Merge branch 'it4i-barbora'

g/GROMACS/GROMACS-2016.5-intel-2017c-hybrid-single-PLUMED-2.3.8.eb

@@ -0,0 +1,37 @@
+# IT4Innovations 2010
+# LK
+
+name = 'GROMACS'
+version = '2016.5'
+versionsuffix = '-hybrid-single-PLUMED-2.3.8'
+
+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', '3.5.2', '', True),
+]
+
+dependencies = [
+    ('Boost', '1.67.0', '-serial'),
+    ('PLUMED', '2.3.8')
+]
+
+sanity_check_paths = {
+    'files': ['bin/gmx_mpi'],
+    'dirs': [''],
+}
+
+moduleclass = 'bio'

g/GROMACS/GROMACS-2020.2-intel-2020a-PLUMED-2.6.1.eb

@@ -0,0 +1,38 @@
+# IT4Innovations 2020
+# LK
+
+name = 'GROMACS'
+version = '2020.2'
+local_plum_ver = '2.6.1'
+versionsuffix = '-PLUMED-%s' % local_plum_ver
+
+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.
+
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
+"""
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+#atches = [
+#   'GROMACS-2018_fix_search_for_nvml_include.patch',
+#   'GROMACS-2018_amend_search_for_nvml_lib.patch',
+#
+
+builddependencies = [
+    ('CMake', '3.16.4'),
+]
+
+dependencies = [
+    ('PLUMED', local_plum_ver, '-Python-3.8.2'),
+]
+
+moduleclass = 'bio'

p/PLUMED/PLUMED-2.3.8-intel-2017c.eb

@@ -0,0 +1,47 @@
+# IT4Innovations 2020
+# LK
+
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.3.8'
+
+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'),
+    ('GSL', '2.5'),
+    ('libmatheval', '1.1.11', '', True),
+]
+
+preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
+configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all'
+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'

p/PLUMED/PLUMED-2.6.1-intel-2020a-Python-3.8.2.eb

@@ -0,0 +1,59 @@
+# by Ward Poelmans <wpoely86@gmail.com>
+
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.6.1'
+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': '2020a'}
+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'),
+    ('libmatheval', '1.1.11'),
+    ('Python', '3.8.2'),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+    ('Boost', '1.72.0'),
+]
+
+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'