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new file: a/ANSYS/ANSYS-2022R1-intel-2020b-alamerini.eb

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new file:   a/AOCC/AOCC-4.1.0-GCCcore-12.2.0.eb
	new file:   a/AOCL/AOCL-4.1.0-CCcore-12.2.0.eb
	new file:   a/Amber/Amber-22.4-foss-2022a-AmberTools-23-CUDA-11.7.0.eb
	new file:   c/Clang/Clang-17.0.2-GCCcore-12.2.0-CUDA-12.2.0.eb
	new file:   c/Clang/Clang-17.0.2-GCCcore-12.2.0.eb
	new file:   g/GROMACS/GROMACS-2023-foss-2022a-CUDA-12.0.0-PLUMED-2.9.0.eb
	new file:   g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-12.0.0-v2.eb
	new file:   l/LAMMPS/LAMMPS-15Jun2023-foss-2022a-kokkos-sm80.eb
	new file:   l/LAMMPS/LAMMPS-2Aug2023-foss-2022a-kokkos-sm80.eb
	new file:   l/LAMMPS/LAMMPS-2Aug2023-foss-2022a-kokkos.eb
	new file:   l/LAMMPS/LAMMPS-2Aug2023_update1-foss-2021b-CUDA-12.2.0-kokkos.eb
	new file:   l/LAMMPS/LAMMPS-2Aug2023_update1-foss-2021b-kokkos.eb
	new file:   m/MATLAB/MATLAB-2023b.eb
	new file:   n/NCCL/NCCL-2.18.3-GCCcore-11.3.0-CUDA-12.2.0.eb
	new file:   o/OVITO/OVITO-3.9.2-gompi-2022a-basic.eb
	new file:   o/OVITO/OVITO-3.9.2-gompi-2022b-basic.eb
	new file:   o/OpenMolcas/OpenMolcas-23.06-intel-2022a-noGA.eb
	modified:   o/OpenMolcas/OpenMolcas-23.06-intel-2022a.eb
	new file:   p/PLUMED/PLUMED-2.9.0-foss-2022a.eb
	new file:   q/Qt6/Qt6-6.5.3-GCCcore-12.2.0.eb
	new file:   "q/Qt6/\\"
	new file:   u/UCX-CUDA/UCX-CUDA-1.14.1-GCCcore-11.3.0-CUDA-12.2.0.eb
This commit is contained in:
Lukas Krupcik 2023-10-30 11:35:42 +01:00
parent 5199a98b32
commit cef77e125f
23 changed files with 1845 additions and 3 deletions
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# IT4Innovations
# LK 2023
name = 'ANSYS'
version = '2022R1'
versionsuffix = '-alamerini'
homepage = 'http://www.ansys.com'
description = """ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is
a promise of something greater. """
toolchain = {'name': 'intel', 'version': '2020b'}
# create a zip file from the 3 install iso files.
# make sure all files of the iso's are in the same directory.
sources = ['ANSYS-2022.1.tar.gz']
checksums = ['94d4700c66189a774f9b06b0e7a89e64']
dependencies = [
('libGLU', '9.0.1'),
# ('libnsl', '1.3.0'), # moc nove pro CentOS 7!!!
]
import os
license_server = os.getenv('EB_ANSYS_LICENSE_SERVER', '150.217.19.173')
license_server_port = os.getenv('EB_ANSYS_LICENSE_SERVER_PORT', '2325:1055')
moduleclass = 'tools'

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# IT4Innovations
# LK 2023
name = 'AOCC'
version = '4.1.0'
homepage = 'https://developer.amd.com/amd-aocc/'
description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0"
# Clang also depends on libstdc++ during runtime, but this dependency is
# already specified as the toolchain.
toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
source_urls = ['https://download.amd.com/developer/eula/aocc/aocc-4-1/']
sources = ['aocc-compiler-%(version)s.tar']
checksums = ['5b04bfdb751c68dfb9470b34235d76efa80a6b662a123c3375b255982cb52acd']
clangversion = '16'
dependencies = [
('binutils', '2.39'),
('ncurses', '6.3'),
('zlib', '1.2.12'),
('libxml2', '2.10.3'),
]
moduleclass = 'compiler'

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# IT4Innovations
# LK 2023
# --include-easyblocks=/apps/all/AOCL/3.0-6-GCCcore-10.2.0/easybuild/reprod/easyblocks/aocl.py
name = 'AOCL'
version = '4.1.0'
homepage = 'https://developer.amd.com/amd-aocc/'
description = """AMD provides a free set of thoroughly optimized and threaded math routines for HPC,
scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling,
computational fluid dynamics, financial analysis, oil and gas applications and more. """
toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
source_urls = ['https://download.amd.com/developer/eula/aocl/aocl-4-1/']
sources = ['aocl-linux-aocc-%(version)s.tar.gz']
checksums = ['25c3d86970a355205de0d139a23e251f070dd76242114b98390fe8f90503e810']
dependencies = [
('binutils', '2.39'),
('ncurses', '6.3'),
('zlib', '1.2.12'),
('libxml2', '2.10.3'),
('AOCC', '4.1.0'),
]
moduleclass = 'numlib'

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# IT4Innovations
# LK 2023
name = 'Amber'
local_amber_ver = 22
local_ambertools_ver = 23
# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php
patchlevels = (3, 0) # (AmberTools, Amber)
version = '%s.%s' % (local_amber_ver, patchlevels[1])
versionsuffix = '-AmberTools-%s.%s-CUDA-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0])
homepage = 'https://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing
molecular dynamics and structure prediction."""
toolchain = {'name': 'foss', 'version': '2022a'}
toolchainopts = {'usempi': True, 'openmp': True}
sources = [
'%%(name)s%s.tar.bz2' % local_amber_ver,
{'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'},
]
patches = [
{'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'},
# {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'},
# {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'},
# {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'},
{'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'},
# {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'},
'Amber-22_reduce_precision_of_kmmd_test.patch',
'Amber-22_remove_undeclared_redundant_variable.patch',
]
checksums = [
'3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2
'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d', # AmberTools23.tar.bz2
'473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch
# AmberTools-20_fix_missing_MPI_LIBRARY_error.patch
'0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc',
# AmberTools-20_fix_xblas_missing_make_dependency.patch
'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65',
'9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch
# AmberTools-21_fix_DGESVD_workspace_query.patch
# '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd',
'1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch
# 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch
# AmberTools-21_fix_more_blas_argument_problems.patch
'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c',
# 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch
# AmberTools-21_fix_potential_use_before_init.patch
'377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139',
# AmberTools-21_fix_rism_argument_mismatch.patch
'14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1',
# AmberTools-21_fix_xray_fftpack_arg_mismatch.patch
'99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f',
'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch
# AmberTools-22_fix_missing_error_check_on_test_run.patch
# 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475',
'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch
# Amber-22_remove_undeclared_redundant_variable.patch
'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb',
]
builddependencies = [
('CMake', '3.23.1'),
('Bison', '3.8.2'),
('flex', '2.6.4'),
('make', '4.3'),
]
dependencies = [
('zlib', '1.2.12'),
('bzip2', '1.0.8'),
('Python', '3.10.4'),
('SciPy-bundle', '2022.05'), # mpi4py required for MMPBSA
('Perl', '5.34.1'),
('Boost', '1.79.0'),
('libreadline', '8.1.2'),
('matplotlib', '3.5.2'),
('netCDF', '4.9.0'),
('netCDF-Fortran', '4.6.0'),
('PnetCDF', '1.12.3'),
('Tkinter', '3.10.4'),
('X11', '20220504'),
('CUDA', '11.7.0', '', SYSTEM),
('NCCL', '2.12.12', '-CUDA-%(cudaver)s'),
('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'),
]
# Some CUDA tests differs from expected results
runtest = False
static = False
moduleclass = 'chem'

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# IT4Innovations
# LK 2023
name = 'Clang'
version = '17.0.2'
versionsuffix = '-CUDA-12.2.0'
homepage = 'https://clang.llvm.org/'
description = """C, C++, Objective-C compiler, based on LLVM. Does not
include C++ standard library -- use libstdc++ from GCC."""
# Clang also depends on libstdc++ during runtime, but this dependency is
# already specified as the toolchain.
toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"]
sources = [
'llvm-project-%(version)s.src.tar.xz',
]
checksums = [
{'llvm-project-17.0.2.src.tar.xz': '351562b14d42fcefcbf00cc1f327680a1062bbbf67a1e1ca6acb64c473b06394'},
]
builddependencies = [
('CMake', '3.24.3'),
('Perl', '5.36.0'),
# Including Python bindings would require this as a runtime dep
('Python', '3.10.8'),
]
dependencies = [
# since Clang is a compiler, binutils is a runtime dependency too
('binutils', '2.39'),
('hwloc', '2.8.0'),
('libxml2', '2.10.3'),
('ncurses', '6.3'),
('GMP', '6.2.1'),
('Z3', '4.12.2'),
('CUDA', '12.2.0', '', True),
]
# enabling RTTI makes the flang compiler need to link to libc++ so instead of
# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90
# you would need
# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++
enable_rtti = False
assertions = True
python_bindings = False
skip_all_tests = True
llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi']
llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang']
moduleclass = 'compiler'

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# IT4Innovations
# LK 2023
name = 'Clang'
version = '17.0.2'
homepage = 'https://clang.llvm.org/'
description = """C, C++, Objective-C compiler, based on LLVM. Does not
include C++ standard library -- use libstdc++ from GCC."""
# Clang also depends on libstdc++ during runtime, but this dependency is
# already specified as the toolchain.
toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"]
sources = [
'llvm-project-%(version)s.src.tar.xz',
]
checksums = [
{'llvm-project-17.0.2.src.tar.xz': '351562b14d42fcefcbf00cc1f327680a1062bbbf67a1e1ca6acb64c473b06394'},
]
builddependencies = [
('CMake', '3.24.3'),
('Perl', '5.36.0'),
# Including Python bindings would require this as a runtime dep
('Python', '3.10.8'),
]
dependencies = [
# since Clang is a compiler, binutils is a runtime dependency too
('binutils', '2.39'),
('hwloc', '2.8.0'),
('libxml2', '2.10.3'),
('ncurses', '6.3'),
('GMP', '6.2.1'),
('Z3', '4.12.2'),
]
# enabling RTTI makes the flang compiler need to link to libc++ so instead of
# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90
# you would need
# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++
enable_rtti = False
assertions = True
python_bindings = False
skip_all_tests = True
llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi']
llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang']
moduleclass = 'compiler'

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# IT4Innovations
# LK 2023
name = 'GROMACS'
version = '2023'
local_plum_ver = '2.9.0'
versionsuffix = '-CUDA-12.2.0-PLUMED-2.9.0'
homepage = 'https://www.gromacs.org'
description = """
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
Newtonian equations of motion for systems with hundreds to millions of
particles.
This is a GPU enabled build, containing both MPI and threadMPI binaries.
It also contains the gmxapi extension for the single precision MPI build.
"""
toolchain = {'name': 'foss', 'version': '2022a'}
toolchainopts = {'openmp': True, 'usempi': True}
source_urls = [
'https://ftp.gromacs.org/pub/gromacs/',
'ftp://ftp.gromacs.org/pub/gromacs/',
]
sources = [SOURCELOWER_TAR_GZ]
patches = [
'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
]
checksums = [
{'gromacs-2023.tar.gz': 'ac92c6da72fbbcca414fd8a8d979e56ecf17c4c1cdabed2da5cfb4e7277b7ba8'},
{'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
{'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
]
builddependencies = [
('CMake', '3.24.3'),
('scikit-build', '0.15.0'),
]
dependencies = [
('CUDA', '12.0.0', '', SYSTEM),
('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'),
('Python', '3.10.4'),
('SciPy-bundle', '2022.05'),
('networkx', '2.8.4'),
('PLUMED', local_plum_ver),
]
configopts = ' -DGMX_MPI=ON'
exts_defaultclass = 'PythonPackage'
exts_default_options = {
'source_urls': [PYPI_SOURCE],
'use_pip': True,
'download_dep_fail': True,
'sanity_pip_check': True,
}
exts_list = [
('gmxapi', '0.4.2', {
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-2023.3.tar.gz',
'start_dir': 'python_packaging/gmxapi',
'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
}),
]
modextrapaths = {
'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
}
moduleclass = 'bio'

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# IT4Innovations
# LK 2023
name = 'GROMACS'
version = '2023.3'
versionsuffix = '-CUDA-%(cudaver)s-v2'
homepage = 'https://www.gromacs.org'
description = """
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
Newtonian equations of motion for systems with hundreds to millions of
particles.
This is a GPU enabled build, containing both MPI and threadMPI binaries.
It also contains the gmxapi extension for the single precision MPI build.
"""
toolchain = {'name': 'foss', 'version': '2022a'}
toolchainopts = {'openmp': True, 'usempi': True}
source_urls = [
'https://ftp.gromacs.org/pub/gromacs/',
'ftp://ftp.gromacs.org/pub/gromacs/',
]
sources = [SOURCELOWER_TAR_GZ]
patches = [
'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
]
checksums = [
{'gromacs-2023.3.tar.gz': '2c9cdd8252ba9aa89a05d7c2d9b07509'},
{'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
'7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
{'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
'6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
]
builddependencies = [
('CMake', '3.24.3'),
('scikit-build', '0.15.0'),
]
dependencies = [
('CUDA', '12.0.0', '', SYSTEM),
('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'),
('Python', '3.10.4'),
('SciPy-bundle', '2022.05'),
('networkx', '2.8.4'),
]
exts_defaultclass = 'PythonPackage'
exts_default_options = {
'source_urls': [PYPI_SOURCE],
'use_pip': True,
'download_dep_fail': True,
'sanity_pip_check': True,
}
exts_list = [
('gmxapi', '0.4.2', {
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-2023.3.tar.gz',
'start_dir': 'python_packaging/gmxapi',
'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
}),
]
modextrapaths = {
'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
}
moduleclass = 'bio'

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# IT4Innovations
# LK 2023
name = 'LAMMPS'
version = '15Jun2023'
versionsuffix = '-kokkos'
_cuda_suffix = '-CUDA-%(cudaver)s'
versionsuffix += _cuda_suffix
cuda_compute_capabilities = ['8.0']
versionsuffix += '-sm80'
homepage = 'https://www.lammps.org'
description = """LAMMPS is a classical molecular dynamics code, and an acronym
for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
used to model atoms or, more generically, as a parallel particle simulator at
the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.
"""
toolchain = {'name': 'foss', 'version': '2022a'}
import os
if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2', 'cstd': 'c++14'}
else:
toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++14'}
# 'https://github.com/lammps/lammps/archive/'
source_urls = [GITHUB_LOWER_SOURCE]
sources = ['patch_%(version)s.tar.gz']
checksums = ['8470ed7b26ccd3728f4b44a7f1c520f1af23a648af685fd30b42b840fdfae2ff']
builddependencies = [
('CMake', '3.23.1'),
('pkgconf', '1.8.0'),
('archspec', '0.1.4'),
]
dependencies = [
('CUDA', '11.7.0', '', SYSTEM),
('UCX-CUDA', '1.12.1', _cuda_suffix),
('NCCL', '2.12.12', _cuda_suffix),
('Python', '3.10.4'),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.1.3'),
('netCDF', '4.9.0'),
('GSL', '2.7'),
('zlib', '1.2.12'),
('gzip', '1.12'),
('cURL', '7.83.0'),
('HDF5', '1.12.2'),
('tbb', '2021.5.0'),
('PCRE', '8.45'),
('libxml2', '2.9.13'),
('FFmpeg', '4.4.2'),
('Voro++', '0.4.6'),
('kim-api', '2.3.0'),
('Eigen', '3.4.0'),
('PLUMED', '2.8.1'),
('ScaFaCoS', '1.0.4'),
('SciPy-bundle', '2022.05'),
# VTK package is auto-disabled if this dep is not available
('VTK', '9.2.2'),
]
install_cmd = 'make install install-python'
# To use additional custom configuration options, use the 'configopts' easyconfig parameter
# See docs and lammps easyblock for more information.
# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos,
# which is claimed to be faster in pure MPI calculations
# configopts = "-DKokkos_ENABLE_SERIAL=yes "
# packages auto-enabled by easyblock
# 'GPU' - if cuda package is present and kokkos is disabled
# 'KOKKOS' - if kokkos is enabled (by default)
# 'INTEL' - if builing on Intel CPU
# 'OPENMP' - if OpenMP swithed on in 'toolchainopts'
# include the following extra packages into the build
general_packages = [
'AMOEBA',
'ASPHERE',
'ATC',
'AWPMD',
'BOCS',
'BODY',
'BPM',
'BROWNIAN',
'CG-DNA',
'CG-SPICA',
'CLASS2',
'COLLOID',
'COLVARS',
'COMPRESS',
'CORESHELL',
'DIELECTRIC',
'DIFFRACTION',
'DIPOLE',
'DPD-BASIC',
'DPD-MESO',
'DPD-REACT',
'DPD-SMOOTH',
'DRUDE',
'EFF',
'ELECTRODE',
'EXTRA-COMPUTE',
'EXTRA-DUMP',
'EXTRA-FIX',
'EXTRA-MOLECULE',
'EXTRA-PAIR',
'FEP',
'GRANULAR',
'H5MD',
'INTERLAYER',
'KIM',
'KSPACE',
'LATBOLTZ',
'LEPTON',
'MACHDYN',
'MANIFOLD',
'MANYBODY',
'MC',
'MEAM',
'MGPT',
'MISC',
'ML-IAP',
'ML-PACE',
'ML-POD',
'ML-RANN',
'ML-SNAP',
'MOFFF',
'MOLECULE',
'MOLFILE',
'MPIIO',
'NETCDF',
'OPT',
'ORIENT',
'PERI',
'PHONON',
'PLUGIN',
'PLUMED',
'POEMS',
'PTM',
'PYTHON',
'QEQ',
'QTB',
'REACTION',
'REAXFF',
'REPLICA',
'RIGID',
'SCAFACOS',
'SHOCK',
'SMTBQ',
'SPH',
'SPIN',
'SRD',
'TALLY',
'UEF',
'VORONOI',
'VTK',
'YAFF',
]
# Excluded packages due to requiring additional (non-trivial) deps
# - ADIOS
# - LATTE and its replacement MDI
# - MESONT (requires very large files downloaded during build)
# - ML-HDNNP (requires N2P2)
# - ML-QUIP
# - MSCG
# - QMMM (setup seems complex)
moduleclass = 'chem'

180
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@ -0,0 +1,180 @@
# IT4Innovations
# LK 2023
name = 'LAMMPS'
version = '2Aug2023'
versionsuffix = '-kokkos'
_cuda_suffix = '-CUDA-%(cudaver)s'
versionsuffix += _cuda_suffix
cuda_compute_capabilities = ['8.0']
versionsuffix += '-sm80'
homepage = 'https://www.lammps.org'
description = """LAMMPS is a classical molecular dynamics code, and an acronym
for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
used to model atoms or, more generically, as a parallel particle simulator at
the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.
"""
toolchain = {'name': 'foss', 'version': '2022a'}
import os
if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2', 'cstd': 'c++14'}
else:
toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++14'}
# 'https://github.com/lammps/lammps/archive/'
source_urls = [GITHUB_LOWER_SOURCE]
sources = ['stable_%(version)s_update1.tar.gz']
checksums = ['0e5568485e5ee080412dba44a1b7a93f864f1b5c75121f11d528854269953ed0']
builddependencies = [
('CMake', '3.23.1'),
('pkgconf', '1.8.0'),
('archspec', '0.1.4'),
]
dependencies = [
('CUDA', '11.7.0', '', SYSTEM),
('UCX-CUDA', '1.12.1', _cuda_suffix),
('NCCL', '2.12.12', _cuda_suffix),
('Python', '3.10.4'),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.1.3'),
('netCDF', '4.9.0'),
('GSL', '2.7'),
('zlib', '1.2.12'),
('gzip', '1.12'),
('cURL', '7.83.0'),
('HDF5', '1.12.2'),
('tbb', '2021.5.0'),
('PCRE', '8.45'),
('libxml2', '2.9.13'),
('FFmpeg', '4.4.2'),
('Voro++', '0.4.6'),
('kim-api', '2.3.0'),
('Eigen', '3.4.0'),
('PLUMED', '2.8.1'),
('ScaFaCoS', '1.0.4'),
('SciPy-bundle', '2022.05'),
# VTK package is auto-disabled if this dep is not available
('VTK', '9.2.2'),
]
install_cmd = 'make install install-python'
# To use additional custom configuration options, use the 'configopts' easyconfig parameter
# See docs and lammps easyblock for more information.
# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos,
# which is claimed to be faster in pure MPI calculations
# configopts = "-DKokkos_ENABLE_SERIAL=yes "
# packages auto-enabled by easyblock
# 'GPU' - if cuda package is present and kokkos is disabled
# 'KOKKOS' - if kokkos is enabled (by default)
# 'INTEL' - if builing on Intel CPU
# 'OPENMP' - if OpenMP swithed on in 'toolchainopts'
# include the following extra packages into the build
general_packages = [
'AMOEBA',
'ASPHERE',
'ATC',
'AWPMD',
'BOCS',
'BODY',
'BPM',
'BROWNIAN',
'CG-DNA',
'CG-SPICA',
'CLASS2',
'COLLOID',
'COLVARS',
'COMPRESS',
'CORESHELL',
'DIELECTRIC',
'DIFFRACTION',
'DIPOLE',
'DPD-BASIC',
'DPD-MESO',
'DPD-REACT',
'DPD-SMOOTH',
'DRUDE',
'EFF',
'ELECTRODE',
'EXTRA-COMPUTE',
'EXTRA-DUMP',
'EXTRA-FIX',
'EXTRA-MOLECULE',
'EXTRA-PAIR',
'FEP',
'GRANULAR',
'H5MD',
'INTERLAYER',
'KIM',
'KSPACE',
'LATBOLTZ',
'LEPTON',
'MACHDYN',
'MANIFOLD',
'MANYBODY',
'MC',
'MEAM',
'MGPT',
'MISC',
'ML-IAP',
'ML-PACE',
'ML-POD',
'ML-RANN',
'ML-SNAP',
'MOFFF',
'MOLECULE',
'MOLFILE',
'MPIIO',
'NETCDF',
'OPT',
'ORIENT',
'PERI',
'PHONON',
'PLUGIN',
'PLUMED',
'POEMS',
'PTM',
'PYTHON',
'QEQ',
'QTB',
'REACTION',
'REAXFF',
'REPLICA',
'RIGID',
'SCAFACOS',
'SHOCK',
'SMTBQ',
'SPH',
'SPIN',
'SRD',
'TALLY',
'UEF',
'VORONOI',
'VTK',
'YAFF',
]
# Excluded packages due to requiring additional (non-trivial) deps
# - ADIOS
# - LATTE and its replacement MDI
# - MESONT (requires very large files downloaded during build)
# - ML-HDNNP (requires N2P2)
# - ML-QUIP
# - MSCG
# - QMMM (setup seems complex)
moduleclass = 'chem'

172
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@ -0,0 +1,172 @@
# IT4Innovations
# LK 2023
name = 'LAMMPS'
version = '2Aug2023'
versionsuffix = '-kokkos'
homepage = 'https://www.lammps.org'
description = """LAMMPS is a classical molecular dynamics code, and an acronym
for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
used to model atoms or, more generically, as a parallel particle simulator at
the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.
"""
toolchain = {'name': 'foss', 'version': '2022a'}
import os
if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2'}
else:
toolchainopts = {'openmp': True, 'usempi': True}
# 'https://github.com/lammps/lammps/archive/'
source_urls = [GITHUB_LOWER_SOURCE]
sources = ['stable_%(version)s_update1.tar.gz']
checksums = ['0e5568485e5ee080412dba44a1b7a93f864f1b5c75121f11d528854269953ed0']
builddependencies = [
('CMake', '3.23.1'),
('pkgconf', '1.8.0'),
('archspec', '0.1.4'),
]
dependencies = [
('Python', '3.10.4'),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.1.3'),
('netCDF', '4.9.0'),
('GSL', '2.7'),
('zlib', '1.2.12'),
('gzip', '1.12'),
('cURL', '7.83.0'),
('HDF5', '1.12.2'),
('tbb', '2021.5.0'),
('PCRE', '8.45'),
('libxml2', '2.9.13'),
('FFmpeg', '4.4.2'),
('Voro++', '0.4.6'),
('kim-api', '2.3.0'),
('Eigen', '3.4.0'),
('PLUMED', '2.8.1'),
('ScaFaCoS', '1.0.4'),
('SciPy-bundle', '2022.05'),
# VTK package is auto-disabled if this dep is not available
('VTK', '9.2.2'),
]
# To use additional custom configuration options, use the 'configopts' easyconfig parameter
# See docs and lammps easyblock for more information.
# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos,
# which is claimed to be faster in pure MPI calculations
# configopts = "-DKokkos_ENABLE_SERIAL=yes "
# packages auto-enabled by easyblock
# 'GPU' - if cuda package is present and kokkos is disabled
# 'KOKKOS' - if kokkos is enabled (by default)
# 'INTEL' - if builing on Intel CPU
# 'OPENMP' - if OpenMP swithed on in 'toolchainopts'
# include the following extra packages into the build
general_packages = [
'AMOEBA',
'ASPHERE',
'ATC',
'AWPMD',
'BOCS',
'BODY',
'BPM',
'BROWNIAN',
'CG-DNA',
'CG-SPICA',
'CLASS2',
'COLLOID',
'COLVARS',
'COMPRESS',
'CORESHELL',
'DIELECTRIC',
'DIFFRACTION',
'DIPOLE',
'DPD-BASIC',
'DPD-MESO',
'DPD-REACT',
'DPD-SMOOTH',
'DRUDE',
'EFF',
'ELECTRODE',
'EXTRA-COMPUTE',
'EXTRA-DUMP',
'EXTRA-FIX',
'EXTRA-MOLECULE',
'EXTRA-PAIR',
'FEP',
'GRANULAR',
'H5MD',
'INTERLAYER',
'KIM',
'KSPACE',
'LATBOLTZ',
'LEPTON',
'MACHDYN',
'MANIFOLD',
'MANYBODY',
'MC',
'MDI',
'MEAM',
'MGPT',
'MISC',
'ML-IAP',
'ML-PACE',
'ML-POD',
'ML-RANN',
'ML-SNAP',
'MOFFF',
'MOLECULE',
'MOLFILE',
'MPIIO',
'NETCDF',
'OPT',
'ORIENT',
'PERI',
'PHONON',
'PLUGIN',
'PLUMED',
'POEMS',
'PTM',
'PYTHON',
'QEQ',
'QTB',
'REACTION',
'REAXFF',
'REPLICA',
'RIGID',
'SCAFACOS',
'SHOCK',
'SMTBQ',
'SPH',
'SPIN',
'SRD',
'TALLY',
'UEF',
'VORONOI',
'VTK',
'YAFF',
]
# Excluded packages due to requiring additional (non-trivial) deps
# - ADIOS
# - LATTE
# - MESONT (requires very large files downloaded during build)
# - ML-HDNNP (requires N2P2)
# - ML-QUIP
# - MSCG
# - QMMM (setup seems complex)
moduleclass = 'chem'

172
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@ -0,0 +1,172 @@
# IT4Innovations
# LK 2023
name = 'LAMMPS'
version = '2Aug2023'
versionsuffix = '-CUDA-12.2.0-kokkos'
homepage = 'https://www.lammps.org'
description = """LAMMPS is a classical molecular dynamics code, and an acronym
for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
used to model atoms or, more generically, as a parallel particle simulator at
the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.
"""
toolchain = {'name': 'foss', 'version': '2021b'}
import os
if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2', 'pic': True}
else:
toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
# 'https://github.com/lammps/lammps/archive/'
source_urls = [GITHUB_LOWER_SOURCE]
sources = ['stable_%(version)s_update1.tar.gz']
checksums = ['0e5568485e5ee080412dba44a1b7a93f864f1b5c75121f11d528854269953ed0']
builddependencies = [
('CMake', '3.22.1'),
('pkg-config', '0.29.2'),
('archspec', '0.1.3'),
]
dependencies = [
('Python', '3.9.6'),
('CUDA', '12.2.0', '', True),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.0.6'),
('netCDF', '4.8.1'),
('GSL', '2.7'),
('zlib', '1.2.11'),
('gzip', '1.10'),
('cURL', '7.78.0'),
('HDF5', '1.12.1'),
('tbb', '2020.3'),
('PCRE', '8.45'),
('libxml2', '2.9.10'),
('FFmpeg', '4.3.2'),
('Voro++', '0.4.6'),
('kim-api', '2.3.0'),
('Eigen', '3.4.0'),
('PLUMED', '2.7.3'),
('ScaFaCoS', '1.0.1'),
('SciPy-bundle', '2021.10'),
# VTK package is auto-disabled if this dep is not available
('VTK', '9.1.0'),
]
# To use additional custom configuration options, use the 'configopts' easyconfig parameter
# See docs and lammps easyblock for more information.
# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos,
# which is claimed to be faster in pure MPI calculations
# configopts = "-DKokkos_ENABLE_SERIAL=yes "
# GCC 11/12 defaults to C++17 standard, need to be consistent
configopts = "-DKokkos_CXX_STANDARD=17 "
# packages auto-enabled by easyblock
# 'GPU' - if cuda package is present and kokkos is disabled
# 'KOKKOS' - if kokkos is enabled (by default)
# include the following extra packages into the build
general_packages = [
'ASPHERE',
'AMOEBA',
'ATC',
'AWPMD',
'BOCS',
'BODY',
'BPM',
'BROWNIAN',
'CG-DNA',
'CG-SDK',
'CLASS2',
'COLLOID',
'COLVARS',
'COMPRESS',
'CORESHELL',
'DIELECTRIC',
'DIFFRACTION',
'DIPOLE',
'DPD-BASIC',
'DPD-MESO',
'DPD-REACT',
'DPD-SMOOTH',
'DRUDE',
'EFF',
'ELECTRODE',
'EXTRA-COMPUTE',
'EXTRA-DUMP',
'EXTRA-FIX',
'EXTRA-MOLECULE',
'EXTRA-PAIR',
'FEP',
'GRANULAR',
'H5MD',
'INTERLAYER',
'KIM',
'KSPACE',
'LATBOLTZ',
'MANIFOLD',
'MACHDYN',
'MANYBODY',
'MC',
'MEAM',
'MGPT',
'MISC',
'ML-IAP',
'ML-PACE',
'ML-RANN',
'ML-SNAP',
'MOFFF',
'MOLECULE',
'MOLFILE',
'MPIIO',
'NETCDF',
'OPENMP',
'ORIENT',
'PERI',
'PHONON',
'PLUGIN',
'PLUMED',
'POEMS',
'PTM',
'PYTHON',
'QEQ',
'QTB',
'REACTION',
'REAXFF',
'REPLICA',
'RIGID',
'SCAFACOS',
'SHOCK',
'SMTBQ',
'SPH',
'SPIN',
'SRD',
'TALLY',
'UEF',
'VORONOI',
'VTK',
'YAFF',
]
# Excluded packages due to requiring additional (non-trivial) deps
# - ADIOS
# - LATTE
# - MESONT (requires very large files downloaded during build)
# - ML-HDNNP (requires N2P2)
# - ML-QUIP
# - MSCG
# - QMMM (setup seems complex)
moduleclass = 'chem'

169
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@ -0,0 +1,169 @@
# IT4Innovations
# LK 2023
name = 'LAMMPS'
version = '2Aug2023'
versionsuffix = '-kokkos'
homepage = 'https://www.lammps.org'
description = """LAMMPS is a classical molecular dynamics code, and an acronym
for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
used to model atoms or, more generically, as a parallel particle simulator at
the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.
"""
toolchain = {'name': 'foss', 'version': '2021b'}
import os
if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2', 'pic': True}
else:
toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
# 'https://github.com/lammps/lammps/archive/'
source_urls = [GITHUB_LOWER_SOURCE]
sources = ['stable_%(version)s_update1.tar.gz']
checksums = ['0e5568485e5ee080412dba44a1b7a93f864f1b5c75121f11d528854269953ed0']
builddependencies = [
('CMake', '3.22.1'),
('pkg-config', '0.29.2'),
('archspec', '0.1.3'),
]
dependencies = [
('Python', '3.9.6'),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.0.6'),
('netCDF', '4.8.1'),
('GSL', '2.7'),
('zlib', '1.2.11'),
('gzip', '1.10'),
('cURL', '7.78.0'),
('HDF5', '1.12.1'),
('tbb', '2020.3'),
('PCRE', '8.45'),
('libxml2', '2.9.10'),
('FFmpeg', '4.3.2'),
('Voro++', '0.4.6'),
('kim-api', '2.3.0'),
('Eigen', '3.4.0'),
('PLUMED', '2.7.3'),
('ScaFaCoS', '1.0.1'),
('SciPy-bundle', '2021.10'),
# VTK package is auto-disabled if this dep is not available
('VTK', '9.1.0'),
]
# To use additional custom configuration options, use the 'configopts' easyconfig parameter
# See docs and lammps easyblock for more information.
# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos,
# which is claimed to be faster in pure MPI calculations
# configopts = "-DKokkos_ENABLE_SERIAL=yes "
# packages auto-enabled by easyblock
# 'GPU' - if cuda package is present and kokkos is disabled
# 'KOKKOS' - if kokkos is enabled (by default)
# include the following extra packages into the build
general_packages = [
'ASPHERE',
'AMOEBA',
'ATC',
'AWPMD',
'BOCS',
'BODY',
'BPM',
'BROWNIAN',
'CG-DNA',
'CG-SDK',
'CLASS2',
'COLLOID',
'COLVARS',
'COMPRESS',
'CORESHELL',
'DIELECTRIC',
'DIFFRACTION',
'DIPOLE',
'DPD-BASIC',
'DPD-MESO',
'DPD-REACT',
'DPD-SMOOTH',
'DRUDE',
'EFF',
'ELECTRODE',
'EXTRA-COMPUTE',
'EXTRA-DUMP',
'EXTRA-FIX',
'EXTRA-MOLECULE',
'EXTRA-PAIR',
'FEP',
'GRANULAR',
'H5MD',
'INTERLAYER',
'KIM',
'KSPACE',
'LATBOLTZ',
'MANIFOLD',
'MACHDYN',
'MANYBODY',
'MC',
'MEAM',
'MGPT',
'MISC',
'ML-IAP',
'ML-PACE',
'ML-RANN',
'ML-SNAP',
'MOFFF',
'MOLECULE',
'MOLFILE',
'MPIIO',
'NETCDF',
'OPENMP',
'ORIENT',
'PERI',
'PHONON',
'PLUGIN',
'PLUMED',
'POEMS',
'PTM',
'PYTHON',
'QEQ',
'QTB',
'REACTION',
'REAXFF',
'REPLICA',
'RIGID',
'SCAFACOS',
'SHOCK',
'SMTBQ',
'SPH',
'SPIN',
'SRD',
'TALLY',
'UEF',
'VORONOI',
'VTK',
'YAFF',
]
# Excluded packages due to requiring additional (non-trivial) deps
# - ADIOS
# - LATTE
# - MESONT (requires very large files downloaded during build)
# - ML-HDNNP (requires N2P2)
# - ML-QUIP
# - MSCG
# - QMMM (setup seems complex)
moduleclass = 'chem'

30
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@ -0,0 +1,30 @@
# IT4Innovations
# LK 2023
name = 'MATLAB'
version = '2023b'
homepage = 'https://www.mathworks.com/products/matlab'
description = """MATLAB is a high-level language and interactive environment
that enables you to perform computationally intensive tasks faster than with
traditional programming languages such as C, C++, and Fortran."""
toolchain = SYSTEM
sources = ['R%s_Linux.iso' % (version)]
checksums = ['f1cc4ae1a2e42a1d22745884aa80bf0d5d8676939ad21741ccff15fade06a881']
download_instructions = 'Download %s from mathworks.com' % sources[0]
#java_options = '-Xmx2048m'
#osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files
# Use EB_MATLAB_KEY environment variable or uncomment and modify license key
# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000'
# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or
# uncomment and modify the following variables for installation with floating license server
license_server = 'lm-praha.metacentrum.cz'
license_server_port = '1712'
moduleclass = 'math'

29
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@ -0,0 +1,29 @@
# IT4Innovations
# LK 2023
name = 'NCCL'
version = '2.18.3'
versionsuffix = '-CUDA-%(cudaver)s'
homepage = 'https://developer.nvidia.com/nccl'
description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective
communication primitives that are performance optimized for NVIDIA GPUs."""
toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
github_account = 'NVIDIA'
source_urls = [GITHUB_SOURCE]
sources = ['v%(version)s-1.tar.gz']
checksums = ['b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96']
builddependencies = [('binutils', '2.38')]
dependencies = [
('CUDA', '12.2.0', '', SYSTEM),
('UCX-CUDA', '1.14.1', versionsuffix),
]
# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
cuda_compute_capabilities = ['8.0']
moduleclass = 'lib'

42
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@ -0,0 +1,42 @@
# IT4Innovations
# LK 2023
easyblock = 'CMakeMake'
name = 'OVITO'
version = '3.9.2'
versionsuffix = '-basic'
homepage = 'https://www.ovito.org'
description = """OVITO is a scientific visualization and data analysis solution for atomistic and other particle-based
models. It helps scientists gain meaningful and quick insights from numerical simulation results."""
toolchain = {'name': 'gompi', 'version': '2022a'}
source_urls = ['https://gitlab.com/stuko/ovito/-/archive/v%(version)s/']
sources = [SOURCELOWER_TAR_GZ]
checksums = ['142da611aded2b660f68a11c034aa8cbe10561a9530ce047a08de2f8de543c8e']
builddependencies = [
('binutils', '2.38'),
('CMake', '3.23.1'),
]
dependencies = [
('Qt6', '6.5.3'),
# ('Qt5', '5.15.5'),
('HDF5', '1.12.2'),
('netCDF', '4.9.0'),
('FFmpeg', '4.4.2'),
('zlib', '1.2.12'),
('Boost', '1.79.0'),
('libglvnd', '1.4.0'),
('Python', '3.10.4'),
]
sanity_check_paths = {
'files': ['bin/ovito'],
'dirs': []
}
moduleclass = 'vis'

54
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@ -0,0 +1,54 @@
# IT4Innovations
# LK 2023
easyblock = 'CMakeMake'
name = 'OVITO'
version = '3.9.2'
versionsuffix = '-basic'
homepage = 'https://www.ovito.org/'
description = """OVITO is a scientific visualization and analysis software for atomistic and particle simulation data."""
toolchain = {'name': 'gompi', 'version': '2022b'}
source_urls = ['https://gitlab.com/stuko/ovito/-/archive/v%(version)s/']
sources = ['ovito-v%(version)s.tar.gz']
checksums = ['32041cd3d023d2e2e24222d61b096743b7f6c5ba6c96b29f7e0fb291ff5b638e']
builddependencies = [
('binutils', '2.39'),
('CMake', '3.24.3'),
]
dependencies = [
('Qt6', '6.5.3'),
# ('Qt5', '5.15.7'),
('HDF5', '1.14.0'),
('netCDF', '4.9.0'),
('FFmpeg', '5.1.2'),
('zlib', '1.2.12'),
('Boost', '1.81.0'),
('libglvnd', '1.6.0'),
('Python', '3.10.8'),
]
import os
if os.environ.get("CLUSTERNAME") in ["BARBORA"]:
postinstallcmds = [
'rm %(installdir)s/lib/ovito/libcrypto.so.1.1',
'ln -s /lib64/libcrypto.so.1.1 %(installdir)s/lib/ovito/',
]
sanity_check_paths = {
'files': ['bin/ovito'],
'dirs': ['bin'],
}
#sanity_check_commands = ['ovito --nogui --noviewports --help']
modextravars = {
'OVITO_LICENSING_VERBOSE': '1',
}
moduleclass = 'vis'

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@ -0,0 +1,63 @@
# IT4Innovations
# LK 2023
easyblock = 'CMakeMake'
name = 'OpenMolcas'
version = '23.06'
versionsuffix = '-noGA'
homepage = "https://gitlab.com/Molcas/OpenMolcas"
description = "OpenMolcas is a quantum chemistry software package"
toolchain = {'name': 'intel', 'version': '2022a'}
toolchainopts = {'usempi': True}
source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/']
sources = ["OpenMolcas-v%(version)s.tar.gz"]
patches = [
'OpenMolcas-21.06_mcpdft_deps.patch',
#'OpenMolcas-22.06-increase_MxShll.patch',
]
checksums = [
{'OpenMolcas-v23.06.tar.gz': 'fe0299ed39af6e84f249f91452c411f9845c9ae4a0ce78641c867dea8056f280'},
{'OpenMolcas-21.06_mcpdft_deps.patch': '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a'},
#{'OpenMolcas-22.06-increase_MxShll.patch': 'e2588bca3d60f0681f6569aedb287166cead3934f02bc41f8daa9ede8dad98e8'},
]
builddependencies = [('CMake', '3.23.1')]
dependencies = [
('HDF5', '1.12.2'),
('Python', '3.10.4'),
]
build_shared_libs = True
_copts = [
'-DLINALG=MKL',
'-DMKLROOT=$MKLROOT',
'-DOPENMP=ON',
'-DTOOLS=ON',
'-DFDE=ON',
'-DMPI=OFF',
'-DGA=OFF',
]
configopts = ' '.join(_copts)
modextrapaths = {'PATH': ''}
modextravars = {
'MOLCAS': '%(installdir)s',
'MOLCAS_DRIVER': '%(installdir)s/pymolcas',
'MOLCAS_SOURCE': '%(installdir)s',
}
#sanity_check_commands = ['cd %(builddir)s/easybuild_obj; ./pymolcas verify']
sanity_check_paths = {
'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT,
'sbin/help_basis', 'pymolcas'],
'dirs': ['data/', 'basis_library/'],
}
moduleclass = 'chem'

15
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View File

@ -35,9 +35,16 @@ dependencies = [
build_shared_libs = True
preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS'
configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT '
configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON '
configopts += '-DTOOLS=ON -DFDE=ON'
_copts = [
'-DLINALG=MKL',
'-DMKLROOT=$MKLROOT',
'-DOPENMP=ON',
'-DTOOLS=ON',
'-DFDE=ON',
'-DMPI=ON',
'-DGA=ON',
]
configopts = ' '.join(_copts)
modextrapaths = {'PATH': ''}
modextravars = {
@ -46,6 +53,8 @@ modextravars = {
'MOLCAS_SOURCE': '%(installdir)s',
}
#sanity_check_commands = ['cd %(builddir)s/easybuild_obj; ./pymolcas verify']
sanity_check_paths = {
'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT,
'sbin/help_basis', 'pymolcas'],

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@ -0,0 +1,64 @@
# IT4Innovations
# LK 2023
easyblock = 'ConfigureMake'
name = 'PLUMED'
version = '2.9.0'
homepage = 'https://www.plumed.org'
description = """PLUMED is an open source library for free energy calculations in molecular systems which
works together with some of the most popular molecular dynamics engines. Free energy calculations can be
performed as a function of many order parameters with a particular focus on biological problems, using
state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
"""
toolchain = {'name': 'foss', 'version': '2022a'}
toolchainopts = {'usempi': 'True'}
source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
sources = [SOURCE_TGZ]
checksums = ['534db9ccb9446844f3e99ecdff091ad79c014ce9c4afe212c1536e19f85ab0d1']
builddependencies = [
('xxd', '8.2.4220'),
]
dependencies = [
('zlib', '1.2.12'),
('GSL', '2.7'),
('Python', '3.10.4'),
('SciPy-bundle', '2022.05'),
('Boost', '1.79.0'),
]
preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
configopts += '--enable-boost_graph --enable-boost_serialization '
configopts += '--enable-asmjit '
configopts += '--enable-mpi '
prebuildopts = 'source sourceme.sh && '
# make sure that ld.gold linker is used
# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
# (problem with intel build but maintain consistency between easyconfigs)
buildopts = 'LD_RO="ld.gold -r -o"'
# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
sanity_check_paths = {
'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
'dirs': [],
}
sanity_check_commands = ["python -c 'import plumed'"]
modextrapaths = {
'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
'PLUMED_ROOT': 'lib/plumed',
'PYTHONPATH': 'lib/plumed/python',
}
moduleclass = 'chem'

92
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@ -0,0 +1,92 @@
# IT4Innovations
# LK 2023
easyblock = 'CMakeNinja'
name = 'Qt6'
version = '6.5.3'
homepage = 'https://qt.io/'
description = "Qt is a comprehensive cross-platform C++ application framework."
toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X)
toolchainopts = {'vectorize': False}
source_urls = [
'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/',
'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/',
'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/',
]
sources = ['qt-everywhere-src-%(version)s.tar.xz']
patches = [
'Qt6-6.5.2_fix_OF-Gentoo.patch',
]
checksums = [
{'qt-everywhere-src-6.5.3.tar.xz': '7cda4d119aad27a3887329cfc285f2aba5da85601212bcb0aea27bd6b7b544cb'},
{'Qt6-6.5.2_fix_OF-Gentoo.patch': '62c4b1abdeac69f40fd48f5e46f470f9f9c328fdb02ab8aceb9aa1885ad8c601'},
]
builddependencies = [
('binutils', '2.39'),
('pkgconf', '1.9.3'),
('CMake', '3.24.3'),
('Ninja', '1.11.1'),
# deps for QtWebEngine
('Bison', '3.8.2'),
('flex', '2.6.4'),
('gperf', '3.1'),
('re2c', '3.0'),
]
dependencies = [
('double-conversion', '3.2.1'),
('GLib', '2.75.0'),
('PCRE2', '10.40'),
('libpng', '1.6.38'),
('LibTIFF', '4.4.0'),
('libwebp', '1.3.1'),
('JasPer', '4.0.0'),
('HarfBuzz', '5.3.1'),
('SQLite', '3.39.4'),
('graphite2', '1.3.14'),
# ('assimp', '5.2.5'), # for Qt 3D
('FFmpeg', '5.1.2'),
('X11', '20221110'),
('fontconfig', '2.14.1'),
('zlib', '1.2.12'),
('Python', '3.10.8'),
# ('Python-bundle-PyPI', '2023.06'), # WebEngine
# ('freetype', '2.12.1'), # WebEngine
('DBus', '1.15.2'),
# ('libevent', '2.1.12'), # WebEngine
('libGLU', '9.0.2'),
# ('libjpeg-turbo', '2.1.4'), # WebEngine
# ('NSS', '3.85'), # WebEngine, required
# ('snappy', '1.1.9'), # WebEngine
('OpenSSL', '1.1', '', SYSTEM),
# ('ICU', '72.1'), # WebEngine, optional
# ('nodejs', '18.12.1'), # WebEngine, required
# ('gRPC', '1.52.2'), # WebEngine needs older Abseil/gRPC/protobuf
]
preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt &&' # Typo
preconfigopts += 'sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ' \
'../qt-everywhere-src-6.5.3/qtwebengine/src/gn/CMakeLists.txt &&'
configopts = '-Wno-dev '
configopts += '-DFEATURE_qtpdf_build=OFF ' # Requires CUPS
configopts += '-DQT_AVOID_CMAKE_ARCHIVING_API=ON '
configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON '
#configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7
# Removed from Qt6.0.0 but may be added back in the future
# configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7
sanity_check_paths = {
'files': ['bin/qmake6', 'lib/libQt6Core.%s' % SHLIB_EXT ],
'dirs': ['include/QtCore' ],
}
sanity_check_commands = ['qmake6 --help']
moduleclass = 'devel'

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@ -0,0 +1,92 @@
# IT4Innovations
# LK 2023
easyblock = 'CMakeNinja'
name = 'Qt6'
version = '6.5.3'
homepage = 'https://qt.io/'
description = "Qt is a comprehensive cross-platform C++ application framework."
toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X)
toolchainopts = {'vectorize': False}
source_urls = [
'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/',
'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/',
'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/',
]
sources = ['qt-everywhere-src-%(version)s.tar.xz']
patches = [
'Qt6-6.5.2_fix_OF-Gentoo.patch',
]
checksums = [
{'qt-everywhere-src-6.5.2.tar.xz': 'cde57be663d0f875759797298bdc37a936d517c39f2013e4e6ece5e12edeed12'},
{'Qt6-6.5.2_fix_OF-Gentoo.patch': '62c4b1abdeac69f40fd48f5e46f470f9f9c328fdb02ab8aceb9aa1885ad8c601'},
]
builddependencies = [
('binutils', '2.39'),
('pkgconf', '1.9.3'),
('CMake', '3.24.3'),
('Ninja', '1.11.1'),
# deps for QtWebEngine
('Bison', '3.8.2'),
('flex', '2.6.4'),
('gperf', '3.1'),
('re2c', '3.0'),
]
dependencies = [
('double-conversion', '3.2.1'),
('GLib', '2.75.0'),
('PCRE2', '10.40'),
('libpng', '1.6.38'),
('LibTIFF', '4.4.0'),
('libwebp', '1.3.1'),
('JasPer', '4.0.0'),
('HarfBuzz', '5.3.1'),
('SQLite', '3.39.4'),
('graphite2', '1.3.14'),
# ('assimp', '5.2.5'), # for Qt 3D
('FFmpeg', '5.1.2'),
('X11', '20221110'),
('fontconfig', '2.14.1'),
('zlib', '1.2.12'),
('Python', '3.10.8'),
# ('Python-bundle-PyPI', '2023.06'), # WebEngine
('freetype', '2.12.1'), # WebEngine
('DBus', '1.15.2'),
('libevent', '2.1.12'), # WebEngine
('libGLU', '9.0.2'),
('libjpeg-turbo', '2.1.4'), # WebEngine
('NSS', '3.85'), # WebEngine, required
('snappy', '1.1.9'), # WebEngine
('OpenSSL', '1.1', '', SYSTEM),
('ICU', '72.1'), # WebEngine, optional
('nodejs', '18.12.1'), # WebEngine, required
# ('gRPC', '1.52.2'), # WebEngine needs older Abseil/gRPC/protobuf
]
preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt &&' # Typo
preconfigopts += 'sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ' \
'../qt-everywhere-src-6.5.2/qtwebengine/src/gn/CMakeLists.txt &&'
configopts = '-Wno-dev '
configopts += '-DFEATURE_qtpdf_build=OFF ' # Requires CUPS
configopts += '-DQT_AVOID_CMAKE_ARCHIVING_API=ON '
configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON '
#configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7
# Removed from Qt6.0.0 but may be added back in the future
# configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7
sanity_check_paths = {
'files': ['bin/qmake6', 'lib/libQt6Core.%s' % SHLIB_EXT, 'lib/libQt6WebEngineCore.%s' % SHLIB_EXT],
'dirs': ['include/QtCore', 'include/QtWebEngineCore'],
}
sanity_check_commands = ['qmake6 --help']
moduleclass = 'devel'

51
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@ -0,0 +1,51 @@
# IT4Innovations
# LK 2023
easyblock = 'EB_UCX_Plugins'
name = 'UCX-CUDA'
version = '1.14.1'
versionsuffix = '-CUDA-%(cudaver)s'
homepage = 'http://www.openucx.org/'
description = """Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
This module adds the UCX CUDA support.
"""
toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
toolchainopts = {'pic': True}
source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s']
sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}]
patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch']
checksums = [
('457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93',
'baa0634cafb269a3112f626eb226bcd2ca8c9fcf0fec3b8e2a3553baad5f77aa'), # ucx-1.14.1.tar.gz
{'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch':
'457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'},
]
builddependencies = [
('binutils', '2.38'),
('Autotools', '20220317'),
('pkgconf', '1.8.0'),
]
dependencies = [
('zlib', '1.2.12'),
('UCX', '1.14.1'),
('CUDA', '12.2.0', '', SYSTEM),
('GDRCopy', '2.3'),
]
configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs '
configopts += '--without-java --without-go --disable-doxygen-doc '
import os
if os.environ.get("CLUSTERNAME") in ["KAROLINA", "BARBORA"]:
configopts += '--with-xpmem --with-knem=/opt/knem-1.1.4.90mlnx1'
moduleclass = 'lib'