Merge branch 'it4i-salomon'

Former-commit-id: 338bd38dff8fc50aa66d51e6385b793f9c2aa4af

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'

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'

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'

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'