From 0c35a58c352210c1dc40a65cf0c23ea163478df5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 10 Sep 2018 15:25:03 +0200 Subject: [PATCH] new file: b/Boost/Boost-1.68.0-intel-2017c-serial.eb new file: g/GROMACS/GROMACS-2018.1-intel-2017c-hybrid-single-PLUMED.eb new file: g/GROMACS/GROMACS-2018.3-intel-2017c-hybrid-single-PLUMED.eb new file: p/PLUMED/PLUMED-2.4.2-intel-2017c.eb Former-commit-id: dbbb5aed810ab212c041daaff6eaf84bb1e56ad7 --- b/Boost/Boost-1.68.0-intel-2017c-serial.eb | 28 +++++++++++++ ...2018.1-intel-2017c-hybrid-single-PLUMED.eb | 36 ++++++++++++++++ ...2018.3-intel-2017c-hybrid-single-PLUMED.eb | 36 ++++++++++++++++ p/PLUMED/PLUMED-2.4.2-intel-2017c.eb | 42 +++++++++++++++++++ 4 files changed, 142 insertions(+) create mode 100644 b/Boost/Boost-1.68.0-intel-2017c-serial.eb create mode 100644 g/GROMACS/GROMACS-2018.1-intel-2017c-hybrid-single-PLUMED.eb create mode 100644 g/GROMACS/GROMACS-2018.3-intel-2017c-hybrid-single-PLUMED.eb create mode 100644 p/PLUMED/PLUMED-2.4.2-intel-2017c.eb diff --git a/b/Boost/Boost-1.68.0-intel-2017c-serial.eb b/b/Boost/Boost-1.68.0-intel-2017c-serial.eb new file mode 100644 index 00000000..65c4c213 --- /dev/null +++ b/b/Boost/Boost-1.68.0-intel-2017c-serial.eb @@ -0,0 +1,28 @@ +# IT4Innovations 2018 + +name = 'Boost' +version = '1.68.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2017c'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + + +dependencies = [ + ('bzip2', '1.0.6', '', True), + ('zlib', '1.2.11', '', True), +] + +configopts = '--with-libraries=serialization' +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/g/GROMACS/GROMACS-2018.1-intel-2017c-hybrid-single-PLUMED.eb b/g/GROMACS/GROMACS-2018.1-intel-2017c-hybrid-single-PLUMED.eb new file mode 100644 index 00000000..0513ef2e --- /dev/null +++ b/g/GROMACS/GROMACS-2018.1-intel-2017c-hybrid-single-PLUMED.eb @@ -0,0 +1,36 @@ +# IT4Innovations 2018 + +name = 'GROMACS' +version = '2018.1' +versionsuffix = '-hybrid-single-PLUMED' + +homepage = 'http://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.""" + +toolchain = {'name': 'intel', 'version': '2017c'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +#preconfigopts = 'plumed patch -p -e gromacs-2016.5 &&' +#preconfigopts = 'plumed patch -p --runtime &&' + +configopts = ' -DGMX_GPU=OFF -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=OFF -DGMX_SIMD=AVX2_256 -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON' + +builddependencies = [ + ('CMake', '3.9.1', '', True), +] + +dependencies = [ + ('Boost', '1.68.0', '-serial'), + ('PLUMED', '2.4.2') +] + +sanity_check_paths = { + 'files': ['bin/gmx_mpi'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/g/GROMACS/GROMACS-2018.3-intel-2017c-hybrid-single-PLUMED.eb b/g/GROMACS/GROMACS-2018.3-intel-2017c-hybrid-single-PLUMED.eb new file mode 100644 index 00000000..26af7ea9 --- /dev/null +++ b/g/GROMACS/GROMACS-2018.3-intel-2017c-hybrid-single-PLUMED.eb @@ -0,0 +1,36 @@ +# IT4Innovations 2018 + +name = 'GROMACS' +version = '2018.3' +versionsuffix = '-hybrid-single-PLUMED' + +homepage = 'http://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.""" + +toolchain = {'name': 'intel', 'version': '2017c'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +#preconfigopts = 'plumed patch -p -e gromacs-2016.5 &&' +#preconfigopts = 'plumed patch -p --runtime &&' + +configopts = ' -DGMX_GPU=OFF -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=OFF -DGMX_SIMD=AVX2_256 -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON' + +builddependencies = [ + ('CMake', '3.9.1', '', True), +] + +dependencies = [ + ('Boost', '1.68.0', '-serial'), + ('PLUMED', '2.4.2') +] + +sanity_check_paths = { + 'files': ['bin/gmx_mpi'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/p/PLUMED/PLUMED-2.4.2-intel-2017c.eb b/p/PLUMED/PLUMED-2.4.2-intel-2017c.eb new file mode 100644 index 00000000..3e6fd4e3 --- /dev/null +++ b/p/PLUMED/PLUMED-2.4.2-intel-2017c.eb @@ -0,0 +1,42 @@ +# IT4Innovations 2018 + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.4.2' + +homepage = 'http://www.plumed-code.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': '2017c'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11', '', True), + ('GSL', '2.5'), + ('libmatheval', '1.1.11', '', True), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem'