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new file: g/GROMACS/GROMACS-2018.8-fosscuda-2020b-PLUMED-2.5.6-patch.eb
new file: g/GROMACS/GROMACS-2020.4-fosscuda-2020b-PLUMED-2.7.0-patch.eb new file: p/PLUMED/PLUMED-2.5.6-fosscuda-2020b-patch.eb new file: p/PLUMED/PLUMED-2.7.0-fosscuda-2020b-patch.eb new file: p/PLUMED/PLUMED-2.7.0-fosscuda-2020b.eb
This commit is contained in:
Lukas Krupcik
parent
ab7894c947
commit
052bd50a5b
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# IT4Innovations
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# LK 2021
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name = 'GROMACS'
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version = '2018.8'
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versionsuffix = '-PLUMED-2.5.6-patch'
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homepage = 'https://www.gromacs.org'
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description = """
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
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Newtonian equations of motion for systems with hundreds to millions of
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particles.
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This is a GPU enabled build, containing both MPI and threadMPI builds.
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It also contains the gmxapi extension for the single precision MPI build.
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"""
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toolchain = {'name': 'fosscuda', 'version': '2020b'}
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toolchainopts = {'openmp': True, 'usempi': True}
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source_urls = [
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'https://ftp.gromacs.org/pub/gromacs/',
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'ftp://ftp.gromacs.org/pub/gromacs/',
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]
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patches = [
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'GROMACS-2018_fix_search_for_nvml_include.patch',
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'GROMACS-2018_amend_search_for_nvml_lib.patch',
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]
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sources = ['gromacs-%(version)s-plumed-2.5.6.tar.gz']
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checksums = [
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'64d3613b5d346a2dd7118e289f87937d',
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'59d59316337ce08134d600b44c6501240f2732826ea5699f4b0ae83bb1ae0bd3', # GROMACS-2018_fix_search_for_nvml_include.patch
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'769cf8aab2e76bb1b36befa4b60df0b975a35877994218725426bb2c597f321b', # GROMACS-2018_amend_search_for_nvml_lib.patch
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]
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builddependencies = [
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('CMake', '3.18.4'),
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('scikit-build', '0.11.1'),
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]
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dependencies = [
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('Python', '3.8.6'),
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('SciPy-bundle', '2020.11'),
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('networkx', '2.5'),
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('PLUMED', '2.5.6', '-patch'),
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]
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exts_defaultclass = 'PythonPackage'
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modextrapaths = {
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'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
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}
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moduleclass = 'bio'
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# IT4Innovations
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# LK 2021
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name = 'GROMACS'
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version = '2020.4'
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versionsuffix = '-PLUMED-2.7.0-patch'
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homepage = 'https://www.gromacs.org'
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description = """
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
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Newtonian equations of motion for systems with hundreds to millions of
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particles.
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This is a GPU enabled build, containing both MPI and threadMPI builds.
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It also contains the gmxapi extension for the single precision MPI build.
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"""
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toolchain = {'name': 'fosscuda', 'version': '2020b'}
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toolchainopts = {'openmp': True, 'usempi': True}
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source_urls = [
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'https://ftp.gromacs.org/pub/gromacs/',
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'ftp://ftp.gromacs.org/pub/gromacs/',
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]
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sources = ['gromacs-%(version)s-plumed-2.7.0.tar.gz']
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patches = [
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'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch',
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'GROMACS-2019_increase_test_timeout_for_GPU.patch',
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# 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch',
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# 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch',
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]
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checksums = [
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'adfecf6b60414cdb722e6f4165818cf0', # gromacs-2020.4-plumed-2.7.0.tar.gz
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# GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch
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'406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275',
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# GROMACS-2019_increase_test_timeout_for_GPU.patch
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'0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234',
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# GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch
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'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49',
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# GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch
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'89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb',
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]
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builddependencies = [
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('CMake', '3.18.4'),
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('scikit-build', '0.11.1'),
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]
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dependencies = [
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('Python', '3.8.6'),
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('SciPy-bundle', '2020.11'),
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('networkx', '2.5'),
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('PLUMED', '2.7.0', '-patch'),
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]
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exts_defaultclass = 'PythonPackage'
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exts_default_options = {
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'source_urls': [PYPI_SOURCE],
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'use_pip': True,
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'download_dep_fail': True,
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'sanity_pip_check': True,
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}
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modextrapaths = {
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'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
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}
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moduleclass = 'bio'
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60
p/PLUMED/PLUMED-2.5.6-fosscuda-2020b-patch.eb
Normal file
60
p/PLUMED/PLUMED-2.5.6-fosscuda-2020b-patch.eb
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# IT4Innovations
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# LK 2021
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easyblock = 'ConfigureMake'
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name = 'PLUMED'
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version = '2.5.6'
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versionsuffix = '-patch'
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homepage = 'https://www.plumed.org'
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description = """PLUMED is an open source library for free energy calculations in molecular systems which
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works together with some of the most popular molecular dynamics engines. Free energy calculations can be
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performed as a function of many order parameters with a particular focus on biological problems, using
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state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
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The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
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"""
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toolchain = {'name': 'fosscuda', 'version': '2020b'}
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toolchainopts = {'usempi': 'True'}
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#source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
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sources = ['plumed-2.5.6-patch.tar.gz']
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checksums = ['ede6af7b7c82678b9579d5aedd8049fc']
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dependencies = [
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('zlib', '1.2.11'),
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('GSL', '2.6'),
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('Python', '3.8.6'),
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('SciPy-bundle', '2020.11'),
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('Boost', '1.74.0'),
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]
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preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
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configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
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configopts += '--enable-boost_graph --enable-boost_serialization '
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configopts += '--enable-asmjit '
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prebuildopts = 'source sourceme.sh && '
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# make sure that ld.gold linker is used
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# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
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# (problem with intel build but maintain consistency between easyconfigs)
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buildopts = 'LD_RO="ld.gold -r -o"'
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# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
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preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
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sanity_check_paths = {
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'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
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'dirs': [],
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}
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sanity_check_commands = ["python -c 'import plumed'"]
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modextrapaths = {
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'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
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'PLUMED_ROOT': 'lib/plumed',
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'PYTHONPATH': 'lib/plumed/python',
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}
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moduleclass = 'chem'
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60
p/PLUMED/PLUMED-2.7.0-fosscuda-2020b-patch.eb
Normal file
60
p/PLUMED/PLUMED-2.7.0-fosscuda-2020b-patch.eb
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# IT4Innovations
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# LK 2021
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easyblock = 'ConfigureMake'
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name = 'PLUMED'
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version = '2.7.0'
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versionsuffix = '-patch'
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homepage = 'https://www.plumed.org'
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description = """PLUMED is an open source library for free energy calculations in molecular systems which
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works together with some of the most popular molecular dynamics engines. Free energy calculations can be
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performed as a function of many order parameters with a particular focus on biological problems, using
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state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
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The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
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"""
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toolchain = {'name': 'fosscuda', 'version': '2020b'}
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toolchainopts = {'usempi': 'True'}
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#source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
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sources = ['plumed-2.7.0-patch.tar.gz']
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checksums = ['bbe5afe56ee624c46251735158a69353']
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dependencies = [
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('zlib', '1.2.11'),
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('GSL', '2.6'),
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('Python', '3.8.6'),
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('SciPy-bundle', '2020.11'),
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('Boost', '1.74.0'),
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]
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preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
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configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
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configopts += '--enable-boost_graph --enable-boost_serialization '
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configopts += '--enable-asmjit '
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prebuildopts = 'source sourceme.sh && '
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# make sure that ld.gold linker is used
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# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
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# (problem with intel build but maintain consistency between easyconfigs)
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buildopts = 'LD_RO="ld.gold -r -o"'
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# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
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preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
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sanity_check_paths = {
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'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
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'dirs': [],
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}
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sanity_check_commands = ["python -c 'import plumed'"]
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modextrapaths = {
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'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
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'PLUMED_ROOT': 'lib/plumed',
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'PYTHONPATH': 'lib/plumed/python',
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}
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moduleclass = 'chem'
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58
p/PLUMED/PLUMED-2.7.0-fosscuda-2020b.eb
Normal file
58
p/PLUMED/PLUMED-2.7.0-fosscuda-2020b.eb
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@ -0,0 +1,58 @@
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# IT4Innovations
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# LK 2021
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easyblock = 'ConfigureMake'
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name = 'PLUMED'
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version = '2.7.0'
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homepage = 'https://www.plumed.org'
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description = """PLUMED is an open source library for free energy calculations in molecular systems which
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works together with some of the most popular molecular dynamics engines. Free energy calculations can be
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performed as a function of many order parameters with a particular focus on biological problems, using
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state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
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The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
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"""
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toolchain = {'name': 'fosscuda', 'version': '2020b'}
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toolchainopts = {'usempi': 'True'}
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source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
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sources = [SOURCE_TGZ]
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dependencies = [
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('zlib', '1.2.11'),
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('GSL', '2.6'),
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('Python', '3.8.6'),
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('SciPy-bundle', '2020.11'),
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('Boost', '1.74.0'),
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]
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preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
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configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
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configopts += '--enable-boost_graph --enable-boost_serialization '
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configopts += '--enable-asmjit '
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prebuildopts = 'source sourceme.sh && '
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# make sure that ld.gold linker is used
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# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
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# (problem with intel build but maintain consistency between easyconfigs)
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buildopts = 'LD_RO="ld.gold -r -o"'
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# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
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preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
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sanity_check_paths = {
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'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
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'dirs': [],
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}
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sanity_check_commands = ["python -c 'import plumed'"]
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modextrapaths = {
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'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
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'PLUMED_ROOT': 'lib/plumed',
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'PYTHONPATH': 'lib/plumed/python',
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}
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moduleclass = 'chem'
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