From dde97d4fde6abab56e5766752ec7eb5785ddd4ff Mon Sep 17 00:00:00 2001 From: Lukas Krupcik Date: Wed, 14 Feb 2024 12:24:49 +0100 Subject: [PATCH] new file: g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-v2.eb new file: g/GROMACS/GROMACS-2024-foss-2022a-CUDA-12.0.0-v2.eb new file: h/HyperQueue/HyperQueue-0.18.0.eb new file: s/stda/stda-1.6.3.eb new file: x/xtb4stda/xtb4stda-1.0.eb --- ...ROMACS-2023.4-foss-2022a-CUDA-12.0.0-v2.eb | 75 +++++++++++++++++++ .../GROMACS-2024-foss-2022a-CUDA-12.0.0-v2.eb | 75 +++++++++++++++++++ h/HyperQueue/HyperQueue-0.18.0.eb | 28 +++++++ s/stda/stda-1.6.3.eb | 27 +++++++ x/xtb4stda/xtb4stda-1.0.eb | 30 ++++++++ 5 files changed, 235 insertions(+) create mode 100644 g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-v2.eb create mode 100644 g/GROMACS/GROMACS-2024-foss-2022a-CUDA-12.0.0-v2.eb create mode 100644 h/HyperQueue/HyperQueue-0.18.0.eb create mode 100644 s/stda/stda-1.6.3.eb create mode 100644 x/xtb4stda/xtb4stda-1.0.eb diff --git a/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-v2.eb b/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-v2.eb new file mode 100644 index 00000000..30bbaf5e --- /dev/null +++ b/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-v2.eb @@ -0,0 +1,75 @@ +# IT4Innovations +# BS 2024 + +name = 'GROMACS' +version = '2023.4' +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-2023.4.tar.gz': '4034a8b5ceca56b193afcc5f598824fd'}, + {'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-2023.4.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/g/GROMACS/GROMACS-2024-foss-2022a-CUDA-12.0.0-v2.eb b/g/GROMACS/GROMACS-2024-foss-2022a-CUDA-12.0.0-v2.eb new file mode 100644 index 00000000..549ae6ed --- /dev/null +++ b/g/GROMACS/GROMACS-2024-foss-2022a-CUDA-12.0.0-v2.eb @@ -0,0 +1,75 @@ +# IT4Innovations +# BS 2024 + +name = 'GROMACS' +version = '2024' +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-2024.tar.gz': '6fd5bedba9f84e5b397b4cbe5720ae1e'}, + {'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-2024.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/h/HyperQueue/HyperQueue-0.18.0.eb b/h/HyperQueue/HyperQueue-0.18.0.eb new file mode 100644 index 00000000..cc92e0e7 --- /dev/null +++ b/h/HyperQueue/HyperQueue-0.18.0.eb @@ -0,0 +1,28 @@ +# IT4Innovations +# LK 2024 + +easyblock = 'PackedBinary' + +name = 'HyperQueue' +version = '0.18.0' + +homepage = 'https://it4innovations.github.io/hyperqueue/' +description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks + and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs + and distributes them to fully utilize allocated notes. + You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/It4innovations/hyperqueue/releases/download/v%(version)s/'] +sources = ['hq-v%(version)s-linux-x64.tar.gz'] +checksums = ['4aea552dfa7cdccb8e7a1f86493b3098e4c100d4a2fbe694aea20ffaf50ad80a'] + +sanity_check_paths = { + 'files': ['hq'], + 'dirs': [], +} + +sanity_check_commands = ['hq --version'] + +moduleclass = 'devel' diff --git a/s/stda/stda-1.6.3.eb b/s/stda/stda-1.6.3.eb new file mode 100644 index 00000000..a595138a --- /dev/null +++ b/s/stda/stda-1.6.3.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2024 +# LK 2024 + +easyblock = 'Binary' + +name = 'stda' +version = '1.6.3' + +homepage = 'https://github.com/grimme-lab/stda' +description = """stda program for computing excited states and response functions via simplified TD-DFT methods (sTDA, sTD-DFT, and SF-sTD-DFT) """ + +toolchain = SYSTEM + +source_urls = ['https://github.com/grimme-lab/stda/releases/download/v%(version)s/'] +sources = ['%(name)s_v%(version)s'] +checksums = ['9701f1d08e79dd560f44fbae61d126eaacd944eb8f67fca0820621b90033af80'] + +install_cmd = 'mkdir %(installdir)s/bin && ' +install_cmd += 'mv %(name)s_v%(version)s %(installdir)s/bin/%(name)s ' + +sanity_check_paths = { + 'files': ['bin/stda'], + 'dirs': [], +} + +moduleclass = 'chem' + diff --git a/x/xtb4stda/xtb4stda-1.0.eb b/x/xtb4stda/xtb4stda-1.0.eb new file mode 100644 index 00000000..3758773c --- /dev/null +++ b/x/xtb4stda/xtb4stda-1.0.eb @@ -0,0 +1,30 @@ +# IT4Innovations +# LK 2024 + +easyblock = 'Binary' + +name = 'xtb4stda' +version = '1.0' + +homepage = 'https://github.com/grimme-lab/xtb4stda' +description = """Program to calculate the ground state with sTDA-xTB to be used in further stda calculations""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/grimme-lab/stda/releases/download/v1.6.3/'] +sources = ['%(name)s'] +checksums = ['aa5ba03321607dccc0bd01196876a16c5825100672c0acc0ac06631eb40b7d8e'] + +dependencies = [ + ('stda', '1.6.3') +] + +install_cmd = 'mkdir %(installdir)s/bin && ' +install_cmd += 'mv %(name)s %(installdir)s/bin/%(name)s ' + +sanity_check_paths = { + 'files': ['bin/xtb4stda'], + 'dirs': [], +} + +moduleclass = 'chem'