diff --git a/h/hypothesis/hypothesis-6.14.6-GCCcore-10.2.0.eb b/h/hypothesis/hypothesis-6.14.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000..f22f40ab --- /dev/null +++ b/h/hypothesis/hypothesis-6.14.6-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +# IT4Innovations 2021 +# LK + +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.14.6' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2586eae07e48b35ab5a2d61d607d29ba76939ce140c427d66ccf5db4ddc788d2'] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/n/NAMD/NAMD-2.9-intel-2017c-mpi.eb b/n/NAMD/NAMD-2.9-intel-2017c-mpi.eb new file mode 100644 index 00000000..ded7c744 --- /dev/null +++ b/n/NAMD/NAMD-2.9-intel-2017c-mpi.eb @@ -0,0 +1,27 @@ +name = 'NAMD' +version = '2.9' +versionsuffix = '-mpi' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" + +# AMD/intel cpu +toolchain = {'name': 'intel', 'version': '2017c'} +import os +if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: + toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'} +# 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) && " +else: + toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + + +sources = ['NAMD_%(version)s_Source.tar.gz'] + +dependencies = [ + ('Tcl', '8.6.7', '', ('GCC', '6.3.0-2.27')), + ('FFTW', '3.3.8', '', True), +] + +charm_arch = 'mpi-linux-x86_64' + +moduleclass = 'chem' diff --git a/p/PSI4/PSI4-1.3.2-intel-2020a-Python-3.8.2-karolina.eb b/p/PSI4/PSI4-1.3.2-intel-2020a-Python-3.8.2-karolina.eb new file mode 100644 index 00000000..dee130ac --- /dev/null +++ b/p/PSI4/PSI4-1.3.2-intel-2020a-Python-3.8.2-karolina.eb @@ -0,0 +1,55 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + local_computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True, 'optarch': 'march=core-avx2'} + +source_urls = ['https://github.com/psi4/psi4/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['PSI4-1.3.2_fix_cmake_release.patch'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + # PCMSolver recent versions fail with recent intel local_compilers. + # Tried with intel/201{7,8}b, and versions 1.1.12, and 1.2.1 + # See in more details: https://github.com/PCMSolver/pcmsolver/issues/159 + # ('PCMSolver', '1.2.1'), + ('CheMPS2', '1.8.9'), + ('HDF5', '1.10.6', '', ('iimpi', '2020a')), + # Tests are failing with pytest 3.9.2 + ('pytest', '6.0.1', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('deepdiff', '4.0.6', versionsuffix), +] + +builddependencies = [ + ('CMake', '3.16.4'), + # Perl needed for the ctest test suite during the installation, not for the pytest test suite after the installation + # ('Perl', '5.28.0'), +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python mudule to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python3.7/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON -DENABLE_CheMPS2=ON ' + +# runtest uses ctest, and some of the thests have to be manually local_compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +modextrapaths = {'PYTHONPATH': 'lib/python3.7/site-packages'} + +moduleclass = 'chem' diff --git a/p/pybind11/pybind11-2.7.1-GCCcore-10.2.0.eb b/p/pybind11/pybind11-2.7.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000..0ea87246 --- /dev/null +++ b/p/pybind11/pybind11-2.7.1-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +# IT4Innovations 2021 +# LK + +name = 'pybind11' +version = '2.7.1' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['616d1c42e4cf14fa27b2a4ff759d7d7b33006fdc5ad8fd603bb2c22622f27020'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Eigen', '3.3.8'), +] +dependencies = [('Python', '3.8.6')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/p/pytest/pytest-6.0.1-intel-2020a-Python-3.8.2.eb b/p/pytest/pytest-6.0.1-intel-2020a-Python-3.8.2.eb index 42a2f1a1..0067212e 100644 --- a/p/pytest/pytest-6.0.1-intel-2020a-Python-3.8.2.eb +++ b/p/pytest/pytest-6.0.1-intel-2020a-Python-3.8.2.eb @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': ['lib/python3.8/site-packages/%(name)s-%(version)s-py3.8.egg'], } -moduleclass = 'python' +moduleclass = 'lib' diff --git a/s/SciPy-bundle/SciPy-bundle-2020.03-AOCC-3.1.0-OAMD-2021a.eb b/s/SciPy-bundle/SciPy-bundle-2020.03-AOCC-3.1.0-OAMD-2021a.eb new file mode 100644 index 00000000..a7fead8f --- /dev/null +++ b/s/SciPy-bundle/SciPy-bundle-2020.03-AOCC-3.1.0-OAMD-2021a.eb @@ -0,0 +1,58 @@ +# IT4Innovations 2021 +# LK + +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.03-AOCC-3.1.0' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'OAMD', 'version': '2021a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [('hypothesis', '5.41.2', '', ('GCCcore', '10.2.0'))] + +dependencies = [ + ('Python', '3.8.6', '', ('GCCcore', '10.2.0')), + ('pybind11', '2.6.0', '', ('GCCcore', '10.2.0')), # required by scipy +] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('numpy', '1.18.3', { + 'patches': ['numpy-1.18.2-mkl.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': [ + 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.2.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + ], + }), + ('scipy', '1.4.1', { + 'patches': ['scipy-1.4.1-fix-pthread.patch'], + 'checksums': [ + 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz + '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + ], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('pandas', '1.0.3', { + 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/s/SciPy-bundle/test-SciPy-bundle-2021.10-AOCC-3.1.0-OAMD-2021a.eb b/s/SciPy-bundle/test-SciPy-bundle-2021.10-AOCC-3.1.0-OAMD-2021a.eb new file mode 100644 index 00000000..f97effba --- /dev/null +++ b/s/SciPy-bundle/test-SciPy-bundle-2021.10-AOCC-3.1.0-OAMD-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.10' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'OAMD', 'version': '2021a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.14.6', '', ('GCCcore', '10.2.0')), + ('UnZip', '6.0', '', ('GCCcore', '10.2.0')), +] + +dependencies = [ + ('Python', '3.8.6', '', ('GCCcore', '10.2.0')), + ('pybind11', '2.7.1', '', ('GCCcore','10.2.0')), # required by scipy +] + +use_pip = True + +preconfigopts = [ 'export MKL_DEBUG_CPU_TYPE=5 && '] +#exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('numpy', '1.21.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'patches': ['numpy-1.20.3_skip-ppc-long-complex-test.patch'], + 'checksums': [ + '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip + # numpy-1.20.3_skip-ppc-long-complex-test.patch + '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.2', { + 'checksums': ['f81fcefa8b982624a31c9e4ec7761325a88a0eba60d36d1da90e47f8fe3c67f7'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + ('scipy', '1.7.1', { + 'checksums': ['6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764'], + }), + ('mpi4py', '3.1.1', { + 'checksums': ['e11f8587a3b93bb24c8526addec664b586b965d83c0882b884c14dc3fd6b9f5c'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.3.4', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['a2aa18d3f0b7d538e21932f637fbfe8518d085238b429e4790a35e1e44a96ffc'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang'