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
2025-04-04 06:11:36 +01:00 · 2024-02-14 12:24:49 +01:00 · 2024-02-14 12:24:49 +01:00 · dde97d4fde
commit dde97d4fde
parent 65193dff9c
5 changed files with 235 additions and 0 deletions
--- 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
@ -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'
--- 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
@ -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'
--- a/h/HyperQueue/HyperQueue-0.18.0.eb
+++ 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'
--- a/s/stda/stda-1.6.3.eb
+++ 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'
+
--- a/x/xtb4stda/xtb4stda-1.0.eb
+++ 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'