Commit 4f6f1bf4 authored by Lukáš Krupčík's avatar Lukáš Krupčík

new file: a/ABySS/ABySS-2.0.2-foss-2018a-Py-2.7.eb

	new file:   a/ASE/ASE-3.15.0-Python-2.7.13-base-test.eb
	new file:   a/ASE/ASE-3.15.0-Python-3.6.4-base-test.eb
	new file:   b/Bash/Bash-4.4-GCC-6.3.0-2.27.eb
	new file:   b/Bash/Bash-4.4-intel-2017b.eb
	new file:   b/Boost/Boost-1.66.0-foss-2018a-Py-2.7.eb
	new file:   f/foss/foss-2018a.eb
	new file:   n/numpy/numpy-1.14.1-Py-3.6.eb
	new file:   n/numpy/numpy-1.14.1-mkl.patch
	new file:   o/OpenMPI/OpenMPI-3.0.0-GCC-6.3.0-2.27.eb
	new file:   s/SQLite/SQLite-3.21.0.eb
parent 78c56942
easyblock = 'ConfigureMake'
name = 'ABySS'
version = '2.0.2'
homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss'
description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"""
toolchain = {'name': 'foss', 'version': '2018a'}
toolchainopts = {'usempi': True}
source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/']
sources = [SOURCELOWER_TAR_GZ]
checksums = ['d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df']
dependencies = [
('Boost', '1.66.0', '-Py-2.7'),
('sparsehash', '2.0.3'),
('SQLite', '3.21.0', '', True),
]
configopts = " --enable-maxk=256 "
sanity_check_paths = {
'files': ["bin/ABYSS", "bin/ABYSS-P"],
'dirs': []
}
moduleclass = 'bio'
# IT4Innovations 2017
easyblock = 'PythonPackage'
name = 'ASE'
version = '3.15.0'
versionsuffix = '-Python-%(pyver)s-base-test'
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': 'dummy', 'version': ''}
source_urls = [PYPI_LOWER_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
dependencies = [
('Python', '2.7.13'),
# ('numpy', '1.13.0', '-Python-2.7.13-base'),
# ('scipy', '0.19.1', '-Python-2.7.13-base'),
# ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
]
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'
# IT4Innovations 2017
easyblock = 'PythonPackage'
name = 'ASE'
version = '3.15.0'
versionsuffix = '-Python-%(pyver)s-base-test'
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': 'dummy', 'version': ''}
source_urls = [PYPI_LOWER_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
dependencies = [
('Python', '3.6.1'),
# ('numpy', '1.13.0', '-Python-2.7.13-base'),
# ('scipy', '0.19.1', '-Python-2.7.13-base'),
# ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
]
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'
# IT4Innovations 2018
easyblock = 'ConfigureMake'
name = 'Bash'
version = '4.4'
homepage = 'http://www.gnu.org/software/bash'
description = """Bash is an sh-compatible command language interpreter that executes commands
read from the standard input or from a file. Bash also incorporates useful features from the
Korn and C shells (ksh and csh)."""
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [GNU_SOURCE]
dependencies = [
('libreadline', '7.0', '', True),
]
configopts = " --enable-readline --enable-job-control --enable-history "
sanity_check_paths = {
'files': ["bin/bash"],
'dirs': []
}
moduleclass = 'tools'
# IT4Innovations 2018
easyblock = 'ConfigureMake'
name = 'Bash'
version = '4.4'
homepage = 'http://www.gnu.org/software/bash'
description = """Bash is an sh-compatible command language interpreter that executes commands
read from the standard input or from a file. Bash also incorporates useful features from the
Korn and C shells (ksh and csh)."""
toolchain = {'name': 'intel', 'version': '2017b'}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [GNU_SOURCE]
dependencies = [
('libreadline', '7.0', '', True),
]
configopts = " --enable-readline --enable-job-control --enable-history "
sanity_check_paths = {
'files': ["bin/bash"],
'dirs': []
}
moduleclass = 'tools'
# IT4Innovations 2018
name = 'Boost'
version = '1.66.0'
versionsuffix = '-Py-2.7'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2018a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6', '', True),
('zlib', '1.2.11', '', True),
('Py', '2.7', '', True)
]
configopts = '--with-python=$EBROOTPYTHON/bin/python'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'
easyblock = 'Toolchain'
name = 'foss'
version = '2018a'
homepage = '(none)'
description = """GNU Compiler Collection (GCC) based compiler toolchain, including
OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
gccver = '6.3.0-2.27'
blaslib = 'OpenBLAS'
blasver = '0.2.20'
blas = '%s-%s' % (blaslib, blasver)
# toolchain used to build foss dependencies
comp_mpi_tc_name = 'gompi'
comp_mpi_tc = (comp_mpi_tc_name, version)
# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain
# because of toolchain preparation functions
# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds
dependencies = [
('GCC', gccver),
('OpenMPI', '3.0.0', '', ('GCC', gccver)),
(blaslib, blasver, '', ('GCC', gccver)),
('FFTW', '3.3.7', '', comp_mpi_tc),
('ScaLAPACK', '2.0.2', '-%s' % blas, comp_mpi_tc),
]
moduleclass = 'toolchain'
# IT4Innovations 2018
easyblock = 'PythonPackage'
name = 'numpy'
version = '1.14.1'
homepage = 'http://www.numpy.org'
description = """NumPy is the fundamental package needed for scientific computing with Python."""
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = ['https://github.com/numpy/numpy/releases/download/v%(version)s']
sources = ['%(name)s-%(version)s.tar.gz']
patches = [
'numpy-1.12.0-mkl.patch',
# 'numpy-1.14.1-mkl.patch'
]
builddependencies = [
# ('mkl', '2017.4.239', '', True),
('intel', '2017a', '', True),
]
#prebuildopts = 'mv site.cfg.example site.cfg && export MKL_THREADING_LAYER=GNU && ' # ' export CFLAGS="-fopenmp -m64 -mtune=native -O3 -Wl,--no-as-needed" && export CXXFLAGS="-fopenmp -m64 -mtune=native -O3 -Wl,--no-as-needed" && export LDFLAGS="-ldl -lm" && export FFLAGS="-fopenmp -m64 -mtune=native -O3" && '
sanity_check_paths = {
'files': [],
'dirs': ['lib/python3.6/site-packages/numpy-%(version)s-py3.6-linux-x86_64.egg/numpy'],
}
sanity_check_commands = [('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')]
moduleclass = 'python'
--- site.cfg.example.old 2018-02-20 00:16:17.000000000 +0100
+++ site.cfg.example 2018-03-09 10:47:51.496213510 +0100
@@ -159,11 +159,11 @@
# https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl
# Assuming you installed the mkl in /opt/intel/compilers_and_libraries_2018/linux/mkl,
# for 64 bits code at Linux:
-# [mkl]
-# library_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64
-# include_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/include
-# mkl_libs = mkl_rt
-# lapack_libs = 
+[mkl]
+library_dirs = /apps/all/mkl/2017.4.239/mkl/lib/intel64
+include_dirs = /apps/all/mkl/2017.4.239/mkl/include
+mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core
+lapack_libs = mkl_lapack95_lp64
#
# For 32 bit code at Linux:
# [mkl]
easyblock = 'ConfigureMake'
name = 'OpenMPI'
version = '3.0.0'
homepage = 'http://www.open-mpi.org/'
description = """The Open MPI Project is an open source MPI-2 implementation."""
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads']
sources = [SOURCELOWER_TAR_GZ]
checksums = ['0bbb279b88edc25bbded39520dab6d4b32020277a6088fb1456c9437a8231cf8']
builddependencies = [
('Java', '1.8.0_144', '', True)
]
dependencies = [
('hwloc', '1.11.7'),
('zlib', '1.2.11', '', True),
]
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 ' # dont disable dlopen! https://github.com/open-mpi/ompi/issues/3630
configopts += '--with-tm=/opt/pbs/default ' # Enable PBS
configopts += '--enable-mpi-java ' # Java support RT#4090
configopts += '--enable-mpi-cxx ' # Enable building the C++ MPI bindings
# for PBS Pro 13
preconfigopts = 'export LIBS="-ldl" && '
# to enable SLURM integration (site-specific)
# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr'
# 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': [],
}
modextravars = {'OMPI_MCA_btl_openib_if_include': 'mlx4_0',
'OMPI_MCA_oob_tcp_if_include': '10.0.0.0/8',
}
moduleclass = 'mpi'
# IT4Innovations 2018
easyblock = 'ConfigureMake'
name = 'SQLite'
version = '3.21.0'
homepage = 'http://www.sqlite.org/'
description = 'SQLite: SQL Database Engine in a C Library'
toolchain = {'name': 'dummy', 'version': ''}
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,
'sqlite-amalgamation-%s.zip' % version_str,
]
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'
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