mirror of
https://code.it4i.cz/sccs/easyconfigs-it4i.git
synced 2025-04-07 23:42:12 +01:00
Merge branch 'it4i-karolina'
This commit is contained in:
Lukas Krupcik
commit
294025ae44
99
a/Amber/Amber-22.0-foss-2021b-AmberTools-23.0.eb
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99
a/Amber/Amber-22.0-foss-2021b-AmberTools-23.0.eb
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# IT4Innovations
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# LK 2023
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name = 'Amber'
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local_amber_ver = 22
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local_ambertools_ver = 23
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# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php
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patchlevels = (3, 0) # (AmberTools, Amber)
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version = '%s.%s' % (local_amber_ver, patchlevels[1])
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versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0])
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homepage = 'https://ambermd.org/amber.html'
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description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing
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molecular dynamics and structure prediction."""
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toolchain = {'name': 'foss', 'version': '2021b'}
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toolchainopts = {'usempi': True, 'openmp': True}
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sources = [
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'%%(name)s%s.tar.bz2' % local_amber_ver,
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{'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'},
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]
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patches = [
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{'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'},
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# {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'},
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# {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'},
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# {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'},
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{'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'},
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#{'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'},
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'Amber-22_reduce_precision_of_kmmd_test.patch',
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'Amber-22_remove_undeclared_redundant_variable.patch',
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]
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checksums = [
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'3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2
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'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d', # AmberTools23.tar.bz2
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'473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch
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# AmberTools-20_fix_missing_MPI_LIBRARY_error.patch
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'0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc',
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# AmberTools-20_fix_xblas_missing_make_dependency.patch
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'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65',
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'9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch
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# AmberTools-21_fix_DGESVD_workspace_query.patch
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#'560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd',
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'1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch
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#'d1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch
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# AmberTools-21_fix_more_blas_argument_problems.patch
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'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c',
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#'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch
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# AmberTools-21_fix_potential_use_before_init.patch
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'377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139',
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# AmberTools-21_fix_rism_argument_mismatch.patch
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'14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1',
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# AmberTools-21_fix_xray_fftpack_arg_mismatch.patch
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'99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f',
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'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch
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# AmberTools-22_fix_missing_error_check_on_test_run.patch
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#'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475',
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'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch
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# Amber-22_remove_undeclared_redundant_variable.patch
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'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb',
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]
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builddependencies = [
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('CMake', '3.21.1'),
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('Bison', '3.7.6'),
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('flex', '2.6.4'),
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('make', '4.3'),
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]
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dependencies = [
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('zlib', '1.2.11'),
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('bzip2', '1.0.8'),
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('Python', '3.9.6'),
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('SciPy-bundle', '2021.10'), # mpi4py required for MMPBSA
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('Perl', '5.34.0'),
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('Boost', '1.77.0'),
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('libreadline', '8.1'),
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('matplotlib', '3.4.3'),
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('netCDF', '4.8.1'),
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('netCDF-Fortran', '4.5.3'),
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('PnetCDF', '1.12.3'),
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('Tkinter', '3.9.6'),
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('X11', '20210802'),
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]
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# All tests are expected to pass or be skipped
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runtest = True
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static = False
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moduleclass = 'chem'
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28
h/HyperQueue/HyperQueue-0.16.0.eb
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h/HyperQueue/HyperQueue-0.16.0.eb
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# IT4Innovations
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# LK 2023
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easyblock = 'PackedBinary'
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name = 'HyperQueue'
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version = '0.16.0'
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homepage = 'https://it4innovations.github.io/hyperqueue/'
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description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks
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and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs
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and distributes them to fully utilize allocated notes.
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You thus do not have to manually aggregate your tasks into SLURM/PBS jobs."""
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toolchain = SYSTEM
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source_urls = ['https://github.com/It4innovations/hyperqueue/releases/download/v%(version)s/']
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sources = ['hq-v%(version)s-linux-x64.tar.gz']
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checksums = ['b832fb3ba6c18855d253789d0125aa1581ec2fc9586ca98cbeadb9dc6ae153ba']
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sanity_check_paths = {
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'files': ['hq'],
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'dirs': [],
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}
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sanity_check_commands = ['hq --version']
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moduleclass = 'devel'
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170
l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-SNAP.eb
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170
l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-SNAP.eb
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# IT4Innovations
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# LK 2023
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name = 'LAMMPS'
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version = '23Jun2022'
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versionsuffix = '-kokkos-SNAP'
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homepage = 'https://www.lammps.org'
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description = """LAMMPS is a classical molecular dynamics code, and an acronym
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for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
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potentials for solid-state materials (metals, semiconductors) and soft matter
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(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
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used to model atoms or, more generically, as a parallel particle simulator at
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the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
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parallel using message-passing techniques and a spatial-decomposition of the
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simulation domain. The code is designed to be easy to modify or extend with new
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functionality.
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"""
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toolchain = {'name': 'foss', 'version': '2021b'}
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import os
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if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
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toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2', 'pic': True}
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else:
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toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
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# 'https://github.com/lammps/lammps/archive/'
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source_urls = [GITHUB_LOWER_SOURCE]
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sources = ['stable_%(version)s_update1.tar.gz']
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checksums = ['58e3b2b984f8935bb0db5631e143be2826c45ffd48844f7c394f36624a3e17a2']
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builddependencies = [
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('CMake', '3.22.1'),
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('pkg-config', '0.29.2'),
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('archspec', '0.1.3'),
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]
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dependencies = [
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('Python', '3.9.6'),
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('libpng', '1.6.37'),
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('libjpeg-turbo', '2.0.6'),
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('netCDF', '4.8.1'),
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('GSL', '2.7'),
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('zlib', '1.2.11'),
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('gzip', '1.10'),
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('cURL', '7.78.0'),
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('HDF5', '1.12.1'),
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('tbb', '2020.3'),
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('PCRE', '8.45'),
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('libxml2', '2.9.10'),
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('FFmpeg', '4.3.2'),
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('Voro++', '0.4.6'),
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('kim-api', '2.3.0'),
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('Eigen', '3.4.0'),
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('PLUMED', '2.7.3'),
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('ScaFaCoS', '1.0.1'),
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('SciPy-bundle', '2021.10'),
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# VTK package is auto-disabled if this dep is not available
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('VTK', '9.1.0'),
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]
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# To use additional custom configuration options, use the 'configopts' easyconfig parameter
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# See docs and lammps easyblock for more information.
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# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
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# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos,
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# which is claimed to be faster in pure MPI calculations
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# configopts = "-DKokkos_ENABLE_SERIAL=yes "
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configopts = "-DLAMMPS_EXCEPTIONS=yes -DBUILD_SHARED_LIBS=yes -DMLIAP_ENABLE_PYTHON=yes "
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configopts += "-DPKG_PYTHON=yes -DPYTHON_EXECUTABLE:FILEPATH=`which python` "
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# packages auto-enabled by easyblock
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# 'GPU' - if cuda package is present and kokkos is disabled
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# 'KOKKOS' - if kokkos is enabled (by default)
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# include the following extra packages into the build
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general_packages = [
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'ASPHERE',
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'AMOEBA',
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'ATC',
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'AWPMD',
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'BOCS',
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'BODY',
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'BPM',
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'BROWNIAN',
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'CG-DNA',
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'CG-SDK',
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'CLASS2',
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'COLLOID',
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'COLVARS',
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'COMPRESS',
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'CORESHELL',
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'DIELECTRIC',
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'DIFFRACTION',
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'DIPOLE',
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'DPD-BASIC',
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'DPD-MESO',
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'DPD-REACT',
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'DPD-SMOOTH',
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'DRUDE',
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'EFF',
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'ELECTRODE',
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'EXTRA-COMPUTE',
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'EXTRA-DUMP',
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'EXTRA-FIX',
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'EXTRA-MOLECULE',
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'EXTRA-PAIR',
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'FEP',
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'GRANULAR',
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'H5MD',
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'INTERLAYER',
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'KIM',
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'KSPACE',
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'LATBOLTZ',
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'MANIFOLD',
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'MACHDYN',
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'MANYBODY',
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'MC',
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'MEAM',
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'MGPT',
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'MISC',
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'ML-IAP',
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'ML-PACE',
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'ML-RANN',
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'ML-SNAP',
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'MOFFF',
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'MOLECULE',
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'MOLFILE',
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'MPIIO',
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'NETCDF',
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'OPENMP',
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'ORIENT',
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'PERI',
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'PHONON',
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'PLUGIN',
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'PLUMED',
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'POEMS',
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'PTM',
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'PYTHON',
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'QEQ',
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'QTB',
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'REACTION',
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'REAXFF',
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'REPLICA',
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'RIGID',
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'SCAFACOS',
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'SHOCK',
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'SMTBQ',
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'SPH',
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'SPIN',
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'SRD',
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'TALLY',
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'UEF',
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'VORONOI',
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'VTK',
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'YAFF',
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]
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# Excluded packages due to requiring additional (non-trivial) deps
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# - ADIOS
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# - LATTE
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# - MESONT (requires very large files downloaded during build)
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# - ML-HDNNP (requires N2P2)
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# - ML-QUIP
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# - MSCG
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# - QMMM (setup seems complex)
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||||
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||||
moduleclass = 'chem'
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||||
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