From e3a90957c5ccfb618dca0cbc038c52a1a98b10db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 10:14:18 +0100 Subject: [PATCH 1/2] adding easyconfigs: PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb, PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb --- .../PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb | 59 +++++++++++++++++++ .../PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb | 59 +++++++++++++++++++ 2 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..016f139bcba --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,59 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.2' +versionsuffix = '-Python-%(pyver)s' + +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': '2020b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] + +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/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..8335d4aa2e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb @@ -0,0 +1,59 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.2' +versionsuffix = '-Python-%(pyver)s' + +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': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] + +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' From 5fa6638db59c39831447f1466b5b9f44050ebf20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Dec 2020 13:16:20 +0100 Subject: [PATCH 2/2] drop '-Python*' versionsuffix for PLUMED with 2020b toolchain --- ...6.2-foss-2020b-Python-3.8.6.eb => PLUMED-2.6.2-foss-2020b.eb} | 1 - ...2-intel-2020b-Python-3.8.6.eb => PLUMED-2.6.2-intel-2020b.eb} | 1 - 2 files changed, 2 deletions(-) rename easybuild/easyconfigs/p/PLUMED/{PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb => PLUMED-2.6.2-foss-2020b.eb} (98%) rename easybuild/easyconfigs/p/PLUMED/{PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb => PLUMED-2.6.2-intel-2020b.eb} (98%) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb similarity index 98% rename from easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index 016f139bcba..3fb97d9ba7c 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -4,7 +4,6 @@ easyblock = 'ConfigureMake' name = 'PLUMED' version = '2.6.2' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.plumed.org' description = """PLUMED is an open source library for free energy calculations in molecular systems which diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb similarity index 98% rename from easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb index 8335d4aa2e7..16200c8e59a 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb @@ -4,7 +4,6 @@ easyblock = 'ConfigureMake' name = 'PLUMED' version = '2.6.2' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.plumed.org' description = """PLUMED is an open source library for free energy calculations in molecular systems which