new file: e/enum34/enum34-1.1.6-Py-3.6.eb

new file: f/funcsigs/funcsigs-1.0.2-Py-3.6.eb modified: g/GDAL/GDAL-2.3.2-Py-2.7.eb new file: h/hwloc/hwloc-1.11.7-c7.eb new file: k/Keras_Applications/Keras_Applications-1.0.6-Py-3.6.eb new file: k/Keras_Preprocessing/Keras_Preprocessing-1.0.5-Py-3.6.eb new file: m/mock/mock-2.0.0-Py-3.6.eb new file: n/numactl/numactl-2.0.11-c7.eb new file: n/numpy/numpy-1.15.4-Py-3.6.eb modified: o/OpenMPI/OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.eb new file: o/OpenMPI/OpenMPI-2.1.1-c7.eb new file: p/pbr/pbr-5.1.1-Py-3.6.eb new file: p/protobuf-python/protobuf-python-3.6.1-Py-3.6.eb new file: p/protobuf/protobuf-3.6.1-Py-3.6.eb new file: r/RDKit/RDKit-2018.09.1-foss-2017a-Py-2.7.eb new file: t/Tensorflow/Tensorflow-1.12.0-GCC-6.3.0-2.27-Py-3.6.eb
2025-04-07 15:32:11 +01:00 · 2018-11-26 12:10:01 +01:00 · 2018-11-26 12:10:01 +01:00 · 73be42b3f9
commit 73be42b3f9
parent 3d2aed78dc
16 changed files with 421 additions and 3 deletions
--- a/e/enum34/enum34-1.1.6-Py-3.6.eb
+++ b/e/enum34/enum34-1.1.6-Py-3.6.eb
@ -0,0 +1,22 @@
+# 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'
--- a/f/funcsigs/funcsigs-1.0.2-Py-3.6.eb
+++ b/f/funcsigs/funcsigs-1.0.2-Py-3.6.eb
@ -0,0 +1,20 @@
+# 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'
--- a/g/GDAL/GDAL-2.3.2-Py-2.7.eb
+++ b/g/GDAL/GDAL-2.3.2-Py-2.7.eb
@ -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=$EBROOTNETCDF'
--- a/h/hwloc/hwloc-1.11.7-c7.eb
+++ b/h/hwloc/hwloc-1.11.7-c7.eb
@ -0,0 +1,29 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'hwloc'
+version = '1.11.7'
+versionsuffix = '-c7'
+
+homepage = 'http://www.open-mpi.org/projects/hwloc/'
+description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction
+(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including
+NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various
+system attributes such as cache and memory information as well as the locality of I/O devices such as
+network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
+information about modern computing hardware so as to exploit it accordingly and efficiently."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = [
+    'http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/']
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('numactl', '2.0.11', '-c7'),
+]
+
+configopts = "--enable-libnuma=$EBROOTNUMACTL"
+
+moduleclass = 'system'
--- a/k/Keras_Applications/Keras_Applications-1.0.6-Py-3.6.eb
+++ b/k/Keras_Applications/Keras_Applications-1.0.6-Py-3.6.eb
@ -0,0 +1,20 @@
+# 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'
--- a/k/Keras_Preprocessing/Keras_Preprocessing-1.0.5-Py-3.6.eb
+++ b/k/Keras_Preprocessing/Keras_Preprocessing-1.0.5-Py-3.6.eb
@ -0,0 +1,20 @@
+# 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'
--- a/m/mock/mock-2.0.0-Py-3.6.eb
+++ b/m/mock/mock-2.0.0-Py-3.6.eb
@ -0,0 +1,24 @@
+# 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'
--- a/n/numactl/numactl-2.0.11-c7.eb
+++ b/n/numactl/numactl-2.0.11-c7.eb
@ -0,0 +1,33 @@
+# 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'
--- a/n/numpy/numpy-1.15.4-Py-3.6.eb
+++ b/n/numpy/numpy-1.15.4-Py-3.6.eb
@ -0,0 +1,31 @@
+# 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'
--- a/o/OpenMPI/OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.eb
+++ b/o/OpenMPI/OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.eb
@ -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')]
--- a/o/OpenMPI/OpenMPI-2.1.1-c7.eb
+++ b/o/OpenMPI/OpenMPI-2.1.1-c7.eb
@ -0,0 +1,52 @@
+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'
--- a/p/pbr/pbr-5.1.1-Py-3.6.eb
+++ b/p/pbr/pbr-5.1.1-Py-3.6.eb
@ -0,0 +1,20 @@
+# 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'
--- a/p/protobuf-python/protobuf-python-3.6.1-Py-3.6.eb
+++ b/p/protobuf-python/protobuf-python-3.6.1-Py-3.6.eb
@ -0,0 +1,33 @@
+# 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'
--- a/p/protobuf/protobuf-3.6.1-Py-3.6.eb
+++ b/p/protobuf/protobuf-3.6.1-Py-3.6.eb
@ -0,0 +1,32 @@
+# 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'
--- a/r/RDKit/RDKit-2018.09.1-foss-2017a-Py-2.7.eb
+++ b/r/RDKit/RDKit-2018.09.1-foss-2017a-Py-2.7.eb
@ -0,0 +1,41 @@
+# 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'
--- a/t/Tensorflow/Tensorflow-1.12.0-GCC-6.3.0-2.27-Py-3.6.eb
+++ b/t/Tensorflow/Tensorflow-1.12.0-GCC-6.3.0-2.27-Py-3.6.eb
@ -0,0 +1,41 @@
+# 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'