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new file: h/hypothesis/hypothesis-6.14.6-GCCcore-10.2.0.eb
new file: n/NAMD/NAMD-2.9-intel-2017c-mpi.eb new file: p/PSI4/PSI4-1.3.2-intel-2020a-Python-3.8.2-karolina.eb new file: p/pybind11/pybind11-2.7.1-GCCcore-10.2.0.eb modified: p/pytest/pytest-6.0.1-intel-2020a-Python-3.8.2.eb new file: s/SciPy-bundle/SciPy-bundle-2020.03-AOCC-3.1.0-OAMD-2021a.eb new file: s/SciPy-bundle/test-SciPy-bundle-2021.10-AOCC-3.1.0-OAMD-2021a.eb
This commit is contained in:
Lukas Krupcik
parent
904b3e3cc4
commit
fa4b2c02a3
25
h/hypothesis/hypothesis-6.14.6-GCCcore-10.2.0.eb
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h/hypothesis/hypothesis-6.14.6-GCCcore-10.2.0.eb
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# IT4Innovations 2021
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# LK
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easyblock = 'PythonPackage'
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name = 'hypothesis'
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version = '6.14.6'
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homepage = "https://github.com/HypothesisWorks/hypothesis"
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description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized
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by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets
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you find more bugs in your code with less work."""
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toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
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sources = [SOURCE_TAR_GZ]
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checksums = ['2586eae07e48b35ab5a2d61d607d29ba76939ce140c427d66ccf5db4ddc788d2']
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dependencies = [('Python', '3.8.6')]
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use_pip = True
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download_dep_fail = True
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sanity_pip_check = True
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moduleclass = 'tools'
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27
n/NAMD/NAMD-2.9-intel-2017c-mpi.eb
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n/NAMD/NAMD-2.9-intel-2017c-mpi.eb
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name = 'NAMD'
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version = '2.9'
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versionsuffix = '-mpi'
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homepage = 'http://www.ks.uiuc.edu/Research/namd/'
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description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems."""
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# AMD/intel cpu
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toolchain = {'name': 'intel', 'version': '2017c'}
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import os
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if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
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toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'}
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# prebuildopts = "echo %(builddir)s && while read i; do echo $i; sed 's|-xHost|-march=core-avx2|g' -i $i; done < <(grep xHost %(builddir)s -R | cut -d ':' -f 1 | sort -u) && "
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else:
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toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
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sources = ['NAMD_%(version)s_Source.tar.gz']
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dependencies = [
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('Tcl', '8.6.7', '', ('GCC', '6.3.0-2.27')),
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('FFTW', '3.3.8', '', True),
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]
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charm_arch = 'mpi-linux-x86_64'
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moduleclass = 'chem'
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55
p/PSI4/PSI4-1.3.2-intel-2020a-Python-3.8.2-karolina.eb
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p/PSI4/PSI4-1.3.2-intel-2020a-Python-3.8.2-karolina.eb
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easyblock = 'EB_PSI'
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name = 'PSI4'
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version = '1.3.2'
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versionsuffix = '-Python-%(pyver)s'
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homepage = 'http://www.psicode.org/'
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description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for
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efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform
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local_computations with more than 2500 basis functions running serially or in parallel."""
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toolchain = {'name': 'intel', 'version': '2020a'}
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toolchainopts = {'usempi': True, 'optarch': 'march=core-avx2'}
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source_urls = ['https://github.com/psi4/psi4/archive/refs/tags/']
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sources = ['v%(version)s.tar.gz']
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patches = ['PSI4-1.3.2_fix_cmake_release.patch']
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dependencies = [
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('Python', '3.8.2'),
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('SciPy-bundle', '2020.03', versionsuffix),
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# PCMSolver recent versions fail with recent intel local_compilers.
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# Tried with intel/201{7,8}b, and versions 1.1.12, and 1.2.1
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# See in more details: https://github.com/PCMSolver/pcmsolver/issues/159
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# ('PCMSolver', '1.2.1'),
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('CheMPS2', '1.8.9'),
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('HDF5', '1.10.6', '', ('iimpi', '2020a')),
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# Tests are failing with pytest 3.9.2
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('pytest', '6.0.1', versionsuffix),
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('networkx', '2.4', versionsuffix),
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('deepdiff', '4.0.6', versionsuffix),
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]
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builddependencies = [
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('CMake', '3.16.4'),
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# Perl needed for the ctest test suite during the installation, not for the pytest test suite after the installation
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# ('Perl', '5.28.0'),
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]
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configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF '
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# Install python mudule to the standard location instead of lib
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configopts += '-DPYMOD_INSTALL_LIBDIR=/python3.7/site-packages '
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# Add bundled (downloaded) packages
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# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore
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configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON -DENABLE_CheMPS2=ON '
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# runtest uses ctest, and some of the thests have to be manually local_compared
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# to the reference output (those tests are marked failed)
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# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework)
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# runtest = '-L smoke'
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runtest = False
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modextrapaths = {'PYTHONPATH': 'lib/python3.7/site-packages'}
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moduleclass = 'chem'
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26
p/pybind11/pybind11-2.7.1-GCCcore-10.2.0.eb
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p/pybind11/pybind11-2.7.1-GCCcore-10.2.0.eb
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# IT4Innovations 2021
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# LK
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name = 'pybind11'
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version = '2.7.1'
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homepage = 'https://pybind11.readthedocs.io'
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description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
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mainly to create Python bindings of existing C++ code."""
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toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
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source_urls = ['https://github.com/pybind/pybind11/archive/']
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sources = ['v%(version)s.tar.gz']
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checksums = ['616d1c42e4cf14fa27b2a4ff759d7d7b33006fdc5ad8fd603bb2c22622f27020']
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builddependencies = [
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('binutils', '2.35'),
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('CMake', '3.18.4'),
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('Eigen', '3.3.8'),
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]
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dependencies = [('Python', '3.8.6')]
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configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python"
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moduleclass = 'lib'
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@ -26,4 +26,4 @@ sanity_check_paths = {
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'dirs': ['lib/python3.8/site-packages/%(name)s-%(version)s-py3.8.egg'],
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}
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moduleclass = 'python'
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moduleclass = 'lib'
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58
s/SciPy-bundle/SciPy-bundle-2020.03-AOCC-3.1.0-OAMD-2021a.eb
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s/SciPy-bundle/SciPy-bundle-2020.03-AOCC-3.1.0-OAMD-2021a.eb
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# IT4Innovations 2021
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# LK
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easyblock = 'PythonBundle'
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name = 'SciPy-bundle'
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version = '2020.03-AOCC-3.1.0'
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homepage = 'https://python.org/'
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description = "Bundle of Python packages for scientific software"
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toolchain = {'name': 'OAMD', 'version': '2021a'}
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toolchainopts = {'pic': True, 'lowopt': True}
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builddependencies = [('hypothesis', '5.41.2', '', ('GCCcore', '10.2.0'))]
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dependencies = [
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('Python', '3.8.6', '', ('GCCcore', '10.2.0')),
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('pybind11', '2.6.0', '', ('GCCcore', '10.2.0')), # required by scipy
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]
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use_pip = True
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exts_default_options = {'source_urls': [PYPI_SOURCE]}
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# order is important!
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exts_list = [
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('numpy', '1.18.3', {
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'patches': ['numpy-1.18.2-mkl.patch'],
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'source_tmpl': '%(name)s-%(version)s.zip',
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'checksums': [
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'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.2.zip
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'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch
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],
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}),
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('scipy', '1.4.1', {
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'patches': ['scipy-1.4.1-fix-pthread.patch'],
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'checksums': [
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'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz
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'4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch
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],
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}),
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('mpi4py', '3.0.3', {
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'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'],
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}),
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('pandas', '1.0.3', {
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'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'],
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}),
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('mpmath', '1.1.0', {
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'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'],
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}),
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('deap', '1.3.1', {
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'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'],
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}),
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]
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sanity_pip_check = True
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moduleclass = 'lang'
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@ -0,0 +1,76 @@
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easyblock = 'PythonBundle'
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name = 'SciPy-bundle'
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version = '2021.10'
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homepage = 'https://python.org/'
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description = "Bundle of Python packages for scientific software"
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toolchain = {'name': 'OAMD', 'version': '2021a'}
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toolchainopts = {'pic': True, 'lowopt': True}
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builddependencies = [
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('hypothesis', '6.14.6', '', ('GCCcore', '10.2.0')),
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('UnZip', '6.0', '', ('GCCcore', '10.2.0')),
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]
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dependencies = [
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('Python', '3.8.6', '', ('GCCcore', '10.2.0')),
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('pybind11', '2.7.1', '', ('GCCcore','10.2.0')), # required by scipy
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]
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use_pip = True
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preconfigopts = [ 'export MKL_DEBUG_CPU_TYPE=5 && ']
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#exts_default_options = {'source_urls': [PYPI_SOURCE]}
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# order is important!
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exts_list = [
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('numpy', '1.21.3', {
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'sources': ['%(name)s-%(version)s.zip'],
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'patches': ['numpy-1.20.3_skip-ppc-long-complex-test.patch'],
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'checksums': [
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'63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip
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# numpy-1.20.3_skip-ppc-long-complex-test.patch
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'2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4',
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],
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}),
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('ply', '3.11', {
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'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
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}),
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('gast', '0.5.2', {
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'checksums': ['f81fcefa8b982624a31c9e4ec7761325a88a0eba60d36d1da90e47f8fe3c67f7'],
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}),
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('beniget', '0.4.1', {
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'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
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}),
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('pythran', '0.10.0', {
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'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'],
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}),
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('scipy', '1.7.1', {
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'checksums': ['6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764'],
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}),
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('mpi4py', '3.1.1', {
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'checksums': ['e11f8587a3b93bb24c8526addec664b586b965d83c0882b884c14dc3fd6b9f5c'],
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}),
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('numexpr', '2.7.3', {
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'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'],
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}),
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('Bottleneck', '1.3.2', {
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'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'],
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}),
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('pandas', '1.3.4', {
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'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """,
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'checksums': ['a2aa18d3f0b7d538e21932f637fbfe8518d085238b429e4790a35e1e44a96ffc'],
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}),
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('mpmath', '1.2.1', {
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'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'],
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}),
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('deap', '1.3.1', {
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'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'],
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}),
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]
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sanity_pip_check = True
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moduleclass = 'lang'
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