From c1fff69173d9cfda96c2bf1d109e0350342d1f4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Wed, 5 Feb 2020 08:44:31 +0100 Subject: [PATCH] new file: a/attrs/attrs-19.3.0-Py-3.7.eb new file: b/BAGEL/BAGEL-1.2.2-intel-2020a.eb new file: b/Boost/Boost-1.72.0-intel-2020a.eb new file: c/Cython/Cython-0.29.14-Py-system.eb new file: l/libxc/libxc-4.3.4-intel-2020a.eb new file: n/numpy/numpy-1.15.4-Py-system.eb new file: o/ORCA/ORCA-4.1.1-OpenMPI-3.1.3.eb new file: o/OpenMPI/OpenMPI-3.1.3-GCCcore-8.3.0.eb new file: p/Py/Py-system.eb new file: p/pandas/pandas-1.0.0-Py-3.7.eb new file: p/pluggy/pluggy-0.13.1-Py-3.7.eb new file: p/pytest/pytest-5.3.5-Py-3.7.eb new file: p/python-dateutil/python-dateutil-2.8.1-Py-3.7.eb new file: p/pytz/pytz-2019.3-Py-3.7.eb new file: r/ReFrame/ReFrame-2.21-Py-3.7.eb new file: s/six/six-1.14.0-Py-3.7.eb --- a/attrs/attrs-19.3.0-Py-3.7.eb | 23 +++++++++ b/BAGEL/BAGEL-1.2.2-intel-2020a.eb | 38 ++++++++++++++ b/Boost/Boost-1.72.0-intel-2020a.eb | 26 ++++++++++ c/Cython/Cython-0.29.14-Py-system.eb | 22 ++++++++ l/libxc/libxc-4.3.4-intel-2020a.eb | 50 +++++++++++++++++++ n/numpy/numpy-1.15.4-Py-system.eb | 32 ++++++++++++ o/ORCA/ORCA-4.1.1-OpenMPI-3.1.3.eb | 35 +++++++++++++ o/OpenMPI/OpenMPI-3.1.3-GCCcore-8.3.0.eb | 46 +++++++++++++++++ p/Py/Py-system.eb | 17 +++++++ p/pandas/pandas-1.0.0-Py-3.7.eb | 24 +++++++++ p/pluggy/pluggy-0.13.1-Py-3.7.eb | 21 ++++++++ p/pytest/pytest-5.3.5-Py-3.7.eb | 30 +++++++++++ .../python-dateutil-2.8.1-Py-3.7.eb | 27 ++++++++++ p/pytz/pytz-2019.3-Py-3.7.eb | 22 ++++++++ r/ReFrame/ReFrame-2.21-Py-3.7.eb | 30 +++++++++++ s/six/six-1.14.0-Py-3.7.eb | 20 ++++++++ 16 files changed, 463 insertions(+) create mode 100644 a/attrs/attrs-19.3.0-Py-3.7.eb create mode 100644 b/BAGEL/BAGEL-1.2.2-intel-2020a.eb create mode 100644 b/Boost/Boost-1.72.0-intel-2020a.eb create mode 100644 c/Cython/Cython-0.29.14-Py-system.eb create mode 100644 l/libxc/libxc-4.3.4-intel-2020a.eb create mode 100644 n/numpy/numpy-1.15.4-Py-system.eb create mode 100644 o/ORCA/ORCA-4.1.1-OpenMPI-3.1.3.eb create mode 100644 o/OpenMPI/OpenMPI-3.1.3-GCCcore-8.3.0.eb create mode 100644 p/Py/Py-system.eb create mode 100644 p/pandas/pandas-1.0.0-Py-3.7.eb create mode 100644 p/pluggy/pluggy-0.13.1-Py-3.7.eb create mode 100644 p/pytest/pytest-5.3.5-Py-3.7.eb create mode 100644 p/python-dateutil/python-dateutil-2.8.1-Py-3.7.eb create mode 100644 p/pytz/pytz-2019.3-Py-3.7.eb create mode 100644 r/ReFrame/ReFrame-2.21-Py-3.7.eb create mode 100644 s/six/six-1.14.0-Py-3.7.eb diff --git a/a/attrs/attrs-19.3.0-Py-3.7.eb b/a/attrs/attrs-19.3.0-Py-3.7.eb new file mode 100644 index 00000000..e41e32ed --- /dev/null +++ b/a/attrs/attrs-19.3.0-Py-3.7.eb @@ -0,0 +1,23 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'attrs' +version = '19.3.0' + +homepage = 'http://www.attrs.org/' +description = 'Classes Without Boilerplate' + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +options = {'modulename': 'attr'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.7/site-packages/%(name)s-%(version)s-py3.7.egg'], +} + +moduleclass = 'python' diff --git a/b/BAGEL/BAGEL-1.2.2-intel-2020a.eb b/b/BAGEL/BAGEL-1.2.2-intel-2020a.eb new file mode 100644 index 00000000..2313389b --- /dev/null +++ b/b/BAGEL/BAGEL-1.2.2-intel-2020a.eb @@ -0,0 +1,38 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'BAGEL' +version = '1.2.2' + +homepage = "http://www.nubakery.org" +description = """BAGEL (Brilliantly Advanced General Electronic-structure Library) +is a parallel electronic-structure program.""" + +# Note: A compiler bug(?) in template deduction prevents newer versions of icpc to compile this software. +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/nubakery/bagel/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Autotools', '20180311'), +] + +dependencies = [ + ('Boost', '1.72.0'), + ('libxc', '4.3.4'), +] + +# Hack, because bagel-v1.1.1 uses outdated filenames: +preconfigopts = 'sed -i "s|-gcc-mt||g" configure.ac && ' +preconfigopts += './autogen.sh && ' +preconfigopts += 'CXXFLAGS="$CXXFLAGS -DNDEBUG" ' +configopts = ' --with-boost=$BOOST_ROOT --with-mpi=intel --enable-mkl --with-libxc ' + +sanity_check_paths = { + 'files': ['bin/BAGEL', 'lib/libbagel.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/b/Boost/Boost-1.72.0-intel-2020a.eb b/b/Boost/Boost-1.72.0-intel-2020a.eb new file mode 100644 index 00000000..93a07906 --- /dev/null +++ b/b/Boost/Boost-1.72.0-intel-2020a.eb @@ -0,0 +1,26 @@ +# IT4Innovations 2020 + +name = 'Boost' +version = '1.72.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + + +dependencies = [ + ('bzip2', '1.0.8', '', True), + ('zlib', '1.2.11', '', True), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/c/Cython/Cython-0.29.14-Py-system.eb b/c/Cython/Cython-0.29.14-Py-system.eb new file mode 100644 index 00000000..ad72093a --- /dev/null +++ b/c/Cython/Cython-0.29.14-Py-system.eb @@ -0,0 +1,22 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.29.14' + +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.""" + +toolchain = {'name': 'Py', 'version': 'system'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'lang' diff --git a/l/libxc/libxc-4.3.4-intel-2020a.eb b/l/libxc/libxc-4.3.4-intel-2020a.eb new file mode 100644 index 00000000..3b03ab37 --- /dev/null +++ b/l/libxc/libxc-4.3.4-intel-2020a.eb @@ -0,0 +1,50 @@ +# IT4Innovations 2020 + +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['http://www.tddft.org/programs/libxc/down.php?file=4.3.4/'] +sources = ['libxc-4.3.4.tar.gz'] +patches = [ + #'libxc-%(version)s_rename-F03.patch', + 'libxc-%(version)s.patch' +] + +builddependencies = [ + ('CMake', '3.16.2', '', True), + ('Perl', '5.30.0', '', ('GCCcore', '8.3.0')), +] + +separate_build_dir = True + +# rename *.F03 source file since Intel Fortran local_compiler doesn't like that extension +# also requires patch file to rename file in CMakeLists.txt and src/Makefile.in +preconfigopts = "mv ../libxc-%(version)s/src/libxc_master.F03 ../libxc-%(version)s/src/libxc_master_F03.F90 && " + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/n/numpy/numpy-1.15.4-Py-system.eb b/n/numpy/numpy-1.15.4-Py-system.eb new file mode 100644 index 00000000..51f5cacd --- /dev/null +++ b/n/numpy/numpy-1.15.4-Py-system.eb @@ -0,0 +1,32 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'numpy' +version = '1.15.4' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package needed for scientific local_computing with Python.""" + +toolchain = {'name': 'Py', 'version': 'system'} + +source_urls = ['https://github.com/numpy/numpy/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +local_patch = [ + 'numpy-1.8.1-mkl.local_patch', + 'numpy-1.11.0-sse42.local_patch' +] + +dependencies = [ + ('mkl', '2019.5.281', '', True), + ('Cython', '0.29.14'), +] + +sanity_check_paths = {'files': [], 'dirs': [ + 'lib/python2.7/site-packages/%(name)s-%(version)s-py2.7-linux-x86_64.egg/numpy'], } + +sanity_check_commands = [ + ('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')] + +moduleclass = 'python' diff --git a/o/ORCA/ORCA-4.1.1-OpenMPI-3.1.3.eb b/o/ORCA/ORCA-4.1.1-OpenMPI-3.1.3.eb new file mode 100644 index 00000000..3a003b11 --- /dev/null +++ b/o/ORCA/ORCA-4.1.1-OpenMPI-3.1.3.eb @@ -0,0 +1,35 @@ +# IT4Innovations 2020 + +easyblock = "PackedBinary" + +name = "ORCA" +version = '4.1.1' +versionsuffix = '-OpenMPI-3.1.3' + +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 = SYSTEM + +# Download from https://orcaforum.kofo.mpg.de +sources = ['orca_4_1_1_linux_x86-64_openmpi313.tar.xz'] + +dependencies = [('OpenMPI', '3.1.3', '-GCCcore-8.3.0')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', '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' diff --git a/o/OpenMPI/OpenMPI-3.1.3-GCCcore-8.3.0.eb b/o/OpenMPI/OpenMPI-3.1.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000..6fe824f0 --- /dev/null +++ b/o/OpenMPI/OpenMPI-3.1.3-GCCcore-8.3.0.eb @@ -0,0 +1,46 @@ +# IT4Innovations 2019 + +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '3.1.3' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [ + 'http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('hwloc', '1.11.12'), + ('zlib', '1.2.11'), + ('binutils', '2.32'), + ('UCX', '1.6.1'), +] + +configopts = '--with-tm=/opt/pbs ' # Enable PBS +configopts += '--with-ucx=$EBROOTUCX ' + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', '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': 'mlx5_0', + 'OMPI_MCA_btl_tcp_if_include': '10.33.4.0/24', + 'OMPI_MCA_orte_base_help_aggregate': '0', + } + +moduleclass = 'mpi' diff --git a/p/Py/Py-system.eb b/p/Py/Py-system.eb new file mode 100644 index 00000000..281403ed --- /dev/null +++ b/p/Py/Py-system.eb @@ -0,0 +1,17 @@ +# IT4Innovations 2019 + +easyblock = "Toolchain" + +name = 'Py' +version = 'system' + +homepage = 'https://www.python.org' +description = """Python 2.7 toolchain""" + +toolchain = SYSTEM + +dependencies = [ + ('GCC', '8.3.0-2.32'), +] + +moduleclass = 'toolchain' diff --git a/p/pandas/pandas-1.0.0-Py-3.7.eb b/p/pandas/pandas-1.0.0-Py-3.7.eb new file mode 100644 index 00000000..3e797b45 --- /dev/null +++ b/p/pandas/pandas-1.0.0-Py-3.7.eb @@ -0,0 +1,24 @@ +# IT4Innovations 2018 + +easyblock = "PythonPackage" +name = 'pandas' +version = '1.0.0' + +homepage = 'https://pypi.python.org/pypi/pandas' +description = 'Powerful data structures for data analysis, time series,and statistics.' + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.18.1'), + ('pytz', '2019.3'), + ('python-dateutil', '2.8.1'), +] + +sanity_check_paths = {'files': [], 'dirs': [ + 'lib/python3.7/site-packages/%(name)s-%(version)s-py3.7-linux-x86_64.egg'], } + +moduleclass = 'python' diff --git a/p/pluggy/pluggy-0.13.1-Py-3.7.eb b/p/pluggy/pluggy-0.13.1-Py-3.7.eb new file mode 100644 index 00000000..3d6cf425 --- /dev/null +++ b/p/pluggy/pluggy-0.13.1-Py-3.7.eb @@ -0,0 +1,21 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'pluggy' +version = '0.13.1' + +homepage = 'https://github.com/pytest-dev/pluggy' +description = 'Plugin and hook calling mechanisms for python.' + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.7/site-packages/%(name)s-%(version)s-py3.7.egg'], +} + +moduleclass = 'python' diff --git a/p/pytest/pytest-5.3.5-Py-3.7.eb b/p/pytest/pytest-5.3.5-Py-3.7.eb new file mode 100644 index 00000000..c73e6381 --- /dev/null +++ b/p/pytest/pytest-5.3.5-Py-3.7.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'pytest' +version = '5.3.5' + +homepage = 'http://pytest.org' +description = 'Simple powerful testing with Python' + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +#download_dep_fail = True +use_pip = False + +dependencies = [ + ('six', '1.14.0'), + ('pluggy', '0.13.1'), + ('attrs', '19.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.7/site-packages/%(name)s-%(version)s-py3.7.egg'], +} + +moduleclass = 'python' diff --git a/p/python-dateutil/python-dateutil-2.8.1-Py-3.7.eb b/p/python-dateutil/python-dateutil-2.8.1-Py-3.7.eb new file mode 100644 index 00000000..7d503704 --- /dev/null +++ b/p/python-dateutil/python-dateutil-2.8.1-Py-3.7.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2020 + +easyblock = "PythonPackage" +name = 'python-dateutil' +version = '2.8.1' + +homepage = 'https://github.com/dateutil/dateutil' +description = 'Useful extensions to the standard Python datetime features.' + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [ + 'https://github.com/dateutil/dateutil/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('six', '1.14.0'), +] + +options = {'modulename': 'dateutil'} + +sanity_check_paths = { + 'files': ['lib/python3.7/site-packages/python_dateutil-%(version)s-py3.7.egg'], + 'dirs': [], +} + +moduleclass = 'python' diff --git a/p/pytz/pytz-2019.3-Py-3.7.eb b/p/pytz/pytz-2019.3-Py-3.7.eb new file mode 100644 index 00000000..45f351e2 --- /dev/null +++ b/p/pytz/pytz-2019.3-Py-3.7.eb @@ -0,0 +1,22 @@ +# IT4Innovations 2020 + +easyblock = "PythonPackage" +name = 'pytz' +version = '2019.3' + +homepage = 'http://pytz.sourceforge.net/' +description = """pytz brings the Olson tz database into Python. This library allows + accurate and cross platform timezone calculations using Python 2.4 or higher.""" + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [ + 'https://files.pythonhosted.org/packages/82/c3/534ddba230bd4fbbd3b7a3d35f3341d014cca213f369a9940925e7e5f691/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/python3.7/site-packages/%(name)s-%(version)s-py3.7.egg'], + 'dirs': [], +} + +moduleclass = 'python' diff --git a/r/ReFrame/ReFrame-2.21-Py-3.7.eb b/r/ReFrame/ReFrame-2.21-Py-3.7.eb new file mode 100644 index 00000000..173ea643 --- /dev/null +++ b/r/ReFrame/ReFrame-2.21-Py-3.7.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'ReFrame' +version = '2.21' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = ['https://pypi.python.org/packages/source/R/ReFrame-HPC'] +sources = ['ReFrame-HPC-%(version)s.tar.gz'] + +download_dep_fail = True +use_pip = False + +dependencies = [ + ('pytest', '5.3.5'), +] + +sanity_check_paths = { + 'files': ['bin/reframe'], + 'dirs': [] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' diff --git a/s/six/six-1.14.0-Py-3.7.eb b/s/six/six-1.14.0-Py-3.7.eb new file mode 100644 index 00000000..2015263a --- /dev/null +++ b/s/six/six-1.14.0-Py-3.7.eb @@ -0,0 +1,20 @@ +# IT4Innovations 2020 + +easyblock = "PythonPackage" +name = 'six' +version = '1.14.0' + +homepage = 'https://github.com/benjaminp/six' +description = 'Python 2 and 3 local_compatibility library.' + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = ['https://github.com/benjaminp/six/archive/'] +sources = ['%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.7/site-packages/%(name)s-%(version)s-py3.7.egg'], +} + +moduleclass = 'python'