Merge branch 'it4i-salomon'

Former-commit-id: 70cb738cd1e39daee23ef92e1f6ac3389851528b

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'

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'

g/glibc/glibc-2.19-x32.eb

@@ -3,7 +3,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'glibc'
-version = '2.19'
+version = '2.17'
 versionsuffix = '-x32'
 
 homepage = 'https://www.gnu.org/software/libc/'
@@ -11,7 +11,9 @@ description = """The Glibc package contains the main C library. This library pro
 
 toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
 
-m32 = True
+builddependencies = [
+ ('make', '3.82', '', True) 
+]
 
 sources = ['%(name)s-%(version)s.tar.gz']
 source_urls = ['http://ftp.gnu.org/gnu/glibc/']
@@ -19,7 +21,7 @@ source_urls = ['http://ftp.gnu.org/gnu/glibc/']
 preconfigopts = 'mkdir build && '
 preconfigopts += 'cd build && '
 configure_cmd_prefix = '.'
-configopts = '--enable-kernel=2.6.32 --enable-obsolete-rpc --enable-stack-protector=strong'
+configopts = '--enable-kernel=2.6.32 --enable-obsolete-rpc --enable-stack-protector=strong CC="gcc -m32" CXX="g++ -m32" CFLAGS="-O2 -march=i686" CXXFLAGS="-O2 -march=i686" i686-linux-gnu'
 prebuildopts = 'cd build && ' 
 preinstallopts= 'cd build && '
 

g/glibc/libc-2.14-6.3.0.eb

@@ -1,16 +0,0 @@
-easyblock = 'Toolchain'
-
-name = 'libc'
-version = '2.14-6.3.0'
-
-homepage = 'https://www.gnu.org/software/libc/'
-description = """The Glibc package contains the main C library. This library provides the basic routines for allocating memory, searching directories, opening and closing files, reading and writing files, string handling, pattern matching, arithmetic, and so on."""
-
-toolchain = {'name': 'dummy', 'version': ''}
-
-dependencies = [
-    ('GCCcore', '6.3.0'),
-    ('glibc', '2.14')
-]
-
-moduleclass = 'toolchain'

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'