From 6f3f85ca4caa1ecd63e67be211f91de8ea32b368 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 21 May 2018 13:16:25 +0200 Subject: [PATCH] new file: g/GROMACS/GROMACS-2016.4-intel-2017c-hybrid-single-PLUMED-2.4.1.eb new file: g/GROMACS/GROMACS-2016.5-intel-2017c-hybrid-single-PLUMED-2.4.1.eb modified: g/glibc/glibc-2.19-x32.eb new file: p/PLUMED/PLUMED-2.4.1-intel-2017c.eb Former-commit-id: 01ff540be1b45dfb24942589040cec3d5d9bfb3c --- ...-intel-2017c-hybrid-single-PLUMED-2.4.1.eb | 36 ++++++++++++++++ ...-intel-2017c-hybrid-single-PLUMED-2.4.1.eb | 36 ++++++++++++++++ g/glibc/glibc-2.19-x32.eb | 2 +- p/PLUMED/PLUMED-2.4.1-intel-2017c.eb | 42 +++++++++++++++++++ 4 files changed, 115 insertions(+), 1 deletion(-) create mode 100644 g/GROMACS/GROMACS-2016.4-intel-2017c-hybrid-single-PLUMED-2.4.1.eb create mode 100644 g/GROMACS/GROMACS-2016.5-intel-2017c-hybrid-single-PLUMED-2.4.1.eb create mode 100644 p/PLUMED/PLUMED-2.4.1-intel-2017c.eb diff --git a/g/GROMACS/GROMACS-2016.4-intel-2017c-hybrid-single-PLUMED-2.4.1.eb b/g/GROMACS/GROMACS-2016.4-intel-2017c-hybrid-single-PLUMED-2.4.1.eb new file mode 100644 index 00000000..52cb2eef --- /dev/null +++ b/g/GROMACS/GROMACS-2016.4-intel-2017c-hybrid-single-PLUMED-2.4.1.eb @@ -0,0 +1,36 @@ +# IT4Innovations 2018 + +name = 'GROMACS' +version = '2016.4' +versionsuffix = '-hybrid-single-PLUMED-2.4.1' + +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 = ['ftp://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', '3.5.2', '', True), +] + +dependencies = [ + ('Boost', '1.67.0', '-serial'), + ('PLUMED', '2.4.1') +] + +sanity_check_paths = { + 'files': ['bin/gmx_mpi'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/g/GROMACS/GROMACS-2016.5-intel-2017c-hybrid-single-PLUMED-2.4.1.eb b/g/GROMACS/GROMACS-2016.5-intel-2017c-hybrid-single-PLUMED-2.4.1.eb new file mode 100644 index 00000000..931cc379 --- /dev/null +++ b/g/GROMACS/GROMACS-2016.5-intel-2017c-hybrid-single-PLUMED-2.4.1.eb @@ -0,0 +1,36 @@ +# IT4Innovations 2018 + +name = 'GROMACS' +version = '2016.5' +versionsuffix = '-hybrid-single-PLUMED-2.4.1' + +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 = ['ftp://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', '3.5.2', '', True), +] + +dependencies = [ + ('Boost', '1.67.0', '-serial'), + ('PLUMED', '2.4.1') +] + +sanity_check_paths = { + 'files': ['bin/gmx_mpi'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/g/glibc/glibc-2.19-x32.eb b/g/glibc/glibc-2.19-x32.eb index 2f81f0a4..ef2d1ca8 100644 --- a/g/glibc/glibc-2.19-x32.eb +++ b/g/glibc/glibc-2.19-x32.eb @@ -11,7 +11,7 @@ description = """The Glibc package contains the main C library. This library pro toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} -m32 = True +multilib = True sources = ['%(name)s-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/glibc/'] diff --git a/p/PLUMED/PLUMED-2.4.1-intel-2017c.eb b/p/PLUMED/PLUMED-2.4.1-intel-2017c.eb new file mode 100644 index 00000000..c4b0de99 --- /dev/null +++ b/p/PLUMED/PLUMED-2.4.1-intel-2017c.eb @@ -0,0 +1,42 @@ +# IT4Innovations 2018 + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.4.1' + +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', '2.4'), + ('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'