Commit a65b1f73 authored by Lukáš Krupčík's avatar Lukáš Krupčík

new file: duplicate.sh

	deleted:    a/ABAQUS/ABAQUS-2017-hotfix-1721.eb
	deleted:    a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb
	deleted:    a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb
	deleted:    a/ARB/ARB-5.5-goolf-1.4.10.eb
	deleted:    c/CUDA/CUDA-7.5.18.eb
	deleted:    g/GSL/GSL-2.3-intel-2017a.eb
	deleted:    h/HPL/HPL-2.2-intel-2017b.eb
	deleted:    m/Mesa/Mesa-12.0.2-intel-2016b.eb
	deleted:    remove_list
	deleted:    s/ScientificPython/ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb
	deleted:    s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb
	deleted:    test.sh
	deleted:    x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb
	deleted:    x/xcb-proto/xcb-proto-1.11.eb
parent 839e4496
name = 'ABAQUS'
version = '2017'
hotfix = '1721'
versionsuffix = '-hotfix-%s' % hotfix
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."""
toolchain = {'name': 'dummy', 'version': ''}
sources = [
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-6.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.6-6.tar',
# hotfixes
'%%(version)s.FP.CFA.%s.Part_3DEXP_SimulationServices.Linux64.tar' % hotfix,
'%%(version)s.FP.CFA.%s.Part_SIMULIA_Abaqus_CAE.Linux64.tar' % hotfix,
]
moduleclass = 'cae'
##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
# 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 = 'AMOS'
version = '3.1.0'
homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
toolchain = {'name': 'goolf', 'version': '1.4.10'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')]
patches = ['AMOS-3.1.0_GCC-4.7.patch']
dependencies = [
('expat', '2.1.0'),
('MUMmer', '3.23'),
]
sanity_check_paths = {
'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'],
'dirs': []
}
parallel = 1 # make crashes otherwise
moduleclass = 'bio'
##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
# 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 = 'AMOS'
version = '3.1.0'
homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
toolchain = {'name': 'ictce', 'version': '5.3.0'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')]
dependencies = [
('expat', '2.1.0'),
('MUMmer', '3.23'),
]
sanity_check_paths = {
'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'],
'dirs': []
}
parallel = 1 # make crashes otherwise
moduleclass = 'bio'
name = 'ARB'
version = '5.5'
homepage = 'http://www.arb-home.de/'
description = """The ARB software is a graphically oriented package comprising various tools for sequence database
handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked
to the respective sequence entries is structured according to phylogeny or other user defined criteria."""
toolchain = {'name': 'goolf', 'version': '1.4.10'}
# download from http://download.arb-home.de/release/arb_5.5, and rename to include version
sources = ['%(namelower)s-%(version)s-src.tgz']
patches = [
'%(name)s-%(version)s_xmkmf.patch',
'%(name)s-%(version)s_xflags.patch',
]
dependencies = [
('libpng', '1.6.6'),
('LibTIFF', '4.0.3'),
('Java', '1.7.0_15', '', True),
('lynx', '2.8.7'),
('makedepend', '1.0.4'),
('imake', '1.0.5'),
('libXt', '1.1.4'),
('motif', '2.3.4'), # libXm
('libXpm', '3.5.11'),
('libXaw', '1.0.12'),
('Perl', '5.16.3'),
('libxslt', '1.1.28'),
('freeglut', '2.8.1'),
('Sablotron', '1.0.3'),
('libxml2', '2.9.1'),
]
moduleclass = 'bio'
name = 'CUDA'
version = '7.5.18'
homepage = 'https://developer.nvidia.com/cuda-toolkit'
description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
computing platform and programming model created by NVIDIA and implemented by the
graphics processing units (GPUs) that they produce. CUDA gives developers access
to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/']
sources = ['%(namelower)s_%(version)s_linux.run']
moduleclass = 'system'
......@@ -37,4 +37,6 @@ done
echo ""
for read in `cat duplicate`; do grep "$read" it4i; done | sort -u > remove_list
rm duplicate it4i develop
for rm in `cat remove_list | cut -d ';' -f 2`; do find . -name $rm -exec rm {} \;; done
rm duplicate it4i develop remove_list
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'
name = 'HPL'
version = '2.2'
homepage = 'http://www.netlib.org/benchmark/hpl/'
description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits)
arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available
implementation of the High Performance Computing Linpack Benchmark."""
toolchain = {'name': 'intel', 'version': '2017b'}
toolchainopts = {'usempi': True}
sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://www.netlib.org/benchmark/%(namelower)s']
checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440']
# fix Make dependencies, so parallel build also works
patches = ['HPL_parallel-make.patch']
moduleclass = 'tools'
# the purpose of the easyconfig is to build a Mesa for software rendering,
# not hardware rendering. This means you want at least SSE4.2. We build:
# - llvmpipe: the high-performance Gallium LLVM driver
# - swr: Intel's OpenSWR
# it will try to use the llvmpipe by default. It you want swr, do:
# GALLIUM_DRIVER=swr
easyblock = 'ConfigureMake'
name = 'Mesa'
version = '12.0.2'
homepage = 'http://www.mesa3d.org/'
description = """Mesa is an open-source implementation of the OpenGL specification -
a system for rendering interactive 3D graphics."""
toolchain = {'name': 'intel', 'version': '2016b'}
# swr detects and builds parts specific for AVX and AVX2. If we use
# -xHost, this always gets overwritten and will fail.
toolchainopts = {'optarch': False}
sources = [SOURCELOWER_TAR_XZ]
source_urls = [
'https://mesa.freedesktop.org/archive/%(version)s',
'ftp://ftp.freedesktop.org/pub/mesa/%(version)s',
'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s',
]
builddependencies = [
('flex', '2.6.0'),
('Bison', '3.0.4'),
('Autotools', '20150215'),
('pkg-config', '0.29.1'),
('Mako', '1.0.4', '-Python-2.7.12'),
('libxml2', '2.9.4', '-Python-2.7.12'),
]
dependencies = [
('zlib', '1.2.8'),
('nettle', '3.2'),
('libdrm', '2.4.70'),
('LLVM', '3.8.1'),
('X11', '20160819'),
]
# GLU is not part anymore of Mesa package!
configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri"
configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl"
configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs "
sanity_check_paths = {
'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT,
'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT,
'include/GL/glext.h', 'include/GL/gl_mangle.h',
'include/GL/glx.h', 'include/GL/osmesa.h',
'include/GL/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'
0515e2cba0b6b96e9a955ad98a991119;SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb
11f2dc760748e6e004378c8e2b277b70;XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb
1af592f5c53593710e9a65d4aecaa8f6;ABAQUS-2017-hotfix-1721.eb
22df523f7cc85cc59ef94b864ba42cb8;HPL-2.2-intel-2017b.eb
37a67325bd697ba16456d47f96a809e9;GSL-2.3-intel-2017a.eb
42c0a56911761bebefa424a6580e80fe;ARB-5.5-goolf-1.4.10.eb
454e580a5ededc4fc3ef984aac28bfe9;Mesa-12.0.2-intel-2016b.eb
4f649bd51dadf7c43d0b5118db54d915;AMOS-3.1.0-goolf-1.4.10.eb
515233dc386f6b025bc6c88ec8377c65;xcb-proto-1.11.eb
a47f78ce229d82b7818feb0d9e2e9480;CUDA-7.5.18.eb
d5a4360bcafc8486b843c83767044a7d;ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb
e8b947919b8aeb4a6a394d6831f5d6a4;AMOS-3.1.0-ictce-5.3.0.eb
easyblock = 'PythonPackage'
name = 'ScientificPython'
version = '2.9.4'
versionsuffix = '-Python-%(pyver)s'
homepage = 'https://sourcesup.cru.fr/projects/scientific-py/'
description = """ScientificPython is a collection of Python modules for scientific computing.
It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization,
and parallelization."""
toolchain = {'name': 'intel', 'version': '2016a'}
source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570']
sources = [SOURCE_TAR_GZ]
dependencies = [
('Python', '2.7.11'),
# older version of numpy than the one included in Python module required
# cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for
('numpy', '1.8.2', versionsuffix),
]
options = {'modulename': 'Scientific'}
sanity_check_paths = {
'files': [],
'dirs': ['lib/python%(pyshortver)s/site-packages/Scientific'],
}
moduleclass = 'math'
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'
easyblock = 'PerlModule'
name = 'XML-Parser'
version = '2.44'
versionsuffix = '-Perl-%(perlver)s'
homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/'
description = """This is a Perl extension interface to James Clark's XML parser, expat."""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/']
sources = [SOURCE_TAR_GZ]
dependencies = [
('Perl', '5.22.1'),
('expat', '2.1.1')
]
options = {'modulename': 'XML::Parser'}
sanity_check_paths = {
'files': [],
'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'],
}
moduleclass = 'data'
easyblock = 'ConfigureMake'
name = 'xcb-proto'
version = '1.11'
homepage = 'http://xcb.freedesktop.org/'
description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint,
latency hiding, direct access to the protocol, improved threading support, and extensibility."""
# even though xcb-proto is installed with configure-make-make install, nothing is actually built;
# only .py files are installed using Python, and some .xlm flies copied, so OK to use dummy toolchain
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://xcb.freedesktop.org/dist/']
sources = [SOURCELOWER_TAR_GZ]
allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2])
sanity_check_paths = {
'files': ['lib/pkgconfig/xcb-proto.pc'],
'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver]
}
moduleclass = 'devel'
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