Commit f4790d74 authored by Lukáš Krupčík's avatar Lukáš Krupčík

Merge branch 'it4i-salomon'

parents 3d2aed78 73be42b3
Pipeline #5453 passed with stage
in 28 seconds
# IT4Innovations 2018
easyblock = "PythonPackage"
name = 'enum34'
version = '1.1.6'
homepage = 'https://pypi.python.org/pypi/enum34'
description = 'An enumeration is a set of symbolic names (members) bound to unique, constant values.'
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ]
options = {'modulename': 'enum'}
sanity_check_paths = {
'files': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6.egg'],
'dirs': [],
}
moduleclass = 'python'
# IT4Innovations 2018
easyblock = "PythonPackage"
name = 'funcsigs'
version = '1.0.2'
homepage = 'https://pypi.python.org/pypi/enum34'
description = 'An enumeration is a set of symbolic names (members) bound to unique, constant values.'
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = [PYPI_SOURCE]
sources = ['funcsigs-1.0.2.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['lib/python3.6/site-packages/'],
}
moduleclass = 'python'
......@@ -31,6 +31,7 @@ dependencies = [
('zlib', '1.2.11', '', True),
('cURL', '7.61.1'),
('PCRE', '8.42'),
('PROJ_4', '4.9.2'),
]
configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-netcdf=$EBROOTNETCDF'
......
# IT4Innovations 2018
easyblock = 'ConfigureMake'
name = 'hwloc'
version = '1.11.7'
versionsuffix = '-c7'
homepage = 'http://www.open-mpi.org/projects/hwloc/'
description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction
(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including
NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various
system attributes such as cache and memory information as well as the locality of I/O devices such as
network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
information about modern computing hardware so as to exploit it accordingly and efficiently."""
toolchain = {'name': 'dummy', 'version': ''}
source_urls = [
'http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/']
sources = [SOURCE_TAR_GZ]
dependencies = [
('numactl', '2.0.11', '-c7'),
]
configopts = "--enable-libnuma=$EBROOTNUMACTL"
moduleclass = 'system'
# IT4Innovations 2018
easyblock = "PythonPackage"
name = 'Keras_Applications'
version = '1.0.6'
homepage = 'https://pypi.python.org/pypi/enum34'
description = 'An enumeration is a set of symbolic names (members) bound to unique, constant values.'
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = [PYPI_SOURCE]
sources = ['Keras_Applications-1.0.6.tar.gz']
sanity_check_paths = {
'files': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6.egg'],
'dirs': [],
}
moduleclass = 'python'
# IT4Innovations 2018
easyblock = "PythonPackage"
name = 'Keras_Preprocessing'
version = '1.0.5'
homepage = 'https://pypi.python.org/pypi/enum34'
description = 'An enumeration is a set of symbolic names (members) bound to unique, constant values.'
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = [PYPI_SOURCE]
sources = ['Keras_Preprocessing-1.0.5.tar.gz']
sanity_check_paths = {
'files': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6.egg'],
'dirs': [],
}
moduleclass = 'python'
# IT4Innovations 2018
easyblock = "PythonPackage"
name = 'mock'
version = '2.0.0'
homepage = 'https://pypi.python.org/pypi/enum34'
description = 'An enumeration is a set of symbolic names (members) bound to unique, constant values.'
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = [PYPI_SOURCE]
sources = ['mock-2.0.0.tar.gz']
dependencies = [
('six', '1.11.0'),
]
sanity_check_paths = {
'files': [],
'dirs': ['lib/python3.6/site-packages/mock-2.0.0-py3.6.egg-info/'],
}
moduleclass = 'python'
# IT4Innovations 2018
easyblock = 'ConfigureMake'
name = 'numactl'
version = '2.0.11'
versionsuffix= '-c7'
homepage = 'http://oss.sgi.com/projects/libnuma/'
description = """The numactl program allows you to run your application program on specific cpu's and memory nodes.
It does this by supplying a NUMA memory policy to the operating system before running your program.
The libnuma library provides convenient ways for you to add NUMA memory policies into your own program."""
toolchain = {'name': 'dummy', 'version': ''}
toolchainopts = {'pic': True}
source_urls = ['https://github.com/numactl/numactl/archive/']
sources = [SOURCE_TAR_GZ]
#preconfigopts = "./autogen.sh && "
sanity_check_paths = {
'files': [
'bin/numactl',
'bin/numastat',
'lib/libnuma.%s' %
SHLIB_EXT,
'lib/libnuma.a'],
'dirs': [
'share/man',
'include']}
moduleclass = 'tools'
# IT4Innovations 2018
easyblock = 'PythonPackage'
name = 'numpy'
version = '1.15.4'
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 = [SOURCE_TAR_GZ]
patch = [
'numpy-1.8.1-mkl.patch',
'numpy-1.11.0-sse42.patch'
]
dependencies = [
('mkl', '2017.4.239', '', True),
]
sanity_check_paths = {'files': [], 'dirs': [
'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/numpy'], }
sanity_check_commands = [
('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')]
moduleclass = 'python'
......@@ -17,17 +17,16 @@ source_urls = [
dependencies = [('hwloc', '1.11.7')]
configopts = '--with-threads=posix --enable-shared --enable-static --enable-mpi-thread-multiple --with-verbs'
configopts = '--with-threads=posix --enable-shared --enable-static --enable-mpi-thread-multiple --with-verbs '
# suppress failure modes in relation to mpirun path
configopts += '--enable-mpirun-prefix-by-default '
configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support
# statically link component, don't do dynamic loading
configopts += '--disable-dlopen '
configopts += '--with-tm=/opt/pbs/default ' # Enable PBS
configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify
# for PBS Pro 13
preconfigopts = 'export LIBS="-ldl" && export CC="$CC -noswitcherror" && export CXX="$CXX -noswitcherror" && '
preconfigopts = 'export LIBS="-ldl" && export CC="pgcc -noswitcherror" && export CXX="pgc++ -noswitcherror" && export FC="pgfortran -noswitcherror" && '
# needed for --with-verbs
osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')]
......
easyblock = 'ConfigureMake'
name = 'OpenMPI'
version = '2.1.1'
versionsuffix = '-c7'
homepage = 'http://www.open-mpi.org/'
description = """The Open MPI Project is an open source MPI-3.1 implementation."""
toolchain = {'name': 'dummy', 'version': ''}
source_urls = [
'http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads']
sources = [SOURCELOWER_TAR_GZ]
dependencies = [
('hwloc', '1.11.7', '-c7')
]
# for PBS Pro 13
preconfigopts = 'export LIBS="-ldl" && '
configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs '
# suppress failure modes in relation to mpirun path
configopts += '--enable-mpirun-prefix-by-default '
configopts += '--with-hwloc=$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
# needed for --with-verbs
osdependencies = [('libibverbs-dev', 'rdma-core-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 = "PythonPackage"
name = 'pbr'
version = '5.1.1'
homepage = 'https://pypi.python.org/pypi/enum34'
description = 'An enumeration is a set of symbolic names (members) bound to unique, constant values.'
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = [PYPI_SOURCE]
sources = ['pbr-5.1.1.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['lib/python3.6/site-packages/'],
}
moduleclass = 'python'
# IT4Innovations 2017
easyblock = 'PythonPackage'
name = 'protobuf-python'
version = '3.6.1'
homepage = 'https://github.com/google/protobuf/'
description = """Python Protocol Buffers runtime library."""
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = ['https://github.com/google/protobuf/archive/v%(version)s']
sources = [SOURCE_TAR_GZ]
dependencies = [
('protobuf', version)
]
# use_setup_py_develop = True
start_dir = 'python'
installopts = '--cpp_implementation'
sanity_check_paths = {
'files': [],
'dirs': ['lib/python3.6/site-packages'],
}
options = {'modulename': 'google.protobuf'}
moduleclass = 'devel'
# IT4Innovations 2018
easyblock = 'ConfigureMake'
name = 'protobuf'
version = '3.6.1'
homepage = 'https://code.google.com/p/protobuf/'
description = """Google Protocol Buffers"""
toolchain = {'name': 'Py', 'version': '3.6'}
toolchainopts = {'pic': True}
sources = ['%(name)s-python-%(version)s.tar.gz']
source_urls = [
'https://github.com/google/protobuf/releases/download/v%(version)s/']
# after instalation: python3 setup.py install --cpp_implementation
postinstallcmds = [
'cp %(builddir)s/%(name)s-%(version)s/ %(installdir)s/build -R',
]
sanity_check_paths = {
'files': ['bin/protoc'],
'dirs': [],
}
modextravars = {
'PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION': 'cpp',
}
moduleclass = 'devel'
# IT4Innovations 2018
easyblock = 'CMakeMake'
name = 'RDKit'
version = '2018.09.1'
versionsuffix = '-Py-2.7'
homepage = "https://www.rdkit.org"
description = """Open source toolkit for cheminformatics
Business-friendly BSD license
Core data structures and algorithms in C++
Python (2.x and 3.x) wrappers generated using Boost.Python
Java and C# wrappers generated with SWIG
2D and 3D molecular operations
Descriptor generation for machine learning
Molecular database cartridge for PostgreSQL
Cheminformatics nodes for KNIME (distributed from the KNIME community site: https://www.knime.com/rdkit)
"""
toolchain = {'name': 'foss', 'version': '2017a'}
source_urls = ['https://github.com/rdkit/rdkit/archive/']
sources = ['Release_2018_09_1.tar.gz']
dependencies = [
('CMake', '3.11.4', '', ('GCC', '6.3.0-2.27')),
('Py', '2.7', '', True),
('Boost', '1.66.0', '-Py-2.7'),
('SQLite', '3.25.2', '', ('GCC', '6.3.0-2.27')),
('numpy', '1.15.4', '-Py-2.7', True),
]
separate_build_dir = True
sanity_check_paths = {
'files': [],
'dirs': ['rdkit'],
}
moduleclass = 'chem'
# IT4Innovations 2018
easyblock = 'PythonPackage'
name = 'Tensorflow'
version = '1.12.0'
versionsuffix = '-Py-3.6'
homepage = 'https://www.tensorflow.org/'
description = "An open-source software library for Machine Intelligence"
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
#source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/']
sources = [
'tensorflow-%(version)s-cp36-cp36mu-linux_x86_64.whl',
]
dependencies = [
('Py', '3.6', '', True),
('OpenMPI', '2.1.1'),
('protobuf', '3.6.1', '-Py-3.6', True),
('numpy', '1.15.4', '-Py-3.6', True),
('protobuf-python', '3.6.1', '-Py-3.6', True),
('absl-py', '0.1.10', '-Py-3.6', True),
('Keras_Applications', '1.0.6', '-Py-3.6', True),
('Keras_Preprocessing', '1.0.5', '-Py-3.6', True),
('mock', '2.0.0', '-Py-3.6', True),
('pbr', '5.1.1', '-Py-3.6', True),
('funcsigs', '1.0.2', '-Py-3.6', True),
]
use_pip = True
unpack_sources = False
sanity_check_paths = {
'files': ['bin/tensorboard'],
'dirs': ['lib/python3.6/site-packages/tensorflow-1.12.0.dist-info/'],
}
moduleclass = 'lib'
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