diff --git a/g/GROMACS/GROMACS-2018.8-fosscuda-2020b-PLUMED-2.5.6-patch.eb b/g/GROMACS/GROMACS-2018.8-fosscuda-2020b-PLUMED-2.5.6-patch.eb new file mode 100644 index 00000000..5a002cb6 --- /dev/null +++ b/g/GROMACS/GROMACS-2018.8-fosscuda-2020b-PLUMED-2.5.6-patch.eb @@ -0,0 +1,58 @@ +# IT4Innovations +# LK 2021 + +name = 'GROMACS' +version = '2018.8' +versionsuffix = '-PLUMED-2.5.6-patch' + +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 builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] + +patches = [ + 'GROMACS-2018_fix_search_for_nvml_include.patch', + 'GROMACS-2018_amend_search_for_nvml_lib.patch', +] + +sources = ['gromacs-%(version)s-plumed-2.5.6.tar.gz'] + +checksums = [ + '64d3613b5d346a2dd7118e289f87937d', + '59d59316337ce08134d600b44c6501240f2732826ea5699f4b0ae83bb1ae0bd3', # GROMACS-2018_fix_search_for_nvml_include.patch + '769cf8aab2e76bb1b36befa4b60df0b975a35877994218725426bb2c597f321b', # GROMACS-2018_amend_search_for_nvml_lib.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('PLUMED', '2.5.6', '-patch'), +] + +exts_defaultclass = 'PythonPackage' + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/g/GROMACS/GROMACS-2020.4-fosscuda-2020b-PLUMED-2.7.0-patch.eb b/g/GROMACS/GROMACS-2020.4-fosscuda-2020b-PLUMED-2.7.0-patch.eb new file mode 100644 index 00000000..39cdd379 --- /dev/null +++ b/g/GROMACS/GROMACS-2020.4-fosscuda-2020b-PLUMED-2.7.0-patch.eb @@ -0,0 +1,70 @@ +# IT4Innovations +# LK 2021 + +name = 'GROMACS' +version = '2020.4' +versionsuffix = '-PLUMED-2.7.0-patch' + +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 builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = ['gromacs-%(version)s-plumed-2.7.0.tar.gz'] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', +# 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', +# 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'adfecf6b60414cdb722e6f4165818cf0', # gromacs-2020.4-plumed-2.7.0.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('PLUMED', '2.7.0', '-patch'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/p/PLUMED/PLUMED-2.5.6-fosscuda-2020b-patch.eb b/p/PLUMED/PLUMED-2.5.6-fosscuda-2020b-patch.eb new file mode 100644 index 00000000..510dfd99 --- /dev/null +++ b/p/PLUMED/PLUMED-2.5.6-fosscuda-2020b-patch.eb @@ -0,0 +1,60 @@ +# IT4Innovations +# LK 2021 + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.6' +versionsuffix = '-patch' + +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': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': 'True'} + +#source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = ['plumed-2.5.6-patch.tar.gz'] +checksums = ['ede6af7b7c82678b9579d5aedd8049fc'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), +] + +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 ' +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' diff --git a/p/PLUMED/PLUMED-2.7.0-fosscuda-2020b-patch.eb b/p/PLUMED/PLUMED-2.7.0-fosscuda-2020b-patch.eb new file mode 100644 index 00000000..42778b85 --- /dev/null +++ b/p/PLUMED/PLUMED-2.7.0-fosscuda-2020b-patch.eb @@ -0,0 +1,60 @@ +# IT4Innovations +# LK 2021 + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.0' +versionsuffix = '-patch' + +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': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': 'True'} + +#source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = ['plumed-2.7.0-patch.tar.gz'] +checksums = ['bbe5afe56ee624c46251735158a69353'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), +] + +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 ' +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' diff --git a/p/PLUMED/PLUMED-2.7.0-fosscuda-2020b.eb b/p/PLUMED/PLUMED-2.7.0-fosscuda-2020b.eb new file mode 100644 index 00000000..2b6d23ff --- /dev/null +++ b/p/PLUMED/PLUMED-2.7.0-fosscuda-2020b.eb @@ -0,0 +1,58 @@ +# IT4Innovations +# LK 2021 + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.0' + +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': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), +] + +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 ' +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'