pyver)s'), - ('matplotlib', '1.5.1', '-Python-%(pyver)s') + ('matplotlib', '1.5.1', '-freetype-2.6.3') ] sanity_check_paths = { @@ -29,4 +29,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'bio' +moduleclass = 'data' -- GitLab From cc70804b27f7ce9391e362ed0f27237036e51aed Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 20 Mar 2017 10:18:39 +0100 Subject: [PATCH 207/566] adding easyconfigs: QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb --- .../QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..703fb053f6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'QuTiP' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://qutip.org' +description = """QuTiP is open-source software for simulating the dynamics of open quantum systems.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://qutip.org/downloads/%(version)s/'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From a797616eb175ed6650e8247579bb4f1a2f0fcbef Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 12:37:28 +0100 Subject: [PATCH 208/566] Bowtie2 - With a patch to change the Makefile to use better compiler options for Intel, also based on a suggestion on the Allinea blog --- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 45 +++++++++++++++++++ .../Bowtie2-2.2.9_optimize-intel.patch | 22 +++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb new file mode 100644 index 0000000000..3817ce9c24 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp: Patch for better optimization with the +# Intel compilers, based on +# https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.9' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +patches = ['Bowtie2-%(version)s_optimize-intel.patch'] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "LICENSE", "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch new file mode 100644 index 0000000000..7c5a3cf076 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch @@ -0,0 +1,22 @@ +# Adapt Bowtie2 makefile to use compiler flags that are suited for icpc. +# Options are derived from the options that EasyBuild choses. +# In particular, the compile is no longer restricted to SSE2 but now +# uses -xHost so that AVX/AVX2 instructions will be attempted were appropriate, +# as suggested by https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance +# Author: Kurt Lust, UAntwerp. +--- bowtie2-2.2.9-orig/Makefile 2016-03-10 16:15:50.000000000 +0100 ++++ bowtie2-2.2.9/Makefile 2017-03-20 11:06:20.521070416 +0100 +@@ -165,11 +165,9 @@ + $(error bowtie2 compilation requires a 64-bit platform ) + endif + +-SSE_FLAG=-msse2 +- +-DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) ++DEBUG_FLAGS = -std=c++11 -O0 -g3 -xHost -ftz -fp-speculation=safe -fp-model source + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" +-RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 ++RELEASE_FLAGS = -std=c++11 -O2 -xHost -ftz -fp-speculation=safe -fp-model source + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -- GitLab From 8a32fc2baa2a1f2e1780adbc366e0ecf34401c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 13:20:17 +0100 Subject: [PATCH 209/566] adding easyconfigs: imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb --- ...ed-learn-0.2.1-intel-2016b-Python-3.5.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..399d48b06b --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'imbalanced-learn' +version = '0.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('scikit-learn', '0.18.1', versionsuffix), +] + +options = {'modulename': 'imblearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 2e7c9ddb5a373c9ffdb28645e29f2708c8380efb Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 14:02:30 +0100 Subject: [PATCH 210/566] Bowtie2 for Intel: Changed the easyconfig so that the patch from the previous commit is not needed; removed the patch. --- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 6 ++++- .../Bowtie2-2.2.9_optimize-intel.patch | 22 ------------------- 2 files changed, 5 insertions(+), 23 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index 3817ce9c24..28ad38c224 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -27,7 +27,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -patches = ['Bowtie2-%(version)s_optimize-intel.patch'] +toolchainopts = {'cstd': 'c++11'} + +# Make sure that the Makefile uses options for intel rather than the ones for gcc coded +# in the Makefile by setting RELEASE_FLAGS. +buildopts = 'RELEASE_FLAGS="$CXXFLAGS"' files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch deleted file mode 100644 index 7c5a3cf076..0000000000 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch +++ /dev/null @@ -1,22 +0,0 @@ -# Adapt Bowtie2 makefile to use compiler flags that are suited for icpc. -# Options are derived from the options that EasyBuild choses. -# In particular, the compile is no longer restricted to SSE2 but now -# uses -xHost so that AVX/AVX2 instructions will be attempted were appropriate, -# as suggested by https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance -# Author: Kurt Lust, UAntwerp. ---- bowtie2-2.2.9-orig/Makefile 2016-03-10 16:15:50.000000000 +0100 -+++ bowtie2-2.2.9/Makefile 2017-03-20 11:06:20.521070416 +0100 -@@ -165,11 +165,9 @@ - $(error bowtie2 compilation requires a 64-bit platform ) - endif - --SSE_FLAG=-msse2 -- --DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) -+DEBUG_FLAGS = -std=c++11 -O0 -g3 -xHost -ftz -fp-speculation=safe -fp-model source - DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" --RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 -+RELEASE_FLAGS = -std=c++11 -O2 -xHost -ftz -fp-speculation=safe -fp-model source - RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" - NOASSERT_FLAGS = -DNDEBUG - FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -- GitLab From 379f4c31ce260b1cbc92362a30c6426e81c4ef14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 14:19:45 +0100 Subject: [PATCH 211/566] adding easyconfigs: SWASH-3.14-intel-2016b-mpi.eb, SWASH-3.14-intel-2017a-mpi.eb --- .../s/SWASH/SWASH-3.14-intel-2016b-mpi.eb | 31 +++++++++++++++++++ .../s/SWASH/SWASH-3.14-intel-2017a-mpi.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb new file mode 100644 index 0000000000..82347e4014 --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '3.14' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb new file mode 100644 index 0000000000..6b97716f50 --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '3.14' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' -- GitLab From 69933991035c5ce2ac99a843390487cd68109eca Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 14:38:47 +0100 Subject: [PATCH 212/566] Bowtie2: Modified the comments as requested in the pull request comments. --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index 28ad38c224..fa3d31dfa4 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -6,9 +6,8 @@ # Ottawa Hospital Research Institute - Bioinformatics Team # Modified by: Adam Huffman # The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp: Patch for better optimization with the -# Intel compilers, based on -# https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance +# Modified by: Kurt Lust, UAntwerp: Overwrite compiler options used in the GNU-based +# Makefile with the preferred options for intel compilers. easyblock = 'MakeCp' -- GitLab From b97f2f6df4dd995e89280b15598056f4c66db77c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 15:11:03 +0100 Subject: [PATCH 213/566] adding easyconfigs: EasyBuild-3.1.2.eb --- .../e/EasyBuild/EasyBuild-3.1.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb new file mode 100644 index 0000000000..eaadea3b41 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.1.2' + +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/ef/c7/640c6d791ba452321c0d1371b6626486bb495e0645bb896d33c78a09f810', + # vsc-base + 'https://pypi.python.org/packages/da/90/ee40b1a6a5bfed24139042c737500a9b45db0373a6735e76481fc860fe37', + # easybuild-framework + 'https://pypi.python.org/packages/fa/00/6a47862b38e6d921071d305deab4c494ae2eae58556c90c95e520fea28b9/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/d6/55/9b6634b01fbc26edb9f5af39b06acbe7ec843da438ba5ac3063937934b3e', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/5a/4c/ea8faa46c7874a3d20f28e2d222a1f4a5e97a4f8052add338a785755ec89', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.25.tar.gz', + 'vsc-base-2.5.7.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 80350c7b4c07f77f07a1b646bbc4f45cec83d619 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 18:06:38 +0100 Subject: [PATCH 214/566] bump version to v3.2.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0512590286..0683e432c9 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 = '3.1.2' +VERSION = '3.2.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From bf8085add933e30949220dbef4b6caba7ab1c34c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 21 Mar 2017 15:19:13 +0800 Subject: [PATCH 215/566] adding easyconfigs: QuantumESPRESSO-6.1-intel-2017a.eb --- .../QuantumESPRESSO-6.1-intel-2017a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb new file mode 100644 index 0000000000..4a105c34ef --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb @@ -0,0 +1,59 @@ +name = 'QuantumESPRESSO' +version = '6.1' + +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': '2017a'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'qe-%(version)s.tar.gz', + 'wannier90-2.1.0.tar.gz', + 'qe-gipaw-6.1.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', + 'West-2.0.1.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://www.wannier.org/code/', # wannier90-2.1.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/240/1075/', # qe-6.1.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://www.west-code.org/downloads/', # West-2.0.1.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/208/932/', # yambo-3.4.2.tgz +] + +patches = [ + 'QuantumESPRESSO-5.4.0_yambo-fixes.patch', +] + +# source checksums +checksums = [ + 'db398edcad76e085f8c8a3f6ecb7aaab', # qe-6.1.tar.gz + '07a81c002b41d6d0f97857e55c57d769', # wannier90-2.1.0.tar.gz + '178055353e59eb4dd8bebe27331f2927', # qe-gipaw-6.1.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + '000abe6a5dccd1e722d1767c3dcd3996', # West-2.0.1.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 epw gipaw want west yambo xspectra' # plumed + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' -- GitLab From 0a20d53f1dc9beebcf2f9938f2d84c9963a997a3 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 21 Mar 2017 11:00:13 +0100 Subject: [PATCH 216/566] fix versionsuffix dependency matplotlib --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index e7e4443ff3..efecae95e8 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.11'), ('ROOT','v6.08.02','-Python-%(pyver)s'), - ('matplotlib', '1.5.1', '-freetype-2.6.3') + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3') ] sanity_check_paths = { -- GitLab From d1b093ed3d64f2b8d2bf4a6c35a9f356da607c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 13:06:07 +0100 Subject: [PATCH 217/566] sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock --- .../b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb | 7 +++--- .../b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb | 7 +++--- .../b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 8 +------ .../b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 8 +------ .../b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 12 +--------- .../b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb | 3 +-- .../b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 22 ++----------------- 19 files changed, 26 insertions(+), 197 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb index 13ddeb08e1..f334c5a116 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb @@ -12,17 +12,18 @@ name = 'Bowtie2' version = '2.0.2' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -# N.B. the download option above -> required for sourceforge + +# to add scripts folder to $PATH just uncomment this line +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb index 7f8fbd5ca6..fa8a4e145b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb @@ -12,7 +12,6 @@ name = 'Bowtie2' version = '2.0.2' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool @@ -20,10 +19,12 @@ description = """Bowtie 2 is an ultrafast and memory-efficient tool toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -# N.B. the download option above -> required for sourceforge + +# to add scripts folder to $PATH just uncomment this line +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 9469af37f5..a81247d559 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.0.5' @@ -16,6 +14,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] @@ -24,11 +23,6 @@ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), "doc", "example", "scripts"] -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 264b5296c0..00cfc5cb06 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.0.6' @@ -16,6 +14,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] @@ -24,11 +23,6 @@ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), "doc", "example", "scripts"] -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index f3e4ae2e16..8f006d9054 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.1.0' @@ -16,19 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), - "doc", "example", "scripts"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb index 975220fa34..de611ce79f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb @@ -12,14 +12,13 @@ name = 'Bowtie2' version = '2.1.0' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2', '2.1.0'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} # note: SOURCEFORGE_SOURCE constant doesn't work here because of bowtie-bio used in URL source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 3ccec7b3ec..9dc4955f2b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.0' @@ -16,20 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index 37790b2b2b..535fcdd94e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.2' @@ -16,20 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb index 48fab89b05..8e2370c316 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.4' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb index 3f2240e2f4..b011315af8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.5' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb index 0bb8d3c531..4dca70247f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.5' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb index ab7844bff7..6cd8cef8b8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.6' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb index 9167bcb56a..5c6e44e1e9 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.6' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb index 063d865aaf..7cd080fdb1 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.7' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb index 7309705748..e6c1bebf90 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.8' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb index 4a280ff234..4982ab4d19 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.8' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb index 7f469a05ee..cf2e82b71c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.9' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb index c03250720b..637e625710 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = "2.2.9" @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index fa3d31dfa4..826bc88a15 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -6,10 +6,7 @@ # Ottawa Hospital Research Institute - Bioinformatics Team # Modified by: Adam Huffman # The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp: Overwrite compiler options used in the GNU-based -# Makefile with the preferred options for intel compilers. - -easyblock = 'MakeCp' +# Modified by: Kurt Lust, UAntwerp name = 'Bowtie2' version = '2.2.9' @@ -22,26 +19,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -toolchainopts = {'cstd': 'c++11'} - -# Make sure that the Makefile uses options for intel rather than the ones for gcc coded -# in the Makefile by setting RELEASE_FLAGS. -buildopts = 'RELEASE_FLAGS="$CXXFLAGS"' - -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "LICENSE", "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line #modextrapaths = {'PATH': 'scripts'} -- GitLab From e5d137194f7e4d46ed8578d0a0a25f4c2c4be089 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:25:53 +0100 Subject: [PATCH 218/566] adding easyconfigs: JasPer-2.0.12-intel-2017a.eb --- .../j/JasPer/JasPer-2.0.12-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb new file mode 100644 index 0000000000..668f15ccad --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.12' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/jasper', 'lib64/libjasper.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'vis' -- GitLab From 721d136ab9753a345adfd377e5f391fbd0e97833 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:40:34 +0100 Subject: [PATCH 219/566] adding easyconfigs: HDF5-1.10.0-patch1-intel-2017a.eb, Szip-2.1-intel-2017a.eb --- .../h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb | 22 ++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2017a.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb new file mode 100644 index 0000000000..bc132a2144 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb new file mode 100644 index 0000000000..7a02acddee --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.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': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From b5f873be346781802822e6f839239e35ebb22dff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:49:54 +0100 Subject: [PATCH 220/566] adding easyconfigs: netCDF-4.4.1.1-intel-2017a.eb, netCDF-Fortran-4.4.4-intel-2017a.eb, cURL-7.53.1-GCCcore-6.3.0.eb, Doxygen-1.8.13-GCCcore-6.3.0.eb --- .../c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb | 34 +++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb | 23 +++++++++++++ .../netCDF-Fortran-4.4.4-intel-2017a.eb | 17 ++++++++++ .../n/netCDF/netCDF-4.4.1.1-intel-2017a.eb | 34 +++++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..09811fccde --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.53.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..00e9535d4b --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +name = 'Doxygen' +version = '1.8.13' + +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': 'GCCcore', 'version': '6.3.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb new file mode 100644 index 0000000000..fa3d6fe963 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb @@ -0,0 +1,17 @@ +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': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb new file mode 100644 index 0000000000..d30a65ec63 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.10.0-patch1'), + ('cURL', '7.53.1'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 5762444b72a33f59fe9ba453c4d5eca6ffb80f25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 16:31:10 +0100 Subject: [PATCH 221/566] collapse checksums to a single line to make @wpoely86 happy --- easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb | 4 +--- easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb | 4 +--- easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb | 4 +--- 6 files changed, 6 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 43105b8275..396cb5364f 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index fe52e32d1e..19a10c8362 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -15,9 +15,7 @@ toolchain = {'version': '2015a', 'name': 'foss'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index 24e009d090..9cbc7f2bbf 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index daf551f8aa..97bdf43906 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -15,9 +15,7 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index aae5a5fed7..5b2faed557 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index e201bb7758..ba5d709769 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), -- GitLab From 1e610f306de5153e933712cb219a377d1dfe9947 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 19:49:40 +0100 Subject: [PATCH 222/566] use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb | 4 ++-- 2 files 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 aba6939866..f931b781ea 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 @@ -15,8 +15,8 @@ source_urls = [homepage] # see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False -# compilation fails when configuring with --enable-avx-128-fma -use_fma = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False runtest = 'check' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb index 07c5fa9224..da857e5ca5 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -21,8 +21,8 @@ patches = [ # http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False -# compilation fails when configuring with --enable-avx-128-fma -use_fma = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False runtest = 'check' -- GitLab From baae366171417e854889d108e8f266afeaec8e98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 22:26:58 +0100 Subject: [PATCH 223/566] adding easyconfigs: WRF-3.8.0-intel-2016b-dmpar.eb, tcsh-6.20.00-GCCcore-5.4.0.eb --- .../t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 41 +++++++++++++++++++ .../w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb | 39 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..1413bb1d34 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.20.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb new file mode 100644 index 0000000000..9f07b0effa --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '3.8.0' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version_major_minor)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.20.00')] + +dependencies = [ + ('JasPer', '2.0.10'), + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF_tests_limit-runtimes.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRF-%(version)s_known_problems.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' -- GitLab From b8c0b56d34346a63dbd7933630ad5ef2e8e68299 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 22:39:04 +0100 Subject: [PATCH 224/566] fix netCDF version in dependencies --- easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb index 9f07b0effa..09959e26a3 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb @@ -22,7 +22,7 @@ builddependencies = [('tcsh', '6.20.00')] dependencies = [ ('JasPer', '2.0.10'), - ('netCDF', '4.4.1.1'), + ('netCDF', '4.4.1'), ('netCDF-Fortran', '4.4.4'), ] -- GitLab From 800c673582b5a3203d6a073f4a2800e82199ee9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Mar 2017 20:04:21 +0100 Subject: [PATCH 225/566] adding easyconfigs: ACTC-1.1-intel-2016b.eb --- .../a/ACTC/ACTC-1.1-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb new file mode 100644 index 0000000000..88e0e00942 --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ACTC' +version = '1.1' + +homepage = 'https://sourceforge.net/projects/actc' +description = "ACTC converts independent triangles into triangle strips or fans." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +installopts = "INCDEST=%(installdir)s/include/ac/ LIBDEST=%(installdir)s/lib && " +installopts += "mv %(installdir)s/lib/tc.h %(installdir)s/include/ac/ && " +installopts += "mkdir %(installdir)s/bin && cp -a {tcsample,tctest,tctest2} %(installdir)s/bin && " +installopts += "cp -a {COPYRIGHT,manual.html,prims.gif,README} %(installdir)s/" + +sanity_check_paths = { + 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 933287b2503f1828df80efc7277958dcf53f559f Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Mar 2017 19:21:18 +0000 Subject: [PATCH 226/566] renamed recipe to match convention --- ...2016a-download.eb => PETSc-3.7.5-intel-2016a-download_deps.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-download.eb => PETSc-3.7.5-intel-2016a-download_deps.eb} (100%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb -- GitLab From cb193298f3defbc6c268e7e7f2aa6f1f42156fdf Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Mar 2017 19:21:59 +0000 Subject: [PATCH 227/566] renamed recipe to match convention --- ...ownload_deps.eb => PETSc-3.7.5-intel-2016a-downloaded_deps.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-download_deps.eb => PETSc-3.7.5-intel-2016a-downloaded_deps.eb} (100%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb -- GitLab From d78a9a2c5fb56e58eb9c44aa60ad3365b503b0d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 10:26:12 +0100 Subject: [PATCH 228/566] adding easyconfigs: OpenMPI-2.1.0-GCC-6.3.0-2.28.eb, hwloc-1.11.6-GCC-6.3.0-2.28.eb, GCC-6.3.0-2.28.eb --- easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb | 25 ++++++++++++++ .../h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb | 23 +++++++++++++ .../o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb | 34 +++++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..bac0785b8c --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.3.0' + +binutilsver = '2.28' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..93ceada29d --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.6' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +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=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..f0864ac518 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.1.0' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['c058052b53d209c7521079e3d2da613b'] + +dependencies = [('hwloc', '1.11.6')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_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' -- GitLab From 3f38e052bc47c21c631e125a8bf556792bce9e0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 11:26:13 +0100 Subject: [PATCH 229/566] correctly update $CPATH in ACTC easyconfig --- easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb index 88e0e00942..c94517dc29 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = {'CPATH': 'include/ac'} + moduleclass = 'lib' -- GitLab From 5d143002ba0dde7c4e197453c88c488e9c431ea8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 11:49:15 +0100 Subject: [PATCH 230/566] adding easyconfigs: HISAT2-2.0.5-intel-2017a.eb, NGS-1.3.0-intel-2017a.eb, ncbi-vdb-2.8.2-intel-2017a.eb, file-5.30-intel-2017a.eb --- .../f/file/file-5.30-intel-2017a.eb | 25 ++++++++++++ .../h/HISAT2/HISAT2-2.0.5-intel-2017a.eb | 36 ++++++++++++++++++ .../n/NGS/NGS-1.3.0-intel-2017a.eb | 35 +++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb | 38 +++++++++++++++++++ 4 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb new file mode 100644 index 0000000000..cab481c6f4 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.30' + +homepage = 'http://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb new file mode 100644 index 0000000000..a0d6f2ef27 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.5' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +patches = ['HISAT2-%(version)s_intel-fixes.patch'] + +checksums = ['b6d867e1f8463012d1de3d1472573906'] + +dependencies = [ + ('NGS', '1.3.0'), + ('ncbi-vdb', '2.8.2'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb new file mode 100644 index 0000000000..8d0219a742 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.3.0' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_121', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb new file mode 100644 index 0000000000..5bfe59a4db --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.8.2' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.30'), # provides libmagic + ('HDF5', '1.10.0-patch1'), + ('NGS', '1.3.0'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 399938d27b6370d98c81312cd0c3699e76360be8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:20:18 +0100 Subject: [PATCH 231/566] add missing patch file for HISAT2 --- .../h/HISAT2/HISAT2-2.0.5_intel-fixes.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch new file mode 100644 index 0000000000..571fc956b3 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch @@ -0,0 +1,15 @@ +fix Intel compiler error due to wrong cast to void*, should be int* +author: Kenneth Hoste (HPC-UGent) +--- hisat2-2.0.5/processor_support.h.orig 2017-03-23 11:39:02.647104669 +0100 ++++ hisat2-2.0.5/processor_support.h 2017-03-23 11:39:23.727376802 +0100 +@@ -44,8 +44,8 @@ + + try { + #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) ) +- __cpuid((void *) ®s,0); // test if __cpuid() works, if not catch the exception +- __cpuid((void *) ®s,0x1); // POPCNT bit is bit 23 in ECX ++ __cpuid((int *) ®s,0); // test if __cpuid() works, if not catch the exception ++ __cpuid((int *) ®s,0x1); // POPCNT bit is bit 23 in ECX + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else -- GitLab From 0caaed423383193b70eb9765c15c4d55ba479f66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:21:08 +0100 Subject: [PATCH 232/566] {bio}[intel/2017a] SAMtools 1.4 --- .../s/SAMtools/SAMtools-1.4-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb new file mode 100644 index 0000000000..86a737bc61 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), +] + +moduleclass = 'bio' -- GitLab From f9903bade05e9e83af1538b4ebe64a3916fc55cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:21:29 +0100 Subject: [PATCH 233/566] also patch XZ 5.2.3 to include symbols required by rpm command --- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb index 0e517cfb0f..735c3cbe5b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-5.2.2_compat-libs.patch'] + builddependencies = [ ('gettext', '0.19.8.1', '', True), # use same binutils version that was used when building GCCcore toolchain -- GitLab From 732a70a17a353521a2a9128c5acb8d766c06417c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 13:43:23 +0100 Subject: [PATCH 234/566] use MakeCp for ACTC --- .../easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb index c94517dc29..47b6a5d46f 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'ACTC' version = '1.1' @@ -11,14 +11,14 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -skipsteps = ['configure'] - buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' -installopts = "INCDEST=%(installdir)s/include/ac/ LIBDEST=%(installdir)s/lib && " -installopts += "mv %(installdir)s/lib/tc.h %(installdir)s/include/ac/ && " -installopts += "mkdir %(installdir)s/bin && cp -a {tcsample,tctest,tctest2} %(installdir)s/bin && " -installopts += "cp -a {COPYRIGHT,manual.html,prims.gif,README} %(installdir)s/" +files_to_copy = [ + (['tcsample', 'tctest', 'tctest2'], 'bin'), + (['tc.h'], 'include/ac'), + (['libactc.a'], 'lib'), + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', +] sanity_check_paths = { 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', -- GitLab From 27497f51ac83dddbba0c8be081f7d94ebe9a26d1 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 23 Mar 2017 13:07:11 +0000 Subject: [PATCH 235/566] changed toolchain so that HDF5 1.8.18 is found by the bot --- ...oaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded_deps.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-downloaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded_deps.eb} (96%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb similarity index 96% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb index 111a8d2edd..f864b6e767 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb @@ -6,7 +6,7 @@ homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] -- GitLab From cd45943e036bb52b2bab419b4d529947949eb272 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 14:30:07 +0100 Subject: [PATCH 236/566] {vis}[intel/2016b] VMD 1.9.3 --- .../v/VMD/VMD-1.9.3-intel-2016b.eb | 34 +++++ .../v/VMD/VMD-1.9.3_configure.patch | 116 ++++++++++++++++++ 2 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb new file mode 100644 index 0000000000..2a5279436b --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +name = 'VMD' +version = '1.9.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain= {'name': 'intel' , 'version': '2016b'} + +# downloading requires registration +sources = [('%(namelower)s-%(version)s.src.tar.gz', "tar xfv %s")] + +patches = [ + 'VMD-%(version)s_configure.patch', +] + +dependencies = [ + ('Tcl', '8.6.5'), + ('Tk', '8.6.5'), + ('FLTK', '1.3.3'), + ('Python', '2.7.12'), + ('Mesa', '12.0.2'), + ('netCDF', '4.4.1.1'), + ('FFmpeg', '3.1.3'), + ('ImageMagick', '7.0.3-1'), + ('ACTC', '1.1'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch new file mode 100644 index 0000000000..23f1311b5b --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch @@ -0,0 +1,116 @@ +fix hardcoded stuff in VMD configure script +authors: Stephane Thiell (Stanford University), Kenneth Hoste (HPC-UGent) +--- vmd-1.9.3/configure.orig 2016-12-01 08:11:33.000000000 +0100 ++++ vmd-1.9.3/configure 2017-03-23 13:36:41.501910996 +0100 +@@ -466,7 +476,7 @@ + + $arch_cc = "cc"; + $arch_ccpp = "CC"; +-$arch_nvcc = "/usr/local/cuda-8.0/bin/nvcc"; ++$arch_nvcc = "nvcc"; + $arch_nvccflags = "--ptxas-options=-v " . + "-gencode arch=compute_30,code=compute_30 " . + "-gencode arch=compute_30,code=sm_35 " . +@@ -581,17 +591,17 @@ + # location of Mesa library and include files; basically does the same + # as OpenGL. This is based on the default instructions from the Mesa + # README; the include files should by default be in /usr/local/include/GL. +-$mesa_dir = "$vmd_library_dir/Mesa"; ++$mesa_dir = $ENV{'EBROOTMESA'}; + $mesa_include = "-I$mesa_dir/include"; + $mesa_library = "-L$mesa_dir/lib_$config_arch"; + #$mesa_libs = "-lMesaGL -lMesaGLU"; +-$mesa_libs = "-lMesaGL"; ++$mesa_libs = "-lGL -lGLU"; + $mesa_defines = "-DUSELINEAXES -DVMDMESA -DVMDOPENGL"; + @mesa_cc = (); + @mesa_cu = (); +-@mesa_ccpp = @opengl_ccpp; +-@mesa_h = @opengl_h; +-@mesa_extra = @opengl_extra; ++@mesa_ccpp = (); ++@mesa_h = (); ++@mesa_extra = (); + + + # +@@ -666,10 +676,10 @@ + + ################ FLTK GUI + $fltk_defines = "-DVMDGUI -DVMDFLTK"; +-$fltk_dir = "$vmd_library_dir/fltk"; ++$fltk_dir = $ENV{'EBROOTFLTK'}; + $fltk_include = "-I$fltk_dir/include"; + $fltk_library = "-L$fltk_dir/$config_arch"; +-$fltk_libs = "-lfltk -lX11"; ++$fltk_libs = "-lfltk -lX11 -lXfixes -lXcursor -lXinerama"; + #@fltk_cc = ('forms_ui.c'); + @fltk_cu = (); + @fltk_ccpp = ( 'ColorFltkMenu.C', +@@ -729,8 +739,8 @@ + if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } + $tcl_library = "-L$stock_tcl_library_dir"; + if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } +-$tcl_libs = "-ltcl8.5"; +-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } ++$tcl_libs = "-ltcl8.6"; ++if ($config_tk) { $tcl_libs = "-ltk8.6 -lX11 " . $tcl_libs; } + + @tcl_cc = (); + @tcl_cu = (); +@@ -922,7 +932,7 @@ + # This option enables the use of CUDA GPU acceleration functions. + ####################### + $cuda_defines = "-DVMDCUDA -DMSMPOT_CUDA"; +-$cuda_dir = "/usr/local/cuda-8.0"; ++$cuda_dir = "$CUDA_HOME"; + $cuda_include = ""; + $cuda_library = ""; + $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static"; +@@ -1042,7 +1052,7 @@ + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.6.3-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.8.0-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.9.0-linux64"; +-$liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-4.0.1-linux64"; ++$liboptix_dir = "$ENV{'EBROOTOPTIX'}"; + # NCSA Blue Waters + # $liboptix_dir = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.6.3-linux64"; + # $liboptix_dir = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.8.0-linux64"; +@@ -1310,8 +1320,8 @@ + ####################### + $actc_defines = "-DVMDACTC"; + $actc_dir = "$vmd_library_dir/actc"; +-$actc_include = "-I$actc_dir/include"; +-$actc_library = "-L$actc_dir/lib_$config_arch"; ++$actc_include = "-I$actc_dir"; ++$actc_library = "-L$actc_dir"; + $actc_libs = "-lactc"; + @actc_cc = (); + @actc_cu = (); +@@ -1388,7 +1398,7 @@ + $python_defines = "-DVMDPYTHON"; + $python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir"; + $python_library = "-L$stock_python_library_dir"; +-$python_libs = "-lpython2.5 -lpthread"; ++$python_libs = "-lpython2.7 -lpthread"; + @python_h = ('PythonTextInterp.h', + 'VMDTkinterMenu.h', + 'py_commands.h', +@@ -2173,7 +2183,7 @@ + + if ($config_static) { + $arch_lopts = "-static"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib -lXext -lX11"; ++ $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11"; + } else { + $arch_lopts = ""; + # -rpath causes problems for people running Chromium.. +@@ -2303,7 +2313,7 @@ + # they likely serve no useful purpose going forward. + if (!$config_opengl_dispatch) { + $opengl_dep_libs = "-L/usr/X11R6/lib64 -lGL -lX11"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib64 -lXext -lX11"; ++ $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11"; + } + + # this is to make tcl happy -- GitLab From 84b686e27ad0f9e554a6cf078d652a77c11913b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 17:03:48 +0100 Subject: [PATCH 237/566] style fixes in PETSc easyconfig that downloads deps --- ...ETSc-3.7.5-intel-2016b-downloaded-deps.eb} | 31 ++++++------------- 1 file changed, 9 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016b-downloaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded-deps.eb} (68%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb similarity index 68% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb index f864b6e767..87e4b65750 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb @@ -1,6 +1,6 @@ name = 'PETSc' version = '3.7.5' -versionsuffix = '-downloaded_deps' +versionsuffix = '-downloaded-deps' homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -12,32 +12,19 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] +# (build) dependencies provided through EasyBuild builddependencies = [('CMake', '3.5.2')] -shared_libs = 1 -pic = 1 - -downloadinstall = True - -# For these dependencies, we do not download them dependencies = [('HDF5','1.8.18')] -configopts = "" -configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " -configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" # external packages that are downloaded with --download-=1 and --download--static=1 -download_deps_static = [ - 'hypre', - 'metis', - 'ml', - 'mumps', - 'parmetis', - 'prometheus', - 'ptscotch', - 'suitesparse', - 'superlu', - 'superlu_dist' -] +download_deps_static = ['hypre', 'metis', 'ml', 'mumps', 'parmetis', 'prometheus', 'ptscotch', 'suitesparse', + 'superlu', 'superlu_dist'] # triangle cannot be downloaded with --download-triangle-static because it fails download_deps = ['triangle'] +configopts = "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " +configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +shared_libs = True + moduleclass = 'numlib' -- GitLab From bca436c37aa54ec9ae171066f4d480a701f664f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 17:41:36 +0100 Subject: [PATCH 238/566] add checksum for VMD 1.9.3 sources --- easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb index 2a5279436b..3e3df4bec4 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb @@ -13,11 +13,11 @@ description = """VMD is a molecular visualization program for displaying, animat toolchain= {'name': 'intel' , 'version': '2016b'} # downloading requires registration -sources = [('%(namelower)s-%(version)s.src.tar.gz', "tar xfv %s")] +sources = ['vmd-%(version)s.src.tar.gz'] -patches = [ - 'VMD-%(version)s_configure.patch', -] +patches = ['VMD-%(version)s_configure.patch'] + +checksums = ['5706f88b9b77cc5fafda6fef3a82d6fa'] dependencies = [ ('Tcl', '8.6.5'), -- GitLab From 3d41143457e45e0b7c720954adf981364f9ab72a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 18:44:18 +0100 Subject: [PATCH 239/566] fix easyconfig filename for VMD --- ....9.3-intel-2016b.eb => VMD-1.9.3-intel-2016b-Python-2.7.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/VMD/{VMD-1.9.3-intel-2016b.eb => VMD-1.9.3-intel-2016b-Python-2.7.12.eb} (100%) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb rename to easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb -- GitLab From 3e03d88c9300b4a346ca39a28fbbad235b9e75f7 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 24 Mar 2017 12:33:43 -0400 Subject: [PATCH 240/566] Added SAMtools-1.4-goolf-1.4.10.eb and ncurses-6.0-goolf-1.4.10.eb, the second one is a dependece of the first. By Daniel Navarro-Gomez, MEEI Bioinformatics Center new file: easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb new file: easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb --- .../n/ncurses/ncurses-6.0-goolf-1.4.10.eb | 38 ++++++++++++++++++ .../s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb | 40 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..6b10da13e5 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +# Modified for goolf-1.4.10 by: Daniel Navarro-Gomez, MEEI Bioinformatics Center (MBC) + +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': 'goolf', 'version': '1.4.10'} +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', + # 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/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..f620000661 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +# Modified for goolf-1.4.10 by: Daniel Navarro-Gomez, MEEI Bioinformatics Center (MBC) +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +# +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.7'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 8f63e326929541c6c9f8911357c81019aea0bde8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Fri, 24 Mar 2017 19:27:45 +0000 Subject: [PATCH 241/566] added recipe for repasthpc --- .../r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000..d01d3cb5a2 --- /dev/null +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'RepastHPC' +version = '2.2.0' + +homepage = 'https://repast.github.io/' +description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: +Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ["repast_hpc-%s.tgz" % version] +source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version] + +dependencies = [ + ('netCDF-C++','4.2'), + ('Boost', '1.60.0'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' + +sanity_check_paths = { + 'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version], + 'dirs': ['include','lib','bin/zombie', 'bin/rumor'], +} + +moduleclass = 'bio' -- GitLab From 933e11553203ffe64b2c29128734b3631ce6fe77 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 12:00:12 +0800 Subject: [PATCH 242/566] adding easyconfigs: Wannier90-2.1.0-intel-2017a.eb --- .../Wannier90/Wannier90-2.1.0-intel-2017a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb new file mode 100644 index 0000000000..4945212393 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] +checksums = ['07a81c002b41d6d0f97857e55c57d769'] + +prebuildopts = 'cp ./config/make.inc.ifort ./make.inc && ' + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 33de8679402f5de09a5ce0d7bcdb5bbddd34f302 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 18:03:08 +0800 Subject: [PATCH 243/566] adding easyconfigs: DFTB+-1.3.1-intel-2017a.eb --- .../d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb new file mode 100644 index 0000000000..35d80f5918 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'DFTB+' +version = '1.3.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the + Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been + developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with + ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of + magnitude in speed.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://www.dftb-plus.info/download/dftb-13'] # requires registration +sources = [ + 'dftbplus-%(version)s-src.tar.xz', + 'dftbplus-%(version)s-extlib.tar.xz', + 'dftbplus-%(version)s-autotest.tar.xz', +] + +checksums = [ + 'b821ed7406a2a4b35c0a48974e18667f', # dftbplus-1.3.1-src.tar.xz + '2333f1ff826a3c4776e1e77a28f17004', # dftbplus-1.3.1-extlib.tar.xz + 'abaf8a2f94c74a13a0d8d19e9b022e40', # dftbplus-1.3.1-autotest.tar.xz +] + +dependencies = [ + ('arpack-ng', '3.4.0'), +] + +subdir = '%dftbplus-%(version)s' + +prebuildopts = "sed 's/ARCH = x86_64-linux-intel/ARCH = user/' Makefile.user.template > Makefile.user && " +prebuildopts += "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " +prebuildopts += "sed -i 's|LNOPT = -static|#LNOPT = -static|' sysmakes/make.user && " +prebuildopts += "sed -i 's|/opt/intel/mkl/10.2.6.038/lib/em64t|$(MKLROOT)|' sysmakes/make.user && " +prebuildopts += "cd prg_dftb && " + +files_to_copy = [(['prg_dftb/_obj_user/dftb+'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dftb+'], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From 341613bcd83198517aa20bc7e728f356df2ad5f4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 18:09:07 +0800 Subject: [PATCH 244/566] adding easyconfigs: BerkeleyGW-1.2.0-intel-2017a.eb --- .../BerkeleyGW-1.2.0-intel-2017a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb new file mode 100644 index 0000000000..21a5da2750 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'BerkeleyGW' +version = "1.2.0" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] # requires registration +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['0bfcac62ebe486374b37d04a131453d7'] + +skipsteps = ['configure'] + +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' + +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' + +# "all-flavors" cleans and compiles everything again +preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && ' + +installopts = 'INSTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/' + prog + '.' + flavor + '.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics'] + for flavor in ['real', 'cplx']], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From f9818b855274e1615306b3fde48bcbdbc3b27865 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 23:45:22 +0800 Subject: [PATCH 245/566] simplify prebuildopts --- easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb index 35d80f5918..15d96ddf6e 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -31,12 +31,11 @@ dependencies = [ subdir = '%dftbplus-%(version)s' -prebuildopts = "sed 's/ARCH = x86_64-linux-intel/ARCH = user/' Makefile.user.template > Makefile.user && " -prebuildopts += "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " -prebuildopts += "sed -i 's|LNOPT = -static|#LNOPT = -static|' sysmakes/make.user && " -prebuildopts += "sed -i 's|/opt/intel/mkl/10.2.6.038/lib/em64t|$(MKLROOT)|' sysmakes/make.user && " +prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " prebuildopts += "cd prg_dftb && " +buildopts = "ARCH=user MKL_LIBDIR=$MKLROOT LNOPT= " + files_to_copy = [(['prg_dftb/_obj_user/dftb+'], 'bin')] sanity_check_paths = { -- GitLab From 92fd0795325dd52804826307a09bcc0fcd9cf979 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Mar 2017 17:54:49 +0200 Subject: [PATCH 246/566] adding easyconfigs: ED2-20170201-intel-2017a.eb --- .../e/ED2/ED2-20170201-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb new file mode 100644 index 0000000000..e02aad07d9 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'ED2' +version = '20170201' +commit = '0146fa4' + +homepage = 'https://github.com/EDmodel/ED2' +description = """The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model + incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/EDmodel/ED2/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = ['ED2.patch'] + +dependencies = [('HDF5', '1.10.0-patch1')] + +start_dir = 'ED/build' + +# rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options +prebuildopts = "sed -i 's/^make OPT/#make OPT/g' install.sh && ./install.sh --kind E --platform intel --gitoff && " +prebuildopts += "cd bin-opt-E && " + +buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' " +buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' + +files_to_copy = [(['ED/build/ed_2.1-opt'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ed_2.1-opt'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From 5ec6dcd34db0e99be4c4ba8a7cae4a12b533d4c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Mar 2017 18:18:56 +0200 Subject: [PATCH 247/566] add patches for ED2 --- .../e/ED2/ED2-20170201-intel-2017a.eb | 8 ++++--- .../easyconfigs/e/ED2/ED2_fix-type.patch | 13 ++++++++++ .../e/ED2/ED2_install-without-make.patch | 24 +++++++++++++++++++ 3 files changed, 42 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/e/ED2/ED2_fix-type.patch create mode 100644 easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb index e02aad07d9..eed367500a 100644 --- a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb @@ -14,15 +14,17 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/EDmodel/ED2/archive/'] sources = ['%s.tar.gz' % commit] -patches = ['ED2.patch'] +patches = [ + 'ED2_install-without-make.patch', + 'ED2_fix-type.patch', +] dependencies = [('HDF5', '1.10.0-patch1')] start_dir = 'ED/build' # rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options -prebuildopts = "sed -i 's/^make OPT/#make OPT/g' install.sh && ./install.sh --kind E --platform intel --gitoff && " -prebuildopts += "cd bin-opt-E && " +prebuildopts = "./install.sh --kind E --platform intel --gitoff && cd bin-opt-E && " buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' " buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' diff --git a/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch b/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch new file mode 100644 index 0000000000..4f73ca3487 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch @@ -0,0 +1,13 @@ +fix type for argument to h5dget_type_f call +see https://github.com/EDmodel/ED2/issues/153 and https://github.com/crollinson/ED2/commit/48b9e8132b992460aa8afeca222fd4c12f01cfe4 +--- ED/src/utils/hdf5_utils.F90.orig 2017-02-01 22:00:01.000000000 +0100 ++++ ED/src/utils/hdf5_utils.F90 2017-03-27 11:56:38.579744327 +0200 +@@ -432,7 +432,7 @@ + character(len=2) :: ctype + + logical :: convert = .false. +- integer :: type_id ++ integer(HID_T) :: type_id + real(kind=8), allocatable, dimension(:) :: dvaraTEMP + + ! Find which data type will be read diff --git a/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch b/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch new file mode 100644 index 0000000000..601e93e788 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch @@ -0,0 +1,24 @@ +avoid install.sh calling 'make' (and hard set GIT_EXIST) +author: Kenneth Hoste (HPC-UGent) +--- ED/build/install.sh.orig 2017-03-27 12:00:10.321077952 +0200 ++++ ED/build/install.sh 2017-03-27 11:59:40.200888391 +0200 +@@ -94,8 +94,8 @@ + esac + + # Tag executables with a git version and branch name if possible. +-GIT_EXIST=`git rev-parse --is-inside-work-tree` +-if [ ${GIT_EXIST} == "true" -a ${USE_GIT} ] ++GIT_EXIST="" ++if [ "${GIT_EXIST}" == "true" -a ${USE_GIT} ] + then + GIT_TAG=`git branch -v | awk '/\*/ {print "-" $2 "-" $3}'` + GIT_TAG=`echo ${GIT_TAG} | tr -d '()/[]'` +@@ -122,7 +122,7 @@ + touch dependency.mk + + #----- Launch the compiler. ---------------------------------------------------------------# +-make OPT=${OPT} KIND_COMP=${KIND} ${CLEAN} GIT_TAG=${GIT_TAG} ++#make OPT=${OPT} KIND_COMP=${KIND} ${CLEAN} GIT_TAG=${GIT_TAG} + make_exit_code=$? + #------------------------------------------------------------------------------------------# + -- GitLab From 1af6f173acf17c4edddfd3ce10b770e71ddb0346 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Mon, 27 Mar 2017 19:22:16 +0000 Subject: [PATCH 248/566] cosmetic changes --- .../r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb index d01d3cb5a2..d533ab1e52 100644 --- a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -4,25 +4,27 @@ name = 'RepastHPC' version = '2.2.0' homepage = 'https://repast.github.io/' -description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: -Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.""" +description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation +platforms that have collectively been under continuous development for over 15 years: +Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based +modeling system that is designed for use on large computing clusters and supercomputers.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} -sources = ["repast_hpc-%s.tgz" % version] -source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version] +sources = ["repast_hpc-%(version)s.tgz"] +source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%(version)s'] dependencies = [ - ('netCDF-C++','4.2'), + ('netCDF-C++', '4.2'), ('Boost', '1.60.0'), ] configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' sanity_check_paths = { - 'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version], - 'dirs': ['include','lib','bin/zombie', 'bin/rumor'], + 'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ], + 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], } moduleclass = 'bio' -- GitLab From 2d8c701f3270602f9db0b3edb5cd4a4de7009159 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 28 Mar 2017 10:03:12 +0800 Subject: [PATCH 249/566] disable stdc-predef.h pre-include --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb index 21a5da2750..6db03e17ee 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -21,8 +21,8 @@ prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' -buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' -buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" ' +buildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' # "all-flavors" cleans and compiles everything again -- GitLab From e64ee749935ed6de93fde54097f4bcc9caeca1b9 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 28 Mar 2017 15:29:46 +0800 Subject: [PATCH 250/566] cleanup --- easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb index 15d96ddf6e..7f8e07f325 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -29,10 +29,7 @@ dependencies = [ ('arpack-ng', '3.4.0'), ] -subdir = '%dftbplus-%(version)s' - -prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " -prebuildopts += "cd prg_dftb && " +prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && cd prg_dftb && " buildopts = "ARCH=user MKL_LIBDIR=$MKLROOT LNOPT= " -- GitLab From a629ee133ac546cb1145364ab4dcafd4405b08f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 11:20:23 +0200 Subject: [PATCH 251/566] adding easyconfigs: WRF-Fire-20170221-intel-2016b-dmpar.eb --- .../WRF-Fire-20170221-intel-2016b-dmpar.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb new file mode 100644 index 0000000000..eeb28fe474 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb @@ -0,0 +1,23 @@ +name = 'WRF-Fire' +version = '20170221' +commit = 'f2db7a0' +buildtype = 'dmpar' +versionsuffix = '-' + buildtype + +homepage = 'http://www.openwfm.org/wiki/WRF-SFIRE' +description = """WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a + surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire + line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and + terrain slope. The fire spread is implemented by the level set method.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/openwfm/wrf-fire/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('netCDF-Fortran', '4.4.4'), +] + + +moduleclass = 'geo' -- GitLab From af3b49f341a5e52e48df92f6cfe65a3cf316c78f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 11:49:11 +0200 Subject: [PATCH 252/566] add maxparallel = 10 --- .../w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb index eeb28fe474..55b59e1608 100644 --- a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb @@ -19,5 +19,7 @@ dependencies = [ ('netCDF-Fortran', '4.4.4'), ] +# limit max. parallelism for build (WRF-Fire will cap to 2 if > 20) +maxparallel = 10 moduleclass = 'geo' -- GitLab From e9b358bfb426d73b3a04eae8b2a57dfb47e8ede6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 12:41:24 +0200 Subject: [PATCH 253/566] adding easyconfigs: Doris-4.02-intel-2017a.eb --- .../d/Doris/Doris-4.02-intel-2017a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb new file mode 100644 index 0000000000..37cf20fd5b --- /dev/null +++ b/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'Doris' +version = '4.02' + +homepage = 'http://doris.tudelft.nl/' +description = "Delft object-oriented radar interferometric software" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://doris.tudelft.nl/software/'] +sources = ['doris_v%(version)s.tar.gz'] + +dependencies = [ + ('FFTW', '3.3.6'), +] + +moduleclass = 'geo' -- GitLab From b3fc425e503d838764466ab63d3321642070e1c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:31:38 +0200 Subject: [PATCH 254/566] adding easyconfigs: h5py-2.7.0-intel-2016b-Python-2.7.12.eb --- .../h5py-2.7.0-intel-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..adc15ffb81 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', '1.10.0-patch1'), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From ad6485b3fbe49817a1543a16dbb87ad2b171c876 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:32:03 +0200 Subject: [PATCH 255/566] adding easyconfigs: SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb --- ...piceyPy-1.1.0-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9ffb950100 --- /dev/null +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'SpiceyPy' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/AndrewAnnex/SpiceyPy' +description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'geo' -- GitLab From 6f50fca325bea7be094393d39e28bdc2c94b19ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:32:29 +0200 Subject: [PATCH 256/566] adding easyconfigs: FFTW-3.3.6-intel-2016b.eb --- .../f/FFTW/FFTW-3.3.6-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb new file mode 100644 index 0000000000..14ebd120a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb @@ -0,0 +1,29 @@ +name = 'FFTW' +version = '3.3.6' + +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} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] + +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' -- GitLab From 4757aa658eebdd42897f500ee38fbea0e652d2c4 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Mar 2017 12:52:24 +0000 Subject: [PATCH 257/566] escaped % --- easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb index d533ab1e52..fc07069bff 100644 --- a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' sanity_check_paths = { - 'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ], + 'files': ['lib/librelogo-%%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%%(version)s.%s' % SHLIB_EXT ], 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], } -- GitLab From 61c407afe0e0c14abfcbb085a78030d4a1b6bf86 Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 29 Mar 2017 08:58:45 +0800 Subject: [PATCH 258/566] remove -qopenmp and enable openmp toolchain option --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb index 6db03e17ee..94e1cd433d 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -9,7 +9,7 @@ description = """The BerkeleyGW Package is a set of computer codes that calculat nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['http://www.berkeleygw.org/releases/'] # requires registration sources = ['BGW-%(version)s.tar.gz'] @@ -21,7 +21,7 @@ prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' -buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" ' +buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS" MKLPATH="$MKLROOT" ' buildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' -- GitLab From e665b67632d148ef30590adec9b871b6cc74c9b1 Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 29 Mar 2017 14:31:28 +0800 Subject: [PATCH 259/566] remove the other -qopenmp --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb index 94e1cd433d..2eb57382c1 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -20,7 +20,7 @@ skipsteps = ['configure'] prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' -buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'FOPTS="$FFLAGS" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS" MKLPATH="$MKLROOT" ' buildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' -- GitLab From 1fd96d8483783fe062547963cb0baee7a49ed8db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 18:32:53 +0200 Subject: [PATCH 260/566] adding easyconfigs: ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb --- .../ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..367e778dfc --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ROI_PAC' +version = '3.0.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://roipac.org/' +description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data + to produce differential interferograms""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# download requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC +sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] + +# FIXME: http://roipac.org/cgi-bin/moin.cgi/Patches + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('FFTW', '3.3.6'), + ('GETORB', '2.3.2'), + ('Perl', '5.24.0'), +] + +start_dir = 'ROI_PAC' + +postinstallcmds = [ + # symlink to getorb requires in /bin subdirectory + "cd %(installdir)s/bin && ln -s $(which getorb)", + # also copy scripts and make sure they're excutable + "cp -a INT_SCR/* %(installdir)s/bin", + # fix shebang in Perl scripts + "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//bin/*.pl", +] + +sanity_check_paths = { + 'files': ['bin/getorb', 'bin/make_raw.pl', 'bin/roi'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'bin'} +modextravars = { + 'INT_BIN': '%(installdir)s/bin', + 'INT_SCR': '%(installdir)s/bin', +} + +moduleclass = 'geo' -- GitLab From fc0f4ff96ff2a60bbb800af32366c28229941270 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 18:34:36 +0200 Subject: [PATCH 261/566] adding easyconfigs: jemalloc-4.5.0-intel-2017a.eb --- .../j/jemalloc/jemalloc-4.5.0-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb new file mode 100644 index 0000000000..45f685672f --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.5.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' -- GitLab From 16bdb31b1f2f30a4a25c0a601176e39348a2a341 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 20:04:44 +0200 Subject: [PATCH 262/566] add easyconfig for GETORB dependency for ROI_PAC --- .../g/GETORB/GETORB-2.3.2-intel-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb new file mode 100644 index 0000000000..61b3b12249 --- /dev/null +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GETORB' +version = '2.3.2' + +homepage = 'http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml' +description = "GETORB software package contains programs to handle the orbital data records (ODRs)" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.deos.tudelft.nl/ers/precorbs/tools/'] +sources = ['getorb_%(version)s.tar.gz'] + +skipsteps = ['configure'] + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/getorb', 'bin/lodr', 'bin/mdate'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 5ae48b9b752d2c302000a1a64f9ed58c9da4f585 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 10:31:21 +0200 Subject: [PATCH 263/566] disable parallel building for GETORB, tends to break --- easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb index 61b3b12249..2e648643f9 100644 --- a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb @@ -13,6 +13,8 @@ sources = ['getorb_%(version)s.tar.gz'] skipsteps = ['configure'] +parallel = 1 + preinstallopts = "mkdir %(installdir)s/bin && " installopts = 'BIN_DIR=%(installdir)s/bin' -- GitLab From 07b52f5f937b0962931ac68e1ff50ef6567a3ddb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 10:57:46 +0200 Subject: [PATCH 264/566] apply fixes for ROI_PAC described at http://roipac.org/cgi-bin/moin.cgi/Patches --- .../ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb index 367e778dfc..30adf12039 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -10,10 +10,14 @@ description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for pro toolchain = {'name': 'intel', 'version': '2016b'} -# download requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC +# download of ROI_PAC tarball requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] -# FIXME: http://roipac.org/cgi-bin/moin.cgi/Patches +# make_raw_alos.pl via http://roipac.org/cgi-bin/moin.cgi/ALOS_PALSAR?action=AttachFile&do=get&target=make_raw_alos.pl +patches = [ + 'ROI_PAC-%(version)s_fix-IntSim.patch', + ('make_raw_alos.pl', 'ROI_PAC/INT_SCR'), +] builddependencies = [('Autotools', '20150215')] dependencies = [ @@ -24,6 +28,8 @@ dependencies = [ start_dir = 'ROI_PAC' +installopts = "&& cd fip && $CC $CFLAGS -o add_rmgAmpPhs add_rmgAmpPhs.c && cp -a add_rmgAmpPhs %(installdir)s/bin" + postinstallcmds = [ # symlink to getorb requires in /bin subdirectory "cd %(installdir)s/bin && ln -s $(which getorb)", @@ -34,7 +40,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/getorb', 'bin/make_raw.pl', 'bin/roi'], + 'files': ['bin/add_rmgAmpPhs', 'bin/getorb', 'bin/make_raw.pl', 'bin/make_raw_alos.pl', 'bin/roi'], 'dirs': [], } -- GitLab From c1fc2295bb7312211e795a36fa9bb466465ef66d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:49:06 +0200 Subject: [PATCH 265/566] also define $MY_BIN and $ROI_PAC in ROI_PAC easyconfig --- .../r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb index 30adf12039..89a80fb749 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -48,6 +48,10 @@ modextrapaths = {'PERL5LIB': 'bin'} modextravars = { 'INT_BIN': '%(installdir)s/bin', 'INT_SCR': '%(installdir)s/bin', + 'MY_BIN': '%(installdir)s/bin', + 'ROI_PAC': '%(installdir)s', } +modloadmsg = "To define: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" + moduleclass = 'geo' -- GitLab From 58efec1edfc3367d40113a41898e9c66a597f816 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:53:29 +0200 Subject: [PATCH 266/566] add easyconfig for SQLite 3.17.0 as dep for Python 2.7.13 --- .../s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..41b5a58bd2 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.17.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.sqlite.org/2017/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From fb829371d5936654f861cad99145ed7ca41ab1f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:58:41 +0200 Subject: [PATCH 267/566] no need to patch libreadline 7.0 --- .../easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb index a64400af8e..66d703c987 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -15,8 +15,6 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] -patches = ['libreadline-%(version)s-bugfix.patch'] - builddependencies = [('binutils', '2.27')] dependencies = [('ncurses', '6.0')] -- GitLab From ca1a4fafff488db98e9293a6d4f93b9ee6cde90f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 13:11:17 +0200 Subject: [PATCH 268/566] update extensions in Python 2.7.13 easyconfig, mainly to include numpy 1.12.1 and scipy 0.19.0 --- .../p/Python/Python-2.7.13-intel-2017a.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 31e0d3d932..8d585acc42 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -28,7 +28,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! -# package versions updated March 6th 2017 +# package versions updated March 30th 2017 exts_list = [ # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, # see https://github.com/pypa/setuptools/issues/980 @@ -42,13 +42,14 @@ exts_list = [ ('nose', '1.3.7', { 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), - ('numpy', '1.12.0', { + ('numpy', '1.12.1', { 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], }), - ('scipy', '0.18.1', { + ('scipy', '0.19.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', }), ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], @@ -90,7 +91,7 @@ exts_list = [ ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], }), - ('cryptography', '1.7.2', { + ('cryptography', '1.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], }), ('paramiko', '2.1.2', { @@ -111,8 +112,9 @@ exts_list = [ ('mock', '2.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], }), - ('pytz', '2016.10', { + ('pytz', '2017.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'source_tmpl': '%(name)s-%(version)s.zip', }), ('pandas', '0.19.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], -- GitLab From c51102c55e1c7cb3641db800e8c2ac005121464d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 16:39:09 +0200 Subject: [PATCH 269/566] adding easyconfigs: Mesa-17.0.2-intel-2017a.eb, LLVM-4.0.0-intel-2017a.eb, nettle-3.3-intel-2017a.eb, libdrm-2.4.76-intel-2017a.eb, Mako-1.0.6-intel-2017a-Python-2.7.13.eb, libxml2-2.9.4-intel-2017a-Python-2.7.13.eb --- .../l/LLVM/LLVM-4.0.0-intel-2017a.eb | 42 +++++++++++++ .../l/libdrm/libdrm-2.4.76-intel-2017a.eb | 24 +++++++ ...libxml2-2.9.4-intel-2017a-Python-2.7.13.eb | 24 +++++++ .../Mako-1.0.6-intel-2017a-Python-2.7.13.eb | 22 +++++++ .../m/Mesa/Mesa-17.0.2-intel-2017a.eb | 63 +++++++++++++++++++ .../n/nettle/nettle-3.3-intel-2017a.eb | 28 +++++++++ 6 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb new file mode 100644 index 0000000000..5fba0f28fc --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '4.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Python', '2.7.13'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb new file mode 100644 index 0000000000..be5c5321ff --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.76' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('X11', '20170129'), +] + +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-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..8eeb402547 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.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': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), + ('Python', '2.7.13'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9bae465168 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +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-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb new file mode 100644 index 0000000000..70b8bcc2b4 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -0,0 +1,63 @@ +# 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 = '17.0.2' + +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': 'intel', 'version': '2017a'} +# 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/', + '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', '2.6.3'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Mako', '1.0.6', '-Python-2.7.13'), + ('libxml2', '2.9.4', '-Python-2.7.13'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.3'), + ('libdrm', '2.4.76'), + ('LLVM', '4.0.0'), + ('X11', '20170129'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --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/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-3.3-intel-2017a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb new file mode 100644 index 0000000000..d8f9e8fc31 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.3' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.2'), +] + +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 65ed10a7fb122fd9bbde169b3234337aedb587c9 Mon Sep 17 00:00:00 2001 From: John Donners Date: Thu, 30 Mar 2017 18:55:11 +0200 Subject: [PATCH 270/566] adding easyconfigs: SCOTCH-6.0.4-intel-2016b.eb --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb index 20bc255b1a..5df84b7224 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' -- GitLab From dd3c0ab7262f61bf0d5187f1ce8307bd4c3afda4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 10:34:22 +0200 Subject: [PATCH 271/566] adding easyconfigs: PGI-17.3-GCC-6.3.0-2.28.eb --- .../p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..fd7e68ba06 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '17.3' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['6eefc42f85e756cbaba76467ed640902'] + +gccver = '6.3.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From 22f66c09d8737d5987422a44069c798e5702ac5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 11:52:19 +0200 Subject: [PATCH 272/566] adding easyconfigs: VTune-2017_update2.eb --- .../easyconfigs/v/VTune/VTune-2017_update2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb new file mode 100644 index 0000000000..5db4d180ba --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb @@ -0,0 +1,15 @@ +name = 'VTune' +version = '2017_update2' + +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'] +checksums = ['1ef91898e107a1da015305def80091e4'] + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From 21c7598a04c602939937779d872a9e59ca0f717c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 15:43:48 +0200 Subject: [PATCH 273/566] add patch to fix build of Mesa 17.0.2 with Intel compilers --- .../easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb | 3 +++ .../m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch | 14 ++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index 70b8bcc2b4..f2828371e3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -26,6 +26,7 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] builddependencies = [ ('flex', '2.6.3'), @@ -49,6 +50,8 @@ configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm -- configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " +buildopts = 'V=1' + 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, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch new file mode 100644 index 0000000000..d0aae3dd9c --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch @@ -0,0 +1,14 @@ +strip out '-fp-model source' as a whole, rather than only stripping out '-fp-model' which leads to compilation errors: +"File not found: 'source'" + +author: Ward Poelmans (VUB) +--- mesa-17.0.2/configure.orig 2017-03-31 15:08:32.677119063 +0200 ++++ mesa-17.0.2/configure 2017-03-31 15:09:03.797577051 +0200 +@@ -22317,6 +22317,7 @@ + -e 's/\s\+-O\S*//g' \ + -e 's/\s\+-g\S*//g' \ + -e 's/-fno-rtti\>/-Fno-rtti/g' \ ++ -e 's/\s\+-fp-model \S*//g' \ + -e 's/\s\+-f\S*//g' \ + -e 's/-Fno-rtti\>/-fno-rtti/g' \ + -e 's/^ //' -- GitLab From d9dad61ddaf59e678a9abf97cc7fa9ee16318a9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:28:15 +0200 Subject: [PATCH 274/566] adding easyconfigs: scp-0.10.2-intel-2016b-Python-2.7.12.eb --- .../scp-0.10.2-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1372c5db1e --- /dev/null +++ b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'scp' +version = '0.10.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jbardin/scp.py' +description = """The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol.""" + +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' -- GitLab From f0df52802c6a87777ca2ca60a7ceff6f977cb419 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:28:41 +0200 Subject: [PATCH 275/566] adding easyconfigs: Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb --- ...Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..c0dc9e45f8 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From 77ccc1df9abe43202a2a677829df4cda59bf6b04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:34:12 +0200 Subject: [PATCH 276/566] {data}[intel/2017a] GDAL v2.1.3 + updated deps --- .../GDAL-2.1.3-intel-2017a-Python-2.7.13.eb | 48 +++++++++++++++++++ .../GDAL-2.1.3_fix-uchar-definition.patch | 9 ++++ .../GEOS-3.6.1-intel-2017a-Python-2.7.13.eb | 28 +++++++++++ .../l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 33 +++++++++++++ .../libjpeg-turbo-1.5.1-intel-2017a.eb | 30 ++++++++++++ .../l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb | 29 +++++++++++ .../n/NASM/NASM-2.12.02-intel-2017a.eb | 31 ++++++++++++ .../p/PCRE/PCRE-8.40-intel-2017a.eb | 18 +++++++ .../SWIG-3.0.12-intel-2017a-Python-2.7.13.eb | 20 ++++++++ 9 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..07385fe881 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '2.0.12'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch new file mode 100644 index 0000000000..c70a977531 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch @@ -0,0 +1,9 @@ +--- gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h.orig 2017-03-31 17:06:52.996122910 +0200 ++++ gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h 2017-03-31 17:07:06.356370202 +0200 +@@ -34,4 +34,6 @@ + + jas_stream_t *JPEG2000_VSIL_fopen(const char *filename, const char *mode); + ++#define uchar unsigned char ++ + #endif diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4483d7a5d0 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.13')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb new file mode 100644 index 0000000000..9087c14aa4 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.7' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb new file mode 100644 index 0000000000..921c5c073d --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.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': '2017a'} +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/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..85ea50b710 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.29' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +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/n/NASM/NASM-2.12.02-intel-2017a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb new file mode 100644 index 0000000000..a4d8935beb --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.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 = '2.12.02' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +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/p/PCRE/PCRE-8.40-intel-2017a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb new file mode 100644 index 0000000000..b2df6c9ad9 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.40' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..b90543199e --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.12' +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': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PCRE', '8.40'), +] + +moduleclass = 'devel' -- GitLab From bbf0a5bf2bdef4672f51a6750df57ef02ed6bb41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:51:28 +0200 Subject: [PATCH 277/566] adding easyconfigs: LIBSVM-3.22-intel-2016b.eb --- .../l/LIBSVM/LIBSVM-3.22-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb new file mode 100644 index 0000000000..26b2999f95 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.22' + +homepage = 'http://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Qt', '4.8.7')] + +buildopts = ' && cd svm-toy/qt && make MOC=$EBROOTQT/bin/moc ' +buildopts += 'CFLAGS="$CFLAGS -I$EBROOTQT/include -I$EBROOTQT/include/QtGui -lQtGui -lQtCore" && cd -' + +files_to_copy = [(['svm-*'], 'bin'), 'tools'] + +sanity_check_paths = { + 'files': ['bin/svm-%s' % x for x in ['predict', 'scale', 'train']] + ['bin/svm-toy/qt/svm-toy'], + 'dirs': ['bin/svm-toy', 'tools'], +} + +modextrapaths = { + 'PATH': ['bin', 'bin/svm-toy/qt'], +} + +moduleclass = 'lib' -- GitLab From e9b30261c84e53d6c1d33de470ad822df6a81c07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:15:56 +0200 Subject: [PATCH 278/566] consistently add zlib as dependency in SCOTCH easyconfigs --- .../s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb | 4 ++++ .../s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb | 4 ++++ 17 files changed, 68 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb index f7e1fa75af..fb8bdd5fe8 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/28978/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb index 63e54d60a9..a840cb128c 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb @@ -12,4 +12,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/28978/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb index adc2bceafc..36e2a02cae 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb index 8e693c1ca4..b9f3cfb699 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb index b0d4836a13..60cfca1ccb 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb index b9f29b45c5..1a0f934621 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb index 89020e5a6b..4e6810fc24 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb index f4c56ce013..68499c20c9 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34099/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index f5bdd9828b..8e49ec9738 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb index 3f65d37408..6646f63b1d 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb index 431d04e9df..6627e15ad7 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb index 9fb7233435..e19c44686d 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb index b61aa3728e..4bbf975f93 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb index a98a4841f7..173ec5abc6 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb index ba1a0a43d1..a9f67fc882 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb @@ -12,4 +12,8 @@ toolchainopts = {'pic': True, 'i8': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb index 34df491afd..5f4f35c9c0 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb index a90bb75fa5..30e51cb632 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' -- GitLab From e11ecadb7b25a413b83103555ebe21477c841adb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:40:48 +0200 Subject: [PATCH 279/566] adding easyconfigs: cairo-1.14.8-intel-2017a.eb, pixman-0.34.0-GCCcore-6.3.0.eb, GLib-2.52.0-intel-2017a.eb --- .../c/cairo/cairo-1.14.8-intel-2017a.eb | 43 +++++++++++++++++++ .../g/GLib/GLib-2.52.0-intel-2017a.eb | 34 +++++++++++++++ .../p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb | 23 ++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb new file mode 100644 index 0000000000..6f9eb993e3 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.8' + +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': '2017a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libpng', '1.6.29'), + ('freetype', '2.7.1'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.52.0'), + ('X11', '20170129'), +] + +# 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/GLib/GLib-2.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb new file mode 100644 index 0000000000..dcffcd7dec --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.52.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.4'), + ('PCRE', '8.40'), +] + +builddependencies = [('Python', '2.7.13')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..185ce92b1d --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +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': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 8cea6ea8a6ecbc4dd325a0acdce97bd43aba31af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:41:22 +0200 Subject: [PATCH 280/566] adding easyconfigs: ED2-20170201-intel-2017a-serial.eb --- .../e/ED2/ED2-20170201-intel-2017a-serial.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb new file mode 100644 index 0000000000..0ba1a5a27b --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'ED2' +version = '20170201' +commit = '0146fa4' +versionsuffix = '-serial' + +homepage = 'https://github.com/EDmodel/ED2' +description = """The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model + incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/EDmodel/ED2/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = [ + 'ED2_install-without-make.patch', + 'ED2_fix-type.patch', +] + +dependencies = [('HDF5', '1.10.0-patch1')] + +start_dir = 'ED/build' + +# rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options +prebuildopts = "./install.sh --kind E --platform intel --gitoff && cd bin-opt-E && " + +buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' PAR_DEFS='' " +buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' + +files_to_copy = [(['ED/build/ed_2.1-opt'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ed_2.1-opt'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From 7040ded550b1739b2a37c1ce8193dcb5c9509991 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 19:03:15 +0200 Subject: [PATCH 281/566] adding easyconfigs: R-3.3.3-intel-2017a-X11-20170129.eb, libGLU-9.0.0-intel-2017a.eb, Tk-8.6.6-intel-2017a.eb, PROJ-4.9.3-intel-2017a.eb --- .../l/libGLU/libGLU-9.0.0-intel-2017a.eb | 24 + .../p/PROJ/PROJ-4.9.3-intel-2017a.eb | 30 ++ .../r/R/R-3.3.3-intel-2017a-X11-20170129.eb | 509 ++++++++++++++++++ .../easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb | 27 + 4 files changed, 590 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb new file mode 100644 index 0000000000..7dff238507 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '17.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb new file mode 100644 index 0000000000..07a9a99e42 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb new file mode 100644 index 0000000000..e0614dfdd9 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb @@ -0,0 +1,509 @@ +name = 'R' +version = '3.3.3' +x11ver = '20170129' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.8'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.17.0'), + ('PCRE', '8.40'), + ('libpng', '1.6.29'), # for plotting in R + ('libjpeg-turbo', '1.5.1'), # for plottting in R + ('LibTIFF', '4.0.7'), + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.6'), # for tcltk + ('Tk', '8.6.6'), # for tcltk + ('cURL', '7.53.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +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 March 7th 2017 +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', '0.6-6', ext_options), + ('abind', '1.4-5', 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', '4.1', ext_options), + ('bootstrap', '2017.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.4', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-25', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-10', ext_options), + ('mclust', '5.2.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.4', ext_options), + ('stabledist', '0.7-1', 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', '1.7-5', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.62.0-1', 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), + ('backports', '1.0.5', ext_options), + ('checkmate', '1.8.2', ext_options), + ('Rcpp', '0.12.9', ext_options), + ('cubature', '1.3-6', ext_options), + ('DEoptimR', '1.0-8', ext_options), + ('digest', '0.6.12', ext_options), + ('fastmatch', '1.1-0', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.1.1', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.4-0', ext_options), + ('subplex', '1.2-2', ext_options), + ('stringi', '1.1.2', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.2.0', ext_options), + ('evaluate', '0.10', ext_options), + ('logspline', '2.1.9', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.9-4', ext_options), + ('plotrix', '3.6-4', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-38', ext_options), + ('SparseM', '1.76', ext_options), + ('tripack', '1.3-8', ext_options), + ('irace', '2.1', ext_options), + ('rJava', '0.9-8', ext_options), + ('lattice', '0.20-34', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-28', ext_options), + ('Matrix', '1.2-8', ext_options), + ('png', '0.1-7', ext_options), + ('RcppArmadillo', '0.7.700.0.0', ext_options), + ('plyr', '1.8.4', ext_options), + ('pROC', '1.9.1', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.11', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-2', ext_options), + ('MASS', '7.3-45', ext_options), + ('tree', '1.0-37', ext_options), + ('pls', '2.6-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-8', ext_options), + ('nnet', '7.3-12', ext_options), + ('nlme', '3.1-131', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.9.0', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.29', ext_options), + ('mgcv', '1.8-17', ext_options), + ('colorspace', '1.3-2', ext_options), + ('robustbase', '0.92-7', ext_options), + ('sp', '1.2-4', ext_options), + ('zoo', '1.7-14', ext_options), + ('lmtest', '0.9-35', ext_options), + ('vcd', '1.4-3', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-10', ext_options), + ('survival', '2.40-1', ext_options), + ('mice', '2.30', ext_options), + ('urca', '1.3-0', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.22', ext_options), + ('akima', '0.6-2', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-18', ext_options), + ('mixtools', '1.1.0', ext_options), + ('cluster', '2.0.5', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.19-1', ext_options), + ('codetools', '0.2-15', ext_options), + ('foreach', '1.4.3', ext_options), + ('doMC', '1.3.4', ext_options), + ('DBI', '0.6', ext_options), + ('foreign', '0.8-67', ext_options), + ('gam', '1.14', ext_options), + ('gamlss.data', '5.0-0', ext_options), + ('gamlss.dist', '5.0-0', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-1', ext_options), + ('quantmod', '0.4-7', ext_options), + ('mnormt', '1.5-5', ext_options), + ('mvtnorm', '1.0-6', ext_options), + ('pcaPP', '1.9-61', ext_options), + ('numDeriv', '2016.8-1', ext_options), + ('lava', '1.4.7', ext_options), + ('prodlim', '1.6.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('memoise', '1.0.0', ext_options), + ('plogr', '0.1-1', ext_options), + ('RSQLite', '1.1-2', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-4', ext_options), + ('sfsmisc', '1.1-0', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-3', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-2', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.14', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-38', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.1', ext_options), + ('R.oo', '1.21.0', ext_options), + ('cgdsr', '1.2.5', ext_options), + ('R.utils', '2.5.0', ext_options), + ('R.matlab', '3.6.1', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.4.1', ext_options), + ('reshape2', '1.4.2', ext_options), + ('gtable', '0.2.0', ext_options), + ('munsell', '0.4.3', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.4.1', ext_options), + ('proto', '1.0.0', ext_options), + ('lazyeval', '0.2.0', ext_options), + ('assertthat', '0.1', ext_options), + ('tibble', '1.2', ext_options), + ('ggplot2', '2.2.1', ext_options), + ('gridExtra', '2.2.1', ext_options), + ('chron', '2.3-50', ext_options), + ('data.table', '1.10.4', ext_options), + ('viridis', '0.3.4', ext_options), + ('yaml', '2.1.14', ext_options), + ('jsonlite', '1.3', ext_options), + ('htmltools', '0.3.5', ext_options), + ('htmlwidgets', '0.8', ext_options), + ('knitr', '1.15.1', ext_options), + ('htmlTable', '1.9', ext_options), + ('Hmisc', '4.0-2', ext_options), + ('fastcluster', '1.1.22', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.1.2', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '4.1', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '3.0.1', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.3', ext_options), + ('R6', '2.2.0', ext_options), + ('rjson', '0.2.15', ext_options), + ('sourcetools', '0.1.5', ext_options), + ('shiny', '1.0.0', ext_options), + ('seqinr', '3.3-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-12', ext_options), + ('gmodels', '2.16.2', ext_options), + ('expm', '0.999-1', ext_options), + ('spdep', '0.6-11', ext_options), + ('dplyr', '0.5.0', ext_options), + ('vegan', '2.4-2', ext_options), + ('adegenet', '2.0.1', ext_options), + ('prettyunits', '1.0.2', ext_options), + ('progress', '1.1.2', ext_options), + ('rncl', '0.8.2', ext_options), + ('XML', '3.98-1.5', ext_options), + ('crayon', '1.3.2', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '1.0.2', ext_options), + ('rprojroot', '1.2', ext_options), + ('rmarkdown', '1.3', ext_options), + ('curl', '2.3', ext_options), + ('openssl', '0.9.6', ext_options), + ('httr', '1.2.1', ext_options), + ('reshape', '0.8.6', ext_options), + ('xml2', '1.1.1', ext_options), + ('bold', '0.4.0', ext_options), + ('triebeard', '0.3.0', ext_options), + ('urltools', '1.6.0', ext_options), + ('httpcode', '0.2.0', ext_options), + ('crul', '0.3.0', ext_options), + ('rredlist', '0.3.0', ext_options), + ('rentrez', '1.0.4', ext_options), + ('rotl', '3.0.3', ext_options), + ('solrium', '0.4.0', ext_options), + ('ritis', '0.5.4', ext_options), + ('worrms', '0.1.0', ext_options), + ('natserv', '0.1.4', ext_options), + ('taxize', '0.8.4', ext_options), + ('tidyr', '0.6.1', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.7', ext_options), + ('phylobase', '0.8.2', ext_options), + ('adephylo', '1.1-10', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.19', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-8', ext_options), + ('dismo', '1.1-4', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.4', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.10', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-5', ext_options), + ('rgl', '0.98.1', ext_options), + ('labdsv', '1.8-0', ext_options), + ('stabs', '0.6-2', ext_options), + ('modeltools', '0.2-21', ext_options), + ('strucchange', '1.5-1', ext_options), + ('TH.data', '1.0-8', ext_options), + ('multcomp', '1.4-6', ext_options), + ('coin', '1.1-3', ext_options), + ('party', '1.2-2', ext_options), + ('mboost', '2.7-0', ext_options), + ('msm', '1.6.4', ext_options), + ('nor1mix', '1.2-2', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-9', ext_options), + ('polspline', '1.1.12', ext_options), + ('rms', '5.1-0', ext_options), + ('RWekajars', '3.9.1-1', ext_options), + ('RWeka', '0.4-31', ext_options), + ('slam', '0.1-40', ext_options), + ('tm', '0.7-1', ext_options), + ('TraMineR', '1.8-13', ext_options), + ('chemometrics', '1.4.1', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-6', ext_options), + ('statmod', '1.4.29', ext_options), + ('miscTools', '0.6-22', 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', '1.3.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.51.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '3.0', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-12', ext_options), + ('pbkrtest', '0.4-6', ext_options), + ('car', '2.1-4', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.35', 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', '2.10', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '2.0', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '3.2', ext_options), + ('RGCCA', '2.1', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '4.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.2.0', ext_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('VennDiagram', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '8.0', ext_options), + ('fma', '2.3', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.9-1', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.5-6', ext_options), + ('goftest', '1.0-4', ext_options), + ('spatstat', '1.49-0', ext_options), + ('rgdal', '1.2-5', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.9.9', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.3-1', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-21', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('ModelMetrics', '1.1.0', ext_options), + ('caret', '6.0-73', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.10', ext_options), + ('ggvis', '0.4.3', ext_options), + ('mlr', '2.10', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-9', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.14', 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', '0.6', ext_options), + ('commonmark', '1.2', ext_options), + ('desc', '1.1.0', ext_options), + ('roxygen2', '6.0.1', ext_options), + ('git2r', '0.18.0', ext_options), + ('rversions', '1.0.3', ext_options), + ('withr', '1.0.2', ext_options), + ('devtools', '1.12.0', ext_options), + ('Rook', '1.1-1', ext_options), + ('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.2-3', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-8', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-10', ext_options), + ('ks', '1.10.5', ext_options), + ('logcondens', '2.1.5', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-50', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.4.2', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.6.12', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-23.1097', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.9-3', ext_options), + ('mi', '1.0', ext_options), + ('visNetwork', '1.0.3', ext_options), + ('rgexf', '0.15.3', ext_options), + ('influenceR', '0.1.0', ext_options), + ('DiagrammeR', '0.9.0', ext_options), + ('sem', '3.1-8', ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', 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', '1.4.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.1.1', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('imager', '0.31', ext_options), +] + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb new file mode 100644 index 0000000000..325e35acc9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +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 = [ + ('X11', '20170129'), + ('Tcl', version), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 2d73e37dd1ce05ab3f76e27bbe6c7972f3ff8f4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 19:03:49 +0200 Subject: [PATCH 282/566] add util-linux as dependency to GLib --- .../g/GLib/GLib-2.52.0-intel-2017a.eb | 1 + .../util-linux-2.29.2-intel-2017a.eb | 33 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb index dcffcd7dec..6b20efcba1 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb @@ -17,6 +17,7 @@ dependencies = [ ('gettext', '0.19.8.1'), ('libxml2', '2.9.4'), ('PCRE', '8.40'), + ('util-linux', '2.29.2'), ] builddependencies = [('Python', '2.7.13')] diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb new file mode 100644 index 0000000000..3495ebee0c --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.29.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 98be1ce1add0f4ccea0920abe523f5a7d3182fa8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 20:29:25 +0200 Subject: [PATCH 283/566] adding easyconfigs: X11-20170314-GCCcore-6.3.0.eb, fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb, freetype-2.7.2-GCCcore-6.3.0.eb --- ...fig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb | 27 ++++ .../freetype/freetype-2.7.2-GCCcore-6.3.0.eb | 29 ++++ .../x/X11/X11-20170314-GCCcore-6.3.0.eb | 135 ++++++++++++++++++ 3 files changed, 191 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb new file mode 100644 index 0000000000..cc99c8e530 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' +freetype_ver = '2.7.2' +versionsuffix = '-freetype-%s' % freetype_ver + +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': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', freetype_ver), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..6f9485b3f0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +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/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..28c4d48e99 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -0,0 +1,135 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20170314' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +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', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('fontconfig', '2.12.1', '-freetype-2.7.2'), + ('zlib', '1.2.11'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.1'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.1', { # 2017-01-29 + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.4', common_specs), # 2017-03-14 + ('bigreqsproto', '1.1.2', common_specs), # 2012-03-23 + ('compositeproto', '0.4.2', common_specs), # 2010-10-30 + ('damageproto', '1.2.1', common_specs), # 2010-10-30 + ('dmxproto', '2.3.1', common_specs), # 2011-01-06 + ('dri2proto', '2.8', common_specs), # 2012-07-11 + ('dri3proto', '1.0', common_specs), # 2013-11-01 + ('fixesproto', '5.0', common_specs), # 2011-03-08 + ('fontsproto', '2.1.3', common_specs), # 2014-04-14 + ('glproto', '1.4.17', common_specs), # 2013-12-10 + ('inputproto', '2.3.2', common_specs), # 2016-04-04 + ('kbproto', '1.0.7', common_specs), # 2015-05-01 + ('presentproto', '1.1', common_specs), # 2017-01-26 + ('randrproto', '1.5.0', common_specs), # 2015-05-17 + ('recordproto', '1.14.2', common_specs), # 2012-03-23 + ('renderproto', '0.11.1', common_specs), # 2010-08-10 + ('resourceproto', '1.2.0', common_specs), # 2011-05-28 + ('scrnsaverproto', '1.2.2', common_specs), # 2012-03-23 + ('videoproto', '2.3.3', common_specs), # 2016-03-11 + ('xcmiscproto', '1.2.2', common_specs), # 2012-03-23 + ('xextproto', '7.3.0', common_specs), # 2013-12-27 + ('xf86bigfontproto', '1.2.0', common_specs), # 2009-08-27 + ('xf86dgaproto', '2.1', common_specs), # 2009-10-01 + ('xf86driproto', '2.1.1', common_specs), # 2011-01-06 + ('xf86vidmodeproto', '2.3.1', common_specs), # 2011-01-06 + ('xineramaproto', '1.2.1', common_specs), # 2011-01-06 + ('xproto', '7.0.31', common_specs), # 2016-09-23 + ('libXau', '1.0.8', common_specs), # 2013-05-24 + ('libXdmcp', '1.1.2', common_specs), # 2015-03-21 + ('xcb-proto', '1.12', common_specs), # 2016-05-18 + ('libxcb', '1.12', common_specs), # 2016-05-18 + ('xtrans', '1.3.5', common_specs), # 2014-09-22 + ('libxkbcommon', '0.7.1', { # 2017-01-18 + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.5', common_specs), # 2017-02-26 + ('libXext', '1.3.3', common_specs), # 2014-07-24 + ('libFS', '1.0.7', common_specs), # 2015-05-01 + ('libICE', '1.0.9', common_specs), # 2014-06-07 + ('libSM', '1.2.2', common_specs), # 2013-09-08 + ('libXScrnSaver', '1.2.2', common_specs), # 2012-03-08 + ('libXt', '1.1.5', common_specs), # 2015-05-01 + ('libXmu', '1.1.2', common_specs), # 2013-09-08 + ('libXpm', '3.5.12', common_specs), # 2016-12-15 + ('libXaw', '1.0.13', common_specs), # 2015-05-01 + ('libXfixes', '5.0.3', common_specs), # 2016-10-04 + ('libXcomposite', '0.4.4', common_specs), # 2013-01-03 + ('libXrender', '0.9.10', common_specs), # 2016-10-04 + ('libXcursor', '1.1.14', common_specs), # 2013-05-30 + ('libXdamage', '1.1.4', common_specs), # 2013-01-03 + ('libfontenc', '1.1.3', common_specs), # 2015-05-01 + ('libXfont', '1.5.2', common_specs), # 2016-08-31 + ('libXfont2', '2.0.1', common_specs), # 2015-12-11 + ('libXft', '2.3.2', common_specs), # 2014-06-06 + ('libXi', '1.7.9', common_specs), # 2017-01-23 + ('libXinerama', '1.1.3', common_specs), # 2013-05-31 + ('libXrandr', '1.5.1', common_specs), # 2016-10-04 + ('libXres', '1.0.7', common_specs), # 2013-05-31 + ('libXtst', '1.2.3', common_specs), # 2016-10-04 + ('libXv', '1.0.11', common_specs), # 2016-10-04 + ('libXvMC', '1.0.10', common_specs), # 2016-10-04 + ('libXxf86dga', '1.1.4', common_specs), # 2013-05-31 + ('libXxf86vm', '1.1.4', common_specs), # 2015-02-24 + ('libdmx', '1.1.3', common_specs), # 2013-05-28 + ('libpciaccess', '0.13.4', common_specs), # 2015-05-01 + ('libxkbfile', '1.0.9', common_specs), # 2015-05-01 + ('libxshmfence', '1.2', common_specs), # 2015-01-02 + ('xcb-util', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-image', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-keysyms', '0.4.0', common_specs), # 2014-10-01 + ('xcb-util-renderutil', '0.3.9', common_specs), # 2014-06-13 + ('xcb-util-wm', '0.4.1', common_specs), # 2014-02-19 + ('xcb-util-cursor', '0.1.3', common_specs), # 2016-05-12 +] + +# 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' -- GitLab From 42b1274584aa7936846cd2f34cfd71df6a72f79c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:06:20 +0200 Subject: [PATCH 284/566] no freetype 2.7.2 yet, change versionsuffix to -libpng-1.6.29 --- ....eb => fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb} | 5 ++--- ...3.0.eb => freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb} | 6 ++++-- easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb | 3 ++- 3 files changed, 8 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/fontconfig/{fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb => fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb} (86%) rename easybuild/easyconfigs/f/freetype/{freetype-2.7.2-GCCcore-6.3.0.eb => freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb} (89%) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb similarity index 86% rename from easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb rename to easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb index cc99c8e530..b9da643ed4 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -2,8 +2,7 @@ easyblock = 'ConfigureMake' name = 'fontconfig' version = '2.12.1' -freetype_ver = '2.7.2' -versionsuffix = '-freetype-%s' % freetype_ver +versionsuffix = '-libpng-1.6.29' homepage = 'http://www.freedesktop.org/software/fontconfig' description = """Fontconfig is a library designed to provide system-wide font configuration, customization and @@ -16,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.2.0'), - ('freetype', freetype_ver), + ('freetype', '2.7.1', versionsuffix), ] # use same binutils version that was used when building GCCcore toolchain diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb similarity index 89% rename from easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb rename to easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index 6f9485b3f0..1b0dc16aba 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -1,5 +1,7 @@ name = 'freetype' -version = '2.7.2' +version = '2.7.1' +libpng_ver = '1.6.29' +versionsuffix = '-libpng-%s' % libpng_ver homepage = 'http://freetype.org' description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and @@ -13,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('bzip2', '1.0.6'), - ('libpng', '1.6.29'), + ('libpng', libpng_ver), ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb index 28c4d48e99..dc3461eb7f 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -18,7 +18,8 @@ source_urls = [ dependencies = [ ('bzip2', '1.0.6'), - ('fontconfig', '2.12.1', '-freetype-2.7.2'), + ('fontconfig', '2.12.1', '-libpng-1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), ('zlib', '1.2.11'), ] builddependencies = [ -- GitLab From 6c8b36edb3ad6280a15cc4cfc13bfabebeb5710c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:07:15 +0200 Subject: [PATCH 285/566] bump X11 to version 20170314 in Mesa 17.0.2 easyconfig --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb index be5c5321ff..a8a5a109c8 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2017a'} dependencies = [ - ('X11', '20170129'), + ('X11', '20170314'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index f2828371e3..8bb12d31a3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -42,7 +42,7 @@ dependencies = [ ('nettle', '3.3'), ('libdrm', '2.4.76'), ('LLVM', '4.0.0'), - ('X11', '20170129'), + ('X11', '20170314'), ] # GLU is not part anymore of Mesa package! -- GitLab From 20ef59bf583714a6cf3719bdffc7e2978ad23024 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:10:07 +0200 Subject: [PATCH 286/566] bump X11 dep version in cairo 1.14.8 easyconfig --- easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb index 6f9eb993e3..6be8104cc5 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -21,7 +21,7 @@ dependencies = [ ('pixman', '0.34.0'), ('expat', '2.2.0'), ('GLib', '2.52.0'), - ('X11', '20170129'), + ('X11', '20170314'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -- GitLab From 22f35fb732e032fa70bcedfe12fcf01bffec2f89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:11:57 +0200 Subject: [PATCH 287/566] bump X11 deps to 20170314 --- ...017a-X11-20170129.eb => R-3.3.3-intel-2017a-X11-20170314.eb} | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/R/{R-3.3.3-intel-2017a-X11-20170129.eb => R-3.3.3-intel-2017a-X11-20170314.eb} (99%) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb similarity index 99% rename from easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb rename to easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index e0614dfdd9..6892093317 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -1,6 +1,6 @@ name = 'R' version = '3.3.3' -x11ver = '20170129' +x11ver = '20170314' versionsuffix = '-X11-%s' % x11ver homepage = 'http://www.r-project.org/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb index 325e35acc9..a01bad3db9 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb @@ -15,7 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] dependencies = [ - ('X11', '20170129'), + ('X11', '20170314'), ('Tcl', version), ('zlib', '1.2.11'), ] -- GitLab From 113e1afec23069c309e9b805b51809af27f54de1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:47:22 +0200 Subject: [PATCH 288/566] fix freetype dep in cairo 1.14.8 easyconfig --- easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb index 6be8104cc5..872e069d81 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -17,7 +17,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.11'), ('libpng', '1.6.29'), - ('freetype', '2.7.1'), + ('freetype', '2.7.1', '-libpng-1.6.29'), ('pixman', '0.34.0'), ('expat', '2.2.0'), ('GLib', '2.52.0'), -- GitLab From ad7470594727b093fefd925cf9cf6b40ad5e802f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 22:32:51 +0200 Subject: [PATCH 289/566] include patches for R v3.3.3 extensions to fix compilation with Intel compilers --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 6892093317..75250e8769 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -79,7 +79,7 @@ exts_list = [ ('Rmpi', '0.6-6', ext_options), ('abind', '1.4-5', ext_options), ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), ('bit', '1.1-12', ext_options), ('filehash', '2.3', ext_options), ('ff', '2.2-13', ext_options), @@ -324,7 +324,7 @@ exts_list = [ ('adephylo', '1.1-10', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.19', ext_options), + ('bigmemory', '4.5.19', dict(ext_options.items() + [('patches', ['bigmemory-4.5.19_icpc-wd308.patch'])])), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), ('raster', '2.5-8', ext_options), @@ -407,7 +407,7 @@ exts_list = [ ('VennDiagram', '1.6.17', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), - ('forecast', '8.0', ext_options), + ('forecast', '8.0', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.3', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', ext_options), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), @@ -483,7 +483,7 @@ exts_list = [ ('network', '1.13.0', ext_options), ('statnet.common', '3.3.0', ext_options), ('sna', '2.4', ext_options), - ('glasso', '1.8', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), ('huge', '1.2.7', ext_options), ('d3Network', '0.5.2.1', ext_options), ('ggm', '2.3', ext_options), -- GitLab From d845dddaa77015db0f0b283f52559461647d5738 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 12:02:44 +0200 Subject: [PATCH 290/566] adding easyconfigs: Spack-0.10.0.eb --- easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb new file mode 100644 index 0000000000..3a97b911b1 --- /dev/null +++ b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Spack' +version = '0.10.0' + +homepage = 'https://spack.io/' +description = """Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific + software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, + and all of these builds can coexist on the same machine.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/LLNL/spack/archive/'] +sources = ['v%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/spack'], + 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], +} + +sanity_check_commands = [ + "spack list", + "spack versions gcc", +] + +moduleclass = 'devel' -- GitLab From 5c10b74a26b8517f3c9462ce128ef51f9867bf82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 21:19:46 +0200 Subject: [PATCH 291/566] fix patch for multicool-0.1-10 extension in R 3.3.3 easyconfig --- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 75250e8769..eb14dda6a0 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-10_icpc-wd308.patch', 1)])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch new file mode 100644 index 0000000000..a86f23d77d --- /dev/null +++ b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch @@ -0,0 +1,7 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- multicool/src/Makevars.orig 2017-04-01 21:14:54.299465099 +0200 ++++ multicool/src/Makevars 2017-04-01 21:14:54.299465099 +0200 +@@ -0,0 +1,2 @@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From 23693fca6ad76a06c641d3110ef58445491d73f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 21:32:43 +0200 Subject: [PATCH 292/566] make sure multicool patch level can be derived --- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index eb14dda6a0..06a44541b2 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-10_icpc-wd308.patch', 1)])])), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', ['multicool-0.1-10_icpc-wd308.patch'])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch index a86f23d77d..660089c7d5 100644 --- a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch +++ b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch @@ -1,5 +1,12 @@ add -wd308 compiler option to avoid compiler warning #308 being treated as an error author: Kenneth Hoste (HPC-UGent) +--- multicool/MD5.orig 2017-04-01 21:30:37.105382230 +0200 ++++ multicool/MD5 2017-04-01 21:30:30.095337987 +0200 +@@ -20,3 +20,4 @@ + b18b7e9e5912cf1014aa2c2fa8e86047 *src/compositions.cpp + 994ea793adf2455b973554d9b8dacd99 *src/multicool.cpp + 8e6ea24037e92ec9c30f699f4e3f9b8a *src/multinomial.h ++b1d3a4d02405fe08c7983c479bc27f13 */src/Makevars --- multicool/src/Makevars.orig 2017-04-01 21:14:54.299465099 +0200 +++ multicool/src/Makevars 2017-04-01 21:14:54.299465099 +0200 @@ -0,0 +1,2 @@ -- GitLab From 1db6d2bc186632ac3e477de75e3620300e4364e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 Apr 2017 09:43:12 +0200 Subject: [PATCH 293/566] add patch for imager extension in R 3.3.3 easyconfig --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../r/R/imager-0.3_fix-icpc-bool-cast.patch | 259 ++++++++++++++++++ 2 files changed, 260 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 06a44541b2..01ebe2e855 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -502,7 +502,7 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', ext_options), + ('imager', '0.31', dict(ext_options.items() + [('patches', ['imager-0.3_fix-icpc-bool-cast.patch'])])), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch new file mode 100644 index 0000000000..8d994cb858 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch @@ -0,0 +1,259 @@ +fix Intel compilation errors, partially based on https://github.com/dtschump/CImg/commit/d66a4e7f1b13594a572c22160c20e2bd3f231f6c +author: Kenneth Hoste (HPC-UGent) +--- imager/inst/include/CImg.h.orig 2016-08-31 16:30:10.000000000 +0200 ++++ imager/inst/include/CImg.h 2017-04-01 22:43:25.292695440 +0200 +@@ -17988,7 +17988,7 @@ + unsigned int ind = (unsigned int)mp.opcode[2]; + if (ind!=~0U) ind = (unsigned int)cimg::mod((int)_mp_arg(2),mp.listin.width()); + CImg &img = ind==~0U?mp.imgout:mp.listout[ind]; +- if (img) { ++ if ((bool)img) { + if (mp.opcode[12]!=(ulongT)-1) { + const CImg M(&_mp_arg(12) + 1,dx,dy,dz,(unsigned int)mp.opcode[13],true); + img.draw_image(x,y,z,c,S,M,opacity,(float)_mp_arg(14)); +@@ -18107,10 +18107,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18184,10 +18184,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18257,10 +18257,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18317,10 +18317,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img(ind,cimg::mod(off,whds)); ++ if ((bool)img) return (double)img(ind,cimg::mod(off,whds)); + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18590,7 +18590,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -18662,7 +18662,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -19579,7 +19579,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -19648,7 +19648,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -25664,14 +25664,15 @@ + x0 = ((int)xc%width()) - width(), + y0 = ((int)yc%height()) - height(), + z0 = ((int)zc%depth()) - depth(), +- c0 = ((int)cc%spectrum()) - spectrum(); ++ c0 = ((int)cc%spectrum()) - spectrum(), ++ dx = width(), dy = height(), dz = depth(), dc = spectrum(); + #ifdef cimg_use_openmp + #pragma omp parallel for collapse(3) if (res.size()>=65536) + #endif +- for (int c = c0; c<(int)sc; c+=spectrum()) +- for (int z = z0; z<(int)sz; z+=depth()) +- for (int y = y0; y<(int)sy; y+=height()) +- for (int x = x0; x<(int)sx; x+=width()) ++ for (int c = c0; c<(int)sc; c+=dc) ++ for (int z = z0; z<(int)sz; z+=dz) ++ for (int y = y0; y<(int)sy; y+=dy) ++ for (int x = x0; x<(int)sx; x+=dx) + res.draw_image(x,y,z,c,*this); + } break; + case 1 : { // Neumann boundary. +@@ -47059,7 +47060,7 @@ + const IplImage *img = 0; + for (unsigned int i = 0; iwidthStep - 3*img->width); + assign(img->width,img->height,1,3); + const unsigned char* ptrs = (unsigned char*)img->imageData; +@@ -52636,7 +52637,7 @@ + case 'x' : { // Along the X-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx+=img._width; + dy = cimg::max(dy,img._height); + dz = cimg::max(dz,img._depth); +@@ -52646,7 +52647,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image(pos, ++ if ((bool)img) res.draw_image(pos, + (int)(align*(dy - img._height)), + (int)(align*(dz - img._depth)), + (int)(align*(dc - img._spectrum)), +@@ -52657,7 +52658,7 @@ + case 'y' : { // Along the Y-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy+=img._height; + dz = cimg::max(dz,img._depth); +@@ -52667,7 +52668,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + pos, + (int)(align*(dz - img._depth)), + (int)(align*(dc - img._spectrum)), +@@ -52678,7 +52679,7 @@ + case 'z' : { // Along the Z-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy = cimg::max(dy,img._height); + dz+=img._depth; +@@ -52688,7 +52689,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + (int)(align*(dy - img._height)), + pos, + (int)(align*(dc - img._spectrum)), +@@ -52699,7 +52700,7 @@ + default : { // Along the C-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy = cimg::max(dy,img._height); + dz = cimg::max(dz,img._depth); +@@ -52709,7 +52710,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + (int)(align*(dy - img._height)), + (int)(align*(dz - img._depth)), + pos, +@@ -53957,7 +53958,7 @@ + CImg img; + try { img.load_pnm(filename_tmp2); } + catch (CImgException&) { stop_flag = true; } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + } + cimg::exception_mode(omode); + if (is_empty()) +@@ -54033,7 +54034,7 @@ + CImg img; + try { img.load_png(filename_tmp2); } + catch (CImgException&) { } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + else { // Try to read animated gif. + unsigned int i = 0; + for (bool stop_flag = false; !stop_flag; ++i) { +@@ -54042,7 +54043,7 @@ + CImg img; + try { img.load_png(filename_tmp2); } + catch (CImgException&) { stop_flag = true; } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + } + } + cimg::exception_mode(omode); +--- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 ++++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 +@@ -1,4 +1,5 @@ + + PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 + PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) +- ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 +--- imager/MD5.orig 2016-09-12 15:08:55.000000000 +0200 ++++ imager/MD5 2017-04-01 22:44:16.943021224 +0200 +@@ -31,7 +31,7 @@ + 05e04a3bc5a858c40e001cc65b853dfc *inst/extdata/Leonardo_Birds.jpg + e1328ba2c55d5a72eb77e283c9630b90 *inst/extdata/parrots.png + daa5b7e30235689ad0444df37c88b7ff *inst/extdata/tennis_sif.mpeg +-00de9e6b4c2066d28d7f8d9e251915cd *inst/include/CImg.h ++ea9acc61a3dd73452639c570af543d29 *inst/include/CImg.h + 034a9e8aab9e05094fd31ce9ea3bbae2 *inst/include/imager.h + 0c8aae8db902f96a8f8e323043eb1418 *inst/include/wrappers.h + be39be77874a0181ecd47b1a7a9af5dd *man/FFT.Rd +@@ -140,7 +140,7 @@ + a680472a2ef1eda48c1a9b90488543b5 *man/vanvliet.Rd + 08193940e20b440f614e4c7a2dbf82fb *man/warp.Rd + 429b25a38f282c30d5d178ad9efc3b1f *man/watershed.Rd +-ab8f97aa6f15c67d1029e3eb5091853d *src/Makevars.in ++802ecbe76012c51adf729063804c793a *src/Makevars.in + 5ecf9e8577f31e535dee1c371e75a35f *src/Makevars.win + 78aff3a88c55983a329723eb1174a4ca *src/RcppExports.cpp + 8193f4fecd751c7d310d23b0faacd303 *src/colourspace.cpp -- GitLab From a5f2063b833b5bf00edccfe0167ac1a396850d5d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 Apr 2017 16:03:04 +0200 Subject: [PATCH 294/566] adding easyconfigs: ClusterShell-1.7.3.eb --- .../c/ClusterShell/ClusterShell-1.7.3.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb new file mode 100644 index 0000000000..7a6d8ed9f6 --- /dev/null +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ClusterShell' +version = '1.7.3' + +homepage = 'http://cea-hpc.github.io/clustershell/' +description = """ClusterShell is an event-driven open source Python library, designed to run local or distant commands + in parallel on server farms or on large Linux clusters.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +options = {'modulename': 'ClusterShell'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/clubak', 'bin/clush', 'bin/nodeset'], + 'dirs': ['lib/python%s/site-packages' % pyshortver] +} + +moduleclass = 'tools' -- GitLab From 5663f27a280b6494a5efef3dae1bf526ec75fd1f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 08:13:41 +0100 Subject: [PATCH 295/566] adding easyconfigs: ALLPATHS-LG-52488-foss-2016a.eb --- .../ALLPATHS-LG-52488-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100755 easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb new file mode 100755 index 0000000000..3ba22f9da5 --- /dev/null +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.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 +# +## +# 52488 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'ALLPATHS-LG' +version = '52488' + +homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' +description = """ALLPATHS-LG, the new short read genome assembler.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# source is moved over time, hence multiple URLs below +source_urls = [ + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code', + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06', + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06', +] +sources = ['allpathslg-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From a041d36a1b35a350727fee2733daa96baeb39e8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 10:48:18 +0200 Subject: [PATCH 296/566] adding easyconfigs: Inspector-2017_update2.eb --- .../i/Inspector/Inspector-2017_update2.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb new file mode 100644 index 0000000000..9ea21d95ae --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb @@ -0,0 +1,17 @@ +name = 'Inspector' +version = '2017_update2' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_%(version)s.tar.gz'] +checksums = ['d85a3bbd699b0fc77967fcd5e923ad35'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From b71a103e395e5a84fad3efd2089ffe1748da8238 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 3 Apr 2017 11:05:44 +0200 Subject: [PATCH 297/566] adding easyconfigs: samblaster-0.1.24-goolf-1.7.20.eb --- .../samblaster-0.1.24-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb new file mode 100644 index 0000000000..55c7310c7e --- /dev/null +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'samblaster' +version = '0.1.24' + +homepage = 'https://github.com/GregoryFaust/samblaster' +description = """samblaster: a tool to mark duplicates and extract discordant and split reads from sam files""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] +sources = ['v.%(version)s.tar.gz'] + +files_to_copy = [(['samblaster'], 'bin/'), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/samblaster'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 33a00c24c74c17fb559dcdb9cb4f6b532f95362a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 11:29:09 +0200 Subject: [PATCH 298/566] adding easyconfigs: ImageMagick-7.0.5-4-intel-2017a.eb, Ghostscript-9.21-intel-2017a.eb, LittleCMS-2.8-intel-2017a.eb --- .../Ghostscript-9.21-intel-2017a.eb | 35 ++++++++++++++++ .../ImageMagick-7.0.5-4-intel-2017a.eb | 42 +++++++++++++++++++ .../l/LittleCMS/LittleCMS-2.8-intel-2017a.eb | 23 ++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb new file mode 100644 index 0000000000..e055f488f1 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.21' + +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': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] +sources = ['ghostscript-%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('expat', '2.2.0'), + ('GLib', '2.52.0'), + ('cairo', '1.14.8'), + ('LibTIFF', '4.0.7'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb new file mode 100644 index 0000000000..b01509be3a --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb @@ -0,0 +1,42 @@ +# 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 = '7.0.5-4' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.imagemagick.org/download/releases/'] +checksums = ['473a1e7ae37548eb6fe9cf2b1fb78011'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20170314'), + ('Ghostscript', '9.21'), + ('JasPer', '2.0.12'), + ('libjpeg-turbo', '1.5.1'), + ('LibTIFF', '4.0.7'), + ('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-2017a.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb new file mode 100644 index 0000000000..338a40a66d --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.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': '2017a'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +dependencies = [('libjpeg-turbo', '1.5.1')] + +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 674a1c51476cf8e99d35adf0eff04ac75f62cd02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 12:04:18 +0200 Subject: [PATCH 299/566] add PyYAML as dependency for ClusterShell --- .../c/ClusterShell/ClusterShell-1.7.3.eb | 1 + .../easyconfigs/l/libyaml/libyaml-0.1.7.eb | 28 +++++++++++++++++++ easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb | 25 +++++++++++++++++ 3 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb index 7a6d8ed9f6..26131a5764 100644 --- a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('PyYAML', '3.12')] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] options = {'modulename': 'ClusterShell'} diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb new file mode 100644 index 0000000000..44f94ecc3d --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.7' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb new file mode 100644 index 0000000000..8a6937f145 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libyaml', '0.1.7')] +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +options = {'modulename': 'yaml'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': [('lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver)] +} + +moduleclass = 'lib' -- GitLab From 7859c40ad54c1bb3b76ec5037be59eddf796668b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 11:18:29 +0100 Subject: [PATCH 300/566] Remove obsolete FTP paths --- .../easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb index 3ba22f9da5..a840c61253 100755 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -19,13 +19,12 @@ version = '52488' homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' description = """ALLPATHS-LG, the new short read genome assembler.""" +# Compilation fails with GCC 5.3 (goss-2016b) toolchain = {'name': 'foss', 'version': '2016a'} # source is moved over time, hence multiple URLs below source_urls = [ 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code', - 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06', - 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06', ] sources = ['allpathslg-%(version)s.tar.gz'] -- GitLab From 36b2bfee952f02ce6b499e5f5b7ba8b5d112b5b7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 11:21:44 +0100 Subject: [PATCH 301/566] Fix typo --- .../easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb index a840c61253..0227efebd7 100755 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -19,7 +19,7 @@ version = '52488' homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' description = """ALLPATHS-LG, the new short read genome assembler.""" -# Compilation fails with GCC 5.3 (goss-2016b) +# Compilation fails with GCC 5.3 (foss-2016b) toolchain = {'name': 'foss', 'version': '2016a'} # source is moved over time, hence multiple URLs below -- GitLab From 8c68ce861deb926d89f492e0eaf100c735ef9995 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 17:41:12 +0200 Subject: [PATCH 302/566] adding easyconfigs: deap-0.9.2-intel-2016b-Python-2.7.12.eb --- .../deap-0.9.2-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f639521510 --- /dev/null +++ b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'deap' +version = '0.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deap.readthedocs.org/en/master/' +description = """DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. + It seeks to make algorithms explicit and data structures transparent.""" + +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 = 'tools' -- GitLab From e28163397a26a71ad0c592cafa5b85b4a7b56c78 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 4 Apr 2017 12:14:05 +0930 Subject: [PATCH 303/566] Support for BioKanga 4.3.4 --- .../b/BioKanga/BioKanga-4.3.4-foss-2015b.eb | 30 +++++++++++++++++++ .../b/BioKanga/BioKanga-4.3.4_configure.patch | 29 ++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb new file mode 100644 index 0000000000..da082e4501 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.4' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['BioKanga-4.3.4_configure.patch'] + +builddependencies = [ + ('Autoconf', '2.69'), + ('Automake', '1.15') +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch new file mode 100644 index 0000000000..a88701ea28 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch @@ -0,0 +1,29 @@ +--- ./configure.ac 2017-04-04 11:47:18.067209892 +0930 ++++ ./configure.ac 2017-04-04 11:47:46.719519662 +0930 +@@ -23,11 +23,10 @@ + fasta2dist/Makefile locsw/Makefile quickcount/Makefile csv2feat/Makefile + genalignref2relloci/Makefile genalignloci2core/Makefile maploci2features/Makefile + processcsvfiles/Makefile genalignconf/Makefile Loci2Phylip/Makefile blast2csv/Makefile genrollups/Makefile +- gengoterms/Makefile gengoassoc/Makefile goassoc/Makefile + genWiggle/Makefile gencentroidmetrics/Makefile proccentroids/Makefile DNAseqSitePotential/Makefile SimulateMNase/Makefile + filterreads/Makefile prednucleosomes/Makefile RNAseqSitePotential/Makefile + genDESeq/Makefile fasta2struct/Makefile kangarg/Makefile genultras/Makefile +- LocateROI/Makefile genstructprofile/Makefile genstructstats/Makefile predconfnucs/Makefile gennucstats/Makefile fastafilter/Makefile ++ LocateROI/Makefile genstructprofile/Makefile predconfnucs/Makefile gennucstats/Makefile fastafilter/Makefile + BEDMerge/Makefile BEDFilter/Makefile genElementProfiles/Makefile genzygosity/Makefile genGenomeFromAGP/Makefile genmarkers/Makefile + HammingDist/Makefile genreadsde/Makefile ufilter/Makefile uhamming/Makefile genseqcandidates/Makefile GFFfilter/Makefile loci2dist/Makefile + genNormWiggle/Makefile GTFfilter/Makefile genDiffExpr/Makefile dmpbioseq/Makefile genpseudogenome/Makefile usimdiffexpr/Makefile RNAFragSim/Makefile mergeoverlaps/Makefile +--- Makefile.am 2017-04-04 11:51:40.878045716 +0930 ++++ Makefile.am 2017-04-04 11:51:57.518224861 +0930 +@@ -8,10 +8,9 @@ + genalignref2relloci genalignloci2core maploci2features \ + processcsvfiles genalignconf Loci2Phylip blast2csv genrollups \ + genWiggle proccentroids gencentroidmetrics SimulateMNase predconfnucs \ +- gengoterms gengoassoc goassoc \ + DNAseqSitePotential RNAseqSitePotential prednucleosomes gennucstats \ + uhamming LocateROI genDESeq genGenomeFromAGP kangarg genultras \ +- genstructprofile genstructstats filterreads fasta2struct ufilter genseqcandidates genmarkers GFFfilter \ ++ genstructprofile filterreads fasta2struct ufilter genseqcandidates genmarkers GFFfilter \ + genElementProfiles BEDMerge BEDFilter loci2dist genzygosity genNormWiggle GTFfilter genDiffExpr \ + dmpbioseq genpseudogenome usimdiffexpr genreadsde HammingDist RNAFragSim mergeoverlaps fastafilter \ + kangasr kangar kangahrdx kangade kangas kangapr csv2sqlite biokanga locmarkers PEscaffold SSRdiscovery pacbiokanga -- GitLab From ed49e763dc0bd0d51fe8a687cc1dc6056c9ab11d Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 4 Apr 2017 12:34:08 +0930 Subject: [PATCH 304/566] Added missing easyconfig dependencies for foss-2015b toolchain --- .../a/Autoconf/Autoconf-2.69-foss-2015b.eb | 25 ++++++++++++++ .../a/Automake/Automake-1.15-foss-2015b.eb | 33 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb new file mode 100644 index 0000000000..408f488eca --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb new file mode 100644 index 0000000000..543e7a0ba7 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 2c0bd091e388bc06f25908f60bdaf821e2efeb9b Mon Sep 17 00:00:00 2001 From: Edoardo Di Lorenzo Date: Tue, 4 Apr 2017 09:54:03 +0200 Subject: [PATCH 305/566] adding easyconfigs: Cantera-2.3.0-foss-2016b-Python-2.7.12.eb --- .../Cantera-2.3.0-foss-2016b-Python-2.7.12.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..87566ca1da --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,50 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'Cantera-%(version)s_fix-bug-416.patch', + 'Cantera-%(version)s_fix-test-reprod.patch', +] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('SUNDIALS', '2.7.0'), + ('Eigen', '3.3.2'), + ('fmt', '3.0.1'), + ('googletest', '1.8.0'), +] +builddependencies = [ + ('SCons', '2.5.1', versionsuffix), + ('3to2', '1.1.1', versionsuffix), +] + +common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=openblas 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 +installopts = 'install ' + common_opts +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 504315aa55cf670592a7dfaa04a662012782ee73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 10:03:58 +0200 Subject: [PATCH 306/566] {bio}[intel/2016b] Stampy v1.0.31 w/ Python 2.7.12 --- ...Stampy-1.0.31-intel-2016b-Python-2.7.12.eb | 35 ++++++++++++++++ .../Stampy/Stampy-1.0.31_fix-hardcoding.patch | 40 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1c6a84db5e --- /dev/null +++ b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Stampy' +version = '1.0.31' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.well.ox.ac.uk/stampy' +description = """Stampy is a package for the mapping of short reads from illumina sequencing machines onto + a reference genome.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +# download via http://www.well.ox.ac.uk/software-download-registration and rename from Stampy-latest.tgz +sources = ['Stampy-%(version)s.tgz'] +checksums = ['512b2da5a952a65d2e6f70220c4641dc'] + +patches = ['Stampy-%(version)s_fix-hardcoding.patch'] + +dependencies = [('Python', '2.7.12')] + +files_to_copy = ['ext', 'maptools.%s' % SHLIB_EXT, 'plugins', 'README.txt', 'Stampy', 'stampy.py'] + +sanity_check_paths = { + 'files': ['maptools.%s' % SHLIB_EXT, 'stampy.py'], + 'dirs': ['ext', 'plugins', 'Stampy'], +} + +modextrapaths = { + # add top-level install path to $PATH and $PYTHONPATH + 'PATH': [''], + 'PYTHONPATH': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch new file mode 100644 index 0000000000..ce59a23011 --- /dev/null +++ b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch @@ -0,0 +1,40 @@ +--- stampy-1.0.31/makefile.orig 2016-12-01 17:28:32.000000000 +0100 ++++ stampy-1.0.31/makefile 2017-04-04 09:59:04.057705404 +0200 +@@ -3,6 +3,10 @@ + # Compiles with gcc 5.4.0 and Apple LLVM version 6.1.0 + # + ++CC?=gcc ++CXX?=g++ ++CFLAGS?=-O2 ++CXXFLAGS?= + SHELL=/bin/bash + python?=python + platform=`uname` +@@ -31,21 +35,21 @@ + + $(bdir)/c/%.o: + mkdir -p $(bdir)/c +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c c/$*.c -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c c/$*.c -o $@ + + $(bdir)/pyx/%.o: + mkdir -p $(bdir)/pyx + ln -s -f `pwd`/pyx/$(ucs)/$*.c pyx/$*.c +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c pyx/$*.c -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c pyx/$*.c -o $@ + + $(bdir)/%.o: +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c ext/readalign/$*.cc -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c ext/readalign/$*.cc -o $@ + + build-stampy: $(objs) + cp -r build/python2.7/* . + @if [ $(platform) = Linux ]; then \ +- g++ `$(python)-config --ldflags` -pthread -shared $(objs) -o maptools.so ; \ ++ $(CXX) `$(python)-config --ldflags` -pthread -shared $(objs) -o maptools.so ; \ + else \ +- g++ `$(python)-config --ldflags` -pthread -dynamiclib $(objs) -o maptools.so ; \ ++ $(CXX) `$(python)-config --ldflags` -pthread -dynamiclib $(objs) -o maptools.so ; \ + fi + -- GitLab From 104319a4179492a63772b13e76cb8d051b248f09 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:23:37 +0200 Subject: [PATCH 307/566] missing dep --- .../s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb new file mode 100644 index 0000000000..21d1aa5067 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-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': 'foss', '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 f37de2420a9c1c3105717e39e765a76951c55205 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:23:57 +0200 Subject: [PATCH 308/566] missing dep --- .../easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb new file mode 100644 index 0000000000..bab8954a19 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.2' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 3be2fdf53413ebf2aa43b7df16ce006bb80cfd60 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:19 +0200 Subject: [PATCH 309/566] missing dep --- .../easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb new file mode 100644 index 0000000000..6faff2689b --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '3.0.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' -- GitLab From bb9e516ef8adbfa25e3e8b9bc65cd1a2118a0e97 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:36 +0200 Subject: [PATCH 310/566] missing dep --- .../googletest/googletest-1.8.0-foss-2016b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb new file mode 100644 index 0000000000..51ca2d0db0 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.8.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's C++ test framework" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libgmock.a', 'lib/libgmock_main.a', 'lib/libgtest.a', 'lib/libgtest_main.a'], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' -- GitLab From ce46e440b36dd05543bf1c0982a03360faf138a8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:59 +0200 Subject: [PATCH 311/566] missing dep --- .../SCons-2.5.1-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..40cbf3c559 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.1' +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 e653637f60899545e584b8abce4485607356e097 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:25:20 +0200 Subject: [PATCH 312/566] missing dep --- .../3to2-1.1.1-foss-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5236c8830e --- /dev/null +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-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': 'foss', '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' -- GitLab From ad5231b3ecf0c03a913ffabe6c000a7f969d3399 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 4 Apr 2017 13:10:31 +0200 Subject: [PATCH 313/566] adding easyconfigs: Sambamba-0.6.6.eb --- .../easyconfigs/s/Sambamba/Sambamba-0.6.6.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb new file mode 100644 index 0000000000..cd17c8d34d --- /dev/null +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -0,0 +1,32 @@ +# 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 = 'Sambamba' +version = '0.6.6' + +homepage = 'http://lomereiter.github.io/sambamba/' +description = """Sambamba is a high performance modern robust and fast tool (and library), + written in the D programming language, for working with SAM and BAM files. Current functionality + is an important subset of samtools functionality, including view, index, sort, markdup, and depth""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] +sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] + +sanity_check_paths = { + 'files': ['sambamba_v%(version)s'], + 'dirs': [], +} + +modextrapaths = { + 'PATH': "", +} + +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] + +moduleclass = 'bio' -- GitLab From 1a436e8b4ff18fd3e7d68944ff2f6a851cd46d02 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 13:16:24 +0200 Subject: [PATCH 314/566] style fixes --- .../s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb index 55c7310c7e..a99c1c0912 100644 --- a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -16,10 +16,11 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] sources = ['v.%(version)s.tar.gz'] -files_to_copy = [(['samblaster'], 'bin/'), - 'README.md', - 'SAMBLASTER_Supplemental.pdf', - 'LICENSE.txt', +files_to_copy = [ + (['samblaster'], 'bin/'), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', ] sanity_check_paths = { -- GitLab From e96add50c8edc330c81ed35a3bf500d241a9b126 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 13:41:54 +0200 Subject: [PATCH 315/566] adding easyconfigs: Perl-5.24.1-intel-2017a.eb --- .../p/Perl/Perl-5.24.1-intel-2017a.eb | 893 ++++++++++++++++++ 1 file changed, 893 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb new file mode 100644 index 0000000000..a2c5b790f2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -0,0 +1,893 @@ +name = 'Perl' +version = '5.24.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.38', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('File::ShareDir::Install', '0.11', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.16', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.11', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4222', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.28', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.26', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.418', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.044', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.42', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.54', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Simple', '1.302078', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.132', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.047', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.49.1', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.9', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.05', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.03', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.13', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Test::Deep', '1.126', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.32', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Moo', '2.003002', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.84', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.35', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.070', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.21', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2012', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.13', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.25', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.54', { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.31', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Parse::RecDescent', '1.967014', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.40', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.46', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 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['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Test::Output', '1.031', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.14', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.42', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.03', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.009', { + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', 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'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.60', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.88', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.02', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.14', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KJ/KJALB'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.2004', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9164', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.19', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Text::Template', '1.47', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + }), +] + +moduleclass = 'lang' -- GitLab From f47b5a553604438de699f09d452f750f51c4df1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 13:45:47 +0200 Subject: [PATCH 316/566] add comment with info on last update of Perl extensions --- easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index a2c5b790f2..7186e3ec91 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True} source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] +# !! order of extensions is important !! +# extensions updated on April 4th 2017 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', -- GitLab From f94439f39c75c014db0eb230041cbeac2d02d0c2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 4 Apr 2017 14:28:30 +0100 Subject: [PATCH 317/566] adding easyconfigs: matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb --- ...tplotlib-2.0.0-foss-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2f829b0767 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +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 3cb81f831d69775ac510480c8dc116e468e78258 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 4 Apr 2017 14:54:03 +0100 Subject: [PATCH 318/566] adding easyconfigs: MultiQC-0.9-foss-2016b-Python-2.7.12.eb --- .../MultiQC-0.9-foss-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a7a94c8c8c --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Adam Huffman +# The Francis Crick Institute +easyblock = 'PythonPackage' + +name = 'MultiQC' +version = '0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/ewels/MultiQC/archive'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '2.0.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' -- GitLab From e9dd3eee1b8bf54fae66b954aaf7705665188d6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 18:45:56 +0200 Subject: [PATCH 319/566] update imager extensions to 0.40.1 + add patch to fix compilation with Intel compilers --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 3 +- .../r/R/imager-0.3_fix-icpc-bool-cast.patch | 259 --------------- .../r/R/imager-0.40.1_fix-CImg-icpc.patch | 310 ++++++++++++++++++ 3 files changed, 312 insertions(+), 260 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch create mode 100644 easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 01ebe2e855..7c666ff2ec 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -502,7 +502,8 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', dict(ext_options.items() + [('patches', ['imager-0.3_fix-icpc-bool-cast.patch'])])), + ('downloader', '0.4', ext_options), + ('imager', '0.40.1', dict(ext_options.items() + [('patches', ['imager-0.40.1_fix-CImg-icpc.patch'])])), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch deleted file mode 100644 index 8d994cb858..0000000000 --- a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch +++ /dev/null @@ -1,259 +0,0 @@ -fix Intel compilation errors, partially based on https://github.com/dtschump/CImg/commit/d66a4e7f1b13594a572c22160c20e2bd3f231f6c -author: Kenneth Hoste (HPC-UGent) ---- imager/inst/include/CImg.h.orig 2016-08-31 16:30:10.000000000 +0200 -+++ imager/inst/include/CImg.h 2017-04-01 22:43:25.292695440 +0200 -@@ -17988,7 +17988,7 @@ - unsigned int ind = (unsigned int)mp.opcode[2]; - if (ind!=~0U) ind = (unsigned int)cimg::mod((int)_mp_arg(2),mp.listin.width()); - CImg &img = ind==~0U?mp.imgout:mp.listout[ind]; -- if (img) { -+ if ((bool)img) { - if (mp.opcode[12]!=(ulongT)-1) { - const CImg M(&_mp_arg(12) + 1,dx,dy,dz,(unsigned int)mp.opcode[13],true); - img.draw_image(x,y,z,c,S,M,opacity,(float)_mp_arg(14)); -@@ -18107,10 +18107,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18184,10 +18184,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18257,10 +18257,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18317,10 +18317,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img(ind,cimg::mod(off,whds)); -+ if ((bool)img) return (double)img(ind,cimg::mod(off,whds)); - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18590,7 +18590,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -18662,7 +18662,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -19579,7 +19579,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -19648,7 +19648,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -25664,14 +25664,15 @@ - x0 = ((int)xc%width()) - width(), - y0 = ((int)yc%height()) - height(), - z0 = ((int)zc%depth()) - depth(), -- c0 = ((int)cc%spectrum()) - spectrum(); -+ c0 = ((int)cc%spectrum()) - spectrum(), -+ dx = width(), dy = height(), dz = depth(), dc = spectrum(); - #ifdef cimg_use_openmp - #pragma omp parallel for collapse(3) if (res.size()>=65536) - #endif -- for (int c = c0; c<(int)sc; c+=spectrum()) -- for (int z = z0; z<(int)sz; z+=depth()) -- for (int y = y0; y<(int)sy; y+=height()) -- for (int x = x0; x<(int)sx; x+=width()) -+ for (int c = c0; c<(int)sc; c+=dc) -+ for (int z = z0; z<(int)sz; z+=dz) -+ for (int y = y0; y<(int)sy; y+=dy) -+ for (int x = x0; x<(int)sx; x+=dx) - res.draw_image(x,y,z,c,*this); - } break; - case 1 : { // Neumann boundary. -@@ -47059,7 +47060,7 @@ - const IplImage *img = 0; - for (unsigned int i = 0; iwidthStep - 3*img->width); - assign(img->width,img->height,1,3); - const unsigned char* ptrs = (unsigned char*)img->imageData; -@@ -52636,7 +52637,7 @@ - case 'x' : { // Along the X-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx+=img._width; - dy = cimg::max(dy,img._height); - dz = cimg::max(dz,img._depth); -@@ -52646,7 +52647,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image(pos, -+ if ((bool)img) res.draw_image(pos, - (int)(align*(dy - img._height)), - (int)(align*(dz - img._depth)), - (int)(align*(dc - img._spectrum)), -@@ -52657,7 +52658,7 @@ - case 'y' : { // Along the Y-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy+=img._height; - dz = cimg::max(dz,img._depth); -@@ -52667,7 +52668,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - pos, - (int)(align*(dz - img._depth)), - (int)(align*(dc - img._spectrum)), -@@ -52678,7 +52679,7 @@ - case 'z' : { // Along the Z-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy = cimg::max(dy,img._height); - dz+=img._depth; -@@ -52688,7 +52689,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - (int)(align*(dy - img._height)), - pos, - (int)(align*(dc - img._spectrum)), -@@ -52699,7 +52700,7 @@ - default : { // Along the C-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy = cimg::max(dy,img._height); - dz = cimg::max(dz,img._depth); -@@ -52709,7 +52710,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - (int)(align*(dy - img._height)), - (int)(align*(dz - img._depth)), - pos, -@@ -53957,7 +53958,7 @@ - CImg img; - try { img.load_pnm(filename_tmp2); } - catch (CImgException&) { stop_flag = true; } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - } - cimg::exception_mode(omode); - if (is_empty()) -@@ -54033,7 +54034,7 @@ - CImg img; - try { img.load_png(filename_tmp2); } - catch (CImgException&) { } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - else { // Try to read animated gif. - unsigned int i = 0; - for (bool stop_flag = false; !stop_flag; ++i) { -@@ -54042,7 +54043,7 @@ - CImg img; - try { img.load_png(filename_tmp2); } - catch (CImgException&) { stop_flag = true; } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - } - } - cimg::exception_mode(omode); ---- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 -+++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 -@@ -1,4 +1,5 @@ - - PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 - PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) -- -+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -+PKG_CXXFLAGS = -wd308 ---- imager/MD5.orig 2016-09-12 15:08:55.000000000 +0200 -+++ imager/MD5 2017-04-01 22:44:16.943021224 +0200 -@@ -31,7 +31,7 @@ - 05e04a3bc5a858c40e001cc65b853dfc *inst/extdata/Leonardo_Birds.jpg - e1328ba2c55d5a72eb77e283c9630b90 *inst/extdata/parrots.png - daa5b7e30235689ad0444df37c88b7ff *inst/extdata/tennis_sif.mpeg --00de9e6b4c2066d28d7f8d9e251915cd *inst/include/CImg.h -+ea9acc61a3dd73452639c570af543d29 *inst/include/CImg.h - 034a9e8aab9e05094fd31ce9ea3bbae2 *inst/include/imager.h - 0c8aae8db902f96a8f8e323043eb1418 *inst/include/wrappers.h - be39be77874a0181ecd47b1a7a9af5dd *man/FFT.Rd -@@ -140,7 +140,7 @@ - a680472a2ef1eda48c1a9b90488543b5 *man/vanvliet.Rd - 08193940e20b440f614e4c7a2dbf82fb *man/warp.Rd - 429b25a38f282c30d5d178ad9efc3b1f *man/watershed.Rd --ab8f97aa6f15c67d1029e3eb5091853d *src/Makevars.in -+802ecbe76012c51adf729063804c793a *src/Makevars.in - 5ecf9e8577f31e535dee1c371e75a35f *src/Makevars.win - 78aff3a88c55983a329723eb1174a4ca *src/RcppExports.cpp - 8193f4fecd751c7d310d23b0faacd303 *src/colourspace.cpp diff --git a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch new file mode 100644 index 0000000000..8f3e05fe69 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch @@ -0,0 +1,310 @@ +fix compilation issues with Intel compilers in CImg.h +cfr. https://github.com/dtschump/CImg/issues/123 and https://github.com/dahtah/imager/commit/b46e96efe0a9c596c9aca9d786123b10dd83adf2 +also include extra compiler option -wd308 to avoid 'member "std::complex::_M_value" is inaccessible' errors +patched composed by Kenneth Hoste (HPC-UGent) +--- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 ++++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 +@@ -1,4 +1,5 @@ + + PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 + PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) +- ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 +diff --git a/inst/include/CImg.h b/inst/include/CImg.h +index 213d864..922edf8 100755 +--- a/inst/include/CImg.h ++++ b/inst/include/CImg.h +@@ -15161,7 +15161,7 @@ namespace cimg_library_suffixed { + const CImg& img_input=CImg::const_empty(), CImg *const img_output=0, + const CImgList *const list_input=0, CImgList *const list_output=0, + const bool _is_fill=false): +- code(_code),p_break((CImg*)0 - 2), ++ code(_code),p_break((CImg*)(-2*sizeof(CImg))), + imgin(img_input),listin(list_input?*list_input:CImgList::const_empty()), + imgout(img_output?*img_output:CImg::empty()),listout(list_output?*list_output:CImgList::empty()), + img_stats(_img_stats),list_stats(_list_stats),list_median(_list_median),user_macro(0), +@@ -15222,6 +15222,7 @@ namespace cimg_library_suffixed { + memtype.assign(mem._width,1,1,1,0); + for (unsigned int i = 0; i<_cimg_mp_slot_x; ++i) memtype[i] = 1; + memtype[17] = 0; ++ memtype[_cimg_mp_slot_x] = memtype[_cimg_mp_slot_y] = memtype[_cimg_mp_slot_z] = memtype[_cimg_mp_slot_c] = -2; + mempos = _cimg_mp_slot_c + 1; + variable_pos.assign(8); + +@@ -15270,7 +15271,7 @@ namespace cimg_library_suffixed { + } + + _cimg_math_parser(): +- code(_code),p_code_end(0),p_break((CImg*)0 - 2), ++ code(_code),p_code_end(0),p_break((CImg*)(-2*sizeof(CImg))), + imgin(CImg::const_empty()),listin(CImgList::const_empty()), + imgout(CImg::empty()),listout(CImgList::empty()), + img_stats(_img_stats),list_stats(_list_stats),list_median(_list_median),debug_indent(0), +@@ -15301,7 +15302,7 @@ namespace cimg_library_suffixed { + unsigned int *pd = res._data; + int level = 0; + for (const char *ps = expr._data; *ps && level>=0; ++ps) { +- if (!next_is_escaped && *ps=='\\') next_is_escaped = true; ++ if (!is_escaped && !next_is_escaped && *ps=='\\') next_is_escaped = true; + if (!is_escaped && *ps=='\'') { // Non-escaped character + if (!mode && ps>expr._data && *(ps - 1)=='[') next_mode = mode = 2; // Start vector-string + else if (mode==2 && *(ps + 1)==']') next_mode = !mode; // End vector-string +@@ -20498,7 +20499,7 @@ namespace cimg_library_suffixed { + CImg S(&_mp_arg(1) + 1,dx,dy,dz,dc,true); + const float opacity = (float)_mp_arg(12); + +- if (img) { ++ if (img._data) { + if (mp.opcode[13]!=~0U) { // Opacity mask specified + const ulongT sizM = mp.opcode[14]; + if (sizM<(ulongT)dx*dy*dz) +@@ -20605,7 +20606,7 @@ namespace cimg_library_suffixed { + off = (longT)_mp_arg(2), + whds = (longT)img.size(); + if (off>=0 && off=0 && off=0 && off=0 && off::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff=65536)) +- for (int c = c0; c<(int)sc; c+=spectrum()) +- for (int z = z0; z<(int)sz; z+=depth()) +- for (int y = y0; y<(int)sy; y+=height()) +- for (int x = x0; x<(int)sx; x+=width()) ++ for (int c = c0; c<(int)sc; c+=dc) ++ for (int z = z0; z<(int)sz; z+=dz) ++ for (int y = y0; y<(int)sy; y+=dy) ++ for (int x = x0; x<(int)sx; x+=dx) + res.draw_image(x,y,z,c,*this); + } break; + case 1 : { // Neumann +@@ -34824,8 +34826,7 @@ namespace cimg_library_suffixed { + _sigma_x = sigma_x>=0?sigma_x:-sigma_x*_width/100, + _sigma_y = sigma_y>=0?sigma_y:-sigma_y*_height/100, + _sigma_z = sigma_z>=0?sigma_z:-sigma_z*_depth/100, +- __sigma_r = sigma_r>=0?sigma_r:-sigma_r*(edge_max - edge_min)/100, +- _sigma_r = std::max(0.1f,__sigma_r), ++ _sigma_r = sigma_r>=0?sigma_r:-sigma_r*(edge_max - edge_min)/100, + _sampling_x = sampling_x?sampling_x:std::max(_sigma_x,1.0f), + _sampling_y = sampling_y?sampling_y:std::max(_sigma_y,1.0f), + _sampling_z = sampling_z?sampling_z:std::max(_sigma_z,1.0f), +@@ -48076,9 +48077,13 @@ namespace cimg_library_suffixed { + else return load_other(filename); + #else + // Open file and check for PNG validity +- const char *volatile nfilename = filename; // two 'volatile' here to remove a g++ warning due to 'setjmp'. ++#if defined __GNUC__ ++ const char *volatile nfilename = filename; // Use 'volatile' to avoid (wrong) g++ warning. + std::FILE *volatile nfile = file?file:cimg::fopen(nfilename,"rb"); +- ++#else ++ const char *nfilename = filename; ++ std::FILE *nfile = file?file:cimg::fopen(nfilename,"rb"); ++#endif + unsigned char pngCheck[8] = { 0 }; + cimg::fread(pngCheck,8,(std::FILE*)nfile); + if (png_sig_cmp(pngCheck,0,8)) { +@@ -49017,11 +49022,11 @@ namespace cimg_library_suffixed { + rdr.ndim(2)?rdr.ndim(2):1, + rdr.ndim(3)?rdr.ndim(3):1, + rdr.ndim(4)?rdr.ndim(4):1); +- if(typeid(T)==typeid(unsigned char)) ++ if (typeid(T)==typeid(unsigned char)) + rdr.setup_read_byte(); +- else if(typeid(T)==typeid(int)) ++ else if (typeid(T)==typeid(int)) + rdr.setup_read_int(); +- else if(typeid(T)==typeid(double)) ++ else if (typeid(T)==typeid(double)) + rdr.setup_read_double(); + else + rdr.setup_read_float(); +@@ -49312,7 +49317,7 @@ namespace cimg_library_suffixed { + *item = *tmp1 = *tmp2 = 0; + out[0] = std::fscanf(file,"%63s",item._data); + out[0] = out[1] = out[2] = out[3] = out[5] = 1; out[4] = out[6] = out[7] = -1; +- if(cimg::strncasecmp(item,"#INRIMAGE-4#{",13)!=0) ++ if (cimg::strncasecmp(item,"#INRIMAGE-4#{",13)!=0) + throw CImgIOException("CImg<%s>::load_inr(): INRIMAGE-4 header not found.", + pixel_type()); + +@@ -49342,17 +49347,17 @@ namespace cimg_library_suffixed { + tmp2._data); + } + } +- if(out[0]<0 || out[1]<0 || out[2]<0 || out[3]<0) ++ if (out[0]<0 || out[1]<0 || out[2]<0 || out[3]<0) + throw CImgIOException("CImg<%s>::load_inr(): Invalid dimensions (%d,%d,%d,%d) defined in header.", + pixel_type(), + out[0],out[1],out[2],out[3]); +- if(out[4]<0 || out[5]<0) ++ if (out[4]<0 || out[5]<0) + throw CImgIOException("CImg<%s>::load_inr(): Incomplete pixel type defined in header.", + pixel_type()); +- if(out[6]<0) ++ if (out[6]<0) + throw CImgIOException("CImg<%s>::load_inr(): Incomplete PIXSIZE field defined in header.", + pixel_type()); +- if(out[7]<0) ++ if (out[7]<0) + throw CImgIOException("CImg<%s>::load_inr(): Big/Little Endian coding type undefined in header.", + pixel_type()); + } +@@ -52161,9 +52166,16 @@ namespace cimg_library_suffixed { + "save_png(): Unable to save data in '(*FILE)' unless libpng is enabled.", + cimg_instance); + #else +- const char *volatile nfilename = filename; // two 'volatile' here to remove a g++ warning due to 'setjmp'. ++ ++#if defined __GNUC__ ++ const char *volatile nfilename = filename; // Use 'volatile' to avoid (wrong) g++ warning. + std::FILE *volatile nfile = file?file:cimg::fopen(nfilename,"wb"); + volatile double stmin, stmax = (double)max_min(stmin); ++#else ++ const char *nfilename = filename; ++ std::FILE *nfile = file?file:cimg::fopen(nfilename,"wb"); ++ double stmin, stmax = (double)max_min(stmin); ++#endif + + if (_depth>1) + cimg::warn(_cimg_instance +@@ -52188,7 +52200,7 @@ namespace cimg_library_suffixed { + png_error_ptr user_error_fn = 0, user_warning_fn = 0; + png_structp png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING,user_error_ptr, user_error_fn, + user_warning_fn); +- if(!png_ptr){ ++ if (!png_ptr){ + if (!file) cimg::fclose(nfile); + throw CImgIOException(_cimg_instance + "save_png(): Failed to initialize 'png_ptr' structure when saving file '%s'.", +@@ -52921,17 +52933,17 @@ namespace cimg_library_suffixed { + wtr.open(filename, imitate_file); + else { + minc::minc_info di; +- if(width()) di.push_back(minc::dim_info(width(),width()*0.5,-1,minc::dim_info::DIM_X)); +- if(height()) di.push_back(minc::dim_info(height(),height()*0.5,-1,minc::dim_info::DIM_Y)); +- if(depth()) di.push_back(minc::dim_info(depth(),depth()*0.5,-1,minc::dim_info::DIM_Z)); +- if(spectrum()) di.push_back(minc::dim_info(spectrum(),spectrum()*0.5,-1,minc::dim_info::DIM_TIME)); ++ if (width()) di.push_back(minc::dim_info(width(),width()*0.5,-1,minc::dim_info::DIM_X)); ++ if (height()) di.push_back(minc::dim_info(height(),height()*0.5,-1,minc::dim_info::DIM_Y)); ++ if (depth()) di.push_back(minc::dim_info(depth(),depth()*0.5,-1,minc::dim_info::DIM_Z)); ++ if (spectrum()) di.push_back(minc::dim_info(spectrum(),spectrum()*0.5,-1,minc::dim_info::DIM_TIME)); + wtr.open(filename,di,1,NC_FLOAT,0); + } +- if(typeid(T)==typeid(unsigned char)) ++ if (typeid(T)==typeid(unsigned char)) + wtr.setup_write_byte(); +- else if(typeid(T)==typeid(int)) ++ else if (typeid(T)==typeid(int)) + wtr.setup_write_int(); +- else if(typeid(T)==typeid(double)) ++ else if (typeid(T)==typeid(double)) + wtr.setup_write_double(); + else + wtr.setup_write_float(); +@@ -56443,7 +56455,7 @@ namespace cimg_library_suffixed { + } + if (disp.is_resized()) { disp.resize(false); visu0.assign(); } + if (ym>=0 && ym<13) { if (!text_down) { visu.assign(); text_down = true; }} +- else if (ym>=visu.height() - 13) { if(text_down) { visu.assign(); text_down = false; }} ++ else if (ym>=visu.height() - 13) { if (text_down) { visu.assign(); text_down = false; }} + if (!exit_on_anykey && key && key!=cimg::keyESC && + (key!=cimg::keyW || (!disp.is_keyCTRLLEFT() && !disp.is_keyCTRLRIGHT()))) { + key = 0; +@@ -57564,7 +57576,7 @@ namespace cimg_library_suffixed { + if (nlast_frame>=nb_images) nlast_frame = nb_images - 1; + assign(1 + (nlast_frame - nfirst_frame)/nstep_frame); + TIFFSetDirectory(tif,0); +-#if cimg_verbosity>=3 ++#if cimg_verbosity<3 + TIFFSetWarningHandler(0); + TIFFSetErrorHandler(0); + #endif +@@ -58324,7 +58336,6 @@ namespace cimg_library_suffixed { + throw CImgIOException(_cimglist_instance + "save_gzip_external(): Specified filename is (null).", + cimglist_instance); +- + CImg command(1024), filename_tmp(256), body(256); + const char + *ext = cimg::split_filename(filename,body), +--- imager/src/Makevars.in.orig 2017-04-04 18:02:36.525410690 +0200 ++++ imager/src/Makevars.in 2017-04-04 18:04:52.818449342 +0200 +@@ -1,3 +1,5 @@ + PKG_CPPFLAGS = $(SHLIB_OPENMP_CFLAGS) @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ @TIFF_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_use_r -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 -Dcimg_date='""' -Dcimg_time='""' + PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ @TIFF_LIBS@ $(RCPP_LDFLAGS) + ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From 7638aeafcfa7264556a6ad330ed7572759665261 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:08:33 +0200 Subject: [PATCH 320/566] added zlib dependency --- .../easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb index c3aab419f3..773f70da96 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.18')] +dependencies = [ + ('libpng', '1.6.18'), + ('zlib', '1.2.8') +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], -- GitLab From e814354fd0809d35cbf6bf1b85844bb2e267dcfc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:09:15 +0200 Subject: [PATCH 321/566] added zlib dependency --- .../easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb index 76cd412cf3..7436cc5833 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('zlib', '1.2.8') +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], -- GitLab From d90ac78aec452f629244a06ae4ff49c8001e7684 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:10:43 +0200 Subject: [PATCH 322/566] added custom sanity check --- .../easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb index a083925f91..2a604f301f 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb @@ -16,4 +16,11 @@ 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 ab8b2b9c6a5272d9912cff51be3bb22a5eff1b3e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:11:13 +0200 Subject: [PATCH 323/566] added custom sanity checks --- .../easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb index cb4fbebab2..15f766ff31 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb @@ -16,4 +16,11 @@ 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 746c112e1e9293ed92e4ea7192c1f6271ad17621 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:12:12 +0200 Subject: [PATCH 324/566] remove unneeded line --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 14c2e7f378..9cef816ccd 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -24,7 +24,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('six', '1.10.0', { -- GitLab From a00d479e8b57814916e4d9078bda040ef48fe56f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:15:01 +0200 Subject: [PATCH 325/566] delete unneeded LD_LIBRARY_PATH --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 9cef816ccd..9565d51bb3 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -66,7 +66,6 @@ exts_list = [ modextrapaths = { 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], - 'LD_LIBRARY_PATH': ['lib/python%(pyshortver)s/site-packages'] } sanity_check_paths = { -- GitLab From 4b6fe00282e6767b906ebac0a88c360b0c42300d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:15:22 +0200 Subject: [PATCH 326/566] update sanity check --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 9565d51bb3..52da5ecd72 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -70,7 +70,7 @@ modextrapaths = { sanity_check_paths = { 'files': ['bin/multiqc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/multiqc-%(version)s-py%(pyshortver)s.egg'] + 'dirs': ['lib/python%(pyshortver)s/site-packages/'] } moduleclass = 'bio' -- GitLab From cc5d41bc0cc73c26f134801cede7f89961d06811 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:29:23 +0930 Subject: [PATCH 327/566] Easyconfig for Autotools-20150215/foss-2015b --- .../Autotools/Autotools-20150215-foss-2015b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb new file mode 100644 index 0000000000..ab4ec5f149 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' -- GitLab From c65c50b2a84609923b11eebb2dfe79b7c1252752 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:30:11 +0930 Subject: [PATCH 328/566] Added comment/author to patch file --- .../easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch index a88701ea28..735a5b6d0c 100644 --- a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch @@ -1,3 +1,6 @@ +The Open Sourcing and refactoring of BioKanga on GitHub has resulted in some build issues. This +patch removes references to code which nolonger exists in refactored code of v4.3.4 +author: Nathan S. Watson-Haigh (University of Adelaide) --- ./configure.ac 2017-04-04 11:47:18.067209892 +0930 +++ ./configure.ac 2017-04-04 11:47:46.719519662 +0930 @@ -23,11 +23,10 @@ -- GitLab From 62b4678f29b9ba66d2d7334bf916a5871aa08573 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:31:32 +0930 Subject: [PATCH 329/566] Implement changes suggested by Kenneth Hoste. * Changed to use Autotools-20150215/foss-2015b as build dependency. * Use %(version)s variable in patch name instead of hardcoding. --- .../easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb index da082e4501..b413e97fee 100644 --- a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb @@ -13,12 +13,9 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['BioKanga-4.3.4_configure.patch'] +patches = ['BioKanga-%(version)s_configure.patch'] -builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15') -] +builddependencies = [('Autotools', '20150215')] preconfigopts = "autoreconf -f -i && " -- GitLab From fa83d2fc94fcabf75adbd75cde9c2ce86d225162 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:49:56 +0930 Subject: [PATCH 330/566] Adding libtool-2.4.6/foss-2015b missing dep --- .../l/libtool/libtool-2.4.6-foss-2015b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb new file mode 100644 index 0000000000..83d12ef5f8 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' -- GitLab From 71e29e140a369ff5d938a57835bda6f4f53e5d1f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 5 Apr 2017 09:00:59 +0200 Subject: [PATCH 331/566] removed unused patches line --- .../n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb index b4a5ec30e9..a4c16330cb 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb @@ -14,8 +14,6 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -#patches = ['numpy-1.8.0-mkl.patch'] - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From cad67753370e1950e1ee1c63301ea5b159276d0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 11:23:41 +0200 Subject: [PATCH 332/566] bump imager extension to 0.40.1 in R 3.3.3 easyconfig to sync it up with #4427 --- easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 2584758870..3b6ee9a746 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -502,7 +502,8 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', ext_options), + ('downloader', '0.4', ext_options), + ('imager', '0.40.1', ext_options), ] moduleclass = 'lang' -- GitLab From fc93911bf77c7d56dcb1b7fbf7c1e01b91116208 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 5 Apr 2017 13:03:36 +0200 Subject: [PATCH 333/566] style fixes and add symlink to the sanity check --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb index cd17c8d34d..c6c18b59b8 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -18,8 +18,10 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] + sanity_check_paths = { - 'files': ['sambamba_v%(version)s'], + 'files': ['sambamba_v%(version)s', 'sambamba'], 'dirs': [], } @@ -27,6 +29,4 @@ modextrapaths = { 'PATH': "", } -postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] - moduleclass = 'bio' -- GitLab From ff2de14ad7c936a63b9c2b9ba092ff0912669456 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 5 Apr 2017 12:03:45 +0100 Subject: [PATCH 334/566] Add explicit Python extension deps, based on @pescobar's work --- .../MultiQC-0.9-foss-2016b-Python-2.7.12.eb | 54 +++++++++++++++++-- 1 file changed, 50 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb index a7a94c8c8c..4ca3af6861 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -1,7 +1,11 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Adam Huffman # The Francis Crick Institute -easyblock = 'PythonPackage' +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' name = 'MultiQC' version = '0.9' @@ -16,14 +20,56 @@ description = """Aggregate results from bioinformatics analyses across many samp toolchain = {'name': 'foss', 'version': '2016b'} -sources = ['v%(version)s.tar.gz'] -source_urls = ['https://github.com/ewels/MultiQC/archive'] - dependencies = [ ('Python', '2.7.12'), ('matplotlib', '2.0.0', versionsuffix), ] +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('pyparsing', '2.1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('pytz', '2016.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + }), + ('python-dateutil', '2.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + }), + ('PyYAML', '3.12', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', + }), + ('simplejson', '3.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('multiqc', version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['lib/python%(pyshortver)s/site-packages'] -- GitLab From fa8ca0b1d95b064584aaf1b3885d72ebfc7a3366 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 14:26:20 +0200 Subject: [PATCH 335/566] adding easyconfigs: vsc-mympirun-4.0.0b0.eb, vsc-base-2.5.8.eb, IPy-0.83.eb, vsc-install-0.10.25.eb --- easybuild/easyconfigs/i/IPy/IPy-0.83.eb | 23 ++++++++++++ .../easyconfigs/v/vsc-base/vsc-base-2.5.8.eb | 27 ++++++++++++++ .../v/vsc-install/vsc-install-0.10.25.eb | 23 ++++++++++++ .../v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb | 35 +++++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPy/IPy-0.83.eb create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb create mode 100644 easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb diff --git a/easybuild/easyconfigs/i/IPy/IPy-0.83.eb b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb new file mode 100644 index 0000000000..661784d022 --- /dev/null +++ b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'IPy' +version = '0.83' + +homepage = 'https://pypi.python.org/pypi/IPy' +description = """Class and tools for handling of IPv4 and IPv6 addresses and networks""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'IPy'} + +shortpyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/' % shortpyver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb new file mode 100644 index 0000000000..c38a164cb9 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'vsc-base' +version = '2.5.8' + +homepage = 'http://hpcugent.github.com/vsc-base/' +description = """Basic Python libraries used by UGent's HPC group""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +# install as zipped egg to make sure that tools that use this as a dependency are responsive +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'vsc.utils'} + +shortpyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%(pyver)s/site-packages/vsc_base-%%(version)s-py%(pyver)s.egg' % {'pyver': shortpyver}], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb new file mode 100644 index 0000000000..c821c18048 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.10.25' + +homepage = 'http://hpcugent.github.com/vsc-install/' +description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.install'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb new file mode 100755 index 0000000000..58a69d638c --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '4.0.0b0' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = ['vsc-mympirun-%(version)s.tar.gz'] + +dependencies = [ + ('vsc-base', '2.5.8'), + ('IPy', '0.83'), +] +builddependencies = [('vsc-install', '0.10.25')] + +#postinstallcmds = ['echo "import pkg_resources; pkg_resources.declare_namespace(__name__)" > %(installdir)s/lib/vsc/__init__.py'] +#use_easy_install = True + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +#options = {'modulename': 'vsc.mympirun'} +options = {'modulename': 'vsc'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 03f367f888b40140a128276d63c9ff7c7f4779bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 14:30:31 +0200 Subject: [PATCH 336/566] don't patch Makevars.in twice in patch for R imager extension --- .../easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch index 8f3e05fe69..829b112342 100644 --- a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch +++ b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch @@ -2,15 +2,6 @@ fix compilation issues with Intel compilers in CImg.h cfr. https://github.com/dtschump/CImg/issues/123 and https://github.com/dahtah/imager/commit/b46e96efe0a9c596c9aca9d786123b10dd83adf2 also include extra compiler option -wd308 to avoid 'member "std::complex::_M_value" is inaccessible' errors patched composed by Kenneth Hoste (HPC-UGent) ---- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 -+++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 -@@ -1,4 +1,5 @@ - - PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 - PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) -- -+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -+PKG_CXXFLAGS = -wd308 diff --git a/inst/include/CImg.h b/inst/include/CImg.h index 213d864..922edf8 100755 --- a/inst/include/CImg.h -- GitLab From 6806348b71dbd35af608f2da2a6644e741ae03d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:00:10 +0200 Subject: [PATCH 337/566] remove commented out lines, addd sanity check command to check that 'mympirun --help' works --- .../easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb index 58a69d638c..b31dee5a6e 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -17,13 +17,10 @@ dependencies = [ ] builddependencies = [('vsc-install', '0.10.25')] -#postinstallcmds = ['echo "import pkg_resources; pkg_resources.declare_namespace(__name__)" > %(installdir)s/lib/vsc/__init__.py'] -#use_easy_install = True - # we ship something in bin/fake modextrapaths = {'PATH': 'bin/fake'} -#options = {'modulename': 'vsc.mympirun'} +# can't check for 'import vsc.mympirun' because vsc-base may be installed system-wide options = {'modulename': 'vsc'} pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) @@ -32,4 +29,6 @@ sanity_check_paths = { 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], } +sanity_check_commands = ["mympirun --help"] + moduleclass = 'tools' -- GitLab From 372ee603a6f226341a0ee51b8a6b33cdb48156e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:14:17 +0200 Subject: [PATCH 338/566] bump to intel/2017a and Perl 5.24.1 in ROI_PAC easyconfig --- ....2-intel-2016b.eb => GETORB-2.3.2-intel-2017a.eb} | 2 +- ...0.eb => ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb} | 12 ++++++++---- 2 files changed, 9 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/g/GETORB/{GETORB-2.3.2-intel-2016b.eb => GETORB-2.3.2-intel-2017a.eb} (92%) rename easybuild/easyconfigs/r/ROI_PAC/{ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb => ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb} (83%) diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb similarity index 92% rename from easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb rename to easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb index 2e648643f9..f01c7d1564 100644 --- a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb @@ -6,7 +6,7 @@ version = '2.3.2' homepage = 'http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml' description = "GETORB software package contains programs to handle the orbital data records (ODRs)" -toolchain = {'name': 'intel', 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://www.deos.tudelft.nl/ers/precorbs/tools/'] sources = ['getorb_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb similarity index 83% rename from easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb rename to easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb index 89a80fb749..351c02bb8c 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb @@ -8,22 +8,26 @@ homepage = 'http://roipac.org/' description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data to produce differential interferograms""" -toolchain = {'name': 'intel', 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2017a'} # download of ROI_PAC tarball requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] # make_raw_alos.pl via http://roipac.org/cgi-bin/moin.cgi/ALOS_PALSAR?action=AttachFile&do=get&target=make_raw_alos.pl patches = [ - 'ROI_PAC-%(version)s_fix-IntSim.patch', ('make_raw_alos.pl', 'ROI_PAC/INT_SCR'), + 'ROI_PAC-%(version)s_fix-IntSim.patch', +] +checksums = [ + 'db50e9cd99183291eb9cfe7c74750cc6', # ROI_PAC_3_0_1.tgz + '284faa43c12626670810c1e14d393159', # make_raw_alos.pl ] builddependencies = [('Autotools', '20150215')] dependencies = [ ('FFTW', '3.3.6'), ('GETORB', '2.3.2'), - ('Perl', '5.24.0'), + ('Perl', '5.24.1'), ] start_dir = 'ROI_PAC' @@ -52,6 +56,6 @@ modextravars = { 'ROI_PAC': '%(installdir)s', } -modloadmsg = "To define: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" +modloadmsg = "These environment variables should be defined: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" moduleclass = 'geo' -- GitLab From 3db3b7b5770a9f83fd0aa56f48c62b8eb4410f80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:15:16 +0200 Subject: [PATCH 339/566] add missing patch file for ROI_PAC --- .../r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch new file mode 100644 index 0000000000..f9b938a005 --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch @@ -0,0 +1,15 @@ +fix bug in ROI_PAC v3.0.1, cfr. http://roipac.org/cgi-bin/moin.cgi/Patches +--- ./ROI_PAC/intsim/IntSim.f.orig 2017-03-30 10:35:09.702908447 +0200 ++++ ./ROI_PAC/intsim/IntSim.f 2017-03-30 10:36:32.204116436 +0200 +@@ -1339,6 +1339,11 @@ + ntotlonpx = ntotcpx + endif + ++! update these after padding has been applied EJF 2013/5/9 ++ nslatpx = int(dem_pixel_min(1)) ++ nslonpx = int(dem_pixel_min(2)) ++ nlatpx = nint(dem_pixel_max(1)) - nslatpx + 1 ++ nlonpx = nint(dem_pixel_max(2)) - nslonpx + 1 + + write (*,*) + write (*,*) -- GitLab From 231a282bc419ebf00eb44efadcd54d9ca68bfca1 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 4 Apr 2017 18:48:52 +0000 Subject: [PATCH 340/566] Fix pkgconfig patch for Qhull to only let CMake substitute @ --- easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index 53f43a015d..0aa79c3083 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -3,7 +3,7 @@ requires making CMake to fill in the gaps via 'configure_file(... @ONLY)' author: Kenneth Hoste (UGent) --- qhull/CMakeLists.txt.orig 2015-09-21 15:27:38.424110227 +0200 +++ qhull/CMakeLists.txt 2015-09-21 15:27:06.403494984 +0200 -@@ -430,3 +430,9 @@ +@@ -430,3 +430,10 @@ install(FILES html/rbox.man DESTINATION ${MAN_INSTALL_DIR} RENAME rbox.1) install(FILES ${doc_FILES} DESTINATION ${DOC_INSTALL_DIR}) install(DIRECTORY html/ DESTINATION ${DOC_INSTALL_DIR}) @@ -11,6 +11,7 @@ author: Kenneth Hoste (UGent) +CONFIGURE_FILE( + "${CMAKE_CURRENT_SOURCE_DIR}/qhull.pc.in" + "${CMAKE_CURRENT_BINARY_DIR}/qhull.pc" ++ @ONLY +) +INSTALL(FILES "${CMAKE_BINARY_DIR}/qhull.pc" DESTINATION lib/pkgconfig) --- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 -- GitLab From f5d42fd9a077f9483e3e48fae1daee3bd335347e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 00:10:18 +0200 Subject: [PATCH 341/566] fix comment --- .../r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb index 351c02bb8c..d772d057cf 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb @@ -37,7 +37,7 @@ installopts = "&& cd fip && $CC $CFLAGS -o add_rmgAmpPhs add_rmgAmpPhs.c && cp - postinstallcmds = [ # symlink to getorb requires in /bin subdirectory "cd %(installdir)s/bin && ln -s $(which getorb)", - # also copy scripts and make sure they're excutable + # also copy scripts "cp -a INT_SCR/* %(installdir)s/bin", # fix shebang in Perl scripts "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//bin/*.pl", -- GitLab From d8cc0f780474286401a29f65cc0fe227c987b28a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 00:51:01 +0000 Subject: [PATCH 342/566] Octave 4.2.1: add easyconfig for intel 2016b with updated deps incl Qt5 --- .../o/Octave/Octave-4.2.1-intel-2016b.eb | 63 +++++++++++++++++++ .../o/Octave/Octave-4.2.1_intel.patch | 47 ++++++++++++++ 2 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb new file mode 100644 index 0000000000..5ea3487cef --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.2.1' + +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', '2.6.3'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('X11', '20170314'), + ('PCRE', '8.40'), + ('ncurses', '6.0'), + ('libreadline', '7.0'), + ('arpack-ng', '3.4.0'), + ('cURL', '7.52.1'), + ('FLTK', '1.3.3'), + ('fontconfig', '2.12.1'), + ('freetype', '2.7'), + ('GLPK', '4.60'), + ('GL2PS', '1.3.9'), + ('gnuplot', '5.0.5'), + ('Java', '1.8.0_121', '', True), + ('zlib', '1.2.8'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt5', '5.8.0'), + ('HDF5', '1.8.17', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.25'), + ('FFTW', '3.3.6'), +] + +configopts = 'MOC=$EBROOTQT5/bin/moc ' +configopts += 'UIC=$EBROOTQT5/bin/uic ' +configopts += 'RCC=$EBROOTQT5/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' +configopts += '--with-blas="$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-4.2.1_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch new file mode 100644 index 0000000000..872aa06961 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch @@ -0,0 +1,47 @@ +Intel compiler does not understand __builtin_*_overflow +# Oct 25th 2016 by B. Hajgato (Free University Brussels - VUB) +# Apr 4th 2017 by B. Oldeman (Compute Canada) +--- octave-4.2.1/libgnu/xalloc-oversized.h.orig 2017-02-22 18:17:37.000000000 +0000 ++++ octave-4.2.1/libgnu/xalloc-oversized.h 2017-04-04 14:29:22.020046084 +0000 +@@ -43,12 +43,12 @@ + nonnegative. This is a macro, not a function, so that it + works correctly even when SIZE_MAX < N. */ + +-#if 7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p) ++#if (7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p) && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) __builtin_mul_overflow_p (n, s, (size_t) 1) + #elif ((5 <= __GNUC__ \ + || (__has_builtin (__builtin_mul_overflow) \ + && __has_builtin (__builtin_constant_p))) \ +- && !__STRICT_ANSI__) ++ && !__STRICT_ANSI__ && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) \ + (__builtin_constant_p (n) && __builtin_constant_p (s) \ + ? __xalloc_oversized (n, s) \ +--- 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-4.2.1/libgnu/intprops.h.orig 2017-02-22 18:17:35.000000000 +0000 ++++ octave-4.2.1/libgnu/intprops.h 2017-04-04 14:35:17.208604138 +0000 +@@ -242,11 +242,11 @@ + + /* True if __builtin_add_overflow (A, B, P) works when P is non-null. */ + #define _GL_HAS_BUILTIN_OVERFLOW \ +- (5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) ++ ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + + /* True if __builtin_add_overflow_p (A, B, C) works. */ + #define _GL_HAS_BUILTIN_OVERFLOW_P \ +- (7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p)) ++ ((7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p)) && !__INTEL_COMPILER) + + /* The _GL*_OVERFLOW macros have the same restrictions as the + *_RANGE_OVERFLOW macros, except that they do not assume that operands -- GitLab From 8fde62045a9e2e96adb7ce875c72d3b922ee411a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 01:06:14 +0000 Subject: [PATCH 343/566] Fix irresolvable dependencies. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 5ea3487cef..7cb6f50189 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -22,10 +22,10 @@ builddependencies = [ ] dependencies = [ - ('X11', '20170314'), + ('X11', '20160819'), ('PCRE', '8.40'), ('ncurses', '6.0'), - ('libreadline', '7.0'), + ('libreadline', '6.3'), ('arpack-ng', '3.4.0'), ('cURL', '7.52.1'), ('FLTK', '1.3.3'), -- GitLab From 950cd4fa74caec7d7129c9c5f17923778748f88e Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 01:24:41 +0000 Subject: [PATCH 344/566] Avoid conflicts in dependencies. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 7cb6f50189..e845e9c89e 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -15,7 +15,7 @@ patches = ['%(name)s-%(version)s_intel.patch'] builddependencies = [ ('Bison', '3.0.4'), - ('flex', '2.6.3'), + ('flex', '2.6.2'), ('Autotools', '20150215'), ('libtool', '2.4.6'), ('gperf', '3.0.4'), @@ -23,14 +23,14 @@ builddependencies = [ dependencies = [ ('X11', '20160819'), - ('PCRE', '8.40'), + ('PCRE', '8.39'), ('ncurses', '6.0'), ('libreadline', '6.3'), ('arpack-ng', '3.4.0'), ('cURL', '7.52.1'), ('FLTK', '1.3.3'), ('fontconfig', '2.12.1'), - ('freetype', '2.7'), + ('freetype', '2.6.5'), ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), -- GitLab From 16d28a2efc5c9070ab7bc996dd5221a5e676e15b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Apr 2017 07:59:23 +0200 Subject: [PATCH 345/566] adding easyconfigs: Autotools-20150215-GCCcore-5.4.0.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb | 29 +++++++++++++++ .../a/Automake/Automake-1.15-GCCcore-5.4.0.eb | 36 +++++++++++++++++++ .../Autotools-20150215-GCCcore-5.4.0.eb | 18 ++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 20 +++++++++++ 4 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..765fe6f2fd --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..0d4c530534 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..79f6723eb6 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] +# Pure bundle -- no need to specify 'binutils' used when building GCCcore toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..677b163091 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +moduleclass = 'lib' -- GitLab From 5e3ae80f025fa5ee94d3d58603d6b2f037b68c10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 08:52:34 +0200 Subject: [PATCH 346/566] adding easyconfigs: StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb, snaphu-1.4.2-intel-2017a.eb, Triangle-1.6-intel-2017a.eb --- .../StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb | 50 +++++++++++++++++++ .../s/snaphu/snaphu-1.4.2-intel-2017a.eb | 26 ++++++++++ .../t/Triangle/Triangle-1.6-intel-2017a.eb | 34 +++++++++++++ 3 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb create mode 100644 easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..457a515e11 --- /dev/null +++ b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'StaMPS' +version = '3.3b1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://homepages.see.leeds.ac.uk/~earahoo/stamps/' +description = """A software package to extract ground displacements from time series of synthetic aperture radar + (SAR) acquisitions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://homepages.see.leeds.ac.uk/~earahoo/stamps/'] +sources = ['%(name)s_v%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.1'), + ('ROI_PAC', '3.0.1', versionsuffix), + ('Doris', '4.02'), + ('Triangle', '1.6'), + ('snaphu', '1.4.2'), +] + +skipsteps = ['configure'] + +start_dir = 'src' + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS"' + +preinstallopts = 'cp -a ../bin %(installdir)s/bin && ' +installopts = 'INSTALL_DIR=%(installdir)s/bin && cd .. && cp -a {DORIS_SCR,matlab,ROI_PAC_SCR} %(installdir)s/' + +postinstallcmds = [ + # fix shebang in Perl scripts + "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//*_SCR/*.pl", +] + +sanity_check_paths = { + 'files': ['bin/calamp', 'bin/cpxsum', 'bin/pscdem', 'bin/psclonlat', 'bin/pscphase', 'bin/selpsc_patch', + 'bin/selsbc_patch', 'bin/selsbc_patch_new'], + 'dirs': ['DORIS_SCR', 'matlab', 'ROI_PAC_SCR'], +} + +modextravars = { + 'DORIS_SCR': '%(installdir)s/DORIS_SCR', + 'MY_SCR': '%(installdir)s/ROI_PAC_SCR', + 'STAMPS': '%(installdir)s', +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb new file mode 100644 index 0000000000..467c802a40 --- /dev/null +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'snaphu' +version = '1.4.2' + +homepage = 'https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/' +description = """SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping + proposed by Chen and Zebker""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/'] +sources = ['snaphu-v%(version)s.tar.gz'] + +start_dir = 'src' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb new file mode 100644 index 0000000000..166329f4f1 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 974ebcbcc6544aac2c3e1b84ca1fe3529d85bbe9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 09:54:44 +0200 Subject: [PATCH 347/566] {bio}[intel/2017a] BreakDancer 1.4.5 --- .../BreakDancer-1.4.5-intel-2017a.eb | 29 +++++++++++++++++++ ...eakDancer-1.4.5_fix-icpc-compilation.patch | 14 +++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch diff --git a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb new file mode 100644 index 0000000000..2526494ae8 --- /dev/null +++ b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'BreakDancer' +version = '1.4.5' + +homepage = 'http://gmt.genome.wustl.edu/packages/breakdancer' +description = """BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from + next generation paired-end sequencing reads""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/genome/breakdancer/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['BreakDancer-%(version)s_fix-icpc-compilation.patch'] + +dependencies = [('zlib', '1.2.11')] +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=release' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/breakdancer-max'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch new file mode 100644 index 0000000000..e2859dd505 --- /dev/null +++ b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch @@ -0,0 +1,14 @@ +fix for compilation error: +error: no instance of constructor "testing::AssertionResult::AssertionResult" matches the argument list +author: Kenneth Hoste (HPC-UGent) +--- test/lib/io/TestBam.cpp.orig 2017-04-03 18:06:43.355151223 +0200 ++++ test/lib/io/TestBam.cpp 2017-04-03 18:06:09.154756888 +0200 +@@ -107,7 +107,7 @@ + size_t size = in.tellg(); + in.seekg(0, std::ios::beg); + std::vector buf(size); +- ASSERT_TRUE(in.read(buf.data(), size)); ++ ASSERT_TRUE((bool)in.read(buf.data(), size)); + buf.push_back(0); // make sure buffer is null terminated + EXPECT_STREQ(samData.c_str(), buf.data()); + -- GitLab From f092fd499ca51fff05161c17c43d49e84315d7e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 10:07:38 +0200 Subject: [PATCH 348/566] also include $LDFLAGS --- .../s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb | 2 +- easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb index 457a515e11..122fdfc60d 100644 --- a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb @@ -25,7 +25,7 @@ skipsteps = ['configure'] start_dir = 'src' -buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS"' +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS $LDFLAGS"' preinstallopts = 'cp -a ../bin %(installdir)s/bin && ' installopts = 'INSTALL_DIR=%(installdir)s/bin && cd .. && cp -a {DORIS_SCR,matlab,ROI_PAC_SCR} %(installdir)s/' diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb index 8397d4ea59..c65762eb7a 100644 --- a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb @@ -14,7 +14,7 @@ sources = ['snaphu-v%(version)s.tar.gz'] start_dir = 'src' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS $LDFLAGS"' files_to_copy = ['bin', 'config', 'man'] diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb index 467c802a40..3261c207aa 100644 --- a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb @@ -14,7 +14,7 @@ sources = ['snaphu-v%(version)s.tar.gz'] start_dir = 'src' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS $LDFLAGS"' files_to_copy = ['bin', 'config', 'man'] -- GitLab From 94e004a50d650754e599fc04bf206b24cfeb96ab Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Apr 2017 11:33:25 +0200 Subject: [PATCH 349/566] adding easyconfigs: freetype-2.7.1-GCCcore-5.4.0.eb --- .../b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb | 18 ++++++++++++ .../freetype/freetype-2.7.1-GCCcore-5.4.0.eb | 29 +++++++++++++++++++ .../l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb | 29 +++++++++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb | 25 ++++++++++++++++ 4 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..139b8c3f30 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..fee6777ad0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.1' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.28'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +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-1.6.28-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..3d37620c50 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.28' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +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/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..8409e2aa5c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 9b6f95e5909ef012e1853fba226f146c6b9428c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 12:32:58 +0200 Subject: [PATCH 350/566] adding easyconfigs: BLAT-3.5-intel-2017a.eb --- .../b/BLAT/BLAT-3.5-intel-2017a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb new file mode 100644 index 0000000000..7e57ded042 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb @@ -0,0 +1,34 @@ +## +# 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 +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.5' + +homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity + of length 25 bases or more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +source_urls = ['http://users.soe.ucsc.edu/~kent/src'] + +dependencies = [('libpng', '1.6.29')] + +buildopts = 'CC="$CC" COPT= L="$LIBS"' + +files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', + 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 927716f4af5f0146eb885b5debdd96c471bae27e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 12:33:26 +0200 Subject: [PATCH 351/566] adding easyconfigs: BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb --- .../BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..43055f9bb9 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,28 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.1' +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. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.zip' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.24.1'), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' -- GitLab From be8d72e960b3f118bb72ba5070687d21bbf28928 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 13:25:25 +0200 Subject: [PATCH 352/566] adding easyconfigs: Rascaf-1.0.2-intel-2017a.eb, SAMtools-0.1.20-intel-2017a.eb --- .../r/Rascaf/Rascaf-1.0.2-intel-2017a.eb | 33 +++++++++++++++++++ .../s/SAMtools/SAMtools-0.1.20-intel-2017a.eb | 20 +++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb diff --git a/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb new file mode 100644 index 0000000000..8d81791c83 --- /dev/null +++ b/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'Rascaf' +version = '1.0.2' + +homepage = 'https://github.com/mourisl/Rascaf' +description = """Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads + to improve a draft assembly, particularly in the gene regions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/mourisl/Rascaf/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '0.1.20'), +] + +# create fake libbam.a to skip building of included SAMtools +prebuildopts = "touch samtools-0.1.19/libbam.a && " +# empty LINKPATH to avoid that included SAMtools copy is used +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" LINKPATH=""' +parallel = 1 + +files_to_copy = [(['rascaf', 'rascaf-join'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/rascaf', 'bin/rascaf-join'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb new file mode 100644 index 0000000000..75a920a136 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb @@ -0,0 +1,20 @@ +name = 'SAMtools' +version = '0.1.20' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/samtools/%(namelower)s/archive/%(version)s'] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' -- GitLab From 5977c9c92fa12f6fefb43d24dc7ed36a80da51bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 13:41:48 +0200 Subject: [PATCH 353/566] adding easyconfigs: Boost-1.63.0-intel-2017a-Python-2.7.13.eb --- .../Boost-1.63.0-intel-2017a-Python-2.7.13.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e0340fc524 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 11b3a84303b558a60d035b91a785884b116774f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:11:47 +0200 Subject: [PATCH 354/566] adding easyconfigs: SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb --- ...ACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..9d51ecf299 --- /dev/null +++ b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'SSPACE_Basic' +version = '2.1.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/nsoranzo/sspace_basic' +description = "SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/nsoranzo/sspace_basic/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.1'), + ('Bowtie', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['README', 'SSPACE_Basic.pl'], + 'dirs': ['bin', 'tools'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From b921145d0ec6fb2ef6480dbef2b506f4faf241c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:47:04 +0200 Subject: [PATCH 355/566] {bio}[intel/2017a] GapFiller v2.1.1 --- .../GapFiller/GapFiller-2.1.1-intel-2017a.eb | 30 +++++++++++++++++++ .../GapFiller/GapFillter-2.1.1_fix-typo.patch | 13 ++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch diff --git a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb new file mode 100644 index 0000000000..4e408b39dd --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GapFiller' +version = '2.1.1' + +homepage = 'https://sourceforge.net/projects/gapfiller' +description = """GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. + It can be used for both DNA and RNA and it has been tested on Illumina data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['GapFillter-%(version)s_fix-typo.patch'] + +dependencies = [ + ('Boost', '1.63.0', '-Python-2.7.13'), + ('zlib', '1.2.11'), +] + +buildopts = 'bin_PROGRAMS=GapFiller ' +buildopts += 'GapFiller_CFLAGS="$CFLAGS $LDFLAGS -lz" GapFiller_CXXFLAGS="$CXXFLAGS $LDFLAGS -lz"' +installopts = 'bin_PROGRAMS=GapFiller ' + +sanity_check_paths = { + 'files': ['bin/GapFiller'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch b/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch new file mode 100644 index 0000000000..4327a994ef --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch @@ -0,0 +1,13 @@ +fix typo that breaks compilation with Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- gapfiller-2.1.1/src/data_structures/Reads.cpp.orig 2017-04-06 13:30:10.978641815 +0200 ++++ gapfiller-2.1.1/src/data_structures/Reads.cpp 2017-04-06 13:38:39.941387943 +0200 +@@ -154,7 +154,7 @@ + case 1: out.append("C"); break; + case 2: out.append("G"); break; + case 3: out.append("T"); break; +- default: cout << "strange "<< cout << "\n"; ++ default: cout << "strange " << out << "\n"; + } + } + -- GitLab From 1730f76e147bfacab9a328311e2dce727c617736 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:48:15 +0200 Subject: [PATCH 356/566] adding easyconfigs: fqtrim-0.9.5-intel-2017a.eb --- .../f/fqtrim/fqtrim-0.9.5-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb new file mode 100644 index 0000000000..c00d6cd413 --- /dev/null +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'fqtrim' +version = '0.9.5' + +homepage = 'http://ccb.jhu.edu/software/fqtrim/' +description = """fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, + terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing + machines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] +sources = [SOURCE_TAR_GZ] + +buildopts = 'release CC="$CXX" LINKER="$CXX"' + +files_to_copy = [(['fqtrim'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fqtrim'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 799702c12e239d7de2a423c2730bbb120bdbc92a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 16:16:56 +0200 Subject: [PATCH 357/566] adding easyconfigs: DBG2OLC-20170208-intel-2017a.eb --- .../d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb new file mode 100644 index 0000000000..367145a273 --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20170208' +commit = 'b452286' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c827dba5e6c5962a872c23d29dc191513a343168 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 16:03:20 +0000 Subject: [PATCH 358/566] Add --enable-fortran-calling-convention=gfortran to Octave eb. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index e845e9c89e..534dc92f99 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -52,6 +52,8 @@ configopts += 'UIC=$EBROOTQT5/bin/uic ' configopts += 'RCC=$EBROOTQT5/bin/rcc ' configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From 4d1e8dcd8cac962fd799d7c7abd261952559ddef Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 7 Apr 2017 08:55:29 +0200 Subject: [PATCH 359/566] Update METIS-5.1.0-foss-2016b.eb Needed for OpenFOAM # We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb index 1510375706..56000b7259 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb @@ -15,6 +15,9 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + builddependencies = [('CMake', '3.6.1')] configopts = ['', 'shared=1'] -- GitLab From 74b43253719a950a3b13d30a3531754be93587b0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 10 Apr 2017 09:49:43 +0200 Subject: [PATCH 360/566] change qt version dep --- .../ParaView/ParaView-5.3.0-foss-2016b-mpi.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb new file mode 100644 index 0000000000..b50111ff96 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.3.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.17'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 6ac55301bd87882370344c539da5b133642f3089 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 10 Apr 2017 09:51:22 +0200 Subject: [PATCH 361/566] change ParaView version dep --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb index 4f9d282dad..00ba2fa1df 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -1,7 +1,7 @@ name = 'OpenFOAM' version = '4.0' -homepage = 'http://www.openfoam.org/' +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, @@ -22,10 +22,9 @@ dependencies = [ ('ncurses', '6.0'), # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) ('METIS', '5.1.0'), - #('METIS', '5.1.0', '-32bitIDX'), ('SCOTCH', '6.0.4'), ('CGAL', '4.8.1'), - ('ParaView', '5.1.2', '-mpi'), + ('ParaView', '5.3.0', '-mpi'), ] builddependencies = [ -- GitLab From 18cb49ea57b2f04daf6f925cb00e2f9101bd260f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 10 Apr 2017 09:28:35 +0100 Subject: [PATCH 362/566] adding easyconfigs: gnuplot-5.0.5-foss-2016b.eb --- .../g/gnuplot/gnuplot-5.0.5-foss-2016b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100755 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb new file mode 100755 index 0000000000..52cec88efd --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-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': 'foss', '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', '1.6.26'), + ('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 a7fceb3c9b669fb14e2c23952a48482fca1b50c6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 10 Apr 2017 09:31:00 +0100 Subject: [PATCH 363/566] adding easyconfigs: canu-1.4-foss-2016b.eb --- .../easyconfigs/c/canu/canu-1.4-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100755 easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb new file mode 100755 index 0000000000..ff486b7b50 --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '1.4' + +homepage = 'https://github.com/marbl/canu' +description = """Canu is a fork of the Celera Assembler, designed for high-noise single-molecule + sequencing (such as the PacBio RS II or Oxford Nanopore MinION). + + Canu is a hierarchical assembly pipeline which runs in four steps: + + Detect overlaps in high-noise sequences using MHAP + Generate corrected sequence consensus + Trim corrected sequences + Assemble trimmed corrected sequences +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/marbl/canu/archive/'] + +start_dir = 'src' + +files_to_copy = ['Linux-amd64/*'] + +dependencies = [ + ('Java', '1.8.0_112', '', True), + ('Perl', '5.24.0'), + ('gnuplot', '5.0.5'), +] + +sanity_check_paths = { + 'files': ['bin/canu'], + 'dirs': ["bin"] +} + +moduleclass = 'bio' -- GitLab From a38d10acbf7234f434e0c19ff59dc699bc1f57d4 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 10 Apr 2017 10:54:07 +0200 Subject: [PATCH 364/566] Stacks 1.45 build with the foss-2016a toolchain. --- .../s/Stacks/Stacks-1.45-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb new file mode 100644 index 0000000000..4f24751d68 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.45' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 21dee843cc0e8baa54067ef32a50cd458268bc25 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:27:16 +0200 Subject: [PATCH 365/566] Add Qt5/5.8 for intel/2017a --- .../pkg-config-0.29.2-intel-2017a.eb | 27 +++++++++++++++ .../q/Qt5/Qt5-5.8.0-intel-2017a.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb new file mode 100644 index 0000000000..90af56a5b1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.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/q/Qt5/Qt5-5.8.0-intel-2017a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb new file mode 100644 index 0000000000..fc41f1c1fd --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.8.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['Qt5-5.7.1_fix-nan-inf.patch'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.52.0'), + ('libpng', '1.6.29'), + ('X11', '20170314'), #, '', ('GCCcore', '6.3.0')), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From 9406dda37ebe8a116f962078b11b46179fe977e7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:28:50 +0200 Subject: [PATCH 366/566] Added ParaView-5.3.0-intel-2017a-mpi --- .../c/CMake/CMake-3.7.2-intel-2017a.eb | 31 +++++++++++ .../h/HDF5/HDF5-1.8.18-intel-2017a.eb | 26 ++++++++++ .../ParaView-5.3.0-intel-2017a-mpi.eb | 52 +++++++++++++++++++ 3 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb new file mode 100644 index 0000000000..d78b6b43f1 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +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': '2017a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb new file mode 100644 index 0000000000..570e4a8ff2 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb new file mode 100644 index 0000000000..a124946808 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.3.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20170314'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), + ('zlib', '1.2.11'), + ('HDF5', '1.8.18'), + ('Python', '2.7.13'), +] + +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 1f1e58d79e385169568b49542262db25ac27c804 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:37:48 +0200 Subject: [PATCH 367/566] Added CGAL-4.9-intel-2017a-Python-2.7.13 --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 36 ++++ .../e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb | 13 ++ .../m/MPFR/MPFR-3.1.5-20161219.patch | 174 ++++++++++++++++++ .../m/MPFR/MPFR-3.1.5-intel-2017a.eb | 29 +++ 4 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9b23706bf9 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.13'), + ('Boost', '1.63.0', versionsuffix), + ('MPFR', '3.1.5'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..86af55ba48 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch new file mode 100644 index 0000000000..6b2d11466e --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch @@ -0,0 +1,174 @@ +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb new file mode 100644 index 0000000000..94a6262015 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.5' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = [ + 'MPFR_ictce_remove-deprecated-mp.patch', + '%(name)s-%(version)s-20161219.patch', +] + +dependencies = [('GMP', '6.1.2')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 7c2309cf46942ad0342bc4102db6e55fd02cef94 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:40:35 +0200 Subject: [PATCH 368/566] Added OpenFOAM-4.1-intel-2017a --- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 25 ++ .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 339 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 36 ++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb | 18 + 4 files changed, 418 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb new file mode 100644 index 0000000000..352a974db9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -0,0 +1,25 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [('CMake', '3.7.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch new file mode 100644 index 0000000000..6c5fc1671a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -0,0 +1,339 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -41,7 +41,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPV3blockMeshReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -42,7 +42,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPV3FoamReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -16,7 +16,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVReaders + PVblockMeshReader/Allwmake $* +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -42,7 +42,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPVblockMeshReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -43,7 +43,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPVFoamReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc +--- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 +@@ -42,9 +42,8 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && \ +-export FOAM_INST_DIR=$(cd ${BASH_SOURCE%/*/*/*} && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module ++# + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL 2017-04-10 14:51:01.473221230 +0200 +@@ -36,37 +36,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.8 +- +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ] +-then +- +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +- export BOOST_ARCH_PATH=$common_path/$boost_version +- export CGAL_ARCH_PATH=$common_path/$cgal_version +- +- if [ "$FOAM_VERBOSE" -a "$PS1" ] +- then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +- fi +- +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version common_path +- +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools 2017-04-10 14:51:01.473221230 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis OpenFOAM-4.x-version-4.1/etc/config.sh/metis +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/metis 2017-04-10 14:51:01.473221230 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi OpenFOAM-4.x-version-4.1/etc/config.sh/mpi +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/mpi 2017-04-10 14:51:01.473221230 +0200 +@@ -249,6 +249,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview OpenFOAM-4.x-version-4.1/etc/config.sh/paraview +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/paraview 2017-04-10 14:51:01.473221230 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -64,7 +49,7 @@ + #export ParaView_VERSION=4.3.1 + #export ParaView_VERSION=4.4.0 + #export ParaView_VERSION=5.0.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -105,21 +90,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -131,17 +110,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch OpenFOAM-4.x-version-4.1/etc/config.sh/scotch +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/scotch 2017-04-10 14:51:01.473221230 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings OpenFOAM-4.x-version-4.1/etc/config.sh/settings +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/settings 2017-04-10 14:51:01.473221230 +0200 +@@ -56,11 +56,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$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"\ +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options 2017-04-10 14:51:01.473221230 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2017-04-10 14:51:01.474221238 +0200 +@@ -30,10 +30,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options 2017-04-10 14:51:01.474221238 +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 diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb new file mode 100644 index 0000000000..214d84ba90 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '4.1' + +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': '2017a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['318a446c4ae6366c7296b61184acd37c'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '7.0'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.4'), + ('CGAL', '4.9', '-Python-2.7.13'), + ('ParaView', '5.3.0', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.7.2'), + ('flex', '2.6.3'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb new file mode 100644 index 0000000000..56f2a3c362 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' -- GitLab From f0c6c952907f6b57aaef620f887e0e90aabd9940 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:47:12 +0200 Subject: [PATCH 369/566] Downgrade ParaView to 5.2 as OpenFOAM 4.1 does not work with 5.3 They uses something that has been dropped in ParaView 5.3 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 2 +- ...3.0-intel-2017a-mpi.eb => ParaView-5.2.0-intel-2017a-mpi.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/ParaView/{ParaView-5.3.0-intel-2017a-mpi.eb => ParaView-5.2.0-intel-2017a-mpi.eb} (99%) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb index 214d84ba90..2469f2947a 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -24,7 +24,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), ('CGAL', '4.9', '-Python-2.7.13'), - ('ParaView', '5.3.0', '-mpi'), + ('ParaView', '5.2.0', '-mpi'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb similarity index 99% rename from easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb rename to easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index a124946808..addfba2c58 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'ParaView' -version = '5.3.0' +version = '5.2.0' versionsuffix = '-mpi' homepage = "http://www.paraview.org" -- GitLab From 9f863dc507b877ed77968f9d56a47408b7f5e970 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 11 Apr 2017 10:33:06 +0200 Subject: [PATCH 370/566] Switch OpenFOAM 4.1 to Qt 4.x OpenFOAM doesn't work with Qt5 yet... --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 48 ------------------- .../ParaView-5.2.0-intel-2017a-mpi.eb | 4 +- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb | 28 +++++++++++ 4 files changed, 31 insertions(+), 51 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index 9b23706bf9..da60ff72f0 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ dependencies = [ ('MPFR', '3.1.5'), ('GMP', '6.1.2'), ('libGLU', '9.0.0'), - ('Qt5', '5.8.0'), + ('Qt', '4.8.7'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch index 6c5fc1671a..1098db34cb 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -20,30 +20,6 @@ diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/s fi wmake -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -41,7 +41,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPV3blockMeshReaderPanel -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -42,7 +42,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPV3FoamReaderPanel diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake --- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-10-16 16:11:45.000000000 +0200 +++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2017-04-10 14:51:01.472221220 +0200 @@ -56,30 +32,6 @@ diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/grap wmake $targetType vtkPVReaders PVblockMeshReader/Allwmake $* -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -42,7 +42,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPVblockMeshReaderPanel -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -43,7 +43,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPVFoamReaderPanel diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc --- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 +++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index addfba2c58..903174f12f 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -18,7 +18,7 @@ dependencies = [ ('X11', '20170314'), ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), - ('Qt5', '5.8.0'), + ('Qt', '4.8.7'), ('zlib', '1.2.11'), ('HDF5', '1.8.18'), ('Python', '2.7.13'), @@ -43,7 +43,7 @@ configopts += '-DBUILD_TESTING=OFF ' # Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' -configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +configopts += ' -DPARAVIEW_QT_VERSION=4 -DQT_QMAKE_EXECUTABLE=$EBROOTQT/bin/qmake ' # The ParaView server can be cranky, test downloads are quite often failing, especially in the case # of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the # first serial attempt would fail. diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb new file mode 100644 index 0000000000..f45873187d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb @@ -0,0 +1,28 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.52.0'), + ('libpng', '1.6.29'), + ('X11', '20170314'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From cccb215e70aba11ff7b33283085b9a4763b97c58 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 11 Apr 2017 12:00:50 +0200 Subject: [PATCH 371/566] Qt4 also for CGAL --- .../o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 2 +- .../ParaView/ParaView-5.2.0-foss-2016b-mpi.eb | 51 +++++++++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb index 00ba2fa1df..3db67b3e22 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), ('CGAL', '4.8.1'), - ('ParaView', '5.3.0', '-mpi'), + ('ParaView', '5.2.0', '-mpi'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb new file mode 100644 index 0000000000..5dd45f28db --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.2.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qt', '4.8.7'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.17'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 090054ad90088e311860cfdc0b1c228030fe1834 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 11 Apr 2017 12:51:58 +0200 Subject: [PATCH 372/566] Force usage of C++98 for Qt4 with intel/2017a --- easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb index f45873187d..f9818f430a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb @@ -5,6 +5,7 @@ homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++98'} source_urls = [ 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', -- GitLab From d1193f3f30d6139025fa19716905c166ab9520e8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 11 Apr 2017 14:37:55 +0200 Subject: [PATCH 373/566] Qt4 also for CGAL --- .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 281 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb | 36 +++ 2 files changed, 317 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch new file mode 100644 index 0000000000..d7e72b20c9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -0,0 +1,281 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc +--- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 +@@ -42,9 +42,8 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && \ +-export FOAM_INST_DIR=$(cd ${BASH_SOURCE%/*/*/*} && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module ++# + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL 2017-04-10 14:51:01.473221230 +0200 +@@ -36,37 +36,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.8 +- +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ] +-then +- +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +- export BOOST_ARCH_PATH=$common_path/$boost_version +- export CGAL_ARCH_PATH=$common_path/$cgal_version +- +- if [ "$FOAM_VERBOSE" -a "$PS1" ] +- then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +- fi +- +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version common_path +- +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + +#------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools 2017-04-10 14:51:01.473221230 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis OpenFOAM-4.x-version-4.1/etc/config.sh/metis +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/metis 2017-04-10 14:51:01.473221230 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi OpenFOAM-4.x-version-4.1/etc/config.sh/mpi +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/mpi 2017-04-10 14:51:01.473221230 +0200 +@@ -249,6 +249,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview OpenFOAM-4.x-version-4.1/etc/config.sh/paraview +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/paraview 2017-04-10 14:51:01.473221230 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -64,7 +49,7 @@ + #export ParaView_VERSION=4.3.1 + #export ParaView_VERSION=4.4.0 + #export ParaView_VERSION=5.0.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -105,21 +90,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -131,17 +110,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch OpenFOAM-4.x-version-4.1/etc/config.sh/scotch +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/scotch 2017-04-10 14:51:01.473221230 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings OpenFOAM-4.x-version-4.1/etc/config.sh/settings +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/settings 2017-04-10 14:51:01.473221230 +0200 +@@ -56,11 +56,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$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"\ +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options 2017-04-10 14:51:01.473221230 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2017-04-10 14:51:01.474221238 +0200 +@@ -30,10 +30,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options 2017-04-10 14:51:01.474221238 +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 + + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb new file mode 100644 index 0000000000..efc992104f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '4.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['318a446c4ae6366c7296b61184acd37c'] + +patches = ['OpenFOAM-%(version)s-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 18dd07b9caed0bb7fe11b96ec455336759009e7b Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Tue, 11 Apr 2017 11:10:43 -0400 Subject: [PATCH 374/566] Added PLINK-1.9b_4.1-x86_64.eb --- .../p/PLINK/PLINK-1.9b_4.1-x86_64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb new file mode 100644 index 0000000000..fdc904389a --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.9b-4.1-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/1.9/' +description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['plink_linux_x86_64.zip'] +source_urls = ['https://www.cog-genomics.org/static/bin/plink170330/'] + +checksums = ['27e05daa4de39a15a9c7034998a35cc4'] + +files_to_copy = [ + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', +] + +sanity_check_paths = { + 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 798ff8c32a5f67ca08f3607017b8b43ef4a3c9d5 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Tue, 11 Apr 2017 13:09:51 -0400 Subject: [PATCH 375/566] Corrected version name --- easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb index fdc904389a..1454e1f498 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb @@ -1,7 +1,7 @@ easyblock = 'PackedBinary' name = 'PLINK' -version = '1.9b-4.1-x86_64' +version = '1.9b_4.1-x86_64' homepage = 'https://www.cog-genomics.org/plink/1.9/' description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' -- GitLab From f2ad640fea6d4242d77456cb3899a1655a0bc73e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 12 Apr 2017 09:08:20 +0200 Subject: [PATCH 376/566] R extension nloptr need the NLopt lib --- .../n/NLopt/NLopt-2.4.2-intel-2017a.eb | 26 +++++++++++++++++++ .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 1 + 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb new file mode 100644 index 0000000000..a614e1864e --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'NLopt' +version = '2.4.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ab-initio.mit.edu/nlopt/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/libnlopt.a", "include/nlopt.h"], + 'dirs': [""], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 7c666ff2ec..963e074572 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -43,6 +43,7 @@ dependencies = [ ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal ('PROJ', '4.9.3'), # for rgdal ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), -- GitLab From e632d08a417cf5d687a4bfae93373ebc5ba6652b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 12 Apr 2017 09:16:03 +0200 Subject: [PATCH 377/566] Build shared lib for NLopt --- easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb index a614e1864e..607bdc3f75 100644 --- a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://ab-initio.mit.edu/nlopt/'] sources = [SOURCELOWER_TAR_GZ] +configopts = '--enable-shared' + sanity_check_paths = { 'files': ["lib/libnlopt.a", "include/nlopt.h"], 'dirs': [""], -- GitLab From bf0d8f6148716a4b0c12bb67c20d7d189527fb40 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 13 Apr 2017 06:32:52 +0930 Subject: [PATCH 378/566] New easyconfig for BioKanga 4.3.5 --- .../b/BioKanga/BioKanga-4.3.5-foss-2015b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb new file mode 100644 index 0000000000..c614af140d --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.5' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From eef18915f6321f45c5224f19fddb5cc35db4db51 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 10:42:59 +0800 Subject: [PATCH 379/566] adding easyconfigs: atomate-0.4.4-intel-2017a-Python-2.7.13.eb, custodian-1.1.0-intel-2017a-Python-2.7.13.eb, FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb, Flask-0.12-intel-2017a-Python-2.7.13.eb, Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb, gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb, Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb, matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb, monty-0.9.6-intel-2017a-Python-2.7.13.eb, mpmath-0.19-intel-2017a-Python-2.7.13.eb, pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb, pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb, pymongo-3.4.0-intel-2017a-Python-2.7.13.eb, PyYAML-3.12-intel-2017a-Python-2.7.13.eb, requests-2.13.0-intel-2017a-Python-2.7.13.eb, smoqe-0.1.3-intel-2017a-Python-2.7.13.eb, spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb, sympy-1.0-intel-2017a-Python-2.7.13.eb, Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb --- ...atomate-0.4.4-intel-2017a-Python-2.7.13.eb | 28 ++++++++++++ ...stodian-1.1.0-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ ...reWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 31 +++++++++++++ ...aginate-0.4.5-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++ .../Flask-0.12-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ ...nicorn-19.7.1-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ .../Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ ...plotlib-2.0.0-intel-2017a-Python-2.7.13.eb | 44 +++++++++++++++++++ .../monty-0.9.6-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ .../mpmath-0.19-intel-2017a-Python-2.7.13.eb | 34 ++++++++++++++ .../PyYAML-3.12-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++ ...tgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 29 ++++++++++++ ...ymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 32 ++++++++++++++ ...pymongo-3.4.0-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ ...quests-2.13.0-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ .../smoqe-0.1.3-intel-2017a-Python-2.7.13.eb | 25 +++++++++++ ...thon-1.9.9.38-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ .../sympy-1.0-intel-2017a-Python-2.7.13.eb | 33 ++++++++++++++ ...rkzeug-0.12.1-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ 19 files changed, 534 insertions(+) create mode 100644 easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6a33cf7fb2 --- /dev/null +++ b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'atomate' +version = '0.4.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pythonhosted.org/atomate/' +description = """atomate has implementations of FireWorks workflows for Materials Science.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('FireWorks', '1.4.2', versionsuffix), + ('custodian', '1.1.0', versionsuffix), + ('pymatgen', '4.7.3', versionsuffix), + ('pymatgen-db', '0.6.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..45b7389451 --- /dev/null +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'custodian' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/custodian' +description = """A simple JIT job management framework in Python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), + ('monty', '0.9.6', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..526b35054c --- /dev/null +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'FireWorks' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/FireWorks' +description = """FireWorks helps run calculation workflows, with a centralized workflow server + controlling many worker nodes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Flask', '0.12', versionsuffix), + ('Flask-paginate', '0.4.5', versionsuffix), + ('PyYAML', '3.12', versionsuffix), + ('gunicorn', '19.7.1', versionsuffix), + ('monty', '0.9.6', versionsuffix), + ('pymongo', '3.4.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..153e1028fe --- /dev/null +++ b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'Flask-paginate' +version = '0.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Flask-paginate" +description = """Simple paginate support for flask.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_ZIP] + +dependencies = [ + ('Python', '2.7.13'), + ('Flask', '0.12', versionsuffix), +] + +options = {'modulename': 'flask_paginate'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..b305d04f47 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'Flask' +version = '0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Flask" +description = """A microframework based on Werkzeug, Jinja2 and good intentions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Jinja2', '2.9.6', versionsuffix), + ('Werkzeug', '0.12.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6e2be6854a --- /dev/null +++ b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'gunicorn' +version = '19.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/gunicorn" +description = """WSGI HTTP Server for UNIX.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..0069b2587c --- /dev/null +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'Jinja2' +version = '2.9.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Jinja2" +description = """A small but fast and easy to use stand-alone template engine written in pure python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4cff5e718d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +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': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.7.1'), + ('libpng', '1.6.29'), +] + +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/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..64c36ac39f --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'monty' +version = '0.9.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/monty/" +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..db5a0e5289 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '0.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.13')] + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4ff041f5c0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.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': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('libyaml', '0.1.7'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..908d8b8ff5 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'pymatgen-db' +version = '0.6.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymatgen-db' +description = """Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen) + materials analysis library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pymatgen', '4.7.3', versionsuffix), + ('smoqe', '0.1.3', versionsuffix), +] + +options = {'modulename': 'matgendb'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..f8b263a2dd --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pymatgen' +version = '4.7.3' +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': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), + ('matplotlib', '2.0.0', versionsuffix), + ('monty', '0.9.6', versionsuffix), + ('mpmath', '0.19', versionsuffix), + ('requests', '2.13.0', versionsuffix), + ('spglib-python', '1.9.9.38', versionsuffix), + ('sympy', '1.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9bb19f1090 --- /dev/null +++ b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pymongo' +version = '3.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymongo' +description = """Python driver for MongoDB.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..786bbdf2c6 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..a5ff78eb95 --- /dev/null +++ b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'smoqe' +version = '0.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/smoqe' +description = """Simple MongoDB Query Engine (SMoQE).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pymongo', '3.4.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6c2b70d3f7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.9.9.38' +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': '2017a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), +] + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..444574067c --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# patch to fix tests +patches = ['sympy-1.0_tests-unicode.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('mpmath', '0.19', '-Python-%(pyver)s'), +] + +# runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9f007d3773 --- /dev/null +++ b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'Werkzeug' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/WerkZeug" +description = """The Swiss Army knife of Python web development.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' -- GitLab From e64a152e2eba52d015850c2cf549afd467ca0f49 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 11:18:23 +0800 Subject: [PATCH 380/566] use existing libyaml with dummy toolchain --- .../p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb index 4ff041f5c0..73b6477407 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), - ('libyaml', '0.1.7'), + ('libyaml', '0.1.7', '', True), ] options = {'modulename': 'yaml'} -- GitLab From 23807849f1af83d3d0520249a6694f0317f8515f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 13:13:48 +0800 Subject: [PATCH 381/566] remove libpng from matplotlib dependencies (already a dependency of freetype) --- .../m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb index 4cff5e718d..e00702b768 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -17,7 +17,6 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.13'), ('freetype', '2.7.1'), - ('libpng', '1.6.29'), ] exts_list = [ -- GitLab From 86b92838f0b3009d1ec12ffc53e2b7f6993d0974 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Apr 2017 10:20:31 +0100 Subject: [PATCH 382/566] Fix libpng version conflict --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb index 52cec88efd..20416b1946 100755 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb @@ -25,7 +25,7 @@ source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] dependencies = [ ('cairo', '1.14.6'), ('libjpeg-turbo', '1.5.0'), - ('libpng', '1.6.26'), + ('libpng', '1.6.24'), ('libgd', '2.2.3'), ('Pango', '1.40.3'), ('libcerf', '1.5'), -- GitLab From 08e498cb5cc4bf318ed4660616330eb391c4b42c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 11:49:10 +0200 Subject: [PATCH 383/566] adding easyconfigs: bx-python-0.7.4-intel-2017a-Python-2.7.13.eb, LZO-2.10-intel-2017a.eb --- ...-python-0.7.4-intel-2017a-Python-2.7.13.eb | 47 +++++++++++++++++++ .../easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb | 31 ++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..8f02847ea1 --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'bx-python' +version = '0.7.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + + +dependencies = [ + ('Python', '2.7.13'), + ('LZO', '2.10'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " + +exts_list = [ + ('python-lzo', '1.11', { + 'modulename': 'lzo', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], + 'source_tmpl': 'python-lzo-%(version)s.tar.gz', + }), + (name, version, { + 'modulename': 'bx', + 'source_urls': ['https://github.com/bxlab/bx-python/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + }), +] + +# 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': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb new file mode 100644 index 0000000000..801057a84f --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.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 = '2.10' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage + 'download/'] + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +runtest = 'test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'] +} + +moduleclass = 'devel' -- GitLab From ffa2d8c231fe75d6527db2440b07d8f50b250975 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 13:14:06 +0200 Subject: [PATCH 384/566] {math}[intel/2016b] scipy 0.19.0 + numpy 1.12.1 w/ Python 3.5.2 --- .../n/numpy/numpy-1.12.0-mkl.patch | 55 +++++++++++++++++++ .../numpy-1.12.1-intel-2016b-Python-3.5.2.eb | 23 ++++++++ .../scipy-0.19.0-intel-2016b-Python-3.5.2.eb | 19 +++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch new file mode 100644 index 0000000000..3d09924f96 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch @@ -0,0 +1,55 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py +--- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 +@@ -675,7 +675,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -756,6 +756,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py +--- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 +@@ -123,3 +123,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..b83a080a7d --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +patches = ['numpy-1.12.0-mkl.patch'] + +dependencies = [ + ('Python', '3.5.2'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..523cf018d9 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.19.0' +versionsuffix = '-Python-3.5.2' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('numpy', '1.12.1', versionsuffix), +] + +moduleclass = 'math' -- GitLab From e085c578bfb1eac166f793d1b1877a36059d0491 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 13:17:35 +0200 Subject: [PATCH 385/566] adding easyconfigs: Stacks-1.46-intel-2017a.eb, sparsehash-2.0.3-intel-2017a.eb --- .../s/Stacks/Stacks-1.46-intel-2017a.eb | 35 +++++++++++++++++++ .../sparsehash-2.0.3-intel-2017a.eb | 23 ++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb new file mode 100644 index 0000000000..341b4db710 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.46' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '1.4'), + ('sparsehash', '2.0.3'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb new file mode 100644 index 0000000000..32f208ded5 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.3' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """An extremely memory-efficient hash_map + implementation. 2 bits/entry overhead! The SparseHash library + contains several hash-map implementations, including + implementations that optimize for space or speed.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/sparsehash/sparsehash/archive/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 28cf85302f91dcc01e4e373f8d7a8b84ee9a0aff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 10:08:35 +0200 Subject: [PATCH 386/566] adding easyconfigs: MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb, Eigen-3.2.10-intel-2016b.eb --- ...MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bfa4a70408 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'MRtrix' +version = '0.3.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Mesa', '12.0.2'), + ('Qt', '4.8.7'), + ('Eigen', '3.2.10'), +] + +moduleclass = 'bio' -- GitLab From 3ce4bc6da6754819d8706ff8d011551ddc02dbfc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 19 Apr 2017 13:03:43 +0200 Subject: [PATCH 387/566] Add CUDA/8.0.61 --- .../c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..02ed53d7d5 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '8.0.61' + +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': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] + +sources = ['cuda_%(version)s_375.26_linux-run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb new file mode 100644 index 0000000000..b3ad585f70 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '8.0.61' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] + +sources = ['cuda_%(version)s_375.26_linux-run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' -- GitLab From 8307b771d0e3d26a65a442d1e3c761ccb7bdb934 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 19 Apr 2017 13:14:31 +0200 Subject: [PATCH 388/566] Drop Cuda easyconfig with unsupported GCC --- .../c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb deleted file mode 100644 index 02ed53d7d5..0000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'CUDA' -version = '8.0.61' - -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': 'GCCcore', 'version': '6.3.0'} - -source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] - -sources = ['cuda_%(version)s_375.26_linux-run'] - -modextravars = {'CUDA_HOME': '%(installdir)s'} - -moduleclass = 'system' -- GitLab From ad01055ce5e98a5dce7f62d59d7bfd360355cf18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:53:42 +0200 Subject: [PATCH 389/566] adding easyconfigs: JasPer-1.900.1-intel-2017a.eb --- .../j/JasPer/JasPer-1.900.1-intel-2017a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb new file mode 100644 index 0000000000..80e537b9bb --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 98c8fa75eab423831af2b64676302a7ab477997f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:54:13 +0200 Subject: [PATCH 390/566] adding easyconfigs: makedepend-1.0.5-GCCcore-6.3.0.eb, xorg-macros-1.19.1-GCCcore-6.3.0.eb, xproto-7.0.31-GCCcore-6.3.0.eb --- .../makedepend-1.0.5-GCCcore-6.3.0.eb | 26 +++++++++++++++++ .../xorg-macros-1.19.1-GCCcore-6.3.0.eb | 27 +++++++++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb | 29 +++++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb create mode 100755 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b7d5d70c2d --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_UTIL_SOURCE] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb new file mode 100755 index 0000000000..6f48acb154 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.1' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('Autotools', '20150215'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..06e2a620f7 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From e4c9596d4b47c878879c7413a42508d5bd897b29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:58:21 +0200 Subject: [PATCH 391/566] adding easyconfigs: cURL-7.54.0-GCCcore-6.3.0.eb --- .../c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..8d7f087e2b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.54.0' + +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': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From a38dd1652faef8092f063cfcb4a8f8c95aaa21a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:27:11 +0200 Subject: [PATCH 392/566] adding easyconfigs: UDUNITS-2.2.24-intel-2017a.eb --- .../u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb new file mode 100644 index 0000000000..0e89a4b4d6 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +dependencies = [('expat', '2.2.0')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' -- GitLab From b1b868b9fad00772a8c991df2a84b5e91e4488e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:27:39 +0200 Subject: [PATCH 393/566] adding easyconfigs: HDF-4.2.12-intel-2017a.eb --- .../h/HDF/HDF-4.2.12-intel-2017a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb new file mode 100644 index 0000000000..36b03f1853 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.12' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('Szip', '2.1'), + ('libjpeg-turbo', '1.5.1'), +] + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' -- GitLab From db59e7eca44753a4e802ccff209fe89a4804e19d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:28:06 +0200 Subject: [PATCH 394/566] adding easyconfigs: g2lib-1.4.0-intel-2017a.eb, g2clib-1.6.0-intel-2017a.eb --- .../g/g2clib/g2clib-1.6.0-intel-2017a.eb | 17 +++++++++++++++ .../g/g2lib/g2lib-1.4.0-intel-2017a.eb | 21 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb new file mode 100644 index 0000000000..91bbbfa89b --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb @@ -0,0 +1,17 @@ +name = 'g2clib' +version = '1.6.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] + +dependencies = [('JasPer', '1.900.1')] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb new file mode 100644 index 0000000000..c7f92d0e2b --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'g2lib' +version = '1.4.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] + +patches = ['fix_makefile.patch'] + +dependencies = [('JasPer', '1.900.1')] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fpp -I."' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' -- GitLab From 766e37c4509ed9d8de231878b0b1080dc2922fd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:47:38 +0200 Subject: [PATCH 395/566] {geo}[intel/2017a] ESMF 6.3.0rp1 --- .../e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb | 31 +++++++++++++++++++ .../ESMF-6.3.0rp1_fix-file-open-test.patch | 13 ++++++++ .../netCDF-C++4-4.3.0-intel-2017a.eb | 24 ++++++++++++++ 3 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb new file mode 100644 index 0000000000..fec7e0e3f7 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb @@ -0,0 +1,31 @@ +name = 'ESMF' +version = '6.3.0rp1' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = [ + 'ESMF-6.1.1_libopts.patch', + 'ESMF-%(version)s_fix-file-open-test.patch', +] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('netCDF-C++4', '4.3.0'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch new file mode 100644 index 0000000000..62a98e0354 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch @@ -0,0 +1,13 @@ +fix compilation issue with recent compilers +cfr. https://sourceforge.net/p/esmf/esmf/ci/3706bf758012daebadef83d6575c477aeff9c89b/#diff-1 +--- src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp.orig 2017-04-19 13:44:03.384547426 +0200 ++++ src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp 2017-04-19 13:44:16.864674576 +0200 +@@ -105,7 +105,7 @@ + ReadABAQUS::~ReadABAQUS() + { + mdbImpl->release_interface(readMeshIface); +- if (NULL != abFile) ++ if (abFile.is_open()) + abFile.close(); + } + diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb new file mode 100644 index 0000000000..959f14667b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' + +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': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 4133ea658c683e1f2a46a28bb5494b71aa9765e1 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 19 Apr 2017 15:32:06 +0200 Subject: [PATCH 396/566] v6.0 --- .../c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb new file mode 100644 index 0000000000..942648ea47 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '6.0' +cuda_version = '8.0.61' + +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-8.0-linux-x64-v%(version)s.tgz'] + +dependencies = [('CUDA', cuda_version)] + +checksums = [ + '4aacb7acb93c5e4dfa9db814df496219', # cudnn-8.0-linux-x64-v6.0.tgz, Jan 20 2017 download +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' -- GitLab From 695590ab4dad6e11621fcf63d0bf7152afc9ad9d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 18:36:20 +0200 Subject: [PATCH 397/566] adding easyconfigs: libiconv-1.15-intel-2017a.eb --- .../l/libiconv/libiconv-1.15-intel-2017a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb new file mode 100644 index 0000000000..fb6be42e9f --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.15' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' -- GitLab From 2d502840969e2356078da89e05ac197c67ae0306 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:14:45 +0200 Subject: [PATCH 398/566] install libiconv with GCCcore rather than intel toolchain --- ...nv-1.15-intel-2017a.eb => libiconv-1.15-GCCcore-6.3.0.eb} | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/l/libiconv/{libiconv-1.15-intel-2017a.eb => libiconv-1.15-GCCcore-6.3.0.eb} (75%) diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb similarity index 75% rename from easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb rename to easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb index fb6be42e9f..c2a203f1b2 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -6,11 +6,14 @@ version = '1.15' homepage = 'https://www.gnu.org/software/libiconv' description = "Libiconv converts from one character encoding to another through Unicode conversion" -toolchain = {'name': 'intel', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], -- GitLab From b72075148a92dc4187d739278cb11f5f33e40709 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:35:46 +0200 Subject: [PATCH 399/566] adding easyconfigs: numba-0.32.0-intel-2017a-Python-2.7.13.eb --- .../numba-0.32.0-intel-2017a-Python-2.7.13.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..dc868ad142 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.32.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('LLVM', '4.0.0'), +] + +exts_list = [ + ('llvmlite', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# 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/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' -- GitLab From bf7342099c04a56d0715d02cdf2531ee57e1d194 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:58:08 +0200 Subject: [PATCH 400/566] adding easyconfigs: PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb, ZeroMQ-4.2.2-intel-2017a.eb, OpenPGM-5.2.122-intel-2017a.eb, libsodium-1.0.12-intel-2017a.eb --- .../libsodium/libsodium-1.0.12-intel-2017a.eb | 20 +++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb | 30 ++++++++++++++++ ...Q-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb | 30 ++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb | 36 +++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb new file mode 100644 index 0000000000..faf9cf93a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.12' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb new file mode 100644 index 0000000000..d604042523 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] + +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb new file mode 100644 index 0000000000..3ee565a8d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.2' +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': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +dependencies = [ + ('Python', '2.7.13'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb new file mode 100644 index 0000000000..165ba15944 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.2' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['52499909b29604c1e47a86f1cb6a9115'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.29.2'), + ('libsodium', '1.0.12'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 54c21ef39805e3658819582f56a821f29ea5b96c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:58:44 +0200 Subject: [PATCH 401/566] adding easyconfigs: GSL-2.3-intel-2017a.eb --- .../easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb new file mode 100644 index 0000000000..23a2fed6dc --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.3' + +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': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From 5611e1be3e27234852c0429f2a98458f8e3a0e2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 11:42:16 +0200 Subject: [PATCH 402/566] add patch to avoid configparser declaring ownership of backports namespace, fixes #3825 --- ...igparser-3.5.0-foss-2016a-Python-2.7.11.eb | 16 +++------- ...gparser-3.5.0-intel-2016b-Python-2.7.12.eb | 15 ++------- ...igparser-3.5.0-intel-2016b-Python-3.5.2.eb | 7 ++--- ...gparser-3.5.0_no-backports-namespace.patch | 31 +++++++++++++++++++ 4 files changed, 41 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb index 8172078525..f9db925788 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb @@ -12,26 +12,18 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '2.7.11'), -] -builddependencies = [ - ('pip', '8.1.2', versionsuffix), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.11')] +builddependencies = [('pip', '8.1.2', versionsuffix)] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], } -# XXX: hack! for some reason the sanity check imports fail, even though the -# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py -# in backports makes it pass and hopefully does not break anything. -postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] - sanity_check_commands = [ ('python', "-c 'import configparser'"), ('python', "-c 'from backports import configparser'"), diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb index 10fc576297..bed63bcc08 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb @@ -12,26 +12,17 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '2.7.12'), -] -builddependencies = [ - ('pip', '8.1.2', versionsuffix), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.12')] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], } -# XXX: hack! for some reason the sanity check imports fail, even though the -# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py -# in backports makes it pass and hopefully does not break anything. -postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] - sanity_check_commands = [ ('python', "-c 'import configparser'"), ('python', "-c 'from backports import configparser'"), 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 index e3bb6d9e20..113e88c75f 100644 --- 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 @@ -12,12 +12,11 @@ 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'), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '3.5.2')] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch b/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch new file mode 100644 index 0000000000..6deccec5e6 --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch @@ -0,0 +1,31 @@ +don't let configparser define 'backports' namespace, since that interferes with other packaging that provide stuff in 'backports' + +patch obtained from https://github.com/NIXOS/nixpkgs/blob/master/pkgs/development/python-modules/configparser/0001-namespace-fix.patch +see also https://bitbucket.org/ambv/configparser/issues/17/importerror-when-used-with-other-backports +diff --git a/setup.py b/setup.py +index 3b07823..63ed25d 100644 +--- a/setup.py ++++ b/setup.py +@@ -42,7 +42,6 @@ setup( + py_modules=modules, + package_dir={'': 'src'}, + packages=find_packages('src'), +- namespace_packages=['backports'], + include_package_data=True, + zip_safe=False, + install_requires=requirements, +diff --git a/src/backports/__init__.py b/src/backports/__init__.py +index f84d25c..febdb2f 100644 +--- a/src/backports/__init__.py ++++ b/src/backports/__init__.py +@@ -3,9 +3,3 @@ + + from pkgutil import extend_path + __path__ = extend_path(__path__, __name__) +- +-try: +- import pkg_resources +- pkg_resources.declare_namespace(__name__) +-except ImportError: +- pass +-- -- GitLab From cf19458b143e485f7f38567676fccbce91806cd1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 17:12:07 +0200 Subject: [PATCH 403/566] re-add nbconvert extension in IPython easyconfigs --- ...igparser-3.5.0-foss-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ ...rypoints-0.2.2-foss-2016b-Python-2.7.12.eb | 28 +++++++++++++++++ .../IPython-5.1.0-foss-2016b-Python-2.7.12.eb | 12 +++---- ...IPython-5.1.0-intel-2016b-Python-2.7.12.eb | 12 +++---- ...IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 16 +++++----- 5 files changed, 75 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5bd3d25aab --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +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': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] +sources = ['configparser-%(version)s.tar.gz'] + +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.12')] + +use_pip = True + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], +} + +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-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a82113c472 --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.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': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/f8/ad/0e77a853c745a15981ab51fa9a0cb4eca7a7a007b4c1970106ee6ba01e0c/'] +sources = ['entrypoints-0.2.2-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), + ('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-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb index 15948e83d4..ec7c04c10b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -114,11 +112,9 @@ exts_list = [ ('pexpect', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '4.2.0', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('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/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb index 73b84816cd..ad14e82e32 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '15.4.0', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -114,11 +112,9 @@ exts_list = [ ('pexpect', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '4.2.0', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('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/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb index 89001fc17a..01c5f93a20 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '10.1', versionsuffix), ('prompt-toolkit', '1.0.13', versionsuffix), ] @@ -111,11 +109,13 @@ exts_list = [ ('pexpect', '4.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '5.1.1', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('pandocfilters', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + }), + ('nbconvert', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'use_pip': True, + }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), -- GitLab From f142dcdf9ad525403d586d37b3bf68d2a2933032 Mon Sep 17 00:00:00 2001 From: Basil Neff Date: Thu, 20 Apr 2017 17:31:03 +0200 Subject: [PATCH 404/566] Change source_urls of pycrypto to https://pypi.python.org/packages/source/p/pycrypto/: A crypto library should be downloaded via https, python.org seems more reliable than dlitz.net, dlitz.net is currently not online. --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb | 2 +- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb | 2 +- .../p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.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-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-2.7.5-goolf-1.4.10.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-2.7.6-goolf-1.4.10.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 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.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 | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb | 2 +- 61 files changed, 61 insertions(+), 61 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 0cacb5b908..6b56eb27c3 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 @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 c4b91910db..8b4e1559a2 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 @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 6cb74160de..acd58a0881 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 @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 2bf2b3c0c7..e8f04d3c24 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 @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 d616f3a678..f6fb8098a2 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 @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 3bba96e78d..e63f73a086 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 @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 5578abe094..007214e5b0 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 @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index 4289f275f3..8a60745ce6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb index f16c276300..f9d52e68ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 7ca3e0d30a..b14cb9623b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 90aff56172..161e0d5c72 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 540888954b..236dc03eb2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index 500c945db9..61b2cea7f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 66287172c5..15781ef44b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb index 49ed840807..92cc06cd43 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 4fa82a32c1..2bcf51b6e3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -95,7 +95,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 36a33282cc..b4d230688e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 index ceffc4847a..f016ee6e7a 100644 --- 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 @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 index 42a08985d0..7040853aa6 100644 --- 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 @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index ba6ada1467..0f7cc1242b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index f39ab1c056..8305709383 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb index 47c4558b9f..eb4f43f9dd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 8d585acc42..099f1ae1b2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -86,7 +86,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 9cf2d30627..b98190bc1b 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 @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 0d7187668b..6d47c29a41 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 @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 1f04581f6c..5d62c714b3 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 @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 d6acb56cd0..466af1fc83 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 @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 0a6a82b9fe..9112593773 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 @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 78b8331206..b74b1eef65 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 @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 8bc486f394..fa3597eb0f 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 @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 f91d5d9be1..74108af019 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 @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 1589ad3044..7f83fbbc76 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 @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 cc438001ba..d802876700 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 @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 8a3b97a885..8d651bcfeb 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 @@ -84,7 +84,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 ff8c4dd1f7..0ac840f64e 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 @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 400936afa7..8301c629cc 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 535df5f445..fcb554f578 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 @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 15167c0da9..d08ab61505 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 @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 5da8fad6cd..3479838d18 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 @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 a19c3193df..e92ff5d69d 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 @@ -84,7 +84,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 c42116cc9a..0f597d584c 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 e020765a41..2963dc2fc7 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 0e5c8bdaf5..6953cb6dbe 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 50b5d85a22..0f287711fc 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 954cb1d6c9..77b75dd242 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 2117038315..3ba0f79c58 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 de0245d75a..58ac4915cc 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 39c33c3855..f324c5da55 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 @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 dfd615f248..76e8491a9b 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 @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 530b345146..e15e16e66c 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 @@ -62,7 +62,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ] 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 1f4aa039b5..fbcadd2903 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 @@ -62,7 +62,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ] 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 85a061b4b2..aaa2d02a7e 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 @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 43f98bbf39..80c176feab 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 @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 fa4d5db712..e220cd9cc4 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 @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 7f32b2fbd5..1fe2eb4748 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 @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index 34b680443b..3794d8056b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 f17ad6e258..0ea37fde6e 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 @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 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 bba87219ba..6b27ddc007 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 @@ -97,7 +97,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index 3034157afb..0f528e0158 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb index f40c4aab55..2fc712658f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb index 805061ab30..198569f10b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], -- GitLab From 2582246e9f15e21fffde3cf51c5c8e8f192422ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 20:47:44 +0200 Subject: [PATCH 405/566] adding easyconfigs: IPython-5.3.0-intel-2017a-Python-2.7.13.eb --- ...IPython-5.3.0-intel-2017a-Python-2.7.13.eb | 176 ++++++++++++++++++ 1 file changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..62ef063309 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,176 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.3.0' +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': '2017a'} + +dependencies = [ + ('Python', '2.7.13'), + ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'modulename': 'pygments', + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2017.4.17', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'modulename': 'jinja2', + }), + ('jupyter_client', '5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.4', { + '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/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('scandir', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + }), + ('pathlib2', '2.2.1', { + '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', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('pexpect', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('pandocfilters', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'patches': ['configparser-3.5.0_no-backports-namespace.patch'], + 'use_pip': True, + }), + ('entrypoints', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'source_tmpl': 'entrypoints-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('nbconvert', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'use_pip': True, + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('testpath', '0.3', { + 'source_urls': ['https://pypi.python.org/packages/py2.py3/t/testpath/'], + 'source_tmpl': 'testpath-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'source_tmpl': 'wcwidth-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('prompt-toolkit', '1.0.14', { + 'modulename': 'prompt_toolkit', + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'source_tmpl': 'prompt_toolkit-%(version)s-py2-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), + ('ipykernel', '4.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('ipywidgets', '5.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + }), + ('widgetsnbextension', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + }), +] + +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', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' -- GitLab From d9723ff8ec091b57e3ffbf11566782a52a612a75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 21:05:59 +0200 Subject: [PATCH 406/566] adding easyconfigs: ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb, h5py-2.7.0-intel-2017a-Python-2.7.13.eb, pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb, pkg-config-0.29.2-GCCcore-6.3.0.eb --- .../h5py-2.7.0-intel-2017a-Python-2.7.13.eb | 32 +++++++ ...ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb | 88 +++++++++++++++++++ .../pkg-config-0.29.2-GCCcore-6.3.0.eb | 32 +++++++ ...gconfig-1.2.2-intel-2017a-Python-2.7.13.eb | 26 ++++++ 4 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..300f1e3d6e --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.13'), + ('HDF5', '1.10.0-patch1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d74840fcf3 --- /dev/null +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,88 @@ +easyblock = 'Bundle' + +name = 'ipyrad' +version = '0.6.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipyrad.readthedocs.io' +description = """ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic + data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('h5py', '2.7.0', versionsuffix), + ('numba', '0.32.0', versionsuffix), + ('IPython', '5.3.0', versionsuffix), +] + +exts_list = [ + ('imagesize', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize'], + }), + ('alabaster', '0.7.10', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster'], + }), + ('Babel', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer'], + }), + ('docutils', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], + }), + ('Sphinx', '1.5.5', { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx'], + }), + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + ('jupyter', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter'], + }), + ('ipyparallel', '6.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipyparallel'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings'], + }), + ('html5lib', '0.999999999', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib'], + }), + ('bleach', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach'], + }), + ('jupyter-console', '5.1.0', { + 'modulename': 'jupyter_console', + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_console'], + 'source_tmpl': 'jupyter_console-%(version)s.tar.gz', + }), + ('qtconsole', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], + }), + ('futures', '3.1.1', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], + }), + (name, version, { + 'source_urls': ['https://github.com/dereneaton/ipyrad/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + }), +] + +# 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/ipyrad'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b75a0d85ea --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +# 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/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..0df86ffc84 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 0be93bb3b688cde0add034758905359998691a30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 22:04:24 +0200 Subject: [PATCH 407/566] add patch file for configparser as extension in IPython easyconfig --- ...gparser-3.5.0_no-backports-namespace.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch diff --git a/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch b/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch new file mode 100644 index 0000000000..6deccec5e6 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch @@ -0,0 +1,31 @@ +don't let configparser define 'backports' namespace, since that interferes with other packaging that provide stuff in 'backports' + +patch obtained from https://github.com/NIXOS/nixpkgs/blob/master/pkgs/development/python-modules/configparser/0001-namespace-fix.patch +see also https://bitbucket.org/ambv/configparser/issues/17/importerror-when-used-with-other-backports +diff --git a/setup.py b/setup.py +index 3b07823..63ed25d 100644 +--- a/setup.py ++++ b/setup.py +@@ -42,7 +42,6 @@ setup( + py_modules=modules, + package_dir={'': 'src'}, + packages=find_packages('src'), +- namespace_packages=['backports'], + include_package_data=True, + zip_safe=False, + install_requires=requirements, +diff --git a/src/backports/__init__.py b/src/backports/__init__.py +index f84d25c..febdb2f 100644 +--- a/src/backports/__init__.py ++++ b/src/backports/__init__.py +@@ -3,9 +3,3 @@ + + from pkgutil import extend_path + __path__ = extend_path(__path__, __name__) +- +-try: +- import pkg_resources +- pkg_resources.declare_namespace(__name__) +-except ImportError: +- pass +-- -- GitLab From 0c7c4f5c3d8938754cdf2229ab8aa6743d375d6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 23:28:04 +0200 Subject: [PATCH 408/566] add toyplot extension in ipyrad easyconfig file --- ...ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb | 26 +++++++++++++++++- .../Pillow-4.1.0-intel-2017a-Python-2.7.13.eb | 27 +++++++++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb index d74840fcf3..ecce4b3046 100644 --- a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -10,14 +10,15 @@ description = """ipyrad is an interactive toolkit for assembly and analysis of r toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') dependencies = [ ('Python', '2.7.13'), ('h5py', '2.7.0', versionsuffix), ('numba', '0.32.0', versionsuffix), ('IPython', '5.3.0', versionsuffix), + ('Pillow', '4.1.0', versionsuffix), ] exts_list = [ @@ -69,6 +70,29 @@ exts_list = [ 'modulename': 'concurrent.futures', 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], }), + ('arrow', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/arrow'], + }), + ('colormath', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colormath'], + }), + ('multipledispatch', '0.4.9', { + 'source_urls': ['https://pypi.python.org/packages/source/m/multipledispatch'], + }), + ('pypng', '0.0.18', { + 'modulename': 'png', + 'source_urls': ['https://pypi.python.org/packages/source/p/pypng'], + }), + ('olefile', '0.44', { + 'source_urls': ['https://pypi.python.org/packages/source/o/olefile'], + 'source_tmpl': 'olefile-%(version)s.zip', + }), + ('reportlab', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'], + }), + ('toyplot', '0.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toyplot'], + }), (name, version, { 'source_urls': ['https://github.com/dereneaton/ipyrad/archive/'], 'source_tmpl': '%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..f4cf66d2ef --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '4.1.0' +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': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.7'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From 4dd8a3443ae8329b20a05bce182f2386c3053d9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 21 Apr 2017 13:14:18 +0200 Subject: [PATCH 409/566] Go 1.8.1 binary version --- easybuild/easyconfigs/g/Go/Go-1.8.1.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.8.1.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.8.1.eb b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb new file mode 100644 index 0000000000..07ab4f25c4 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.8.1' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +source_urls = ['https://storage.googleapis.com/golang/'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s'} +moduleclass = 'compiler' -- GitLab From 6beb05e877f425ecaafe2fa8cbb60ff583c27dd5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 21 Apr 2017 13:43:25 +0200 Subject: [PATCH 410/566] added AdapterRemoval --- .../AdapterRemoval-2.2.0-foss-2016b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb new file mode 100644 index 0000000000..738b03c0ca --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'MakeCp' + +name = 'AdapterRemoval' +version = '2.2.0' + +homepage = 'https://github.com/MikkelSchubert/%(namelower)s' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/MikkelSchubert/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +files_to_copy = [(['build/%(name)s'], 'bin'), (['build/%(name)s.1'], 'share/man/man1')] + +checksums = ['159e5c7c527dde70eac444a87bf5fbfc'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('AdapterRemoval', '--version')] + +moduleclass = 'bio' -- GitLab From 321af123d5b5f5bb627e1e067dbf730af59b4816 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Apr 2017 13:16:53 +0200 Subject: [PATCH 411/566] adding easyconfigs: ViennaRNA-2.3.5-intel-2017a.eb --- .../ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb new file mode 100644 index 0000000000..daafb8cd29 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.3.5' + +homepage = 'http://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 28d361d3ce47585509674f61b14a5027ac94a1dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Apr 2017 11:00:31 +0200 Subject: [PATCH 412/566] add checksum for ViennaRNA 2.3.5 source tarball --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb index daafb8cd29..fc2a6f62b8 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -25,6 +25,8 @@ toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] +checksums = ['4542120adae9b7abb605e2304c2a1326'] + # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory -- GitLab From 513967084fe5171105b83b20c0cc16466b84346b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 17:12:25 +0800 Subject: [PATCH 413/566] bundle most of the python packages as extensions --- ...stodian-1.1.0-intel-2017a-Python-2.7.13.eb | 9 ++++- ...reWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 33 +++++++++++++++--- ...aginate-0.4.5-intel-2017a-Python-2.7.13.eb | 27 --------------- .../Flask-0.12-intel-2017a-Python-2.7.13.eb | 26 -------------- ...nicorn-19.7.1-intel-2017a-Python-2.7.13.eb | 24 ------------- .../Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb | 24 ------------- .../monty-0.9.6-intel-2017a-Python-2.7.13.eb | 26 -------------- .../mpmath-0.19-intel-2017a-Python-2.7.13.eb | 34 ------------------- ...tgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 9 ++++- ...ymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 32 ++++++++++++++--- ...pymongo-3.4.0-intel-2017a-Python-2.7.13.eb | 24 ------------- ...quests-2.13.0-intel-2017a-Python-2.7.13.eb | 24 ------------- .../smoqe-0.1.3-intel-2017a-Python-2.7.13.eb | 25 -------------- .../sympy-1.0-intel-2017a-Python-2.7.13.eb | 33 ------------------ .../s/sympy/sympy-1.0_tests-unicode.patch | 23 ------------- ...rkzeug-0.12.1-intel-2017a-Python-2.7.13.eb | 24 ------------- 16 files changed, 72 insertions(+), 325 deletions(-) delete mode 100644 easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch delete mode 100644 easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index 45b7389451..2a8be8856b 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -15,7 +15,14 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), - ('monty', '0.9.6', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index 526b35054c..0323b8f8c9 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -15,12 +15,35 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), - ('Flask', '0.12', versionsuffix), - ('Flask-paginate', '0.4.5', versionsuffix), ('PyYAML', '3.12', versionsuffix), - ('gunicorn', '19.7.1', versionsuffix), - ('monty', '0.9.6', versionsuffix), - ('pymongo', '3.4.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('Flask', '0.12', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], + }), + ('Flask-paginate', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], + 'source_tmpl': 'flask-paginate-%(version)s.zip', + 'modulename': 'flask_paginate', + }), + ('Jinja2', '2.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('Werkzeug', '0.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug/'], + }), + ('gunicorn', '19.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], + }), + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), + ('pymongo', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymongo/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 153e1028fe..0000000000 --- a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Flask-paginate' -version = '0.4.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Flask-paginate" -description = """Simple paginate support for flask.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_ZIP] - -dependencies = [ - ('Python', '2.7.13'), - ('Flask', '0.12', versionsuffix), -] - -options = {'modulename': 'flask_paginate'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index b305d04f47..0000000000 --- a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Flask' -version = '0.12' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Flask" -description = """A microframework based on Werkzeug, Jinja2 and good intentions.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), - ('Jinja2', '2.9.6', versionsuffix), - ('Werkzeug', '0.12.1', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 6e2be6854a..0000000000 --- a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'gunicorn' -version = '19.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/gunicorn" -description = """WSGI HTTP Server for UNIX.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 0069b2587c..0000000000 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Jinja2' -version = '2.9.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Jinja2" -description = """A small but fast and easy to use stand-alone template engine written in pure python.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 64c36ac39f..0000000000 --- a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'monty' -version = '0.9.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/monty/" -description = """Monty implements supplementary useful functions for Python that are not part of the standard library. - Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton - and cached_class, and many more.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index db5a0e5289..0000000000 --- a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Author: Adam Huffman -# adam.huffman@crick.ac.uk -# The Francis Crick Institute - -easyblock = 'PythonPackage' - -name = 'mpmath' -version = '0.19' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://mpmath.org/' -description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex - types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation - can be performed just as well at 10-digit or 1000-digit precision, with either real or complex - numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely - high precision work.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] -sources = ['%(version)s.tar.gz'] - -dependencies = [('Python', '2.7.13')] - -runtest = 'python -c "import mpmath; mpmath.runtests();"' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index 908d8b8ff5..b7bde5299a 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -16,7 +16,14 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), ('pymatgen', '4.7.3', versionsuffix), - ('smoqe', '0.1.3', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('smoqe', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], + }), ] options = {'modulename': 'matgendb'} diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index f8b263a2dd..c011699956 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -17,11 +17,35 @@ dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ('matplotlib', '2.0.0', versionsuffix), - ('monty', '0.9.6', versionsuffix), - ('mpmath', '0.19', versionsuffix), - ('requests', '2.13.0', versionsuffix), ('spglib-python', '1.9.9.38', versionsuffix), - ('sympy', '1.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('Flask', '0.12', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], + }), + ('Flask-paginate', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], + 'source_tmpl': 'flask-paginate-%(version)s.zip', + 'modulename': 'flask_paginate', + }), + ('gunicorn', '19.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], + }), + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), + ('mpmath', '0.19', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('sympy', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 9bb19f1090..0000000000 --- a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pymongo' -version = '3.4.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/pymongo' -description = """Python driver for MongoDB.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 786bbdf2c6..0000000000 --- a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'requests' -version = '2.13.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/requests' -description = """Python http for humans.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index a5ff78eb95..0000000000 --- a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'smoqe' -version = '0.1.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/smoqe' -description = """Simple MongoDB Query Engine (SMoQE).""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), - ('pymongo', '3.4.0', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 444574067c..0000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'sympy' -version = '1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://sympy.org/' -description = """SymPy is a Python library for symbolic mathematics. It aims to - become a full-featured computer algebra system (CAS) while keeping the code as - simple as possible in order to be comprehensible and easily extensible. SymPy - is written entirely in Python and does not require any external libraries.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -# patch to fix tests -patches = ['sympy-1.0_tests-unicode.patch'] - -dependencies = [ - ('Python', '2.7.13'), - ('mpmath', '0.19', '-Python-%(pyver)s'), -] - -# runtest = 'python setup.py test' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch deleted file mode 100644 index 87e12a3b40..0000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch +++ /dev/null @@ -1,23 +0,0 @@ -Fix for Unicode error that causes one of the tests to fail - -For reference, see -http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte -and http://nedbatchelder.com/text/unipain/unipain.html - -Patch created by: - -Adam Huffman -The Francis Crick Institute - -diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py ---- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 -+++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 -@@ -164,7 +164,7 @@ - except CalledProcessError as e: - raise CodeWrapError( - "Error while executing command: %s. Command output is:\n%s" % ( -- " ".join(command), e.output.decode())) -+ " ".join(command), e.output.decode('ascii', 'ignore'))) - if not self.quiet: - print(retoutput) - diff --git a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 9f007d3773..0000000000 --- a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Werkzeug' -version = '0.12.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/WerkZeug" -description = """The Swiss Army knife of Python web development.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' -- GitLab From 5cbbbd21c3081ec7f660939e08bb4e12b23b3063 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 18:05:52 +0800 Subject: [PATCH 414/566] restore erroneously deleted file --- .../s/sympy/sympy-1.0_tests-unicode.patch | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch new file mode 100644 index 0000000000..87e12a3b40 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch @@ -0,0 +1,23 @@ +Fix for Unicode error that causes one of the tests to fail + +For reference, see +http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte +and http://nedbatchelder.com/text/unipain/unipain.html + +Patch created by: + +Adam Huffman +The Francis Crick Institute + +diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py +--- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 ++++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 +@@ -164,7 +164,7 @@ + except CalledProcessError as e: + raise CodeWrapError( + "Error while executing command: %s. Command output is:\n%s" % ( +- " ".join(command), e.output.decode())) ++ " ".join(command), e.output.decode('ascii', 'ignore'))) + if not self.quiet: + print(retoutput) + -- GitLab From ce6e45a9eff79478f37e7e8dec137a229cd1c9bc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 18:12:09 +0800 Subject: [PATCH 415/566] use Bundle easyblock for easyconfigs with extensions --- .../custodian-1.1.0-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- .../FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- ...pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 15 ++++++++++----- .../pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- 4 files changed, 40 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index 2a8be8856b..e8bf835f61 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'custodian' version = '1.1.0' @@ -9,22 +9,28 @@ description = """A simple JIT job management framework in Python.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('custodian', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], + }), ('monty', '0.9.6', { 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], }), ] +# 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': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index 0323b8f8c9..f776bdcadf 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'FireWorks' version = '1.4.2' @@ -10,17 +10,18 @@ description = """FireWorks helps run calculation workflows, with a centralized w toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('FireWorks', version, { + 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], + }), ('Flask', '0.12', { 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], }), @@ -46,6 +47,11 @@ exts_list = [ }), ] +# 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': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index b7bde5299a..007db0084d 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'pymatgen-db' version = '0.6.5' @@ -10,23 +10,28 @@ description = """Pymatgen-db is a database add-on for the Python Materials Genom toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('pymatgen', '4.7.3', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('pymatgen-db', '0.6.5', { + 'modulename': 'matgendb', + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen-db/'], + }), ('smoqe', '0.1.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], }), ] -options = {'modulename': 'matgendb'} +# 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': [], diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index c011699956..718deacce4 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'Bundle' name = 'pymatgen' version = '4.7.3' @@ -10,9 +10,6 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), @@ -20,6 +17,7 @@ dependencies = [ ('spglib-python', '1.9.9.38', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ @@ -40,6 +38,9 @@ exts_list = [ ('mpmath', '0.19', { 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], }), + ('pymatgen', version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], + }), ('requests', '2.13.0', { 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], }), @@ -48,6 +49,11 @@ exts_list = [ }), ] +# 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': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] -- GitLab From 07ac52418a3dd86aaa411fb487e172b7c3ae50cb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 25 Apr 2017 15:51:57 +0200 Subject: [PATCH 416/566] {chem} [dummy] ORCA/4.0.0.2 --- .../o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb new file mode 100644 index 0000000000..c9312c4044 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb @@ -0,0 +1,38 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = '4.0.0.2' + +openmpiversion = '2.0.2' +versionsuffix = '-OpenMPI-%s' % openmpiversion + +homepage = 'http://cec.mpg.de/forum/' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Download from https://cec.mpg.de/orcadownload/index.php +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tbz' % (version.replace('.', '_'), openmpiversion.replace('.', ''))] + +checksums = ['a5b8ecdd3d004af4bc8190c986f34e11'] + +dependencies = [('OpenMPI', openmpiversion, '-GCC-6.3.0-2.27')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From fb97882c1ab2909d8026a599a4ca7bf1baf576fc Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:19:15 +0200 Subject: [PATCH 417/566] adding easyconfigs: Python-2.7.12-foss-2017a.eb --- .../p/Python/Python-2.7.12-foss-2017a.eb | 293 ++++++++++++++++++ 1 file changed, 293 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb new file mode 100644 index 0000000000..b8e862c97f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb @@ -0,0 +1,293 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-21_17-31-01 +# Built with EasyBuild version 3.1.1 on 2017-04-20_11-17-51 +# Built with EasyBuild version 3.1.1 on 2017-04-03_09-46-50 +name = 'Python' +version = '2.7.12' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated March 30th 2017 +# setuptools 34.3.3 zip +exts_list = [ + ('setuptools', '23.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.25.2', { + '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', '2.6.0', { + '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', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2017.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "build_time": 2237.89, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--sourcepath='/cluster/easybuild/sources'", 'Python-2.7.12-foss-2017a-updated.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 404321068, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491205609, + "total_memory": 128828, +}] + +# Build statistics +buildstats = [ +{ + "build_time": 2237.89, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--sourcepath='/cluster/easybuild/sources'", 'Python-2.7.12-foss-2017a-updated.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 404321068, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491205609, + "total_memory": 128828, +}, +{ + "build_time": 1966.64, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python/Python-2.7.12-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login24", + "install_size": 404321244, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1492679870, + "total_memory": 128828, +}, +] + +# Build statistics +buildstats = [ +{ + "build_time": 2237.89, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--sourcepath='/cluster/easybuild/sources'", 'Python-2.7.12-foss-2017a-updated.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + 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--enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login24", + "install_size": 404321244, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1492679870, + "total_memory": 128828, +}, +{ + "build_time": 1970.68, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--force', '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python/Python-2.7.12-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 404321549, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1492788660, + "total_memory": 128828, +}, +] -- GitLab From 89f32f26dbe584295199ddd82dcac02a1691aaf6 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:21:09 +0200 Subject: [PATCH 418/566] adding easyconfigs: OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb --- .../OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb new file mode 100644 index 0000000000..773f1229f6 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb @@ -0,0 +1,51 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_19-59-16 +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': '2017a'} + +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' + +# Build statistics +buildstats = [{ + "build_time": 15.4, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1041307, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491328756, + "total_memory": 128828, +}] -- GitLab From cb391d58e57d511606572ea9d503ca1fd6ec9802 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:22:20 +0200 Subject: [PATCH 419/566] adding easyconfigs: LLVM-4.0.0-foss-2017a.eb, LLVM-3.9.1-foss-2017a.eb --- .../l/LLVM/LLVM-3.9.1-foss-2017a.eb | 123 +++++++ .../l/LLVM/LLVM-4.0.0-foss-2017a.eb | 301 ++++++++++++++++++ 2 files changed, 424 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb new file mode 100644 index 0000000000..be174d687f --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb @@ -0,0 +1,123 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-22_13-55-34 +# Built with EasyBuild version 3.1.1 on 2017-04-04_11-30-48 +easyblock = 'CMakeMake' + +name = 'LLVM' +version = "3.9.1" + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' + +# Build statistics +buildstats = [{ + "build_time": 520.33, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 55611227, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491298248, + "total_memory": 128828, +}] + +# Build statistics +buildstats = [ +{ + "build_time": 520.33, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 55611227, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491298248, + "total_memory": 128828, +}, +{ + "build_time": 687.87, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--try-software-version='3.9.1'", "--umask='002'", 'LLVM-3.9.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 55620832, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492862134, + "total_memory": 128828, +}, +] diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb new file mode 100644 index 0000000000..9090d26425 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb @@ -0,0 +1,301 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-22_14-33-26 +# Built with EasyBuild version 3.1.1 on 2017-04-22_13-54-52 +# Built with EasyBuild version 3.1.1 on 2017-04-21_17-49-43 +# Built with EasyBuild version 3.1.1 on 2017-04-04_11-52-35 +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '4.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' + +# Build statistics +buildstats = [{ + "build_time": 751.68, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-4.0.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259484, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491299554, + "total_memory": 128828, +}] + +# Build statistics +buildstats = [ +{ + "build_time": 751.68, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-4.0.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259484, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491299554, + "total_memory": 128828, +}, +{ + "build_time": 392.25, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'LLVM/LLVM-4.0.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259232, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492789782, + "total_memory": 128828, +}, +] + +# Build statistics +buildstats = [ +{ + "build_time": 751.68, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-4.0.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; 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COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259232, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; 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COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259789, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492864405, + "total_memory": 128828, +}, +] -- GitLab From 2c13ce9d66850ecf1c3f0d3eef88fdf57fb26981 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:27:11 +0200 Subject: [PATCH 420/566] adding easyconfigs: Boost-1.63.0-foss-2017a.eb, Boost-1.63.0-foss-2017a-Python-2.7.12.eb --- .../Boost-1.63.0-foss-2017a-Python-2.7.12.eb | 103 ++++++++++++++++++ .../b/Boost/Boost-1.63.0-foss-2017a.eb | 50 +++++++++ 2 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb new file mode 100644 index 0000000000..483520bf60 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb @@ -0,0 +1,103 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-20_15-40-11 +# Built with EasyBuild version 3.1.1 on 2017-04-03_15-24-36 +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "build_time": 1537.69, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 169939518, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491225875, + "total_memory": 128828, +}] + +# Build statistics +buildstats = [ +{ + "build_time": 1537.69, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; 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[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491225875, + "total_memory": 128828, +}, +{ + "build_time": 1585.32, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login24", + "install_size": 169940729, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492695611, + "total_memory": 128828, +}, +] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb new file mode 100644 index 0000000000..daa0767419 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb @@ -0,0 +1,50 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_18-18-26 +name = 'Boost' +version = '1.63.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "build_time": 2759.25, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'GROMACS-5.1.4-foss-2017a-hybrid.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 167262879, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491322705, + "total_memory": 128828, +}] -- GitLab From 0584f74e36a564f4a10893de1e84c542751ebeba Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:27:40 +0200 Subject: [PATCH 421/566] adding easyconfigs: NAMD-2.12-foss-2017a-mpi.eb --- .../n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb new file mode 100644 index 0000000000..13ea1d21a4 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -0,0 +1,50 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_17-10-41 +name = 'NAMD' +version = '2.12' +versionsuffix = '-mpi' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'pic': True} + +sources = ['NAMD_%(version)s_Source.tar.gz'] + +dependencies = [ + ('Tcl', '8.5.12'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +charm_arch = "mpi-linux-x86_64" + +moduleclass = 'chem' + +# Build statistics +buildstats = [{ + "build_time": 269.88, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'NAMD-2.12-foss-2017a-mpi.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 45931470, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491318641, + "total_memory": 128828, +}] -- GitLab From 85190c2bda5be363fb61a927f39ffe2a9911b564 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:28:39 +0200 Subject: [PATCH 422/566] adding easyconfigs: IMB-4.1-foss-2017a.eb --- .../easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb new file mode 100644 index 0000000000..87a1fa9cc3 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -0,0 +1,57 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-21_09-32-59 +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': '2017a'} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' +buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" + +parallel = 1 + +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 = 'perf' + +# Build statistics +buildstats = [{ + "build_time": 17.94, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'IMB-4.1-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1238017, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1492759974, + "total_memory": 128828, +}] -- GitLab From a6aea5c1c8a5f4247519054b20bc9bcbc40399cd Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:29:53 +0200 Subject: [PATCH 423/566] adding easyconfigs: grib_api-1.21.0-foss-2017a.eb --- .../g/grib_api/grib_api-1.21.0-foss-2017a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb new file mode 100644 index 0000000000..c8b9bec5e8 --- /dev/null +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb @@ -0,0 +1,51 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-03_13-34-52 +easyblock = 'ConfigureMake' + +name = 'grib_api' +version = '1.21.0' + +homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home' +description = """The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python + programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of + command line tools is also provided to give quick access to GRIB messages.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] +sources = ['grib_api-%(version)s-Source.tar.gz'] + +dependencies = [ + ('JasPer', '1.900.1'), +] + +configopts = '--with-jasper=$EBROOTJASPER' + +parallel = 1 + +moduleclass = 'data' + +# Build statistics +buildstats = [{ + "build_time": 778.65, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'grib_api-1.16.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 27887407, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491219291, + "total_memory": 128828, +}] -- GitLab From 6c7928b649a58001999f593917825f9e51c5362e Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:31:20 +0200 Subject: [PATCH 424/566] adding easyconfigs: HDF5-1.8.18-foss-2017a.eb --- .../h/HDF5/HDF5-1.8.18-foss-2017a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb new file mode 100644 index 0000000000..10498ad96c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb @@ -0,0 +1,53 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_14-47-11 +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' + +# Build statistics +buildstats = [{ + "build_time": 144.81, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'HDF5-1.8.18-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 25911504, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491310030, + "total_memory": 128828, +}] -- GitLab From b65a2b6bb4c73feb566e0c2ffb9030263b588a14 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 21:49:46 +0200 Subject: [PATCH 425/566] adding easyconfigs: SIONlib-1.7.1-foss-2017a.eb, SIONlib-1.7.1-foss-2017a-tools.eb --- .../SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb | 70 +++++++++++++++++++ .../s/SIONlib/SIONlib-1.7.1-foss-2017a.eb | 64 +++++++++++++++++ 2 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb new file mode 100644 index 0000000000..7d3b72d93e --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -0,0 +1,70 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-35-15 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.1' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. This package provides a stripped-down + installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against a tool requiring + a different SIONlib version.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = ['sionlib-%(version)sl.tar.gz'] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] + +checksums = [ + 'bc2ed625cdf967815007e71e732f38d1', # sionlib-1.7.1l.tar.gz +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 8.34, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a-tools.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1955553, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493148914, + "total_memory": 128828, +}] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb new file mode 100644 index 0000000000..667807f3cc --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -0,0 +1,64 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-34-35 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.1' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. SIONlib provides different interfaces: + parallel access using MPI, OpenMP, or their combination, and sequential access for post-processing + utilities.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)s'] + +checksums = [ + '9d613055896af2792518d6e0cda02588', # sionlib-1.7.1.tar.gz +] + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['sioncom', 'siongen', 'sionser']], + 'dirs': [] +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 14.02, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 4336229, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493148875, + "total_memory": 128828, +}] -- GitLab From 7a5457b4666d8716ecdedc2417d645c451103a60 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 21:50:23 +0200 Subject: [PATCH 426/566] adding easyconfigs: OTF2-2.0-foss-2017a.eb --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb new file mode 100644 index 0000000000..7d56604ccc --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -0,0 +1,67 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-37-09 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 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 = 'OTF2' +version = '2.0' + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +checksums = [ + '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz +] + +builddependencies = [('SIONlib', '1.7.1', '-tools')] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib/libotf2.a", "lib64/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' + +# Build statistics +buildstats = [{ + "build_time": 69.0, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'OTF2-2.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 19885165, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493149028, + "total_memory": 128828, +}] -- GitLab From 979674e2721a618799239d5ea2a795a9481e5aa6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 26 Apr 2017 08:47:16 +0800 Subject: [PATCH 427/566] reorder extensions --- .../custodian-1.1.0-intel-2017a-Python-2.7.13.eb | 6 +++--- .../FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 6 +++--- .../pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 6 +++--- .../pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 9 +++------ 4 files changed, 12 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index e8bf835f61..0c065c7d55 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -18,12 +18,12 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ - ('custodian', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], - }), ('monty', '0.9.6', { 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], }), + ('custodian', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index f776bdcadf..ac5fcef9e1 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -19,9 +19,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ - ('FireWorks', version, { - 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], - }), ('Flask', '0.12', { 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], }), @@ -45,6 +42,9 @@ exts_list = [ ('pymongo', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pymongo/'], }), + ('FireWorks', version, { + 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index 007db0084d..7c6022d3f6 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -19,13 +19,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ + ('smoqe', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], + }), ('pymatgen-db', '0.6.5', { 'modulename': 'matgendb', 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen-db/'], }), - ('smoqe', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], - }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index 718deacce4..86166ed4e4 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -38,15 +38,12 @@ exts_list = [ ('mpmath', '0.19', { 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], }), - ('pymatgen', version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], - }), - ('requests', '2.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), ('sympy', '1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], }), + ('pymatgen', version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -- GitLab From 49691e295bac00c8d5dcfa04e643f66f99257cc4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 26 Apr 2017 13:09:36 +0200 Subject: [PATCH 428/566] {lang} [intel/2017a] PyCUDA/2016.1.2 --- ...CUDA-2016.1.2-intel-2017a-Python-2.7.13.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..102a71dd89 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyCUDA' +version = '2016.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mathema.tician.de/software/pycuda' +description = """PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('CUDA', '8.0.61', '', True), + ('Boost', '1.63.0', versionsuffix), +] + +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ --boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " + +options = {'modulename': '%(namelower)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' -- GitLab From ecf4252a307ec2a48fd8b7a0d54a6f2fdfb77605 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 26 Apr 2017 18:29:34 +0200 Subject: [PATCH 429/566] Wrap line --- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb index 102a71dd89..fd93f89fda 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb @@ -18,7 +18,8 @@ dependencies = [ ('Boost', '1.63.0', versionsuffix), ] -prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ --boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " +prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " options = {'modulename': '%(namelower)s'} -- GitLab From 0a7cde9d50f531ed67fc85d4cfb143fe560f1ee8 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 08:05:52 +0200 Subject: [PATCH 430/566] upgraded 2.7.13 instead --- .../p/Python/Python-2.7.13-foss-2017a.eb | 162 ++++++++++++++++++ 1 file changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb new file mode 100644 index 0000000000..3625e3bbd6 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -0,0 +1,162 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-27_06-34-41 +name = 'Python' +version = '2.7.13' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated March 30th 2017 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('Cython', '0.25.2', { + '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', '2.6.0', { + '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', '4.0.11', { + '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': ['https://pypi.python.org/packages/source/p/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2017.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "build_time": 2019.51, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", "--robot-paths=':/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python-2.7.13-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 409464422, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493267680, + "total_memory": 128828, +}] -- GitLab From 5fc0d21237b193085a426540bd13d4fdd264287c Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 17:00:41 +0200 Subject: [PATCH 431/566] removed built comments --- .../SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb | 27 +------------------ .../s/SIONlib/SIONlib-1.7.1-foss-2017a.eb | 27 +------------------ 2 files changed, 2 insertions(+), 52 deletions(-) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb index 7d3b72d93e..7e537ec0fb 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -1,9 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-35-15 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel # License:: 3-clause BSD ## @@ -43,28 +43,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "build_time": 8.34, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a-tools.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1955553, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493148914, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb index 667807f3cc..46e980be5f 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -1,9 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-34-35 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel # License:: 3-clause BSD ## @@ -37,28 +37,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "build_time": 14.02, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 4336229, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493148875, - "total_memory": 128828, -}] -- GitLab From 898b454611d529f69430652bb58b19dae94a9096 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 17:03:16 +0200 Subject: [PATCH 432/566] removed built comments --- .../easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 27 +---------------- .../i/IMB/IMB-4.1-intel-2017.02.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb index 87a1fa9cc3..0a33899fe9 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-21_09-32-59 easyblock = 'MakeCp' name = 'IMB' @@ -30,28 +29,4 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 17.94, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'IMB-4.1-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1238017, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492759974, - "total_memory": 128828, -}] + diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb new file mode 100644 index 0000000000..65d5fc7e4a --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb @@ -0,0 +1,29 @@ +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': 'intel', 'version': '2017.02'} +toolchainopts = {'usempi': True} + +source_urls = ['https://software.intel.com/sites/default/files/managed/34/aa/'] +sources = ['%(name)s_%(version)s.tgz'] + +prebuildopts = "cd src && " +buildopts = "all" + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' + -- GitLab From 622f881da74b15c05d51e9e56979b3dd518756d8 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 19:49:42 +0200 Subject: [PATCH 433/566] removed built comments from Python-2.7.13-foss-2017a.eb easyconfig --- .../p/Python/Python-2.7.13-foss-2017a.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 3625e3bbd6..166b747669 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-27_06-34-41 name = 'Python' version = '2.7.13' @@ -135,28 +134,3 @@ exts_list = [ moduleclass = 'lang' -# Build statistics -buildstats = [{ - "build_time": 2019.51, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", "--robot-paths=':/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python-2.7.13-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 409464422, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493267680, - "total_memory": 128828, -}] -- GitLab From 4c5f699986938c5a6d6770067bb8a74afb8c904d Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 19:53:37 +0200 Subject: [PATCH 434/566] delete Python-2.7.12-foss-2017a.eb easyconfig file --- .../p/Python/Python-2.7.12-foss-2017a.eb | 293 ------------------ 1 file changed, 293 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb deleted file mode 100644 index b8e862c97f..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb +++ /dev/null @@ -1,293 +0,0 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-21_17-31-01 -# Built with EasyBuild version 3.1.1 on 2017-04-20_11-17-51 -# Built with EasyBuild version 3.1.1 on 2017-04-03_09-46-50 -name = 'Python' -version = '2.7.12' - -homepage = 'http://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively.""" - -toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.11'), - ('libreadline', '6.3'), - ('ncurses', '6.0'), - ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), # this requires a full X11 stack - ('GMP', '6.1.1'), - ('libffi', '3.2.1'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2h'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# order is important! -# package versions updated March 30th 2017 -# setuptools 34.3.3 zip -exts_list = [ - ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], - 'patches': ['numpy-1.8.0-mkl.patch'], - }), - ('scipy', '0.19.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('pbr', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.25.2', { - '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', '2.6.0', { - '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', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.1.0', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('paramiko', '2.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2017.2', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), - ('enum34', '1.1.6', { - 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], - }), - ('bitstring', '3.1.5', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], - }), - ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), -] - -moduleclass = 'lang' - -# Build statistics -buildstats = [{ - "build_time": 2237.89, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--sourcepath='/cluster/easybuild/sources'", 'Python-2.7.12-foss-2017a-updated.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 404321068, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491205609, - "total_memory": 128828, -}] - -# Build statistics -buildstats = [ -{ - "build_time": 2237.89, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--sourcepath='/cluster/easybuild/sources'", 'Python-2.7.12-foss-2017a-updated.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 404321068, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491205609, - "total_memory": 128828, -}, -{ - "build_time": 1966.64, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python/Python-2.7.12-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login24", - "install_size": 404321244, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492679870, - "total_memory": 128828, -}, -] - -# Build statistics -buildstats = [ -{ - "build_time": 2237.89, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--sourcepath='/cluster/easybuild/sources'", 'Python-2.7.12-foss-2017a-updated.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 404321068, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491205609, - "total_memory": 128828, -}, -{ - "build_time": 1966.64, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python/Python-2.7.12-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login24", - "install_size": 404321244, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492679870, - "total_memory": 128828, -}, -{ - "build_time": 1970.68, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--force', '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python/Python-2.7.12-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 404321549, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492788660, - "total_memory": 128828, -}, -] -- GitLab From 5446fcacc7f537b151b6c2e9abf42fa9b9bec5de Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 19:57:59 +0200 Subject: [PATCH 435/566] removed built comments --- .../OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb index 773f1229f6..3f1b8657b8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_19-59-16 easyblock = 'ConfigureMake' name = 'OSU-Micro-Benchmarks' @@ -24,28 +23,3 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 15.4, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1041307, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491328756, - "total_memory": 128828, -}] -- GitLab From 5516323ae59d996cf2489f0c372952e2b4c510d3 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:00:49 +0200 Subject: [PATCH 436/566] correcting title --- easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 166b747669..5abe3e3e7d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -133,4 +133,3 @@ exts_list = [ ] moduleclass = 'lang' - -- GitLab From f1171afab1d0bf1a0ef79b28c4b1ce10e9cbd490 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:27:16 +0200 Subject: [PATCH 437/566] removed built comments, and changed to python-2.7.13 --- .../l/LLVM/LLVM-3.9.1-foss-2017a.eb | 81 +----- .../l/LLVM/LLVM-4.0.0-foss-2017a.eb | 259 +----------------- 2 files changed, 2 insertions(+), 338 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb index be174d687f..6bffed0098 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb @@ -1,5 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-22_13-55-34 -# Built with EasyBuild version 3.1.1 on 2017-04-04_11-30-48 easyblock = 'CMakeMake' name = 'LLVM' @@ -22,7 +20,7 @@ sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ ('CMake', '3.7.2'), - ('Python', '2.7.12'), + ('Python', '2.7.13'), ] dependencies = [ @@ -44,80 +42,3 @@ separate_build_dir = True moduleclass = 'compiler' -# Build statistics -buildstats = [{ - "build_time": 520.33, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 55611227, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491298248, - "total_memory": 128828, -}] - -# Build statistics -buildstats = [ -{ - "build_time": 520.33, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": 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--disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 55620832, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492862134, - "total_memory": 128828, -}, -] diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb index 9090d26425..5a2a5553d5 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb @@ -1,7 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-22_14-33-26 -# Built with EasyBuild version 3.1.1 on 2017-04-22_13-54-52 -# Built with EasyBuild version 3.1.1 on 2017-04-21_17-49-43 -# Built with EasyBuild version 3.1.1 on 2017-04-04_11-52-35 easyblock = 'CMakeMake' name = 'LLVM' @@ -24,7 +20,7 @@ sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ ('CMake', '3.7.2'), - ('Python', '2.7.12'), + ('Python', '2.7.13'), ] dependencies = [ @@ -46,256 +42,3 @@ separate_build_dir = True moduleclass = 'compiler' -# Build statistics -buildstats = [{ - "build_time": 751.68, - "command_line": ["--buildpath='/dev/shm'", 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--with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 141259232, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492862091, - "total_memory": 128828, -}, -] - -# Build statistics -buildstats = [ -{ - "build_time": 751.68, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-4.0.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 141259484, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491299554, - "total_memory": 128828, -}, -{ - "build_time": 392.25, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'LLVM/LLVM-4.0.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 141259232, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492789782, - "total_memory": 128828, -}, -{ - "build_time": 739.5, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'LLVM-4.0.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 141259232, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492862091, - "total_memory": 128828, -}, -{ - "build_time": 395.04, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'LLVM-4.0.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 141259789, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492864405, - "total_memory": 128828, -}, -] -- GitLab From 485b0eb98fcde2bb53fa971f1530deed67ace3a7 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:51:09 +0200 Subject: [PATCH 438/566] removed comments, add jasper 1.900.1-foss-2017a dependency --- .../g/grib_api/grib_api-1.21.0-foss-2017a.eb | 26 ------------------- .../j/JasPer/JasPer-1.900.1-foss-2017a.eb | 22 ++++++++++++++++ 2 files changed, 22 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb index c8b9bec5e8..fa7f84d3e3 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-03_13-34-52 easyblock = 'ConfigureMake' name = 'grib_api' @@ -24,28 +23,3 @@ parallel = 1 moduleclass = 'data' -# Build statistics -buildstats = [{ - "build_time": 778.65, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'grib_api-1.16.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 27887407, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491219291, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb new file mode 100644 index 0000000000..73e404db1c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' + -- GitLab From 0378f98cce404a3d418b2ff997068c303ba29f9d Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:55:18 +0200 Subject: [PATCH 439/566] removed built comments --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 28 +------------------ 1 file changed, 1 insertion(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index 7d56604ccc..c2ecdc414e 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -1,10 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-37-09 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer -# License:: 3-clause BSD +## License:: 3-clause BSD # # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ @@ -40,28 +39,3 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 69.0, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'OTF2-2.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 19885165, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493149028, - "total_memory": 128828, -}] -- GitLab From df93abf1c89c8562763fa53595193975553e6234 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:59:28 +0200 Subject: [PATCH 440/566] removed built comments and added Szip-2.1-foss-2017a.eb dependency --- .../h/HDF5/HDF5-1.8.18-foss-2017a.eb | 27 ------------------- .../easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb | 24 +++++++++++++++++ 2 files changed, 24 insertions(+), 27 deletions(-) create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb index 10498ad96c..1febe1c832 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_14-47-11 name = 'HDF5' version = '1.8.18' @@ -25,29 +24,3 @@ dependencies = [ ] moduleclass = 'data' - -# Build statistics -buildstats = [{ - "build_time": 144.81, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'HDF5-1.8.18-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 25911504, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491310030, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb new file mode 100644 index 0000000000..9365662b36 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' + -- GitLab From 00949b56eb8ba377a3f9adbbc96729483f1d7a0a Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 21:36:16 +0200 Subject: [PATCH 441/566] updated Boost-1.63.0-foss-2017a-Python-2.7.12 to 2.7.13 and removed built comments --- .../Boost-1.63.0-foss-2017a-Python-2.7.13.eb | 24 +++++++++++++++++ .../b/Boost/Boost-1.63.0-foss-2017a.eb | 26 ------------------- 2 files changed, 24 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..49051608e1 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb index daa0767419..ea4624e01d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_18-18-26 name = 'Boost' version = '1.63.0' @@ -23,28 +22,3 @@ boost_mpi = True moduleclass = 'devel' -# Build statistics -buildstats = [{ - "build_time": 2759.25, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'GROMACS-5.1.4-foss-2017a-hybrid.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 167262879, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491322705, - "total_memory": 128828, -}] -- GitLab From 101e7c5c515b350678f51ac93715b0e537db32d2 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 21:38:09 +0200 Subject: [PATCH 442/566] deleted Boost-1.63.0-foss-2017a-Python-2.7.12.eb --- .../Boost-1.63.0-foss-2017a-Python-2.7.12.eb | 103 ------------------ 1 file changed, 103 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb deleted file mode 100644 index 483520bf60..0000000000 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb +++ /dev/null @@ -1,103 +0,0 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-20_15-40-11 -# Built with EasyBuild version 3.1.1 on 2017-04-03_15-24-36 -name = 'Boost' -version = '1.63.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.boost.org/' -description = "Boost provides free peer-reviewed portable C++ source libraries." - -toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'usempi': True, 'pic': True} - -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.11'), - ('Python', '2.7.12'), -] - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' - -# Build statistics -buildstats = [{ - "build_time": 1537.69, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 169939518, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491225875, - "total_memory": 128828, -}] - -# Build statistics -buildstats = [ -{ - "build_time": 1537.69, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 169939518, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491225875, - "total_memory": 128828, -}, -{ - "build_time": 1585.32, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login24", - "install_size": 169940729, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492695611, - "total_memory": 128828, -}, -] -- GitLab From 4eaa887d711737ff20a23ad31aa3dc194c816c33 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Fri, 28 Apr 2017 06:06:57 +0200 Subject: [PATCH 443/566] removed built comments and updated tcl --- .../n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 28 +------------------ .../t/Tcl/Tcl-8.5.19-foss-2017a.eb | 27 ++++++++++++++++++ 2 files changed, 28 insertions(+), 27 deletions(-) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index 13ea1d21a4..6dd67416d3 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_17-10-41 name = 'NAMD' version = '2.12' versionsuffix = '-mpi' @@ -13,7 +12,7 @@ toolchainopts = {'opt': True, 'pic': True} sources = ['NAMD_%(version)s_Source.tar.gz'] dependencies = [ - ('Tcl', '8.5.12'), + ('Tcl', '8.5.19'), ] # /bin/csh is required by 'config' script @@ -23,28 +22,3 @@ charm_arch = "mpi-linux-x86_64" moduleclass = 'chem' -# Build statistics -buildstats = [{ - "build_time": 269.88, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'NAMD-2.12-foss-2017a-mpi.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 45931470, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491318641, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb new file mode 100644 index 0000000000..0514b4e682 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = "8.5.19" + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' + -- GitLab From 1763251c00437c70b3aeff0287d6406648f30897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 10:57:26 +0200 Subject: [PATCH 444/566] align IMB 4.1 easyconfigs for foss/2017a and intel/2017.02 --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 14 +++++--------- .../easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb | 11 +++++------ 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb index 0a33899fe9..bcbb961f34 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -4,29 +4,25 @@ 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. -""" +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': '2017a'} +toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' -prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' -buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" +buildopts = 'all CC="$MPICC"' parallel = 1 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']], + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], 'dirs': ['bin', 'doc'] } moduleclass = 'perf' - - diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb index 65d5fc7e4a..d22113b5a9 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb @@ -10,20 +10,19 @@ description = """The Intel MPI Benchmarks perform a set of MPI performance measu toolchain = {'name': 'intel', 'version': '2017.02'} toolchainopts = {'usempi': True} -source_urls = ['https://software.intel.com/sites/default/files/managed/34/aa/'] sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] -prebuildopts = "cd src && " -buildopts = "all" +start_dir = 'src' +buildopts = 'all CC="$MPICC"' parallel = 1 -files_to_copy = [(['src/IMB-*'], 'bin')] +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], - 'dirs': [], + 'dirs': ['bin', 'doc'] } moduleclass = 'perf' - -- GitLab From 828a4b4be010f44678b5cc7c401ecd2b84ea51d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 11:23:30 +0200 Subject: [PATCH 445/566] adding easyconfigs: Boost-1.64.0-intel-2017a.eb --- .../b/Boost/Boost-1.64.0-intel-2017a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb new file mode 100644 index 0000000000..981136de99 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.64.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From d211df671be83d9fbb2740449366a1874cf44490 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 12:44:47 +0200 Subject: [PATCH 446/566] adding easyconfigs: Python-3.6.1-intel-2017a.eb --- .../p/Python/Python-3.6.1-intel-2017a.eb | 127 ++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb new file mode 100644 index 0000000000..b226f52d51 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb @@ -0,0 +1,127 @@ +name = 'Python' +version = '3.6.1' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('XZ', '5.2.3'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.25.2', { + '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', '2.6.0', { + '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/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.11', { + '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': ['https://pypi.python.org/packages/source/p/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' -- GitLab From 6d38e047d7867b3529d97081d4ff1c69857e504c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 14:50:50 +0200 Subject: [PATCH 447/566] adding easyconfigs: BamTools-2.4.1-intel-2017a.eb, CMake-3.8.0-GCCcore-6.3.0.eb --- .../b/BamTools/BamTools-2.4.1-intel-2017a.eb | 16 +++++++++ .../c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb new file mode 100644 index 0000000000..fd92ae4c8f --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'BamTools' +version = '2.4.1' + +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': 'intel', 'version': '2017a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '3.8.0')] + +files_to_copy = ['bin', 'lib', 'include', 'docs', 'LICENSE', 'README'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..522448447c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.8.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +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', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9d66b3cd3f23021c0083ce763ee46a4b14b0dbb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:01:10 +0200 Subject: [PATCH 448/566] use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb | 8 ++------ easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb | 8 ++------ easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb | 8 ++------ 3 files changed, 6 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb index 4325e0c729..ad3e944f8a 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'gompi', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] runtest = 'check' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb index 14ebd120a4..2c0fe9cb97 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] # no quad precision, requires GCC v4.6 or higher # see also diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb index da857e5ca5..7d5646bd9c 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] # no quad precision, requires GCC v4.6 or higher # see also -- GitLab From 8a0042c90ca5002241acabd21eae93ec86b751a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:24:03 +0200 Subject: [PATCH 449/566] adding easyconfigs: SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb, SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb, METIS-5.1.0-intel-2017a.eb, ParMETIS-4.0.3-intel-2017a.eb --- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 25 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb | 22 ++++++++++++++++ ...iteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb | 19 ++++++++++++++ ...Sparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb | 19 ++++++++++++++ 4 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb new file mode 100644 index 0000000000..91d00f1139 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -0,0 +1,25 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [('CMake', '3.8.0')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb new file mode 100644 index 0000000000..239bd0fcd4 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.8.0')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb new file mode 100644 index 0000000000..3f7ce4f28f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..28aa92c03a --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('ParMETIS', metis_ver)] + +parallel = 1 + +moduleclass = 'numlib' -- GitLab From ab62066363ea6186a345ad2c4c489dc45f355fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:39:36 +0200 Subject: [PATCH 450/566] fix sources spec for HMMER 3.1b2 + minor style fixes --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb | 9 ++++----- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 9 ++++----- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index 0456b6d6ce..c756d8464e 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -28,16 +28,15 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] -sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], 'dirs': [] } -runtest = 'check' - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index da1af277a5..4211dd88a0 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -28,16 +28,15 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] -sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], 'dirs': [] } -runtest = 'check' - moduleclass = 'bio' -- GitLab From 83ab75f708cba109de54b5c963959c07e8f9b33f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:44:19 +0200 Subject: [PATCH 451/566] extend sanity check for HMMER 3.1b2 --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb | 5 +++-- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index c756d8464e..aed3e32ba8 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -35,8 +35,9 @@ runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], - 'dirs': [] + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index 4211dd88a0..66c915507d 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -35,8 +35,9 @@ runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], - 'dirs': [] + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], } moduleclass = 'bio' -- GitLab From 0944579f6e494a7a2e3e626638aa50ea16c951e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:58:00 +0200 Subject: [PATCH 452/566] adding easyconfigs: HMMER-3.1b2-intel-2017a.eb --- .../h/HMMER/HMMER-3.1b2-intel-2017a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb new file mode 100644 index 0000000000..3ca7456fc5 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' -- GitLab From 6c5e0ab7620bddaf2d500c27241863c56198f9a8 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 2 May 2017 20:21:29 +0200 Subject: [PATCH 453/566] adding easyconfigs: OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb --- .../OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100755 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb new file mode 100755 index 0000000000..1e3286223d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' +versionsuffix= '-opa' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['886698becc5bea8c151c0af2074b8392'] + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-psm2 ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libpsm2', 'libpsm2-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' -- GitLab From d8b7170e5bdc9bf19490d270f9877692a2e5d9b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:01:29 +0200 Subject: [PATCH 454/566] {compiler}[dummy] GCCcore 7.1.0 --- .../easyconfigs/g/GCCcore/GCCcore-7.1.0.eb | 54 ++++++ .../mpfr-3.1.5-allpatches-20161219.patch | 176 ++++++++++++++++++ 2 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb new file mode 100644 index 0000000000..6f69a58a66 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '7.1.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.5' + +source_urls = [ + '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 + '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 = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.28'), +] + +patches = [ + ('mpfr-%s-allpatches-20161219.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + 'GCCcore-6.2.0-fix-find-isl.patch', +] + +checksums = [ + '6bf56a2bca9dac9dbbf8e8d1036964a8', # gcc-7.1.0.tar.bz2 + '8ddbb26dc3bd4e2302984debba1406a5', # gmp-6.1.2.tar.bz2 + 'b1d23a55588e3b2a13e3be66bc69fd8d', # mpfr-3.1.5.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch new file mode 100644 index 0000000000..4e70357e4a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch @@ -0,0 +1,176 @@ +# MPFR v3.1.5 patch dated 2017-12-19 +# downloaded via https://gforge.inria.fr/frs/?group_id=136 +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; -- GitLab From 4e6ea8705ba5ea327960feb905feefd9cbdfa3c0 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 2 May 2017 21:11:14 +0200 Subject: [PATCH 455/566] adding easyconfigs: METIS-5.1.0-foss-2017a.eb, ParMETIS-4.0.3-foss-2017a.eb, SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb, SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb --- .../m/METIS/METIS-5.1.0-foss-2017a.eb | 22 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb | 22 +++++++++++++++++++ ...uiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb | 19 ++++++++++++++++ ...eSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb | 19 ++++++++++++++++ 4 files changed, 82 insertions(+) create mode 100755 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb create mode 100755 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb create mode 100755 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb create mode 100755 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb new file mode 100755 index 0000000000..03a730e5cc --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.8.0')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb new file mode 100755 index 0000000000..875f07389d --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.8.0')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb new file mode 100755 index 0000000000..a66251bb0f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('METIS', metis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb new file mode 100755 index 0000000000..7c7dff3356 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +parmetis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % parmetis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('ParMETIS', parmetis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From cf7d72d4c302a22a5ee6946ec7a95f47f1cb9779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:32:15 +0200 Subject: [PATCH 456/566] fix time travelling in MPFR patch, thanks @wpoely86 --- .../easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch index 4e70357e4a..67ff28d57a 100644 --- a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch @@ -1,4 +1,4 @@ -# MPFR v3.1.5 patch dated 2017-12-19 +# MPFR v3.1.5 patch dated 2016-12-19 # downloaded via https://gforge.inria.fr/frs/?group_id=136 diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES --- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 -- GitLab From 42e15f650164f4faee57db07337d9dfeabf46332 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:36:24 +0200 Subject: [PATCH 457/566] {compiler}[dummy] GCC 7.1.0 w/ binutils 2.28 + deps --- .../b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb | 27 ++++++++++++++++++ .../b/binutils/binutils-2.28-GCCcore-7.1.0.eb | 21 ++++++++++++++ .../f/flex/flex-2.6.3-GCCcore-7.1.0.eb | 24 ++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb | 25 +++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-7.1.0.eb | 24 ++++++++++++++++ .../m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 28 +++++++++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb | 25 +++++++++++++++++ 7 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..33d3ae47a6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..10ecc14d7a --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..28c855c205 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb @@ -0,0 +1,24 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..870e7eab31 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '7.1.0' + +binutilsver = '2.28' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..f487ba5530 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb @@ -0,0 +1,24 @@ +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': 'GCCcore', 'version': '7.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..18394615f9 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', 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 = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..bec9454ed8 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 29988a028e00ce8b88a74b367cd1cfcbd1b4db80 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 3 May 2017 11:22:05 +0200 Subject: [PATCH 458/566] PoC for TBB open source --- .../t/tbb/tbb-2017_U5-goolf-1.7.20.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb new file mode 100644 index 0000000000..94782c17c8 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb @@ -0,0 +1,28 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +unpack_options = '--strip-components=1' + +skipsteps = ['configure', 'install'] + +buildininstalldir = True + +buildopts = "compiler=$CC" + +#runtest = 'compiler=$CC test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['.'], +} + +moduleclass = 'lib' -- GitLab From 60038da4530e4cde6809d03d02b289e8ca841a83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:30:23 +0200 Subject: [PATCH 459/566] also build IMB-IO in IMB 4.1 easyconfig using foss/2016b --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index f6d0b1f028..449a0d2750 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -4,26 +4,24 @@ name = 'IMB' version = '4.1' homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' -description = """ -The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point -and global communication operations for a range of message sizes. -""" +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' -prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' -buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" +buildopts = 'all CC="$MPICC"' parallel = 1 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']], + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], 'dirs': ['bin', 'doc'] } -- GitLab From 9d83a3a823af6048779169f9eb4272b540b03097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:33:59 +0200 Subject: [PATCH 460/566] adding easyconfigs: IMB-4.1-intel-2017a.eb --- .../easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb new file mode 100644 index 0000000000..6636a983cd --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb @@ -0,0 +1,28 @@ +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': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': ['bin', 'doc'] +} + +moduleclass = 'perf' -- GitLab From 1521762763e6b6414ffd0859c553dc3337f5a038 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:59:21 +0200 Subject: [PATCH 461/566] fix toolchain version --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 449a0d2750..2b74ec6d38 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -7,7 +7,7 @@ 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': '2016b'} +toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] -- GitLab From a8d022261518aa55ac0044ad7e0b852f1fc55509 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 14:10:11 +0200 Subject: [PATCH 462/566] clean up tbb easyconfig to use enhanced easyblock --- .../easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb index 94782c17c8..f90202e1b4 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb @@ -10,19 +10,4 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/01org/tbb/archive/'] sources = ['%(version)s.tar.gz'] -unpack_options = '--strip-components=1' - -skipsteps = ['configure', 'install'] - -buildininstalldir = True - -buildopts = "compiler=$CC" - -#runtest = 'compiler=$CC test' - -sanity_check_paths = { - 'files': [], - 'dirs': ['.'], -} - moduleclass = 'lib' -- GitLab From b2623eb814ff0c54f95850202907564ac4768734 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 14:20:28 +0200 Subject: [PATCH 463/566] adding easyconfigs: tbb-2017_U5-intel-2017a.eb --- .../easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb new file mode 100644 index 0000000000..fc7398b13b --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb @@ -0,0 +1,13 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +moduleclass = 'lib' -- GitLab From 775f59f8c5345bb4ddb974790de0275d68e88e29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 16:47:33 +0200 Subject: [PATCH 464/566] adding easyconfigs: Node-RED-0.16.2-foss-2017a.eb, nodejs-6.10.3-foss-2017a.eb --- .../n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 28 +++++++++++++++++++ .../n/nodejs/nodejs-6.10.3-foss-2017a.eb | 26 +++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb new file mode 100644 index 0000000000..828c4e612b --- /dev/null +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'Node-RED' +version = '0.16.2' + +homepage = 'http://nodered.org' +description = """Node-RED is a programming tool for wiring together hardware devices, APIs and online services + in new and interesting ways.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/node-red/node-red/releases/download/%(version)s/'] +sources = ['node-red-%(version)s.zip'] + +dependencies = [ + ('nodejs', '6.10.3'), +] + +preinstallopts = 'cd %(namelower)s-%(version)s && ' +install_cmd = 'npm install --prefix %(installdir)s -g' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/node_modules/%(namelower)s'], +} +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb new file mode 100644 index 0000000000..65377857a3 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '6.10.3' + +homepage = 'http://nodejs.org' + +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'lowopt': True} + +source_urls = ['http://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' -- GitLab From 012625a422c61cf81f51b20892b4413d2891039f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 17:20:32 +0200 Subject: [PATCH 465/566] more %(namelower)s --- easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb index 828c4e612b..7531db7616 100644 --- a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -10,7 +10,7 @@ description = """Node-RED is a programming tool for wiring together hardware dev toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['https://github.com/node-red/node-red/releases/download/%(version)s/'] -sources = ['node-red-%(version)s.zip'] +sources = ['%(namelower)s-%(version)s.zip'] dependencies = [ ('nodejs', '6.10.3'), -- GitLab From f9589ba77bc83a6b6e568a99c9de6b0958733f10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 17:27:30 +0200 Subject: [PATCH 466/566] use --help as sanity check command, since --version starts a Node-RED server... --- easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb index 7531db7616..f11db814aa 100644 --- a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -23,6 +23,6 @@ sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['lib/node_modules/%(namelower)s'], } -sanity_check_commands = ['%(namelower)s --version'] +sanity_check_commands = ['%(namelower)s --help'] moduleclass = 'tools' -- GitLab From a3a0e6c3c840bbd9e2ac747879d5fb04bceb7223 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 May 2017 12:21:44 +0800 Subject: [PATCH 467/566] prepare release notes for eb320 --- RELEASE_NOTES | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a56c5c3afe..b25f9e1c1c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,32 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.2.0 (May 5th 2017) +--------------------- + +feature release +- added example easyconfig files for 33 new software packages: + - ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484), + DFTB+ (#4398), Doris (#4404), ED2 (#4402), FireWorks (#4484), GETORB (#4414), GapFiller (#4462), IPy (#4450), + imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), PyCUDA (#4523), + pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), + SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), + VMD (#4391), WRF-Fire (#4403) +- added additional easyconfigs for various supported software packages, including ... +- various enhancements, including: + - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) + - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) +- various bug fixes, including: + - add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs (#4369) + - use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain (#4384) + - fix pkgconfig patch for Qhull to only let CMake substitute (#4451) + - also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for foss/2016b (#4467) + - add dependency NLopt for R extension nloptr (#4481) + - fix issue with configparser and backports namespace blocking inclusion of nbconvert with IPython (#4504) + - change source_urls of pycrypto to encrypted https://pypi.python.org/... (#4505) + - fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (#4531) + + v3.1.2 (March 20th 2017) ------------------------ -- GitLab From 23d840436deca449424710bd1abe199149a27d7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 May 2017 13:50:49 +0800 Subject: [PATCH 468/566] prepare release notes for eb320 --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b25f9e1c1c..f2fbd7d51c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -17,7 +17,8 @@ feature release pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), VMD (#4391), WRF-Fire (#4403) -- added additional easyconfigs for various supported software packages, including ... +- added additional easyconfigs for various supported software packages, including: + - 3to2 1.1.1, ACTC 1.1, ALLPATHS-LG 52488, Autoconf 2.69, Autoconf 2.69, Automake 1.15, Automake 1.15, Autotools 20150215, Autotools 20150215, arpack-ng 3.4.0, atomate 0.4.4, BLAT 3.5, BamTools 2.4.1, BioKanga 4.3.4, BioKanga 4.3.5, BioPerl 1.7.1, Bison 3.0.4, Boost 1.63.0, Boost 1.64.0, Bowtie2 2.2.9, BreakDancer 1.4.5, binutils 2.28, bx-python , bzip2 1.0.6, CMake 3.8.0, CUDA 8.0.61.eb, Cantera 2.3.0, ClusterShell 1.7.3.eb, cURL 7.53.1, cURL 7.54.0, cairo 1.14.8, configparser 3.5.0, cuDNN 6.0, custodian 1.1.0, DBG2OLC 20170208, DFTB+ 1.3.1, Doris 4.02, Doxygen 1.8.13, deap 0.9.2, ED2 20170201, ED2 20170201, ESMF 6.3.0rp1, EasyBuild 3.1.2.eb, Eigen 3.3.2, entrypoints 0.2.2, FFTW 3.3.6, FireWorks 1.4.2, file 5.30, flex 2.6.3, fmt 3.0.1, fontconfig 2.12.1, fqtrim 0.9.5, freetype 2.5.5, freetype 2.6.2, freetype 2.7.1, freetype 2.7.1, GCC 6.3.0, GCC 7.1.0, GCCcore 7.1.0.eb, GDAL 2.1.3, GEOS 3.6.1, GETORB 2.3.2, GLib 2.52.0, GMP 6.1.2, GSL 2.3, GapFiller 2.1.1, Ghostscript 9.21, Go 1.8.1.eb, g2clib 1.6.0, g2lib 1.4.0, gnuplot 5.0.5, googletest 1.8.0, HDF 4.2.12, HDF5 1.10.0, HISAT2 2.0.5, HMMER 3.1b2, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, hwloc 1.11.6, IMB 4.1, IMB 4.1, IMB 4.1, IPy 0.83.eb, IPython 5.3.0, ImageMagick 7.0.5, Inspector 2017_update2.eb, imbalanced-learn 0.2.1, ipyrad 0.6.15, JasPer 1.900.1, JasPer 2.0.12, jemalloc 4.5.0, LIBSVM 3.22, LLVM 4.0.0, LZO 2.10, LibTIFF 4.0.7, LittleCMS 2.8, libGLU 9.0.0, libdrm 2.4.76, libiconv 1.15, libjpeg-turbo 1.5.1, libpng 1.6.18, libpng 1.6.21, libpng 1.6.28, libpng 1.6.29, libreadline 7.0, libsodium 1.0.12, libtool 2.4.6, libtool 2.4.6, libxml2 2.9.4, libyaml 0.1.7.eb, M4 1.4.18, METIS 5.1.0, MRtrix 0.3.15, Mako 1.0.6, Mesa 17.0.2, MultiQC 0.7, MultiQC 0.9, makedepend 1.0.5, matplotlib 1.5.1, matplotlib 2.0.0, matplotlib 2.0.0, NASM 2.12.02, NGS 1.3.0, NLopt 2.4.2, NLopt 2.4.2, ncbi-vdb 2.8.2, ncurses 6.0, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, netCDF 4.4.1.1, nettle 3.3, numba 0.32.0, numpy 1.10.1, numpy 1.12.1, ORCA 4.0.0.2, Octave 4.2.1, OpenMPI 2.1.0, OpenPGM 5.2.122, PCRE 8.40, PETSc 3.7.5, PGI 17.3, PLINK 1.9b_4.1, PROJ 4.9.3, ParMETIS 4.0.3, Perl 5.24.1, Pillow 4.1.0, PyCUDA 2016.1.2, PyYAML 3.12, PyYAML 3.12.eb, PyZMQ 16.0.2, Python 2.7.13, Python 3.6.1, pixman 0.34.0, pkg-config 0.29.2, pkgconfig 1.2.2, pymatgen-db 0.6.5, pymatgen 4.7.3, QuTiP 4.1.0, QuantumESPRESSO 6.1, R 3.3.3, R 3.3.3, ROI_PAC 3.0.1, Rascaf 1.0.2, RepastHPC 2.2.0, rootpy 0.8.0, SAMtools 0.1.20, SAMtools 1.4, SAMtools 1.4, SCons 2.5.1, SIONlib 1.7.1, SIONlib 1.7.1, SQLite 3.17.0, SSPACE_Basic 2.1.1, SUNDIALS 2.7.0, SWASH 3.14, SWASH 3.14, SWIG 3.0.12, Sambamba 0.6.6.eb, Seaborn 0.7.1, Spack 0.10.0.eb, SpiceyPy 1.1.0, StaMPS 3.3b1, Stacks 1.45, Stacks 1.46, Stampy 1.0.31, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, samblaster 0.1.24, scipy 0.19.0, scp 0.10.2, snaphu 1.4.2, sparsehash 2.0.3, spglib-python 1.9.9.38, Tcl 8.6.6, Tk 8.6.6, Triangle 1.6, tbb 2017_U5, tbb 2017_U5, tcsh 6.20.00, UDUNITS 2.2.24, util linux, VMD 1.9.3, VTune 2017_update2.eb, ViennaRNA 2.3.5, vsc-base 2.5.8, vsc-install 0.10.25, vsc-mympirun 4.0.0b0, WRF-Fire 20170221, WRF 3.8.0, Wannier90 2.1.0, X11 20170314, XZ 5.2.2, xorg-macros 1.19.1, xproto 7.0.31, ZeroMQ 4.2.2, zlib 1.2.11, zlib 1.2.11 - various enhancements, including: - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) -- GitLab From 64164034dc03ed67cc9cf24fef855d8a71878eb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 May 2017 09:35:28 +0200 Subject: [PATCH 469/566] add comment on Python as build dep for nodejs --- easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb index 65377857a3..b02123940f 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb @@ -16,6 +16,7 @@ toolchainopts = {'lowopt': True} source_urls = ['http://nodejs.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] +# Python is required (only) as build dependency allow_system_deps = [('Python', SYS_PYTHON_VERSION)] sanity_check_paths = { -- GitLab From c673a9aa8a3d703806f3201b950947d051eba7c5 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 4 May 2017 15:51:53 +0200 Subject: [PATCH 470/566] adding easyconfigs: git-2.12.2-foss-2016b.eb --- .../g/git/git-2.12.2-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb b/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb new file mode 100644 index 0000000000..4708565849 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.12.2' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.49.1'), + ('expat', '2.2.0'), + ('gettext', '0.19.8'), + ('Perl', '5.24.0', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c1912bd137f0ca05f1a33357f119144fe79d8a0e Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 4 May 2017 16:17:20 +0200 Subject: [PATCH 471/566] Added memkind --- .../Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb | 26 ++++++++++++++ .../m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb | 34 +++++++++++++++++++ easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb | 25 ++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..c94e4b8ac3 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "8.27" + +homepage = 'http://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the + GNU operating system. These are the core utilities which are expected to exist on every operating system. + + Contact: sc@fz-juelich.de +""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [('binutils', '2.26')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..30d25870f8 --- /dev/null +++ b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'memkind' +version = '1.5.0' + +homepage = 'http://memkind.github.io' +description = """User Extensible Heap Manager built on top of jemalloc which enables control of memory characteristics +and a partitioning of the heap between kinds of memory. + + Contact: sc@fz-juelich.de +""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/memkind/memkind/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.26'), + ('Coreutils', '8.27'), # needed to ensure that ./build_jemalloc.sh works properly + ('Autotools', '20150215'), # needed to ensure that ./build_jemalloc.sh works properly +] + +dependencies = [ + ('tbb', '2017.4.174', '', True), # optional, to enable the tbb heap manager +] + +# This can be also an EB dependency, but seems unnecesary +osdependencies = [('numactl-devel', 'libnuma-devel ')] + +preconfigopts = './build_jemalloc.sh && ./autogen.sh && ' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb new file mode 100644 index 0000000000..54c9706aa0 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb @@ -0,0 +1,25 @@ +name = 'tbb' +version = '2017.4.174' + +homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +description = """Intel Threading Building Blocks 4.0 (Intel TBB) + is a widely used, award-winning C++ template library for creating reliable, + portable, and scalable parallel applications. + Use Intel TBB for a simple and rapid way of developing robust task-based + parallel applications that scale to available processor cores, are compatible + with multiple environments, and are easier to maintain. + Intel TBB is the most proficient way to implement future-proof parallel applications + that tap into the power and performance of multicore and manycore hardware platforms. + + Contact: sc@fz-juelich.de +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_tbb_%(version)s.tgz'] + +requires_runtime_license = False + +dontcreateinstalldir = True + +moduleclass = 'lib' -- GitLab From c183a7c624985aadebe8e70291df64825a2aaf72 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 4 May 2017 16:19:51 +0200 Subject: [PATCH 472/566] Removed contact info --- .../easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb | 2 -- easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb | 2 -- easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb index c94e4b8ac3..e47ad52ac4 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb @@ -6,8 +6,6 @@ version = "8.27" homepage = 'http://www.gnu.org/software/coreutils/' description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. - - Contact: sc@fz-juelich.de """ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} diff --git a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb index 30d25870f8..5522bebb7b 100644 --- a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb @@ -6,8 +6,6 @@ version = '1.5.0' homepage = 'http://memkind.github.io' description = """User Extensible Heap Manager built on top of jemalloc which enables control of memory characteristics and a partitioning of the heap between kinds of memory. - - Contact: sc@fz-juelich.de """ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb index 54c9706aa0..925ecf0fc9 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb @@ -10,8 +10,6 @@ description = """Intel Threading Building Blocks 4.0 (Intel TBB) with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. - - Contact: sc@fz-juelich.de """ toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 27e05e5536c1a9366d61d1ed9487ad36f7e11df1 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Thu, 4 May 2017 16:26:44 -0400 Subject: [PATCH 473/566] add easyconfig x265-2.4-foss-2016b.eb --- .../easyconfigs/x/x265/x265-2.4-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb new file mode 100644 index 0000000000..d0b1d74b60 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '2.4' + +homepage = 'http://x265.org/' +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': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://ftp.videolan.org/pub/videolan/x265/', + 'http://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [('Yasm', '1.3.0')] + +builddependencies = [('CMake', '3.7.2')] + +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 26710fc9b17f4bbed3ad2f9de260e16ca650da40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 May 2017 22:34:40 +0200 Subject: [PATCH 474/566] bump version to 3.2.0 + tweak release notes --- RELEASE_NOTES | 18 ++++++++++-------- setup.py | 2 +- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f2fbd7d51c..d67162b731 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,34 +3,36 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, +The latest version of easybuild-easyconfig provides 6,943 easyconfig files, for 1,216 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.2.0 (May 5th 2017) --------------------- feature release -- added example easyconfig files for 33 new software packages: +- added example easyconfig files for 34 new software packages: - ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484), DFTB+ (#4398), Doris (#4404), ED2 (#4402), FireWorks (#4484), GETORB (#4414), GapFiller (#4462), IPy (#4450), - imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), PyCUDA (#4523), - pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), - SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), - VMD (#4391), WRF-Fire (#4403) + imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), Node-RED (#4542), + PyCUDA (#4523), pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), + rootpy (#4242), SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), + samblaster (#4435), VMD (#4391), WRF-Fire (#4403) - added additional easyconfigs for various supported software packages, including: - - 3to2 1.1.1, ACTC 1.1, ALLPATHS-LG 52488, Autoconf 2.69, Autoconf 2.69, Automake 1.15, Automake 1.15, Autotools 20150215, Autotools 20150215, arpack-ng 3.4.0, atomate 0.4.4, BLAT 3.5, BamTools 2.4.1, BioKanga 4.3.4, BioKanga 4.3.5, BioPerl 1.7.1, Bison 3.0.4, Boost 1.63.0, Boost 1.64.0, Bowtie2 2.2.9, BreakDancer 1.4.5, binutils 2.28, bx-python , bzip2 1.0.6, CMake 3.8.0, CUDA 8.0.61.eb, Cantera 2.3.0, ClusterShell 1.7.3.eb, cURL 7.53.1, cURL 7.54.0, cairo 1.14.8, configparser 3.5.0, cuDNN 6.0, custodian 1.1.0, DBG2OLC 20170208, DFTB+ 1.3.1, Doris 4.02, Doxygen 1.8.13, deap 0.9.2, ED2 20170201, ED2 20170201, ESMF 6.3.0rp1, EasyBuild 3.1.2.eb, Eigen 3.3.2, entrypoints 0.2.2, FFTW 3.3.6, FireWorks 1.4.2, file 5.30, flex 2.6.3, fmt 3.0.1, fontconfig 2.12.1, fqtrim 0.9.5, freetype 2.5.5, freetype 2.6.2, freetype 2.7.1, freetype 2.7.1, GCC 6.3.0, GCC 7.1.0, GCCcore 7.1.0.eb, GDAL 2.1.3, GEOS 3.6.1, GETORB 2.3.2, GLib 2.52.0, GMP 6.1.2, GSL 2.3, GapFiller 2.1.1, Ghostscript 9.21, Go 1.8.1.eb, g2clib 1.6.0, g2lib 1.4.0, gnuplot 5.0.5, googletest 1.8.0, HDF 4.2.12, HDF5 1.10.0, HISAT2 2.0.5, HMMER 3.1b2, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, hwloc 1.11.6, IMB 4.1, IMB 4.1, IMB 4.1, IPy 0.83.eb, IPython 5.3.0, ImageMagick 7.0.5, Inspector 2017_update2.eb, imbalanced-learn 0.2.1, ipyrad 0.6.15, JasPer 1.900.1, JasPer 2.0.12, jemalloc 4.5.0, LIBSVM 3.22, LLVM 4.0.0, LZO 2.10, LibTIFF 4.0.7, LittleCMS 2.8, libGLU 9.0.0, libdrm 2.4.76, libiconv 1.15, libjpeg-turbo 1.5.1, libpng 1.6.18, libpng 1.6.21, libpng 1.6.28, libpng 1.6.29, libreadline 7.0, libsodium 1.0.12, libtool 2.4.6, libtool 2.4.6, libxml2 2.9.4, libyaml 0.1.7.eb, M4 1.4.18, METIS 5.1.0, MRtrix 0.3.15, Mako 1.0.6, Mesa 17.0.2, MultiQC 0.7, MultiQC 0.9, makedepend 1.0.5, matplotlib 1.5.1, matplotlib 2.0.0, matplotlib 2.0.0, NASM 2.12.02, NGS 1.3.0, NLopt 2.4.2, NLopt 2.4.2, ncbi-vdb 2.8.2, ncurses 6.0, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, netCDF 4.4.1.1, nettle 3.3, numba 0.32.0, numpy 1.10.1, numpy 1.12.1, ORCA 4.0.0.2, Octave 4.2.1, OpenMPI 2.1.0, OpenPGM 5.2.122, PCRE 8.40, PETSc 3.7.5, PGI 17.3, PLINK 1.9b_4.1, PROJ 4.9.3, ParMETIS 4.0.3, Perl 5.24.1, Pillow 4.1.0, PyCUDA 2016.1.2, PyYAML 3.12, PyYAML 3.12.eb, PyZMQ 16.0.2, Python 2.7.13, Python 3.6.1, pixman 0.34.0, pkg-config 0.29.2, pkgconfig 1.2.2, pymatgen-db 0.6.5, pymatgen 4.7.3, QuTiP 4.1.0, QuantumESPRESSO 6.1, R 3.3.3, R 3.3.3, ROI_PAC 3.0.1, Rascaf 1.0.2, RepastHPC 2.2.0, rootpy 0.8.0, SAMtools 0.1.20, SAMtools 1.4, SAMtools 1.4, SCons 2.5.1, SIONlib 1.7.1, SIONlib 1.7.1, SQLite 3.17.0, SSPACE_Basic 2.1.1, SUNDIALS 2.7.0, SWASH 3.14, SWASH 3.14, SWIG 3.0.12, Sambamba 0.6.6.eb, Seaborn 0.7.1, Spack 0.10.0.eb, SpiceyPy 1.1.0, StaMPS 3.3b1, Stacks 1.45, Stacks 1.46, Stampy 1.0.31, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, samblaster 0.1.24, scipy 0.19.0, scp 0.10.2, snaphu 1.4.2, sparsehash 2.0.3, spglib-python 1.9.9.38, Tcl 8.6.6, Tk 8.6.6, Triangle 1.6, tbb 2017_U5, tbb 2017_U5, tcsh 6.20.00, UDUNITS 2.2.24, util linux, VMD 1.9.3, VTune 2017_update2.eb, ViennaRNA 2.3.5, vsc-base 2.5.8, vsc-install 0.10.25, vsc-mympirun 4.0.0b0, WRF-Fire 20170221, WRF 3.8.0, Wannier90 2.1.0, X11 20170314, XZ 5.2.2, xorg-macros 1.19.1, xproto 7.0.31, ZeroMQ 4.2.2, zlib 1.2.11, zlib 1.2.11 + - BamTools 2.4.1, Boost 1.64.0, GCC 7.1.0, IPython 5.3.0, LLVM 4.0.0, Mesa 17.0.2, Octave 4.2.1, OpenMPI 2.1.0, + PETSc 3.7.5, PGI 17.3, Perl 5.24.1, Python 2.7.13 + 3.6.1 (incl. numpy 1.12.1, scipy 0.19.0), R 3.3.3, SuiteSparse 4.5.5 - various enhancements, including: - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) - various bug fixes, including: - add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs (#4369) - use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain (#4384) - - fix pkgconfig patch for Qhull to only let CMake substitute (#4451) + - fix pkgconfig patch for Qhull (#4451) - also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for foss/2016b (#4467) - add dependency NLopt for R extension nloptr (#4481) - fix issue with configparser and backports namespace blocking inclusion of nbconvert with IPython (#4504) - change source_urls of pycrypto to encrypted https://pypi.python.org/... (#4505) - fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (#4531) + - also build IMB-IO in IMB 4.1 easyconfig using foss/2016a (#4539) v3.1.2 (March 20th 2017) diff --git a/setup.py b/setup.py index 0683e432c9..40e8813698 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 = '3.2.0.dev0' +VERSION = '3.2.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 79ac6ae1634c2272cc3f821d2f56ee53ee6d67ee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:10:45 +0200 Subject: [PATCH 475/566] Bump all to CMake 3.8.0 --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- .../c/CMake/CMake-3.7.2-intel-2017a.eb | 31 ------------------- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 2 +- .../ParaView-5.2.0-intel-2017a-mpi.eb | 2 +- 4 files changed, 3 insertions(+), 34 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index da60ff72f0..e83b067d66 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -23,7 +23,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.7.2'), + ('CMake', '3.8.0'), ('Eigen', '3.3.3'), ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb deleted file mode 100644 index d78b6b43f1..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.7.2' - -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': '2017a'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - -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 ['ccmake', 'cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb index 352a974db9..91d00f1139 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -18,7 +18,7 @@ source_urls = [ # We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] -builddependencies = [('CMake', '3.7.2')] +builddependencies = [('CMake', '3.8.0')] configopts = ['', 'shared=1'] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index 903174f12f..8746599786 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -24,7 +24,7 @@ dependencies = [ ('Python', '2.7.13'), ] -builddependencies = [('CMake', '3.7.2')] +builddependencies = [('CMake', '3.8.0')] separate_build_dir = True -- GitLab From 946baf954570a740f5d87d4161d1d75b0bf27b3d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:11:55 +0200 Subject: [PATCH 476/566] Bump CMake in OpenFOAM too to 3.8.0 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb index 2469f2947a..c3f3f806f9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [ ('Bison', '3.0.4'), - ('CMake', '3.7.2'), + ('CMake', '3.8.0'), ('flex', '2.6.3'), ] -- GitLab From fcc2fe709d80ba7fe6a6a2d350398621c54022c7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:19:50 +0200 Subject: [PATCH 477/566] Drop old comment --- easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb index fc41f1c1fd..ab4ae0dab8 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb @@ -26,7 +26,7 @@ configopts = '-skip qtgamepad' dependencies = [ ('GLib', '2.52.0'), ('libpng', '1.6.29'), - ('X11', '20170314'), #, '', ('GCCcore', '6.3.0')), + ('X11', '20170314'), ('libGLU', '9.0.0'), ] -- GitLab From 94fab13de92516a969d7a43238c3571870007b1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 May 2017 17:29:28 +0200 Subject: [PATCH 478/566] adding easyconfigs: EasyBuild-3.2.0.eb --- .../e/EasyBuild/EasyBuild-3.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb new file mode 100644 index 0000000000..d84e16eaba --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.2.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/2c/39/4435097a0b897ca1e3c7f055000ebfa2a5dc3632e606a7cf0088b0caa2ee/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/ce/49/70a1d3f419ffb21dc3a3446bdf63d2a49447753fa4e69ec0a3db5a262e67/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/97/59/b8d166b270f113ae69b0983275dac5da5bfb94bb1082a10bb26e93c78ed7/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.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 b1d56530a5bae608a28c907a43792ed3c9f85ea6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 May 2017 17:58:30 +0200 Subject: [PATCH 479/566] bump to v3.3.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 40e8813698..85590c2983 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 = '3.2.0' +VERSION = '3.3.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 2a8958f86f854c0523d195c3bf3a34edb6615ef6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:26:00 +0200 Subject: [PATCH 480/566] adding easyconfigs: OpenFOAM-2.2.2-intel-2017a.eb, flex-2.5.39-GCCcore-6.3.0.eb --- .../f/flex/flex-2.5.39-GCCcore-6.3.0.eb | 22 +++++++++++ .../o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb | 39 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f579ff8a96 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb @@ -0,0 +1,22 @@ +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': 'GCCcore', 'version': '6.3.0'} +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', '1.4.18')] +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb new file mode 100644 index 0000000000..7d4fcb2a52 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb @@ -0,0 +1,39 @@ +name = 'OpenFOAM' +version = '2.2.2' + +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': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.2.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From 0fee12a842bff40dfac37d47d96db9e9137ffb2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:28:24 +0200 Subject: [PATCH 481/566] adding easyconfigs: OpenFOAM-2.3.1-intel-2017a.eb --- .../o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb new file mode 100644 index 0000000000..22826bc9df --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb @@ -0,0 +1,44 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From d3563b795447df65ba2eaaf239c0f332589a3c50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:29:03 +0200 Subject: [PATCH 482/566] adding easyconfigs: OpenFOAM-2.4.0-intel-2017a.eb --- .../o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb new file mode 100644 index 0000000000..dd2ccbb6b7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.4.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From 8d7635554191701bb4b415e9a5fce845e981f221 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 May 2017 09:52:09 +0200 Subject: [PATCH 483/566] adding easyconfigs: ASE-3.13.0-intel-2017a-Python-2.7.13.eb --- .../ASE-3.13.0-intel-2017a-Python-2.7.13.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..046d2d02c9 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From d3dd9379507508f02b36714605f0a22ae9bc187d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 May 2017 10:16:35 +0200 Subject: [PATCH 484/566] adding easyconfigs: hanythingondemand-3.2.2-cli.eb, hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb --- .../hanythingondemand-3.2.2-cli.eb | 42 +++++++++++++++++++ ...ndemand-3.2.2-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb new file mode 100644 index 0000000000..5c43bd66c7 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.2' +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', '2.5.8'), +] + +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-3.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ef65fdbca6 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.2' +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 ee456a43f1d3f473ea3dcd590add6e5b5193aecc Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 8 May 2017 11:04:19 +0200 Subject: [PATCH 485/566] Update OpenFOAM-4.1-foss-2016b.eb --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb index efc992104f..eea7c1b416 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), ('CGAL', '4.8.1'), - ('ParaView', '5.1.2', '-mpi'), + ('ParaView', '5.2.0', '-mpi'), ] builddependencies = [ -- GitLab From bd572560993ad8dfd0fba752371b66d459df4116 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 8 May 2017 11:05:32 +0200 Subject: [PATCH 486/566] Update ParaView-5.2.0-foss-2016b-mpi.eb --- .../easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb index 5dd45f28db..d4515369c6 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb @@ -33,6 +33,7 @@ configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBR configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_QT_VERSION=4 -DQT_QMAKE_EXECUTABLE=$EBROOTQT/bin/qmake ' # if you want to build server only Paraview, uncomment the following line: # configopts += '-DVTK_USE_X=OFF ' -- GitLab From acb79d1e16b4eb7312bbda5353605e53a86bd33c Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Mon, 8 May 2017 12:00:47 +0200 Subject: [PATCH 487/566] Added tbb open source and numactl as dependencies for memkind --- .../m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb | 11 +++++++---- .../t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb | 17 +++++++++++++++++ 2 files changed, 24 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb index 5522bebb7b..6a31d17221 100644 --- a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb @@ -21,12 +21,15 @@ builddependencies = [ ] dependencies = [ - ('tbb', '2017.4.174', '', True), # optional, to enable the tbb heap manager + ('tbb', '2017_U5'), # optional, to enable the tbb heap manager + ('numactl', '2.0.11') ] -# This can be also an EB dependency, but seems unnecesary -osdependencies = [('numactl-devel', 'libnuma-devel ')] - preconfigopts = './build_jemalloc.sh && ./autogen.sh && ' +sanity_check_paths = { + 'files': ["include/memkind.h", "lib/libmemkind.%s" % SHLIB_EXT], + 'dirs': [], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..0e4e8f19f1 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb @@ -0,0 +1,17 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.26') +] + +moduleclass = 'lib' -- GitLab From 3afbfc7bec4adf121f4e597a3f3d5e2a69d2b449 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 9 May 2017 09:28:23 +0200 Subject: [PATCH 488/566] updated --- .../easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb | 4 ++++ .../SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb | 10 ++++++---- .../SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb | 9 +++++---- 3 files changed, 15 insertions(+), 8 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb old mode 100755 new mode 100644 index 03a730e5cc..24c6a9c29a --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb @@ -15,8 +15,12 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +#We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.path'] + builddependencies = [('CMake', '3.8.0')] configopts = ['', 'shared=1'] moduleclass = 'math' + diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb old mode 100755 new mode 100644 index a66251bb0f..ac3303de2d --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb @@ -1,19 +1,21 @@ name = 'SuiteSparse' version = '4.5.5' -metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % metis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True} +toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -dependencies = [('METIS', metis_ver)] +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] maxparallel = 1 moduleclass = 'numlib' + diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb index 7c7dff3356..a24c57563a 100755 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb @@ -1,18 +1,19 @@ name = 'SuiteSparse' version = '4.5.5' -parmetis_ver = '4.0.3' -versionsuffix = '-ParMETIS-%s' % parmetis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True} +toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -dependencies = [('ParMETIS', parmetis_ver)] +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) +dependencies = [(parmetis, parmetis_ver)] maxparallel = 1 -- GitLab From a171247892a0d7a9b2082a7f6cd472ff99d74b8c Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 9 May 2017 09:40:54 +0200 Subject: [PATCH 489/566] missing files --- .../libpciaccess-0.13.1-goolf-1.4.10.eb | 4 +--- .../libpciaccess-0.13.1-ictce-4.0.6.eb | 24 +++++++++++++++++++ .../libpciaccess-0.13.1-ictce-4.1.13.eb | 24 +++++++++++++++++++ .../libpciaccess-0.13.1-ictce-5.3.0.eb | 4 +--- .../libpciaccess-0.13.1-ictce-5.5.0.eb | 4 +--- .../libpciaccess-0.13.1-intel-2015a.eb | 4 +--- .../libpciaccess-0.13.3-intel-2015a.eb | 4 +--- .../libpciaccess-0.13.4-gimkl-2.11.5.eb | 4 +--- .../libpciaccess-0.13.4-intel-2015b.eb | 4 +--- .../libpciaccess-0.13.4-intel-2016a.eb | 4 +--- 10 files changed, 56 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb index 437954d342..9371a19f2d 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb new file mode 100644 index 0000000000..adbb940942 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.1' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +builddependencies = [ + ('Autoconf', '2.69'), + ('xorg-macros', '1.17'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..67891759ae --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.1' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +builddependencies = [ + ('Autoconf', '2.69'), + ('xorg-macros', '1.17'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb index 834a292992..cbc3f1b46c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb index c3e51b6854..1abedab086 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.5.0'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index 8f259d339a..8970daab0a 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb index 5f22d77a36..a36467cdf5 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb @@ -6,7 +6,7 @@ version = '0.13.3' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb index ea05edcced..449c59f9bf 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'gimkl', 'version': '2.11.5'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb index 1af83efe66..fd0fe49af5 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb index c0a23d9702..69a705ef82 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], -- GitLab From c22ad8a61d53d5c2f32a5f02e6744227475d3416 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 09:46:50 +0200 Subject: [PATCH 490/566] don't re-add archived libpciaccess easyconfigs --- .../libpciaccess-0.13.1-ictce-4.0.6.eb | 24 ------------------- .../libpciaccess-0.13.1-ictce-4.1.13.eb | 24 ------------------- 2 files changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb deleted file mode 100644 index adbb940942..0000000000 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.13.1' - -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -builddependencies = [ - ('Autoconf', '2.69'), - ('xorg-macros', '1.17'), -] - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb deleted file mode 100644 index 67891759ae..0000000000 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.13.1' - -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -builddependencies = [ - ('Autoconf', '2.69'), - ('xorg-macros', '1.17'), -] - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' -- GitLab From 44b396a0cef6d3a4c19f55157e03ab3932b184bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 09:48:20 +0200 Subject: [PATCH 491/566] consistent update of libpciaccess source URLs --- .../l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb | 4 +--- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb | 4 +--- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 01c9c7b5d7..9967c64c68 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'GCC', 'version': '4.7.2'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb index 11ed8ea67d..76bd735f5a 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'foss', 'version': '2016b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb index 9124b553ab..de4d55b188 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], -- GitLab From 3a215d2301ab7fa13a66b9899a3f3e02038d4413 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 9 May 2017 09:49:24 +0200 Subject: [PATCH 492/566] Update METIS-5.1.0-foss-2016a.eb --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb index 2b65f31212..728e632fc1 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb @@ -15,6 +15,9 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + builddependencies = [('CMake', '3.4.3')] configopts = ['', 'shared=1'] -- GitLab From 5e3ebe055d256bd61a2683a4843ab65f80687aea Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 9 May 2017 09:59:39 +0200 Subject: [PATCH 493/566] updated usempi --- easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index 6dd67416d3..b1ee1a4af9 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -7,7 +7,7 @@ description = """NAMD is a parallel molecular dynamics code designed for high-pe large biomolecular systems.""" toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'opt': True, 'pic': True} +toolchainopts = {'usempi': True, 'pic': True} sources = ['NAMD_%(version)s_Source.tar.gz'] @@ -22,3 +22,4 @@ charm_arch = "mpi-linux-x86_64" moduleclass = 'chem' + -- GitLab From ed733c7284cfedc210d707cdf4990d9ea3ff7fa7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 10:34:00 +0200 Subject: [PATCH 494/566] adding easyconfigs: xarray-0.9.5-intel-2017a-Python-3.6.1.eb --- .../xarray-0.9.5-intel-2017a-Python-3.6.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..aba02b5499 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.9.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 1721278ce3b16a5e15f737939f20588ea7dbcf64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 11:02:07 +0200 Subject: [PATCH 495/566] adding easyconfigs: CMake-3.8.1-GCCcore-6.3.0.eb --- .../c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..4eddbf2181 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.8.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +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', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 6493fbb9d6c7df667f875b49dbf17d1b72f4ce8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 11:23:56 +0200 Subject: [PATCH 496/566] adding easyconfigs: googletest-1.8.0-intel-2017a.eb --- .../googletest-1.8.0-intel-2017a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb new file mode 100644 index 0000000000..c0c3624868 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.8.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's C++ test framework" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.8.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libgmock.a', 'lib/libgmock_main.a', 'lib/libgtest.a', 'lib/libgtest_main.a'], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' -- GitLab From cfb7d78f7f0e3039c1c367608fcf6e6527c5ff12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 11:30:33 +0200 Subject: [PATCH 497/566] use GCCcore/6.3.0 toolchain for googletest --- ....0-intel-2017a.eb => googletest-1.8.0-GCCcore-6.3.0.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/googletest/{googletest-1.8.0-intel-2017a.eb => googletest-1.8.0-GCCcore-6.3.0.eb} (79%) diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-GCCcore-6.3.0.eb similarity index 79% rename from easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb rename to easybuild/easyconfigs/g/googletest/googletest-1.8.0-GCCcore-6.3.0.eb index c0c3624868..a63352bc58 100644 --- a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-GCCcore-6.3.0.eb @@ -6,12 +6,15 @@ version = '1.8.0' homepage = 'https://github.com/google/googletest' description = "Google's C++ test framework" -toolchain = {'name': 'intel', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['https://github.com/google/googletest/archive/'] sources = ['release-%(version)s.tar.gz'] -builddependencies = [('CMake', '3.8.1')] +builddependencies = [ + ('binutils', '2.27'), + ('CMake', '3.8.1'), +] separate_build_dir = True -- GitLab From 699236a4da05466e1bf6767f266408f08c5ee8b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 12:43:20 +0200 Subject: [PATCH 498/566] adding easyconfigs: HDF5-1.10.1-intel-2017a.eb --- .../h/HDF5/HDF5-1.10.1-intel-2017a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb new file mode 100644 index 0000000000..d72f14fe00 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.1' + +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': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43a2f9466702fb1db31df98ae6677f15'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From a7bf4c610f903ff28228d6b7ae027f8dea70ac93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 16:18:19 +0200 Subject: [PATCH 499/566] adding easyconfigs: Keras-2.0.4-intel-2017a-Python-3.6.1.eb, Theano-0.9.0-intel-2017a-Python-3.6.1.eb, h5py-2.7.0-intel-2017a-Python-3.6.1.eb, PyYAML-3.12-intel-2017a-Python-3.6.1.eb, pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb, nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb --- .../h5py-2.7.0-intel-2017a-Python-3.6.1.eb | 32 +++++++++++++++++++ .../Keras-2.0.4-intel-2017a-Python-3.6.1.eb | 28 ++++++++++++++++ ...eterized-0.6.0-intel-2017a-Python-3.6.1.eb | 24 ++++++++++++++ .../PyYAML-3.12-intel-2017a-Python-3.6.1.eb | 27 ++++++++++++++++ ...kgconfig-1.2.2-intel-2017a-Python-3.6.1.eb | 26 +++++++++++++++ .../Theano-0.9.0-intel-2017a-Python-3.6.1.eb | 23 +++++++++++++ 6 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..b00f2d835b --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.1'), + ('HDF5', '1.10.1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..45f0be1e64 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Keras' +version = '2.0.4' +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': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('Theano', '0.9.0', versionsuffix), + ('h5py', '2.7.0', '%(versionsuffix)s'), + ('PyYAML', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..7877603edb --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'nose-parameterized' +version = '0.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..6ad31707a9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.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': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('libyaml', '0.1.7', '', True), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..5b31de03c1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..3bd29d9876 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 0b5e6f8788f525168634c28e81bb9ac25fe17f7d Mon Sep 17 00:00:00 2001 From: jrbosch Date: Tue, 9 May 2017 14:00:18 -0400 Subject: [PATCH 500/566] convert to UNIX format --- .../easyconfigs/x/x265/x265-2.4-foss-2016b.eb | 58 +++++++++---------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb index d0b1d74b60..1d2f5fec38 100644 --- a/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb +++ b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb @@ -1,29 +1,29 @@ -easyblock = 'CMakeMake' - -name = 'x265' -version = '2.4' - -homepage = 'http://x265.org/' -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': 'foss', 'version': '2016b'} - -source_urls = [ - 'http://ftp.videolan.org/pub/videolan/x265/', - 'http://download.videolan.org/pub/videolan/x265/', -] -sources = ['%(name)s_%(version)s.tar.gz'] - -dependencies = [('Yasm', '1.3.0')] - -builddependencies = [('CMake', '3.7.2')] - -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' +easyblock = 'CMakeMake' + +name = 'x265' +version = '2.4' + +homepage = 'http://x265.org/' +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': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://ftp.videolan.org/pub/videolan/x265/', + 'http://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [('Yasm', '1.3.0')] + +builddependencies = [('CMake', '3.7.2')] + +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 8ab7c872caf82ab348498376928e3b90480fbfc2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 9 May 2017 21:22:35 +0200 Subject: [PATCH 501/566] adding easyconfigs: GROMACS-2016.1-foss-2017a-PLUMED.eb --- .../GROMACS-2016.1-foss-2017a-PLUMED.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb new file mode 100644 index 0000000000..9fc85b8f3e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb @@ -0,0 +1,41 @@ +## +# 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 +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.1' +versionsuffix = '-PLUMED' + +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. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +dependencies = [ + ('PLUMED', '2.3.0'), +] + +moduleclass = 'bio' -- GitLab From 5d359bd43470955903edd5a7cb2e5ae8871d6894 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 10 May 2017 07:24:00 +0800 Subject: [PATCH 502/566] adding easyconfigs: Siesta-4.0-intel-2017a.eb, Siesta-4.1-b2-intel-2017a.eb --- .../s/Siesta/Siesta-4.0-intel-2017a.eb | 18 ++++++++++++++++++ .../s/Siesta/Siesta-4.1-b2-intel-2017a.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb new file mode 100644 index 0000000000..b92708a1d8 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'Siesta' +version = '4.0' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s/%(version)s/+download/'] + +dependencies = [('netCDF-Fortran', '4.4.4')] + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb new file mode 100644 index 0000000000..5e51c29c8b --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'Siesta' +version = '4.1-b2' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://launchpad.net/%(namelower)s/%(version_major)s.1/%(version)s/+download/'] + +dependencies = [('netCDF-Fortran', '4.4.4')] + +parallel = 1 + +moduleclass = 'phys' -- GitLab From 00cdb166ff15cf4a58f71f10473790e4c3c1436f Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Wed, 10 May 2017 08:48:11 +0200 Subject: [PATCH 503/566] updated comments --- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) mode change 100755 => 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb old mode 100755 new mode 100644 index 1e3286223d..3413573e74 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb @@ -21,7 +21,7 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -# needed for --with-verbs +# needed for --with-psm2 osdependencies = [('libpsm2', 'libpsm2-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] @@ -33,3 +33,5 @@ sanity_check_paths = { } moduleclass = 'mpi' + + -- GitLab From 8d3c267dbee7f7b89edf438bd54e5e1fa7966262 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 10 May 2017 14:56:57 +0800 Subject: [PATCH 504/566] add checksums and make source_url more generic --- easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb | 4 +++- easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb index b92708a1d8..88fc6fad8f 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} sources = [SOURCELOWER_TGZ] -source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s/%(version)s/+download/'] +vl = version.split('-') +source_urls = ['https://launchpad.net/siesta/%s/%%(version)s/+download' % vl[0]] +checksums = ['c4aa5f4cf2eabefaaacd3ef6350ec8fd'] dependencies = [('netCDF-Fortran', '4.4.4')] diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb index 5e51c29c8b..5b2e971198 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://launchpad.net/%(namelower)s/%(version_major)s.1/%(version)s/+download/'] +vl = version.split('-') +source_urls = ['https://launchpad.net/siesta/%s/%%(version)s/+download' % vl[0]] +checksums = ['6dd700aa79b0da39bbd3233c220d630f'] dependencies = [('netCDF-Fortran', '4.4.4')] -- GitLab From c19bdd1337dea376a7db32ce9145cf4dfe132c74 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Wed, 10 May 2017 09:43:32 +0200 Subject: [PATCH 505/566] updated --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb | 2 +- .../SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb | 7 +++---- .../SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb | 7 +++---- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb index 24c6a9c29a..b1648c008c 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb @@ -16,7 +16,7 @@ source_urls = [ ] #We use 32bit for indices and 64bit for content -patches = ['METIS-5.1.0-use-doubles.path'] +patches = ['METIS-5.1.0-use-doubles.patch'] builddependencies = [('CMake', '3.8.0')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb index ac3303de2d..4727d14749 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb @@ -1,5 +1,7 @@ name = 'SuiteSparse' version = '4.5.5' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" @@ -10,10 +12,7 @@ toolchainopts = {'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)] +dependencies = [('METIS', metis_ver)] maxparallel = 1 diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb index a24c57563a..457bb71cde 100755 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb @@ -1,5 +1,7 @@ name = 'SuiteSparse' version = '4.5.5' +parmetis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % parmetis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" @@ -10,10 +12,7 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -parmetis = 'ParMETIS' -parmetis_ver = '4.0.3' -versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) -dependencies = [(parmetis, parmetis_ver)] +dependencies = [('ParMETIS', parmetis_ver)] maxparallel = 1 -- GitLab From 84a87e68b2bfe4a5516557e54910c445299b05f5 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Wed, 10 May 2017 09:56:53 +0200 Subject: [PATCH 506/566] added fftw as dependency --- easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index b1ee1a4af9..8c793e8447 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -13,6 +13,7 @@ sources = ['NAMD_%(version)s_Source.tar.gz'] dependencies = [ ('Tcl', '8.5.19'), + ('FFTW', '3.3.6'), ] # /bin/csh is required by 'config' script -- GitLab From f19f305be53e82db0c019889343e9614fd7042d9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 10 May 2017 15:58:50 +0800 Subject: [PATCH 507/566] remove no longer necessary parallel=1 --- easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb | 2 -- easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb index 88fc6fad8f..c782f5eabf 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb @@ -15,6 +15,4 @@ checksums = ['c4aa5f4cf2eabefaaacd3ef6350ec8fd'] dependencies = [('netCDF-Fortran', '4.4.4')] -parallel = 1 - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb index 5b2e971198..3186618b3a 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb @@ -15,6 +15,4 @@ checksums = ['6dd700aa79b0da39bbd3233c220d630f'] dependencies = [('netCDF-Fortran', '4.4.4')] -parallel = 1 - moduleclass = 'phys' -- GitLab From 38c1c0621a437cf495f525da7c2b4d087790bedc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 13:18:00 +0200 Subject: [PATCH 508/566] adding easyconfigs: Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb, Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb, protobuf-3.3.0-intel-2017a.eb, protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb, protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb --- ...-python-3.3.0-intel-2017a-Python-2.7.13.eb | 29 +++++++++++++++ ...f-python-3.3.0-intel-2017a-Python-3.6.1.eb | 29 +++++++++++++++ .../p/protobuf/protobuf-3.3.0-intel-2017a.eb | 23 ++++++++++++ ...sorflow-1.1.0-intel-2017a-Python-2.7.13.eb | 35 +++++++++++++++++++ ...nsorflow-1.1.0-intel-2017a-Python-3.6.1.eb | 35 +++++++++++++++++++ 5 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e538a8e99b --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..4c753d376f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb new file mode 100644 index 0000000000..10bedd5672 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.3.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb new file mode 100755 index 0000000000..a6aec94f18 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2017a'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/8a/73/74c610decd5e0a1fd7f441a32e3561d21c28ced98fd6d3d9d5c70dbf92ce/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['70a7a29dbef478cbac9a9c839a18227e'] + +dependencies = [ + ('Python', '%s.%s.13' % (pymaj, pymin)), + ('protobuf-python', '3.3.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..f134b5be2b --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2017a'} + +pymaj = '3' +pymin = '6' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/cd/e4/b2a8bcd1fa689489050386ec70c5c547e4a75d06f2cc2b55f45463cd092c/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['1f761290358dfb7fe4ec73140f4d282a'] + +dependencies = [ + ('Python', '%s.%s.1' % (pymaj, pymin)), + ('protobuf-python', '3.3.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 1483de14a6df6e3641b2f740f5931682055045c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 15:08:41 +0200 Subject: [PATCH 509/566] adding easyconfigs: NLTK-3.2.2-intel-2017a-Python-2.7.13.eb --- .../NLTK-3.2.2-intel-2017a-Python-2.7.13.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..1388501b14 --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'NLTK' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 6ec3072ebf8e9ae25a8f5289def75bd636a385b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 15:16:14 +0200 Subject: [PATCH 510/566] adding easyconfigs: pbdagcon-20170330-intel-2017a.eb, BLASR-20170330-intel-2017a.eb, blasr_libcpp-20170426-intel-2017a.eb, pbbam-20170508-intel-2017a.eb, HTSlib-20160107-intel-2017a-PacBio.eb, HDF5-1.8.18-intel-2017a-serial.eb --- .../b/BLASR/BLASR-20170330-intel-2017a.eb | 38 ++++++++++++++ .../blasr_libcpp-20170426-intel-2017a.eb | 41 ++++++++++++++++ .../h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb | 27 ++++++++++ .../HTSlib-20160107-intel-2017a-PacBio.eb | 41 ++++++++++++++++ .../p/pbbam/pbbam-20170508-intel-2017a.eb | 49 +++++++++++++++++++ .../pbdagcon/pbdagcon-20170330-intel-2017a.eb | 40 +++++++++++++++ 6 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb create mode 100644 easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb new file mode 100644 index 0000000000..e63d8bc616 --- /dev/null +++ b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'BLASR' +commit = 'bed926d' +version = '20170330' + +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': 'intel', 'version': '2017a'} +#toolchainopts = {'usempi': True} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('HDF5', '1.8.18', '-serial'), + ('pbbam', '20170508'), + ('blasr_libcpp', '20170426'), +] + +prebuildopts = "./configure.py --with-szlib HDF5_INCLUDE=$EBROOTHDF5/include HDF5_LIB=$EBROOTHDF5/lib && " + +binaries = ['blasr', 'utils/loadPulses', 'utils/pls2fasta', 'utils/samFilter', 'utils/samtoh5', + 'utils/samtom4', 'utils/sawriter', 'utils/sdpMatcher', 'utils/toAfg'] +files_to_copy = [(binaries, 'bin')] + +sanity_check_paths = { + 'files': ['bin/blasr', 'bin/loadPulses', 'bin/pls2fasta', 'bin/samFilter', 'bin/samtoh5', 'bin/samtom4', + 'bin/sawriter', 'bin/sdpMatcher', 'bin/toAfg'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb new file mode 100644 index 0000000000..e172377121 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'blasr_libcpp' +version = '20170426' +commit = 'cd49f36' + +homepage = 'https://github.com/PacificBiosciences/blasr_libcpp' +description = """Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for + analyzing PacBio sequences""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/PacificBiosciences/blasr_libcpp/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('HDF5', '1.8.18', '-serial'), + ('pbbam', '20170508'), +] + +unpack_options = "--strip-components=1" + +skipsteps = ['configure', 'install'] +buildininstalldir = True + +#prebuildopts = "NOPBBAM=1 NOHDF=1 ./configure.py && " +prebuildopts = "./configure.py && " + +sanity_check_paths = { + 'files': ['alignment/libblasr.a', 'alignment/libblasr.%s' % SHLIB_EXT, 'hdf/libpbihdf.a', + 'hdf/libpbihdf.%s' % SHLIB_EXT, 'pbdata/libpbdata.a', 'pbdata/libpbdata.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['alignment', 'hdf', 'pbdata'], + 'LD_LIBRARY_PATH': ['alignment', 'hdf', 'pbdata'], + 'LIBRARY_PATH': ['alignment', 'hdf', 'pbdata'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb new file mode 100644 index 0000000000..ef054b6cdf --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.18' +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': '2017a'} +toolchainopts = {'pic': True, 'usempi': False} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb new file mode 100644 index 0000000000..e9e046ddd8 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '20160107' +commit = '6b6c813' +versionsuffix = '-PacBio' + +homepage = 'https://github.com/PacificBiosciences/htslib' +description = """PacBio fork of C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/PacificBiosciences/htslib/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('cURL', '7.54.0'), +] + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb new file mode 100644 index 0000000000..5e218a3225 --- /dev/null +++ b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'pbbam' +version = '20170508' +commit = 'd62e310' + +homepage = 'http://pbbam.readthedocs.io/' +description = """The pbbam software package provides components to create, query, & edit PacBio BAM files + and associated indices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +gtest_ver = '1.8.0' +source_urls = [ + 'https://github.com/PacificBiosciences/pbbam/archive/', + 'https://github.com/google/googletest/archive/', +] +sources = [ + ('%s.tar.gz' % commit, "tar xfvz %s --strip-components=1"), # pbbam + 'release-%s.tar.gz' % gtest_ver, # googletest +] + +builddependencies = [ + ('CMake', '3.8.1'), + ('Doxygen', '1.8.13'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.64.0'), + ('googletest', '1.8.0'), + ('HTSlib', '20160107', '-PacBio'), +] + +skipsteps = ['install'] + +buildininstalldir = True + +configopts = "-DHTSLIB_ROOTDIR=$EBROOTHTSLIB -DGTEST_SRC_DIR=%%(builddir)s/googletest-release-%s" % gtest_ver + +runtest = 'test' + +postinstallcmds = ["rm -r googletest-release-%s" % gtest_ver] + +sanity_check_paths = { + 'files': ['bin/pbindex', 'bin/pbindexdump', 'bin/pbmerge', 'lib/libpbbam.a'], + 'dirs': ['include/pbbam'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb b/easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb new file mode 100644 index 0000000000..51dd75d3e1 --- /dev/null +++ b/easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'pbdagcon' +version = '20170330' +commit = 'fd8fbad' + +homepage = 'https://github.com/PacificBiosciences/pbdagcon' +description = """pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence + consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'https://github.com/PacificBiosciences/pbdagcon/archive/', + 'https://github.com/PacificBiosciences/DALIGNER/archive/', + 'https://github.com/PacificBiosciences/DAZZ_DB/archive/', +] +sources = [ + '%s.tar.gz' % commit, # pbdagcon + '583de37.tar.gz', # DALIGNER + '7954b44.tar.gz', # DAZZ_DB +] + +dependencies = [ + ('blasr_libcpp', '20170426'), +] + +prebuildopts = "rmdir DAZZ_DB && ln -s %(builddir)s/DAZZ_DB* DAZZ_DB && cd DAZZ_DB && pwd && make && cd .. && " +prebuildopts += "export CPATH=$PWD/DAZZ_DB:$CPATH && export LIBRARY_PATH=$PWD/DAZZ_DB:$LIBRARY_PATH && " +prebuildopts += "rmdir DALIGNER && ln -s %(builddir)s/DALIGNER* DALIGNER && cd DALIGNER && pwd && make && cd .. && " +prebuildopts += "./configure.py && export DALIGNER_SRC=$PWD/DALIGNER && export DAZZ_DB_SRC=$PWD/DAZZ_DB && " + +files_to_copy = [(['src/cpp/pbdagcon'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/pbdagcon'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f433280a21cca4e4c0b1a2495a6fcaa1832c0af2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 15:34:11 +0200 Subject: [PATCH 511/566] adding easyconfigs: pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb, enchant-1.6.1-intel-2017a.eb, hunspell-1.6.1-intel-2017a.eb --- .../e/enchant/enchant-1.6.1-intel-2017a.eb | 25 +++++++++++++++++ .../h/hunspell/hunspell-1.6.1-intel-2017a.eb | 25 +++++++++++++++++ ...enchant-1.6.8-intel-2017a-Python-2.7.13.eb | 27 +++++++++++++++++++ 3 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb new file mode 100644 index 0000000000..13433c2f04 --- /dev/null +++ b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'enchant' +version = '1.6.1' + +homepage = 'https://abiword.github.io/enchant/' +description = """Enchant is a library (and command-line program) that wraps a number of different spelling libraries + and programs with a consistent interface.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/AbiWord/enchant/releases/download/enchant-%s/' % '-'.join(version.split('.'))] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] +dependencies = [('hunspell', '1.6.1')] + +buildopts = "LIBTOOL='libtool --tag=CC'" + +sanity_check_paths = { + 'files': ['bin/enchant', 'lib/libenchant.a', 'lib/libenchant.%s' % SHLIB_EXT], + 'dirs': ['include/enchant', 'lib/enchant'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb new file mode 100644 index 0000000000..808d4c832e --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.6.1' + +homepage = 'http://hunspell.github.io/' +description = """Hunspell is a spell checker and morphological analyzer library and program designed for languages + with rich morphology and complex word compounding or character encoding.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', + 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], + 'dirs': ['include/hunspell'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..44fd59e0fa --- /dev/null +++ b/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pyenchant' +version = '1.6.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pythonhosted.org/pyenchant/' +description = "PyEnchant is a spellchecking library for Python, based on the excellent Enchant library." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('enchant', '1.6.1'), +] + +options = {'modulename': 'enchant'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From ae2102adbb82b9d5a4ba8d501c50ec282682c784 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 16:17:26 +0200 Subject: [PATCH 512/566] adding easyconfigs: pandas-0.20.1-intel-2017a-Python-3.6.1.eb --- .../pandas-0.20.1-intel-2017a-Python-3.6.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..ea5b45bce1 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.20.1' +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': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 6fe5e21171575a9bddd5010a52a597d2b3b8b8f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 16:38:47 +0200 Subject: [PATCH 513/566] adding easyconfigs: scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb, matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb --- ...tplotlib-2.0.1-intel-2017a-Python-3.6.1.eb | 43 +++++++++++++++++++ ...t-learn-0.18.1-intel-2017a-Python-3.6.1.eb | 30 +++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..a1866952ba --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,43 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.1' +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': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.6.1'), + ('freetype', '2.7.1'), +] + +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-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..af24f8502f --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('matplotlib', '2.0.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 33f3a414b01acd8de6e44c737dec0165a534143e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 18:37:10 +0200 Subject: [PATCH 514/566] adding easyconfigs: RAxML-8.2.10-intel-2017a-hybrid-avx2.eb --- .../RAxML-8.2.10-intel-2017a-hybrid-avx2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb new file mode 100644 index 0000000000..55ca13f91f --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.10' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'intel', 'version': '2017a'} +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"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e26314e1b0611d8031c8cec4e5272efc68677fa1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 19:09:28 +0200 Subject: [PATCH 515/566] clean up commented out lines in BLASR & blasr_libcpp easyconfigs, no need to use cstd=c++11 for BLASR --- easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb | 2 -- .../b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb | 1 - 2 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb index e63d8bc616..d6ce3f9ad0 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb @@ -11,8 +11,6 @@ description = """ BLASR (Basic Local Alignment with Successive Refinement) rapid taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ toolchain = {'name': 'intel', 'version': '2017a'} -#toolchainopts = {'usempi': True} -toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] sources = ['%s.tar.gz' % commit] diff --git a/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb index e172377121..c6d9e3ba4f 100644 --- a/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb +++ b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb @@ -23,7 +23,6 @@ unpack_options = "--strip-components=1" skipsteps = ['configure', 'install'] buildininstalldir = True -#prebuildopts = "NOPBBAM=1 NOHDF=1 ./configure.py && " prebuildopts = "./configure.py && " sanity_check_paths = { -- GitLab From 006a5ed25c64d72593d5761c0672a4ba8bd9f34c Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 11 May 2017 15:20:45 +0930 Subject: [PATCH 516/566] EasyConfig for BioKanga v4.3.6 --- .../b/BioKanga/BioKanga-4.3.6-foss-2015b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb new file mode 100644 index 0000000000..e9e6ecd9f9 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.6' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From a0d0507e01ead49ed4189641b597f7f0be1001a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 08:43:03 +0200 Subject: [PATCH 517/566] use 'data' as moduleclass --- .../easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb index 1388501b14..6f5ffa7a5b 100644 --- a/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb @@ -19,4 +19,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'tools' +moduleclass = 'data' -- GitLab From 65fa3ba5ecc8668bfacd8eb7bd9b6141bcaac096 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 08:44:33 +0200 Subject: [PATCH 518/566] blank line between deps & builddeps --- easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb index 13433c2f04..abd8322098 100644 --- a/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb +++ b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb @@ -13,6 +13,7 @@ source_urls = ['https://github.com/AbiWord/enchant/releases/download/enchant-%s/ sources = [SOURCE_TAR_GZ] builddependencies = [('Autotools', '20150215')] + dependencies = [('hunspell', '1.6.1')] buildopts = "LIBTOOL='libtool --tag=CC'" -- GitLab From 64536687d1aaa8c0b42588f54367f04ed6b9da5c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 11 May 2017 14:17:24 +0200 Subject: [PATCH 519/566] adding easyconfigs: goolfc-2017.01.eb --- .../CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb | 24 ++++++++ .../f/FFTW/FFTW-3.3.6-gompic-2017.01.eb | 25 +++++++++ .../easyconfigs/g/gcccuda/gcccuda-2017.01.eb | 21 +++++++ .../easyconfigs/g/gompic/gompic-2017.01.eb | 23 ++++++++ .../easyconfigs/g/goolfc/goolfc-2017.01.eb | 38 +++++++++++++ .../h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb | 23 ++++++++ ...BLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb | 56 +++++++++++++++++++ .../OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb | 34 +++++++++++ ...ic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb | 25 +++++++++ 9 files changed, 269 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2017.01.eb create mode 100644 easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..8bfbdd15f7 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '8.0.61_375.26' + +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 = [ + 'https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/prod/local_installers/', + 'http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/', + 'https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/', +] + +sources = ['%(namelower)s_%(version)s_linux-run'] + +checksums = [ + '33e1bd980e91af4e55f3ef835c103f9b', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb new file mode 100644 index 0000000000..98911ef733 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb @@ -0,0 +1,25 @@ +name = 'FFTW' +version = '3.3.6' + +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': '2017.01'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb new file mode 100644 index 0000000000..1dc8205870 --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2017.01' + +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', '8.0.61_375.26', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb b/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb new file mode 100644 index 0000000000..138f18ef6c --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2017.01' + +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', '8.0.61_375.26', '', comp), # part of gcccuda + ('OpenMPI', '2.0.2', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb new file mode 100644 index 0000000000..b8e965c62e --- /dev/null +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb @@ -0,0 +1,38 @@ +easyblock = "Toolchain" + +name = 'goolfc' +version = '2017.01' + +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-3.7.0' +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', '8.0.61_375.26', '', comp), # part of gompic + ('OpenMPI', '2.0.2', '', ('gcccuda', version)), # part of gompic + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.6', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..547c202aa9 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +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=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb new file mode 100644 index 0000000000..4c55b7dc6c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.7.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$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-2.0.2-gcccuda-2017.01.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb new file mode 100644 index 0000000000..f4abe2cc5c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2017.01'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['886698becc5bea8c151c0af2074b8392'] + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--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-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb new file mode 100644 index 0000000000..8f3ffb84de --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.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': '2017.01'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.7.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff)] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 1ac0a3d24973bb43c15c441e2a7e7dd018d87276 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 21:17:56 +0200 Subject: [PATCH 520/566] adding easyconfigs: R-3.4.0-intel-2017a-X11-20170314.eb --- .../r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 514 ++++++++++++++++++ 1 file changed, 514 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb new file mode 100644 index 0000000000..0f9329d684 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -0,0 +1,514 @@ +name = 'R' +version = '3.4.0' +x11ver = '20170314' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +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" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.8'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.17.0'), + ('PCRE', '8.40'), + ('libpng', '1.6.29'), # for plotting in R + ('libjpeg-turbo', '1.5.1'), # for plottting in R + ('LibTIFF', '4.0.7'), + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.6'), # for tcltk + ('Tk', '8.6.6'), # for tcltk + ('cURL', '7.53.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +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 March 7th 2017 +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', '0.6-6', ext_options), + ('abind', '1.4-5', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.4-1', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '4.1.1', ext_options), + ('bootstrap', '2017.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.5', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-25', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.8', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-10', ext_options), + ('mclust', '5.2.3', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.4', ext_options), + ('stabledist', '0.7-1', 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', '1.7-6', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.62.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.9', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('backports', '1.0.5', ext_options), + ('checkmate', '1.8.2', ext_options), + ('Rcpp', '0.12.10', ext_options), + ('cubature', '1.3-8', ext_options), + ('DEoptimR', '1.0-8', ext_options), + ('digest', '0.6.12', ext_options), + ('fastmatch', '1.1-0', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.1.1', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.4-0', ext_options), + ('subplex', '1.2-2', ext_options), + ('stringi', '1.1.5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.2.0', ext_options), + ('evaluate', '0.10', ext_options), + ('logspline', '2.1.9', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.9-4', ext_options), + ('plotrix', '3.6-5', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-40', ext_options), + ('SparseM', '1.77', ext_options), + ('tripack', '1.3-8', ext_options), + ('irace', '2.3', ext_options), + ('rJava', '0.9-8', ext_options), + ('lattice', '0.20-35', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-28', ext_options), + ('Matrix', '1.2-10', ext_options), + ('png', '0.1-7', ext_options), + ('RcppArmadillo', '0.7.800.2.0', ext_options), + ('plyr', '1.8.4', ext_options), + ('pROC', '1.9.1', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.11', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-2', ext_options), + ('MASS', '7.3-47', ext_options), + ('tree', '1.0-37', ext_options), + ('pls', '2.6-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-8', ext_options), + ('nnet', '7.3-12', ext_options), + ('nlme', '3.1-131', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.3.3.0', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.33', ext_options), + ('mgcv', '1.8-17', ext_options), + ('colorspace', '1.3-2', ext_options), + ('robustbase', '0.92-7', ext_options), + ('sp', '1.2-4', ext_options), + ('zoo', '1.8-0', ext_options), + ('lmtest', '0.9-35', ext_options), + ('vcd', '1.4-3', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-11', ext_options), + ('survival', '2.41-3', ext_options), + ('mice', '2.30', ext_options), + ('urca', '1.3-0', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.22', ext_options), + ('akima', '0.6-2', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-19', ext_options), + ('mixtools', '1.1.0', ext_options), + ('cluster', '2.0.6', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', 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ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.3', ext_options), + ('diveRsity', '1.9.90', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.2.0', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.1', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('downloader', '0.4', ext_options), + ('imager', '0.40.2', dict(ext_options.items() + [('patches', ['imager-0.40.2_icpc-wd308.patch'])])), +] + +moduleclass = 'lang' + -- GitLab From 907e2454dc8d7bb28ef3852a02d94ab0461b1d7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 21:25:15 +0200 Subject: [PATCH 521/566] add missing patch files for kohoner/imager extensions in R v3.4.0 --- .../r/R/imager-0.40.2_icpc-wd308.patch | 21 +++++++++++++++++ .../r/R/kohonen-3.0.2_icpc-wd308.patch | 23 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch create mode 100644 easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch b/easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch new file mode 100644 index 0000000000..bdcf948b63 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch @@ -0,0 +1,21 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- imager/MD5.orig 2017-05-11 19:41:40.494524499 +0200 ++++ imager/MD5 2017-05-11 19:41:57.914534000 +0200 +@@ -178,7 +178,7 @@ + ad2654de31942fed6a81372ca95c69f8 *man/warp.Rd + 175e0ff835838c3a97f4e262ea2e22a9 *man/watershed.Rd + 6d2ea6da4b089e34b2c74fa9915598ad *man/where.Rd +-2d2d7a47e364f82c3a83d1def6997313 *src/Makevars.in ++4b7df5fe6555e13b54525ca11ac3bfb7 *src/Makevars.in + 0921c95e100ceb6edfe481db8258741c *src/Makevars.win + ad6fce36dbcb58ce1a05b98b5a87f263 *src/RcppExports.cpp + cac489a7495799d378cf0c10c8db3ebd *src/colourspace.cpp +--- imager/src/Makevars.in.orig 2017-05-11 19:41:06.494524465 +0200 ++++ imager/src/Makevars.in 2017-05-11 19:41:20.957122000 +0200 +@@ -1,3 +1,5 @@ + PKG_CPPFLAGS = $(SHLIB_OPENMP_CFLAGS) @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ @TIFF_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_use_r -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 -Dcimg_date='""' -Dcimg_time='""' + PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ @TIFF_LIBS@ $(RCPP_LDFLAGS) + ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 diff --git a/easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch b/easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch new file mode 100644 index 0000000000..7c77bb7a74 --- /dev/null +++ b/easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch @@ -0,0 +1,23 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- kohonen/MD5.orig 2017-05-11 18:42:50.494520969 +0200 ++++ kohonen/MD5 2017-05-11 18:43:02.299001000 +0200 +@@ -41,7 +41,7 @@ + 4074da8d1e8ba029d52de2a9ff24124b *man/unit.distances.Rd + c7f0e4739945511e6fcd67289320eab1 *man/wines.Rd + ad838f45c3a9435e7b2229b8cc6682ae *man/yeast.Rd +-74d73c2023015c6b008d9fdd11d60b14 *src/Makevars ++803f88be6a292da8d8ab21bdf420bda0 *src/Makevars + fada3f440c7f59d360c9303e803b1460 *src/RcppExports.cpp + 0b0c395e4a39ef2e6b31d2459c449912 *src/batch-supersom.cpp + 478e89466560e680760d7781c81acbcc *src/distance-functions.cpp +--- kohonen/src/Makevars.orig 2017-05-11 18:42:07.494520926 +0200 ++++ kohonen/src/Makevars 2017-05-11 18:42:34.436276000 +0200 +@@ -1,3 +1,4 @@ +-PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) +-PKG_CXXFLAGS = $(SHLIB_OPENMP_CFLAGS) +-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) -wd308 ++PKG_CXXFLAGS = $(SHLIB_OPENMP_CFLAGS) -wd308 ++PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) -wd308 -- GitLab From f2abe0f2e6cfb51114b25520766aad0dfa32f615 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 21:30:04 +0200 Subject: [PATCH 522/566] adding easyconfigs: R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb --- ...le-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 168 ++++++++++++++++++ 1 file changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..99eea4dc16 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -0,0 +1,168 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('HDF5', '1.10.0-patch1'), # for rhdf5 +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://bioconductor.org/packages/3.5/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.5/data/annotation/src/contrib/', + 'http://bioconductor.org/packages/3.5/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.22.0', bioconductor_options), + ('Biobase', '2.36.2', bioconductor_options), + ('S4Vectors', '0.14.0', bioconductor_options), + ('IRanges', '2.10.0', bioconductor_options), + ('GenomeInfoDbData', '0.99.0', bioconductor_options), + ('GenomeInfoDb', '1.12.0', bioconductor_options), + ('AnnotationDbi', '1.38.0', bioconductor_options), + ('zlibbioc', '1.22.0', bioconductor_options), + ('XVector', '0.16.0', bioconductor_options), + ('Biostrings', '2.44.0', bioconductor_options), + ('GenomicRanges', '1.28.1', bioconductor_options), + ('BiocParallel', '1.10.1', bioconductor_options), + ('Rsamtools', '1.28.0', bioconductor_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('DelayedArray', '0.2.2', bioconductor_options), + ('SummarizedExperiment', '1.6.1', bioconductor_options), + ('GenomicAlignments', '1.12.0', bioconductor_options), + ('ShortRead', '1.34.0', bioconductor_options), + ('graph', '1.54.0', bioconductor_options), + ('affyio', '1.46.0', bioconductor_options), + ('BiocInstaller', '1.26.0', bioconductor_options), + ('preprocessCore', '1.38.1', bioconductor_options), + ('affy', '1.54.0', bioconductor_options), + ('GO.db', '3.4.1', bioconductor_options), + ('limma', '3.32.2', bioconductor_options), + ('RBGL', '1.52.0', bioconductor_options), + ('org.Hs.eg.db', '3.4.1', bioconductor_options), + ('AnnotationForge', '1.18.0', bioconductor_options), + ('KEGG.db', '3.2.3', bioconductor_options), + ('annaffy', '1.48.0', bioconductor_options), + ('gcrma', '2.48.0', bioconductor_options), + ('oligoClasses', '1.38.0', bioconductor_options), + ('edgeR', '3.18.1', bioconductor_options), + ('PFAM.db', '3.4.1', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.10.0', bioconductor_options), + ('qvalue', '2.8.0', bioconductor_options), + ('impute', '1.50.1', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.30.0', bioconductor_options), + ('hgu133plus2.db', '3.2.3', bioconductor_options), + ('illuminaio', '0.18.0', bioconductor_options), + ('rtracklayer', '1.36.0', bioconductor_options), + ('biomaRt', '2.32.0', bioconductor_options), + ('GenomicFeatures', '1.28.0', bioconductor_options), + ('bumphunter', '1.16.0', bioconductor_options), + ('multtest', '2.32.0', bioconductor_options), + ('siggenes', '1.50.0', bioconductor_options), + ('DynDoc', '1.54.0', bioconductor_options), + ('genoset', '1.32.0', bioconductor_options), + ('NOISeq', '2.20.0', bioconductor_options), + ('Rgraphviz', '2.20.0', bioconductor_options), + ('RNASeqPower', '1.16.0', bioconductor_options), + ('annotate', '1.54.0', bioconductor_options), + ('GSEABase', '1.38.0', bioconductor_options), + ('genefilter', '1.58.1', bioconductor_options), + ('Category', '2.38.0', bioconductor_options), + ('GOstats', '2.42.0', bioconductor_options), + ('BSgenome', '1.44.0', bioconductor_options), + ('VariantAnnotation', '1.22.0', bioconductor_options), + ('interactiveDisplayBase', '1.14.0', bioconductor_options), + ('AnnotationHub', '2.8.1', bioconductor_options), + ('AnnotationFilter', '1.0.0', bioconductor_options), + ('ProtGenerics', '1.8.0', bioconductor_options), + ('ensembldb', '2.0.1', bioconductor_options), + ('biovizBase', '1.24.0', bioconductor_options), + ('OrganismDbi', '1.18.0', bioconductor_options), + ('ggbio', '1.24.0', bioconductor_options), + ('geneplotter', '1.54.0', bioconductor_options), + ('DESeq2', '1.16.1', bioconductor_options), + ('ReportingTools', '2.16.0', bioconductor_options), + ('affycoretools', '1.48.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.26.0', bioconductor_options), + ('GenomeGraphs', '1.36.0', bioconductor_options), + ('geneLenDataBase', '1.12.0', bioconductor_options), + ('goseq', '1.28.0', bioconductor_options), + ('KEGGREST', '1.16.0', bioconductor_options), + ('KEGGgraph', '1.34.0', bioconductor_options), + ('KEGGprofile', '1.18.0', bioconductor_options), + ('GEOquery', '2.42.0', bioconductor_options), + ('mixOmics', '6.1.3', ext_options), + ('minfi', '1.22.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.22.0', bioconductor_options), + ('lumi', '2.28.0', bioconductor_options), + ('widgetTools', '1.54.0', bioconductor_options), + ('tkWidgets', '1.54.0', bioconductor_options), + ('Mfuzz', '2.36.0', bioconductor_options), + ('venn', '1.2', ext_options), + ('maSigPro', '1.48.0', bioconductor_options), + ('SPIA', '2.28.0', bioconductor_options), + ('Gviz', '1.20.0', bioconductor_options), + ('cummeRbund', '2.18.0', bioconductor_options), + ('GenomicFiles', '1.12.0', bioconductor_options), + ('derfinderHelper', '1.10.0', bioconductor_options), + ('derfinder', '1.10.3', bioconductor_options), + ('polyester', '1.12.0', bioconductor_options), + ('Rsubread', '1.26.0', bioconductor_options), + ('pcaMethods', '1.68.0', bioconductor_options), + ('marray', '1.54.0', bioconductor_options), + ('CGHbase', '1.36.0', bioconductor_options), + ('sigaR', '1.24.0', bioconductor_options), + ('HCsnip', '1.16.0', bioconductor_options), + ('metagenomeSeq', '1.18.0', bioconductor_options), + ('gdsfmt', '1.12.0', bioconductor_options), + ('SNPRelate', '1.10.1', dict(bioconductor_options.items() + [('patches', ['SNPRelate-1.6.5_no-SSE-intr.patch'])])), + ('rhdf5', '2.20.0', bioconductor_options), + ('biomformat', '1.4.0', bioconductor_options), + ('phyloseq', '1.20.0', bioconductor_options), + ('ALDEx2', '1.8.0', bioconductor_options), + ('RcppParallel', '4.3.20', ext_options), + ('dada2', '1.4.0', bioconductor_options), + ('LEA', '1.8.1', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From 5ada904273c09ec09a905f36c44ee31bc583c9a0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 12 May 2017 09:56:28 +0800 Subject: [PATCH 523/566] prepare release notes for eb321 --- RELEASE_NOTES | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d67162b731..7fd5ec2c84 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,23 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,943 easyconfig files, for 1,216 different software packages, +The latest version of easybuild-easyconfig provides 7,037 easyconfig files, for 1,228 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.2.1 (May 12th 2017) +---------------------- + +bugfix/update release +- added example easyconfig files for 12 new software packages: + - AdapterRemoval (#4509), blasr_libcpp (#4566), canu (#4473), enchant (#4567), hunspell (#4567), memkind (#4544), + NLTK (#4565), pbbam (#4566), pbdagcon (#4566), pyenchant (#4567), Siesta (#4562), xarray (#4556) +- added additional easyconfigs for various supported software packages, including: + - ASE 3.13.0, AdapterRemoval 2.2.0, BLASR 20170330, BerkeleyGW 1.2.0, BioKanga 4.3.6, Boost 1.63.0, Boost 1.63.0, blasr_libcpp 20170426, CGAL 4.8.1, CGAL 4.9, CMake 3.8.1, CUDA 8.0.61_375.26, Coreutils 8.27, canu 1.4, EasyBuild 3.2.0.eb, Eigen 3.3.3, enchant 1.6.1, FFTW 3.3.6, flex 2.5.39, GROMACS 2016.1, gcccuda 2017.01.eb, gompic 2017.01.eb, googletest 1.8.0, goolfc 2017.01.eb, grib_api 1.21.0, HDF5 1.10.1, HDF5 1.8.18, HDF5 1.8.18, HDF5 1.8.18, HTSlib 20160107, h5py 2.7.0, hanythingondemand 3.2.2, hanythingondemand 3.2.2, hunspell 1.6.1, hwloc 1.11.5, JasPer 1.900.1, Keras 2.0.4, LLVM 3.9.1, LLVM 4.0.0, METIS 5.1.0, MPFR 3.1.5, matplotlib 2.0.1, memkind 1.5.0, NAMD 2.11, NAMD 2.12, NLTK 3.2.2, nose parameterized, OSU Micro, OTF2 2.0, OpenBLAS 0.2.19, OpenFOAM 2.2.2, OpenFOAM 2.3.1, OpenFOAM 2.4.0, OpenFOAM 4.0, OpenFOAM 4.1, OpenFOAM 4.1, OpenMPI 2.0.2, OpenMPI 2.0.2, ParMETIS 4.0.3, ParaView 5.2.0, ParaView 5.2.0, ParaView 5.3.0, PyYAML 3.12, Python 2.7.13, pandas 0.20.1, pbbam 20170508, pbdagcon 20170330, pkg config, pkgconfig 1.2.2, protobuf python, protobuf python, protobuf 3.3.0, pyenchant 1.6.8, Qt 4.8.7, Qt5 5.8.0, RAxML 8.2.10, SCOTCH 6.0.4, ScaLAPACK 2.0.2, Siesta 4.0, Siesta 4.1, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, scikit learn, Tcl 8.5.19, Tensorflow 1.1.0, Tensorflow 1.1.0, Theano 0.9.0, tbb 2017.4.174.eb, tbb 2017_U5, x265 2.4, xarray 0.9.5 +- minor enhancements, including: + - update source URLs in libpciaccess easyconfigs (#3960) + - enable use of double precision floating point in METIS 5.1.0 foss/2016a easyconfig (#4555) + + v3.2.0 (May 5th 2017) --------------------- -- GitLab From 9059b01edbf202cc26b0313d7f85c12ba5bd3a02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 08:51:58 +0200 Subject: [PATCH 524/566] fix update date for extensions in R 3.4.0 easyconfig --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 0f9329d684..949ed58bbb 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -13,7 +13,7 @@ source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" -#Actually use Tcl/Tk +# Actually use Tcl/Tk configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" @@ -62,7 +62,7 @@ ext_options = { } # !! order of packages is important !! -# packages updated on March 7th 2017 +# packages updated on May 11th 2017 exts_list = [ # default libraries, only here to sanity check their presence 'base', -- GitLab From 143826bdf5c4a40c95e9bb07bd20bd38f1914964 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 08:53:34 +0200 Subject: [PATCH 525/566] add update date for extensions in R-bundle-Bioconductor 3.5 easyconfig --- .../R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb index 99eea4dc16..80580237a7 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -37,6 +37,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! +# packages updated on May 11th 2017 exts_list = [ ('BiocGenerics', '0.22.0', bioconductor_options), ('Biobase', '2.36.2', bioconductor_options), -- GitLab From 583d4167050a61ca7a9737d49a17bfd7a38910f6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 12 May 2017 09:53:54 +0200 Subject: [PATCH 526/566] {tools}[intel/2016b] imbalanced-learn 0.2.1 /w Python 2.7.12 (REVIEW) --- ...d-learn-0.2.1-intel-2016b-Python-2.7.12.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..6f8572780e --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'imbalanced-learn' +version = '0.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('scikit-learn', '0.18.1', versionsuffix), +] + +options = {'modulename': 'imblearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From d637dc7a1b7d40ae4c70305b74ab3c1d3c7fc18e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 10:26:08 +0200 Subject: [PATCH 527/566] bump version to v3.2.1 and massage release notes --- RELEASE_NOTES | 6 ++++-- setup.py | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 7fd5ec2c84..4b1afa6117 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 7,037 easyconfig files, for 1,228 different software packages, +The latest version of easybuild-easyconfig provides 7,036 easyconfig files, for 1,228 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.2.1 (May 12th 2017) @@ -13,8 +13,10 @@ bugfix/update release - added example easyconfig files for 12 new software packages: - AdapterRemoval (#4509), blasr_libcpp (#4566), canu (#4473), enchant (#4567), hunspell (#4567), memkind (#4544), NLTK (#4565), pbbam (#4566), pbdagcon (#4566), pyenchant (#4567), Siesta (#4562), xarray (#4556) +- added new easyconfigs for existing toolchains: + - goolfc 2017.01 (#4577) - added additional easyconfigs for various supported software packages, including: - - ASE 3.13.0, AdapterRemoval 2.2.0, BLASR 20170330, BerkeleyGW 1.2.0, BioKanga 4.3.6, Boost 1.63.0, Boost 1.63.0, blasr_libcpp 20170426, CGAL 4.8.1, CGAL 4.9, CMake 3.8.1, CUDA 8.0.61_375.26, Coreutils 8.27, canu 1.4, EasyBuild 3.2.0.eb, Eigen 3.3.3, enchant 1.6.1, FFTW 3.3.6, flex 2.5.39, GROMACS 2016.1, gcccuda 2017.01.eb, gompic 2017.01.eb, googletest 1.8.0, goolfc 2017.01.eb, grib_api 1.21.0, HDF5 1.10.1, HDF5 1.8.18, HDF5 1.8.18, HDF5 1.8.18, HTSlib 20160107, h5py 2.7.0, hanythingondemand 3.2.2, hanythingondemand 3.2.2, hunspell 1.6.1, hwloc 1.11.5, JasPer 1.900.1, Keras 2.0.4, LLVM 3.9.1, LLVM 4.0.0, METIS 5.1.0, MPFR 3.1.5, matplotlib 2.0.1, memkind 1.5.0, NAMD 2.11, NAMD 2.12, NLTK 3.2.2, nose parameterized, OSU Micro, OTF2 2.0, OpenBLAS 0.2.19, OpenFOAM 2.2.2, OpenFOAM 2.3.1, OpenFOAM 2.4.0, OpenFOAM 4.0, OpenFOAM 4.1, OpenFOAM 4.1, OpenMPI 2.0.2, OpenMPI 2.0.2, ParMETIS 4.0.3, ParaView 5.2.0, ParaView 5.2.0, ParaView 5.3.0, PyYAML 3.12, Python 2.7.13, pandas 0.20.1, pbbam 20170508, pbdagcon 20170330, pkg config, pkgconfig 1.2.2, protobuf python, protobuf python, protobuf 3.3.0, pyenchant 1.6.8, Qt 4.8.7, Qt5 5.8.0, RAxML 8.2.10, SCOTCH 6.0.4, ScaLAPACK 2.0.2, Siesta 4.0, Siesta 4.1, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, scikit learn, Tcl 8.5.19, Tensorflow 1.1.0, Tensorflow 1.1.0, Theano 0.9.0, tbb 2017.4.174.eb, tbb 2017_U5, x265 2.4, xarray 0.9.5 + - HDF5 1.10.1, NAMD 2.12, OpenFOAM 4.1, pandas 0.20.1, ParaView 5.2.0, R 3.4.0, R-bundle-Bioconductor 3.5, Tensorflow 1.1.0 - minor enhancements, including: - update source URLs in libpciaccess easyconfigs (#3960) - enable use of double precision floating point in METIS 5.1.0 foss/2016a easyconfig (#4555) diff --git a/setup.py b/setup.py index 85590c2983..cdf0d69c62 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 = '3.3.0.dev0' +VERSION = '3.2.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From e531e19778783ca7f5285c4c8d6dc8b2485b8756 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 14:26:56 +0200 Subject: [PATCH 528/566] (re-)bump to v3.3.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cdf0d69c62..85590c2983 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 = '3.2.1' +VERSION = '3.3.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From ee171bc1dce094e97f1862ecc390486b82b7c86f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 14:32:46 +0200 Subject: [PATCH 529/566] adding easyconfigs: EasyBuild-3.2.1.eb --- .../e/EasyBuild/EasyBuild-3.2.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb new file mode 100644 index 0000000000..dfebb15dea --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.2.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/77/a2/34beda6176a1c85e99861f6a5e881c3a5c67e68e1edc50258a7d941195e8/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/3d/02/a5d239cbe7dfaecf712edc4aa53192239db174505e81d4c793e20abd96b6/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/ac/ae/185b876b02b2f2310fe52bb41539d23a00e421e5b19c246779e4b2be03a8/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.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 8aeae6284f5fe6bcb0bb5832f4a1ea0ec04ce5e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 May 2017 19:39:51 +0200 Subject: [PATCH 530/566] adding easyconfigs: NAMD-2.12-intel-2017a-mpi.eb --- .../n/NAMD/NAMD-2.12-intel-2017a-mpi.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb new file mode 100644 index 0000000000..a859f5adf4 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb @@ -0,0 +1,24 @@ +name = 'NAMD' +version = '2.12' +versionsuffix = '-mpi' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['NAMD_%(version)s_Source.tar.gz'] + +dependencies = [ + ('Tcl', '8.6.6'), + ('FFTW', '3.3.6'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +charm_arch = "mpi-linux-x86_64" + +moduleclass = 'chem' -- GitLab From e75dd82ba959670948e38161852763656350f6c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 10:26:16 +0200 Subject: [PATCH 531/566] style fixes: use single quotes, fix order in toolchainopts --- easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb index a859f5adf4..fd5bdbb7ed 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb @@ -7,7 +7,7 @@ description = """NAMD is a parallel molecular dynamics code designed for high-pe large biomolecular systems.""" toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'usempi': True, 'pic': True} +toolchainopts = {'pic': True, 'usempi': True} sources = ['NAMD_%(version)s_Source.tar.gz'] @@ -19,6 +19,6 @@ dependencies = [ # /bin/csh is required by 'config' script osdependencies = ['tcsh'] -charm_arch = "mpi-linux-x86_64" +charm_arch = 'mpi-linux-x86_64' moduleclass = 'chem' -- GitLab From 28a58de9d80083c85473f36012476856d93edcb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 11:20:31 +0200 Subject: [PATCH 532/566] adding easyconfigs: STAR-2.5.3a-intel-2017a.eb --- .../s/STAR/STAR-2.5.3a-intel-2017a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb new file mode 100644 index 0000000000..7bb56d5efd --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb @@ -0,0 +1,43 @@ +# 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 +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.3a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ["bin/STAR", "bin/STARlong"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 61ed4e7c403d624f0d85b986ff9a3818eb6371a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 11:51:15 +0200 Subject: [PATCH 533/566] adding easyconfigs: Velvet-1.2.10-intel-2017a-mt-kmer_37.eb --- .../Velvet-1.2.10-intel-2017a-mt-kmer_37.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb new file mode 100644 index 0000000000..19b58c6e52 --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.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, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_37' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True, 'pic': True} + +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] + +buildopts = "OPENMP=1 MAXKMERLENGTH=%s LONGSEQUENCES=1" % versionsuffix.split('_')[1] + +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + +moduleclass = 'bio' -- GitLab From 7934c12a2e7fc6fd81543a7c8df06a1b6788a6b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 11:52:38 +0200 Subject: [PATCH 534/566] adding easyconfigs: Bpipe-0.9.9.2-intel-2017a.eb, Java-1.8.0_131.eb --- .../b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb | 21 +++++++++++++++++++ .../easyconfigs/j/Java/Java-1.8.0_131.eb | 15 +++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb diff --git a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb new file mode 100644 index 0000000000..b0ee97e8f9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'Bpipe' +version = '0.9.9.2' + +homepage = 'http://docs.bpipe.org/' +description = "Bpipe - a tool for running and managing bioinformatics pipelines" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.bpipe.org/versions/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8.0_131', '', True)] + +sanity_check_paths = { + 'files': ['bin/bpipe', 'lib/bpipe.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb new file mode 100644 index 0000000000..2bb2551e95 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_131' + +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 26cd2367b99136755e104c2dd2b5063f67c5c957 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 16:19:34 +0200 Subject: [PATCH 535/566] adding easyconfigs: netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb, netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb, netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb --- ...tCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb | 25 +++++++++++++ ...F-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb | 18 ++++++++++ .../netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb | 36 +++++++++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..62c2012841 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' +versionsuffix = '-HDF5-1.8.18' + +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': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1', versionsuffix)] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..188697273d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.4' +versionsuffix = '-HDF5-1.8.18' + +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': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1', versionsuffix)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..8bc6d56640 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,36 @@ +name = 'netCDF' +version = '4.4.1.1' +hdf5_ver = '1.8.18' +versionsuffix = '-HDF5-%s' % hdf5_ver + +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': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', hdf5_ver), + ('cURL', '7.53.1'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From c134dc6583580744f6a678ec0671352361d19c91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 16:52:33 +0200 Subject: [PATCH 536/566] adding easyconfigs: Doris-4.04beta4-intel-2017a.eb, Doris-4.06beta2-intel-2017a.eb --- .../d/Doris/Doris-4.04beta4-intel-2017a.eb | 16 ++++++++++++++++ .../d/Doris/Doris-4.06beta2-intel-2017a.eb | 16 ++++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb new file mode 100644 index 0000000000..ad3c1ecff3 --- /dev/null +++ b/easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'Doris' +version = '4.04beta4' + +homepage = 'http://doris.tudelft.nl/' +description = "Delft object-oriented radar interferometric software" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://doris.tudelft.nl/software/'] +sources = ['doris_v%(version)s.tar.gz'] + +dependencies = [ + ('FFTW', '3.3.6'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb new file mode 100644 index 0000000000..190f829952 --- /dev/null +++ b/easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'Doris' +version = '4.06beta2' + +homepage = 'http://doris.tudelft.nl/' +description = "Delft object-oriented radar interferometric software" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://doris.tudelft.nl/software/'] +sources = ['doris_v%(version)s.tar.gz'] + +dependencies = [ + ('FFTW', '3.3.6'), +] + +moduleclass = 'geo' -- GitLab From b1d528ec317c4f012caf7d34c67ec6f25a6008b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 17:11:22 +0200 Subject: [PATCH 537/566] adding easyconfigs: EricScript-0.5.5-intel-2017a-R-3.4.0.eb, ada-2.0-5-intel-2017a-R-3.4.0.eb, BWA-0.7.15-intel-2017a.eb, SAMtools-1.4.1-intel-2017a.eb, BEDTools-2.26.0-intel-2017a.eb, seqtk-1.2-intel-2017a.eb --- .../a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb | 22 +++++++++++ .../b/BEDTools/BEDTools-2.26.0-intel-2017a.eb | 33 +++++++++++++++++ .../b/BWA/BWA-0.7.15-intel-2017a.eb | 32 ++++++++++++++++ .../EricScript-0.5.5-intel-2017a-R-3.4.0.eb | 34 +++++++++++++++++ .../s/SAMtools/SAMtools-1.4.1-intel-2017a.eb | 37 +++++++++++++++++++ .../s/seqtk/seqtk-1.2-intel-2017a.eb | 28 ++++++++++++++ 6 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb create mode 100644 easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..b1735c68ac --- /dev/null +++ b/easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'RPackage' + +name = 'ada' +version = '2.0-5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/ada/index.html' +description = "Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['ada_%(version)s.tar.gz'] + +dependencies = [('R', '3.4.0', '-X11-20170314')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb new file mode 100644 index 0000000000..48be152602 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb new file mode 100644 index 0000000000..04f7fad391 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , 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 +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.15' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..adaed6879a --- /dev/null +++ b/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'Tarball' + +name = 'EricScript' +version = '0.5.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://sites.google.com/site/bioericscript/home' +description = "EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('ada', '2.0-5', versionsuffix), + ('BWA', '0.7.15'), + ('SAMtools', '1.4.1'), + ('BEDTools', '2.26.0'), + ('seqtk', '1.2'), + ('BLAT', '3.5'), +] + +postinstallcmds = ["chmod a+rx %(installdir)s/ericscript.pl"] + +sanity_check_paths = { + 'files': ['ericscript.pl', 'LICENSE', 'README'], + 'dirs': ['lib'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb new file mode 100644 index 0000000000..cd48ea8cde --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb new file mode 100644 index 0000000000..d6c74b18dc --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'seqtk' +version = '1.2' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/lh3/seqtk/archive/'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +files_to_copy = ["seqtk"] + +sanity_check_paths = { + 'files': files_to_copy, + 'dirs': [], +} + +modextrapaths = { + 'PATH': [''], +} + +moduleclass = 'bio' -- GitLab From e1a4963d905de9962b793beed5336e14098d1577 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 19:35:34 +0200 Subject: [PATCH 538/566] {data}[intel/2017a] NCL 6.4.0 (+ deps) --- .../ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb | 32 +++++++ ...0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb | 49 ++++++++++ .../n/NCL/NCL-6.4.0-intel-2017a.eb | 40 ++++++++ .../n/NCL/NCL-6.4.0_fix-types.patch | 94 +++++++++++++++++++ 4 files changed, 215 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..7d428e69ac --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,32 @@ +name = 'ESMF' +version = '6.3.0rp1' +versionsuffix = '-HDF5-1.8.18' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = [ + 'ESMF-6.1.1_libopts.patch', + 'ESMF-%(version)s_fix-file-open-test.patch', +] + +dependencies = [ + ('netCDF', '4.4.1.1', versionsuffix), + ('netCDF-Fortran', '4.4.4', versionsuffix), + ('netCDF-C++4', '4.3.0', versionsuffix), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb new file mode 100644 index 0000000000..26dd6f6835 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.2.0' +hdf5_ver = '1.8.18' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5_ver + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5_ver), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', '-Python-%(pyver)s'), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb new file mode 100644 index 0000000000..69a80fc8ea --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb @@ -0,0 +1,40 @@ +name = 'NCL' +version = '6.4.0' + +homepage = 'http://www.ncl.ucar.edu' +description = """NCL is an interpreted language designed specifically for scientific data analysis and + visualization.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +#toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} +toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c99'} + +# download via https://www.earthsystemgrid.org/dataset/ncl.html +sources = ['%(namelower)s_ncarg-%(version)s.tar.gz'] + +patches = ['NCL-%(version)s_fix-types.patch'] + +hdf5_ver = '1.8.18' +dependencies = [ + ('cURL', '7.53.1'), + ('JasPer', '1.900.1'), + ('g2lib', '1.4.0'), + ('g2clib', '1.6.0'), + ('HDF', '4.2.12'), + ('HDF5', hdf5_ver), + ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5_ver), + ('netCDF-Fortran', '4.4.4', '-HDF5-%s' % hdf5_ver), + ('Szip', '2.1'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('zlib', '1.2.11'), + ('GDAL', '2.2.0', '-Python-2.7.13-HDF5-%s' % hdf5_ver), + ('UDUNITS', '2.2.24'), + ('ESMF', '6.3.0rp1', '-HDF5-%s' % hdf5_ver), + ('bzip2', '1.0.6'), + ('cairo', '1.14.8'), + ('libiconv', '1.15'), + ('GSL', '2.3'), +] +builddependencies = [('makedepend', '1.0.5')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch b/easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch new file mode 100644 index 0000000000..ecdfe831e0 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch @@ -0,0 +1,94 @@ +fix compilation problems due to incorrect type +author: Kenneth Hoste (HPC-UGent) +--- ni/src/lib/nfp/SCRIP2KMLW.c.orig 2017-04-21 11:22:11.523861897 +0200 ++++ ni/src/lib/nfp/SCRIP2KMLW.c 2017-04-21 11:22:17.773923222 +0200 +@@ -8,17 +8,17 @@ + NhlErrorTypes SCRIP2KML_W(void) { + /* Defining the Arguments */ + /* Argument # 0 */ +- string * scrip_filename; ++ NclQuark* scrip_filename; + char * c_scrip_filename; + int ncid; + + /* Argument # 1 */ +- string * kml_filename; ++ NclQuark* kml_filename; + char * c_kml_filename; + FILE * fid; + + /* Argument # 2 */ +- string * gridname; ++ NclQuark* gridname; + char * c_gridname; + + /* End of Defining the Arguments */ +@@ -48,7 +48,7 @@ + + /* Getting Arguments values */ + /* Argument # 0 */ +- scrip_filename = (string *) NclGetArgValue( ++ scrip_filename = (NclQuark*) NclGetArgValue( + 0, + 3, + NULL, +@@ -61,7 +61,7 @@ + c_scrip_filename = NrmQuarkToString(*scrip_filename); + + /* Argument # 1 */ +- kml_filename = (string *) NclGetArgValue( ++ kml_filename = (NclQuark*) NclGetArgValue( + 1, + 3, + NULL, +@@ -74,7 +74,7 @@ + c_kml_filename = NrmQuarkToString(*kml_filename); + + /* Argument # 1 */ +- gridname = (string *) NclGetArgValue( ++ gridname = (NclQuark*) NclGetArgValue( + 2, + 3, + NULL, +@@ -212,4 +212,4 @@ + free(grid_corner_lon); + fclose(fid); + return (NhlNOERROR); +-} +\ No newline at end of file ++} +--- ni/src/lib/nfp/Unstruct2KMLW.c.orig 2017-04-21 11:20:50.403067496 +0200 ++++ ni/src/lib/nfp/Unstruct2KMLW.c 2017-04-21 11:21:34.883504667 +0200 +@@ -7,12 +7,12 @@ + NhlErrorTypes Unstruct2KML_W(void) { + /* Defining the Arguments */ + /* Argument # 0 */ +- string * filename; ++ NclQuark* filename; + char * c_filename; + FILE * fid; + + /* Argument # 1 */ +- string * gridname; ++ NclQuark* gridname; + char * c_gridname; + + /* Argument # 2 */ +@@ -50,7 +50,7 @@ + + /* Getting Arguments values */ + /* Argument # 0 */ +- filename = (string *) NclGetArgValue( ++ filename = (NclQuark*) NclGetArgValue( + 0, + 6, + NULL, +@@ -63,7 +63,7 @@ + c_filename = NrmQuarkToString(*filename); + + /* Argument # 1 */ +- gridname = (string *) NclGetArgValue( ++ gridname = (NclQuark*) NclGetArgValue( + 1, + 6, + NULL, -- GitLab From a870c28a01201cd38a21584c6f614e470204f76b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 20:56:01 +0200 Subject: [PATCH 539/566] add missing patch file for GDAL 2.2.0 with intel/2017a --- .../g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch new file mode 100644 index 0000000000..c876781483 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch @@ -0,0 +1,11 @@ +add definition for uchar type that is not known by Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- gdal-2.2.0/frmts/jpeg2000/jpeg2000_vsil_io.h.orig 2017-05-15 17:23:31.334324922 +0200 ++++ gdal-2.2.0/frmts/jpeg2000/jpeg2000_vsil_io.h 2017-05-15 17:23:52.134563207 +0200 +@@ -34,4 +34,6 @@ + + jas_stream_t *JPEG2000_VSIL_fopen(const char *filename, const char *mode); + ++#define uchar unsigned char ++ + #endif -- GitLab From f350e79564938b994f09e48b09bdbe88964ab95e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 09:30:27 +0200 Subject: [PATCH 540/566] clean up toolchainopts in NCL 6.4.0 easyconfig --- easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb index 69a80fc8ea..9fa92eb87b 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb @@ -6,8 +6,7 @@ description = """NCL is an interpreted language designed specifically for scient visualization.""" toolchain = {'name': 'intel', 'version': '2017a'} -#toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} -toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c99'} +toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} # download via https://www.earthsystemgrid.org/dataset/ncl.html sources = ['%(namelower)s_ncarg-%(version)s.tar.gz'] -- GitLab From 9b014dfe78bf42f2c5f26e82868346b9dd0bff48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 09:58:11 +0200 Subject: [PATCH 541/566] adding easyconfigs: SCons-2.5.1-intel-2017a.eb --- .../s/SCons/SCons-2.5.1-intel-2017a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb new file mode 100644 index 0000000000..cfdd0743d4 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.1' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# SCons requires Python 2, rely on system Python so we can use SCons when module for Python 3.x is loaded +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +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 a7191dd886149d7f146737462f4dc79bc6b58d07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:17:28 +0200 Subject: [PATCH 542/566] adding easyconfigs: SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb --- ...SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..e2776528bd --- /dev/null +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'SpiceyPy' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/AndrewAnnex/SpiceyPy' +description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'geo' -- GitLab From 34a5f16d1c19c76a6275b1e1e76a735243bce8c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:19:34 +0200 Subject: [PATCH 543/566] adding easyconfigs: h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb --- ...l-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb new file mode 100644 index 0000000000..22fe0fbf91 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +hdf5_ver = '1.10.0-patch1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5_ver + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.1'), + ('HDF5', hdf5_ver), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From efa22960a1721b67796cfac831401c5c0f98d8ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:34:27 +0200 Subject: [PATCH 544/566] adding easyconfigs: GDAL-2.2.0-intel-2017a-Python-3.6.1.eb, GEOS-3.6.1-intel-2017a-Python-3.6.1.eb, SWIG-3.0.12-intel-2017a-Python-3.6.1.eb --- .../GDAL-2.2.0-intel-2017a-Python-3.6.1.eb | 48 +++++++++++++++++++ .../GEOS-3.6.1-intel-2017a-Python-3.6.1.eb | 29 +++++++++++ .../SWIG-3.0.12-intel-2017a-Python-3.6.1.eb | 20 ++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..0b26815dc5 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '3.6.1'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '2.0.12'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..786b191d55 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-%(version)s_fix-Python3.patch'] + +dependencies = [('Python', '3.6.1')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..5c78d52fbe --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.12' +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': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('PCRE', '8.40'), +] + +moduleclass = 'devel' -- GitLab From 35513ec7cbaaf931910118fbf7f6567ffb5f5dbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:35:59 +0200 Subject: [PATCH 545/566] add missing patch for GEOS --- .../g/GEOS/GEOS-3.6.1_fix-Python3.patch | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch new file mode 100644 index 0000000000..51d136b71d --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch @@ -0,0 +1,65 @@ +fix configuring with Python 3 +cfr. https://trac.osgeo.org/geos/ticket/774 +--- configure.orig 2016-12-29 17:33:15.229294313 +0100 ++++ configure 2016-12-29 18:33:27.822625611 +0100 +@@ -18329,7 +18329,7 @@ + if ${am_cv_python_version+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_version=`$PYTHON -c "import sys; print sys.version[:3]"` ++ am_cv_python_version=`$PYTHON -c "import sys; print(sys.version[:3])"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_version" >&5 + $as_echo "$am_cv_python_version" >&6; } +@@ -18348,7 +18348,7 @@ + if ${am_cv_python_platform+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_platform=`$PYTHON -c "import sys; print sys.platform"` ++ am_cv_python_platform=`$PYTHON -c "import sys; print(sys.platform)"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_platform" >&5 + $as_echo "$am_cv_python_platform" >&6; } +@@ -18362,7 +18362,7 @@ + if ${am_cv_python_pythondir+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_pythondir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(0,0,prefix='$PYTHON_PREFIX')" 2>/dev/null || ++ am_cv_python_pythondir=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_lib(0,0,prefix='$PYTHON_PREFIX'))" 2>/dev/null || + echo "$PYTHON_PREFIX/lib/python$PYTHON_VERSION/site-packages"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_pythondir" >&5 +@@ -18379,7 +18379,7 @@ + if ${am_cv_python_pyexecdir+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_pyexecdir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(1,0,prefix='$PYTHON_EXEC_PREFIX')" 2>/dev/null || ++ am_cv_python_pyexecdir=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,0,prefix='$PYTHON_EXEC_PREFIX'))" 2>/dev/null || + echo "${PYTHON_EXEC_PREFIX}/lib/python${PYTHON_VERSION}/site-packages"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_pyexecdir" >&5 +@@ -18448,19 +18448,21 @@ + # Check for Python library path + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Python library path" >&5 + $as_echo_n "checking for Python library path... " >&6; } +- for i in "$base_python_path/lib/python$PYTHON_VERSION/config/" "$base_python_path/lib/python$PYTHON_VERSION/" "$base_python_path/lib/python/config/" "$base_python_path/lib/python/" "$base_python_path/" "$base_python_path/libs/" ; do +- python_path=`find $i -name libpython$PYTHON_VERSION.* -print 2> /dev/null | sed "1q"` ++ for i in "$base_python_path/lib/python$PYTHON_VERSION/config/" "$base_python_path/lib/python$PYTHON_VERSION/" "$base_python_path/lib/python/config/" "$base_python_path/lib/python/" "$base_python_path/" "$base_python_path/libs/" "$base_python_path/lib/" ; do ++ python_path=`find $i -name libpython$PYTHON_VERSION*.so* -print 2> /dev/null | sed "1q"` + if test -n "$python_path" ; then + break + fi + done ++ ++ lpython_name=`python -c "import os; print(os.path.split(\"$python_path\")[1].split(\".so\")[0].split(\"lib\")[1])"` + python_path=`echo $python_path | sed "s,/libpython.*$,,"` + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $python_path" >&5 + $as_echo "$python_path" >&6; } + if test -z "$python_path" ; then + as_fn_error $? "cannot find Python library path" "$LINENO" 5 + fi +- PYTHON_LDFLAGS="-L$python_path -lpython$PYTHON_VERSION" ++ PYTHON_LDFLAGS="-L$python_path -l$lpython_name" + + # + python_site=`echo $base_python_path | sed "s/config/site-packages/"` -- GitLab From 7561b619e73b3afa2cc5bc68c2f35e798f09cbc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:37:19 +0200 Subject: [PATCH 546/566] adding easyconfigs: motif-2.3.7-intel-2017a.eb, xbitmaps-1.1.1.eb, flex-2.6.4-GCCcore-6.3.0.eb --- .../f/flex/flex-2.6.4-GCCcore-6.3.0.eb | 24 ++++++++++++ .../m/motif/motif-2.3.7-intel-2017a.eb | 39 +++++++++++++++++++ .../easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb | 19 +++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..c864ccaca1 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb @@ -0,0 +1,24 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['2882e3179748cc9f9c23ec593d6adc8d'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb new file mode 100644 index 0000000000..e0ba802b63 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.7' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('X11', '20170314'), + ('libpng', '1.6.29'), + ('xbitmaps', '1.1.1', '', True), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.29.2'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb new file mode 100644 index 0000000000..b56ca14110 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_DATA_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 0377a1294cf02a92a3163d815860a572958fba73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 11:49:06 +0200 Subject: [PATCH 547/566] {bio}[intel/2017a] TopHat 2.1.1 --- .../t/TopHat/TopHat-2.1.1-intel-2017a.eb | 41 +++++++++++++++++++ .../TopHat-2.1.1_fix-templating-error.patch | 13 ++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb new file mode 100644 index 0000000000..f3be80ad62 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.1' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = [ + 'tophat-2.0.13-zlib.patch', + 'TopHat-2.1.1_fix-templating-error.patch', +] + +dependencies = [ + ('Boost', '1.64.0'), + ('zlib', '1.2.11'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch new file mode 100644 index 0000000000..0abcfeeb26 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch @@ -0,0 +1,13 @@ +fix templating compilation error, let type inference do its job +authors: Kenneth Hoste (HPC-UGent), Ward Poelmans (VUB) +--- tophat-2.1.1/src/tophat_reports.cpp.orig 2017-05-16 11:24:21.776900497 +0200 ++++ tophat-2.1.1/src/tophat_reports.cpp 2017-05-16 11:25:31.958523978 +0200 +@@ -2705,7 +2705,7 @@ + junction_stat.gtf_match = true; + junction_stat.accepted = true; + +- gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); ++ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); + } + } + fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str()); -- GitLab From 0650f1b517d052a4e93fc7b4a99b8d5e421402fd Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 16 May 2017 13:45:29 +0200 Subject: [PATCH 548/566] adding easyconfigs: SeqAn-2.3.2-foss-2016b.eb --- .../s/SeqAn/SeqAn-2.3.2-foss-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb new file mode 100644 index 0000000000..28c6b25215 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb @@ -0,0 +1,37 @@ +# 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 = "CMakeMake" + +name = 'SeqAn' +version = '2.3.2' + +homepage = 'https://www.seqan.de/' +description = """SeqAn is an open source C++ library of efficient algorithms and data structures + for the analysis of sequences with the focus on biological data""" + +# GCC > 5 required. https://github.com/seqan/seqan#prerequisites +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/seqan/seqan/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +# CMake > 3 required. CMake >= 3.4 recommended +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", "rabema_prepare_sam", + "seqan_tcoffee", "s4_join", "samcat", "splazers", "yara_mapper"]], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From dc8ce7b3d0b19c872e7539e880dfaee4786e8553 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 16 May 2017 15:04:01 +0200 Subject: [PATCH 549/566] update CMake dependency to 3.7.2 --- easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb index 28c6b25215..b89f6044b4 100644 --- a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/seqan/seqan/archive/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] # CMake > 3 required. CMake >= 3.4 recommended -builddependencies = [('CMake', '3.4.3')] +builddependencies = [('CMake', '3.7.2')] dependencies = [ ('zlib', '1.2.8'), -- GitLab From ebf4e914abd70d84f09a56acc1c20c3d638a10e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 17:07:13 +0200 Subject: [PATCH 550/566] adding easyconfigs: NCO-4.6.6-intel-2017a.eb, ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb, libdap-3.18.1-intel-2017a.eb, LibUUID-1.0.3-intel-2017a.eb --- .../ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb | 32 +++++++++++++++++ .../l/LibUUID/LibUUID-1.0.3-intel-2017a.eb | 19 ++++++++++ .../l/libdap/libdap-3.18.1-intel-2017a.eb | 32 +++++++++++++++++ .../n/NCO/NCO-4.6.6-intel-2017a.eb | 35 +++++++++++++++++++ 4 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e00f225a13 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_includes.patch'] + +dependencies = [ + ('Java', '1.8.0_131', '', True), + ('Python', '2.7.13'), +] + +configopts = '--disable-examples --disable-csharp ' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb new file mode 100644 index 0000000000..a50ce3901e --- /dev/null +++ b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'LibUUID' +version = '1.0.3' + +homepage = 'http://sourceforge.net/projects/libuuid/' +description = """Portable uuid C library""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/uuid/uuid.h', 'lib/libuuid.a', 'lib/libuuid.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb new file mode 100644 index 0000000000..437ea556cf --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.18.1' + +homepage = 'http://opendap.org/download/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 + and the development versions of DAP3, up to 3.4. + This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.53.1'), + ('libxml2', '2.9.4'), + ('LibUUID', '1.0.3'), +] + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb b/easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb new file mode 100644 index 0000000000..b9edf1373e --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.6.6' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.24'), + ('expat', '2.2.0'), + ('ANTLR', '2.7.7', '-Python-2.7.13'), + ('libdap', '3.18.1'), + ('GSL', '2.3'), + ('netCDF', '4.4.1.1', '-HDF5-1.8.18'), +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap', 'ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' -- GitLab From 06bbccbc6a65622a729a53d4d1b9555487911510 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 17:43:36 +0200 Subject: [PATCH 551/566] {data}[intel/2017a] CDO 1.8.1 + YAXT 0.5.1 --- .../c/CDO/CDO-1.8.1-intel-2017a.eb | 31 +++++++++++++++++++ .../y/YAXT/YAXT-0.5.1-intel-2017a.eb | 23 ++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb new file mode 100644 index 0000000000..f6f33ffc90 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.8.1' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://code.zmaw.de/attachments/download/14271/'] +checksums = ['54498438de788f245d47499efad7966c'] + +dependencies = [ + ('HDF5', '1.8.18'), + ('netCDF', '4.4.1.1', '-HDF5-1.8.18'), + ('YAXT', '0.5.1'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF" +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/^\(LIBS.*\)/\\1 -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb new file mode 100644 index 0000000000..4cdb872a2c --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.5.1' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://www.dkrz.de/redmine/attachments/download/473/'] +checksums = ['2176c5b1096146e58163656b9d83c0b3'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' -- GitLab From 0c48bec1e62a5778a068bd6bb9acdd3e4952f610 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 19:44:51 +0200 Subject: [PATCH 552/566] simplify patching of libcdi Makefiles in CDO easyconfig --- easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb index f6f33ffc90..1e3e7c4c76 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb @@ -21,7 +21,7 @@ dependencies = [ configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF" # fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 -prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/^\(LIBS.*\)/\\1 -lhdf5_hl -lhdf5/g' && " +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " sanity_check_paths = { 'files': ['bin/cdo'], -- GitLab From 4aebea8ec5da414b987f37af99914dddb715ca4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 21:47:14 +0200 Subject: [PATCH 553/566] use 'git diff --name-only' and $TRAVIS_COMMIT_RANGE in Travis config to get list of changed files --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 07cebed738..2fcb5e365f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -40,5 +40,7 @@ install: - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi script: + - echo $TRAVIS_COMMIT_RANGE + - cd $TRAVIS_BUILD_DIR; git diff --name-only $(echo $TRAVIS_COMMIT_RANGE | sed 's/\.//'); cd - > /dev/null - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From bd23642e2d2c6686caaef2b752817389437509a4 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Wed, 17 May 2017 09:36:48 -0400 Subject: [PATCH 554/566] add FFmpeg easyconfig with support to x265 and LAME --- .../f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb | 34 +++++++++++++++++++ .../l/LAME/LAME-3.99.5-foss-2016b.eb | 30 ++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb new file mode 100644 index 0000000000..374f64671c --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.3.1' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.02'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('x264', '20160614'), + ('x265', '2.4'), + ('LAME', '3.99.5'), + ('X11', '20160819'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb new file mode 100644 index 0000000000..042510cf2a --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.99.5' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] + +dependencies = [('ncurses', '6.0')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 0c5e71d70e1d1ec068990eff100d8e053a267dd4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 17 May 2017 15:46:08 +0200 Subject: [PATCH 555/566] adding easyconfigs: MUMmer-4.0.0beta-goolf-1.7.20.eb --- .../m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb new file mode 100644 index 0000000000..8471838376 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +# 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 = 'MUMmer' +version = '4.0.0beta' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +patches = ['mummer-%(version)s.patch'] + +moduleclass = 'bio' -- GitLab From 8e1bf1c361216cb5bc75de261cdc612704e3bdd9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 17 May 2017 15:52:41 +0200 Subject: [PATCH 556/566] added mummer patch --- .../easyconfigs/m/MUMmer/mummer-4.0.0beta.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch diff --git a/easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch b/easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch new file mode 100644 index 0000000000..b95c705ef8 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch @@ -0,0 +1,15 @@ +Fix a compilation error in version 4.0.0beta +https://github.com/gmarcais/mummer/issues/7 + +diff -ru mummer-4.0.0beta.orig/src/essaMEM/mummer.cpp mummer-4.0.0beta/src/essaMEM/mummer.cpp +--- mummer-4.0.0beta.orig/src/essaMEM/mummer.cpp 2017-04-06 19:49:04.000000000 +0200 ++++ mummer-4.0.0beta/src/essaMEM/mummer.cpp 2017-05-17 15:36:51.998784593 +0200 +@@ -218,7 +218,7 @@ + case 22: + #ifdef VERSION + std::cout << VERSION << '\n'; +-#elif ++#else + std::cout << "\n"; + #endif + exit(0); -- GitLab From a9e81f5a5670c4b90ed5cc8f10243742b554c14e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 May 2017 17:40:01 +0200 Subject: [PATCH 557/566] adding easyconfigs: gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb, MPC-1.0.3-intel-2017a.eb --- .../gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++++++ .../m/MPC/MPC-1.0.3-intel-2017a.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d82b9f3a9d --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('Python', '2.7.13'), + ('GMP', '6.1.2'), + ('MPFR', '3.1.5'), + ('MPC', '1.0.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb b/easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb new file mode 100644 index 0000000000..5bddb3e5d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.0.3' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.multiprecision.org/mpc/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.2'), + ('MPFR', '3.1.5'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 0933fa668c99dee172f6ddae2d7349654c35dee6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 09:14:09 +0200 Subject: [PATCH 558/566] adding easyconfigs: scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb, matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb --- ...plotlib-2.0.2-intel-2017a-Python-2.7.13.eb | 43 +++++++++++++++++++ ...-learn-0.18.1-intel-2017a-Python-2.7.13.eb | 30 +++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..fa289dd53b --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,43 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.7.1'), +] + +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-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb new file mode 100755 index 0000000000..388e0e3afa --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('matplotlib', '2.0.2', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 2bfb83215f61d130c7363fcd8412e4ed09b961da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 09:19:36 +0200 Subject: [PATCH 559/566] adding easyconfigs: statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb --- ...smodels-0.8.0-intel-2017a-Python-2.7.13.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..85483b0005 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'statsmodels' +version = '0.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://statsmodels.sourceforge.net/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '2.7.13')] + +exts_list = [ + ('patsy', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'source_tmpl': 'patsy-%(version)s.zip', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], + 'source_tmpl': 'statsmodels-%(version)s.tar.gz', + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' -- GitLab From 7b5e6e94f527f488a3a966a7cc397c250fa2ddf2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 09:20:21 +0200 Subject: [PATCH 560/566] fix typo in statsmodels source url (/sources/ -> /source/) --- .../s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb index 435f33a3bd..484c222815 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb @@ -21,7 +21,7 @@ exts_list = [ 'source_tmpl': 'patsy-%(version)s.zip', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/sources/statsmodels'], + 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], 'source_tmpl': 'statsmodels-%(version)s.zip', }), ] -- GitLab From d76b99582a77ec30e760a41563bb7c12a398c0c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 11:25:50 +0200 Subject: [PATCH 561/566] adding easyconfigs: gnuplot-5.0.6-intel-2017a.eb, Pango-1.40.5-intel-2017a.eb, libgd-2.2.4-intel-2017a.eb, libcerf-1.5-intel-2017a.eb, HarfBuzz-1.3.1-intel-2017a.eb, GObject-Introspection-1.52.0-intel-2017a.eb --- ...Object-Introspection-1.52.0-intel-2017a.eb | 47 +++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.6-intel-2017a.eb | 42 +++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb | 34 ++++++++++++++ .../l/libcerf/libcerf-1.5-intel-2017a.eb | 28 +++++++++++ .../l/libgd/libgd-2.2.4-intel-2017a.eb | 26 ++++++++++ .../p/Pango/Pango-1.40.5-intel-2017a.eb | 31 ++++++++++++ 6 files changed, 208 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb new file mode 100644 index 0000000000..804872f657 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.52.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.13'), + ('GLib', '2.52.0'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('cairo', '1.14.8'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb new file mode 100644 index 0000000000..22b8ccefa5 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.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 = '5.0.6' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.8'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.29'), + ('libgd', '2.2.4'), + ('Pango', '1.40.5'), + ('libcerf', '1.5'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb new file mode 100644 index 0000000000..58049805dd --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.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': '2017a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GLib', '2.52.0'), + ('cairo', '1.14.8'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +builddependencies = [('GObject-Introspection', '1.52.0')] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.eb new file mode 100644 index 0000000000..3c7483ca6e --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.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': '2017a'} + +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' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb new file mode 100644 index 0000000000..1a8de80eb4 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.4' + +homepage = 'https://libgd.github.io/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.12.1', '-libpng-1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb new file mode 100644 index 0000000000..d7561a197b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.5' + +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': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('X11', '20170314'), + ('GLib', '2.52.0'), + ('cairo', '1.14.8'), + ('HarfBuzz', '1.3.1'), +] + +builddependencies = [('GObject-Introspection', '1.52.0')] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From 8a6b28c55b1bd5cc8e88bb7cd1a11b2084cafcff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 13:14:31 +0200 Subject: [PATCH 562/566] adding easyconfigs: Octave-4.2.1-intel-2017a.eb, arpack-ng-3.5.0-intel-2017a.eb, FLTK-1.3.4-intel-2017a.eb, GLPK-4.61-intel-2017a.eb, GL2PS-1.4.0-intel-2017a.eb, Qhull-2015.2-intel-2017a.eb, qrupdate-1.1.2-intel-2017a.eb, GraphicsMagick-1.3.25-intel-2017a.eb, freeglut-3.0.0-intel-2017a.eb, gperf-3.0.4-intel-2017a.eb, xprop-1.2.2-intel-2017a.eb --- .../arpack-ng/arpack-ng-3.5.0-intel-2017a.eb | 25 +++++++ .../f/FLTK/FLTK-1.3.4-intel-2017a.eb | 36 ++++++++++ .../f/freeglut/freeglut-3.0.0-intel-2017a.eb | 35 ++++++++++ .../g/GL2PS/GL2PS-1.4.0-intel-2017a.eb | 32 +++++++++ .../g/GLPK/GLPK-4.61-intel-2017a.eb | 28 ++++++++ .../GraphicsMagick-1.3.25-intel-2017a.eb | 39 +++++++++++ .../g/gperf/gperf-3.0.4-intel-2017a.eb | 22 +++++++ .../o/Octave/Octave-4.2.1-intel-2017a.eb | 65 +++++++++++++++++++ .../q/Qhull/Qhull-2015.2-intel-2017a.eb | 36 ++++++++++ .../q/qrupdate/qrupdate-1.1.2-intel-2017a.eb | 28 ++++++++ .../x/xprop/xprop-1.2.2-intel-2017a.eb | 30 +++++++++ 11 files changed, 376 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb new file mode 100644 index 0000000000..c2f959831c --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.5.0' + +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': '2017a'} +toolchainopts = {'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.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb new file mode 100644 index 0000000000..95391e1838 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb @@ -0,0 +1,36 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.4' + +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': '2017a'} +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', '17.0.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('xprop', '1.2.2'), + ('zlib', '1.2.11'), +] + +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/f/freeglut/freeglut-3.0.0-intel-2017a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb new file mode 100644 index 0000000000..64f67b2563 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.8.1')] + +dependencies = [ + ('X11', '20170314'), + ('libGLU', '9.0.0'), + ('Mesa', '17.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb new file mode 100644 index 0000000000..a2bcb6dc02 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.0' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.8.1'), +] + +dependencies = [ + ('X11', '20170314'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb new file mode 100644 index 0000000000..28b87558fc --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.61' + +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': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.2')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.eb new file mode 100644 index 0000000000..e1b8b64f3a --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.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': '2017a'} +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', '20170314'), + ('bzip2', '1.0.6'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('LibTIFF', '4.0.7'), + ('libxml2', '2.9.4'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('Ghostscript', '9.21'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.eb new file mode 100644 index 0000000000..6b56add6d5 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.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': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb new file mode 100644 index 0000000000..b28e83ac96 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.2.1' + +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': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('X11', '20170314'), + ('PCRE', '8.40'), + ('ncurses', '6.0'), + ('libreadline', '6.3'), + ('arpack-ng', '3.5.0'), + ('cURL', '7.53.1'), + ('FLTK', '1.3.4'), + ('fontconfig', '2.12.1', '-libpng-1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('GLPK', '4.61'), + ('GL2PS', '1.4.0'), + ('gnuplot', '5.0.6'), + ('Java', '1.8.0_131', '', True), + ('zlib', '1.2.11'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt5', '5.8.0'), + ('HDF5', '1.8.18', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.5', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.25'), + ('FFTW', '3.3.6'), +] + +configopts = 'MOC=$EBROOTQT5/bin/moc ' +configopts += 'UIC=$EBROOTQT5/bin/uic ' +configopts += 'RCC=$EBROOTQT5/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +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-intel-2017a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2017a.eb new file mode 100644 index 0000000000..a35971ec3e --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2017a.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': '2017a'} + +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', '3.8.1')] + +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/q/qrupdate/qrupdate-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2017a.eb new file mode 100644 index 0000000000..4f82f6763a --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2017a.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': '2017a'} +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' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.eb new file mode 100644 index 0000000000..773d17a26f --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.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': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('X11', '20170314'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 372b412676c7564c9f93360d7e897bd05491e24d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 19 May 2017 12:27:56 +0200 Subject: [PATCH 563/566] Keras/2.0.4 for Python 2.7.13 --- .../Keras-2.0.4-intel-2017a-Python-2.7.13.eb | 28 +++++++++++++++++++ .../Theano-0.9.0-intel-2017a-Python-2.7.13.eb | 23 +++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..7f78e14b8d --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Keras' +version = '2.0.4' +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': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Theano', '0.9.0', versionsuffix), + ('h5py', '2.7.0', '%(versionsuffix)s'), + ('PyYAML', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6119fbb576 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From c026c35e54a606aa89c99bcb1f4f50c62cfe535c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 19 May 2017 12:44:11 +0200 Subject: [PATCH 564/566] Switch default backend to Theano for keras --- .../k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb index 7f78e14b8d..b475663604 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb @@ -20,6 +20,9 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] +# it defaults to Tensorflow +modextravars = {'KERAS_BACKEND': 'theano'} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], -- GitLab From 0ff5782bb6b544645a89f85b268e3811a17ec77f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 19 May 2017 13:53:35 +0200 Subject: [PATCH 565/566] Sync Py3 and Py2 easyconfigs of Keras --- .../k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb index 45f0be1e64..d338fae1c9 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb @@ -20,6 +20,9 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] +# it defaults to Tensorflow +modextravars = {'KERAS_BACKEND': 'theano'} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], -- GitLab From f28aafad75d4bb0e567b219ba26fd4d4e4687141 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 20 May 2017 10:35:16 +0200 Subject: [PATCH 566/566] get list of added/modified files using 'git diff --name-only' in Travis config --- .travis.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 2fcb5e365f..accc9427b8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -39,8 +39,13 @@ install: - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi +before_script: + - cd $TRAVIS_BUILD_DIR + # pull in develop so we can diff against it + - git fetch -v origin ${TRAVIS_BRANCH}:${TRAVIS_BRANCH} + # get list of filenames for modified/added files, use '...' to compare with merge base of develop and branch + - git diff --name-only --diff-filter=AM ${TRAVIS_BRANCH}...HEAD script: - - echo $TRAVIS_COMMIT_RANGE - - cd $TRAVIS_BUILD_DIR; git diff --name-only $(echo $TRAVIS_COMMIT_RANGE | sed 's/\.//'); cd - > /dev/null + - cd $HOME - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab