Merge branch 'it4i-salomon'

a/ABINIT/ABINIT-8.6.1-intel-2017a.eb

@@ -13,13 +13,13 @@ toolchain = {'name': 'intel', 'version': '2017a'}
 source_urls = ['https://www.abinit.org/sites/default/files/packages/']
 sources = [SOURCELOWER_TAR_GZ]
 
-configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-dft=flavor='libxc' "
+configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' "
 configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" '
 configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" '
 configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" '
 
 dependencies = [
-    ('libxc', '4.0.1'),
+    ('libxc', '4.0.1', '', True),
     ('netCDF', '4.4.1.1'),
     ('netCDF-Fortran', '4.4.4'),
 ]

b/byacc/byacc-20170509.eb

@@ -1,7 +1,9 @@
+# IT4Innovations 2017
+
 easyblock = 'ConfigureMake'
 
 name = 'byacc'
-version = '20160606'
+version = '20170509'
 
 homepage = 'http://invisible-island.net/byacc/byacc.html'
 description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available.
@@ -9,10 +11,12 @@ description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc
 
 toolchain = {'name': 'dummy', 'version': ''}
 
-sources = [SOURCELOWER_TGZ]
-source_urls = ['ftp://invisible-island.net/byacc']
 
-checksums = ['d527c811b360f04a8c5f5a0a90625966']
+# version independent download ! check downloaded version !
+sources = ['byacc.tar.gz']
+source_urls = ['http://invisible-island.net/datafiles/release']
+
+# checksums = ['d527c811b360f04a8c5f5a0a90625966']
 
 sanity_check_paths = {
     'files': ["bin/yacc"],

c/CP2K/CP2K-5.1-intel-2017a.eb

@@ -0,0 +1,44 @@
+# IT4Innovations 2017
+
+name = 'CP2K'
+version = '5.1'
+
+homepage = 'http://www.cp2k.org/'
+description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular
+ simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different
+ methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and
+ classical pair and many-body potentials. """
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = [SOURCEFORGE_SOURCE]
+
+patches = [
+    'CP2K-2.4.0-fix_compile_date_lastsvn.patch',
+]
+
+# everything have to be with same toolchain!
+dependencies = [
+    ('Libint', '1.1.6'),
+    ('libxc', '2.2.2'), # keep version 2.2.2
+    ('PLUMED', '2.3.0'),
+    ('libxsmm', '1.6.4'),
+]
+
+builddependencies = [
+    ('flex', '2.6.4', '', True),
+    ('Bison', '3.0.4', '', True),
+]
+
+# don't use parallel make, results in compilation failure
+# because Fortran module files aren't created before they are needed
+parallel = 1
+
+# regression test reports failures
+ignore_regtest_fails = True
+
+plumed = True
+
+moduleclass = 'chem'

g/GMP/GMP-5.0.5.eb

@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'GMP'
+version = '5.0.5'
+
+homepage = 'http://gmplib.org/'
+description = """GMP is a free library for arbitrary precision arithmetic, 
+ operating on signed integers, rational numbers, and floating point numbers. """
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = [GNU_SOURCE]
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'],
+    'dirs': [],
+}
+
+moduleclass = 'math'

g/guile/guile-1.8.8.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'guile'
+version = '1.8.8'
+
+homepage = 'http://www.gnu.org/software/guile'
+description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions,
+ the official extension language for the GNU operating system."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [GNU_SOURCE]
+
+dependencies = [
+    ('libtool', '2.4.2'),
+    ('GMP', '5.0.5'),
+    ('libunistring', '0.9.3'),
+    ('pkg-config', '0.27.1'),
+    ('libffi', '3.0.13'),
+    ('libreadline', '6.3'),
+]
+
+configopts = " --enable-error-on-warning=no"
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"],
+    'dirs': []
+}
+
+moduleclass = 'devel'

l/Libint/Libint-1.1.6-intel-2017a.eb

@@ -0,0 +1,27 @@
+name = 'Libint'
+version = '1.1.6'
+
+homepage = 'https://sourceforge.net/p/libint/'
+description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
+ matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'pic': True}
+
+sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))]
+source_urls = ['https://github.com/evaleev/libint/archive/']
+
+builddependencies = [('Autotools', '20150215')]
+
+preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && "
+
+configopts = "--enable-deriv --enable-r12"
+
+sanity_check_paths = {
+    'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] +
+             ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] +
+             ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]],
+    'dirs': [],
+}
+
+moduleclass = 'chem'

l/libmatheval/libmatheval-1.1.11.eb

@@ -0,0 +1,35 @@
+# IT4Innovations 2017
+
+easyblock = 'ConfigureMake'
+
+name = 'libmatheval'
+version = '1.1.11'
+
+homepage = 'http://www.gnu.org/software/libmatheval/'
+description = """GNU libmatheval is a library (callable from C and Fortran) to parse
+ and evaluate symbolic expressions input as text."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+toolchainopts = {'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [GNU_SOURCE]
+
+dependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.0.4'),
+    ('byacc', '20170509'),
+    ('guile', '1.8.8'),
+]
+
+configopts = '--with-pic '
+
+# fix for guile-config being broken because shebang line contains full path to bin/guile
+configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"'
+
+sanity_check_paths = {
+    'files': ['lib/libmatheval.a', 'include/matheval.h'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

l/libtool/libtool-2.4.2.eb

@@ -0,0 +1,17 @@
+# Built with EasyBuild version 2.1.1 on 2015-09-08_14-18-26
+# Built with EasyBuild version 2.1.1 on 2015-08-17_08-12-48
+easyblock = 'ConfigureMake'
+
+name = 'libtool'
+version = '2.4.2'
+
+homepage = 'http://www.gnu.org/software/libtool'
+description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries
+ behind a consistent, portable interface."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()]
+
+moduleclass = 'lib'

l/libxc/libxc-2.2.2-intel-2017a.eb

@@ -0,0 +1,34 @@
+# IT4Innovations 2017
+
+easyblock = 'ConfigureMake'
+
+name = 'libxc'
+version = '2.2.2'
+
+homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc'
+description = """Libxc is a library of exchange-correlation functionals for density-functional theory.
+ The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'opt': True}
+
+sources = [SOURCE_TAR_GZ]
+source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc']
+
+configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared'
+
+# From the libxc mailing list
+# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect
+# a fully working testsuite soon (unless someone wants to volunteer to do
+# it, of course  ) In the meantime, unless the majority of the tests
+# fail, your build should be fine.
+#runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+parallel = 1
+
+moduleclass = 'chem'

l/libxsmm/libxsmm-1.6.4-intel-2017a.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'libxsmm'
+version = '1.6.4'
+
+homepage = 'https://github.com/hfp/libxsmm'
+description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications
+targeting Intel Architecture (x86)."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+sources = ['%(version)s.tar.gz']
+source_urls = ['https://github.com/hfp/libxsmm/archive/']
+
+# install both static and dynamic version
+installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0']
+
+skipsteps = ['configure']
+maxparallel = 1
+
+sanity_check_paths = {
+    'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT],
+    'dirs': ['share']
+}
+
+moduleclass = 'math'

l/libxsmm/libxsmm-1.6.4.eb

@@ -0,0 +1,28 @@
+# IT4Innovations 2017
+
+easyblock = 'ConfigureMake'
+
+name = 'libxsmm'
+version = '1.6.4'
+
+homepage = 'https://github.com/hfp/libxsmm'
+description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications
+targeting Intel Architecture (x86)."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['%(version)s.tar.gz']
+source_urls = ['https://github.com/hfp/libxsmm/archive/']
+
+# install both static and dynamic version
+installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0']
+
+skipsteps = ['configure']
+maxparallel = 1
+
+sanity_check_paths = {
+    'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT],
+    'dirs': ['share']
+}
+
+moduleclass = 'math'

p/PLUMED/PLUMED-2.3.0-intel-2017a.eb

@@ -0,0 +1,42 @@
+# by Ward Poelmans <wpoely86@gmail.com>
+
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.3.0'
+
+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': '2017a'}
+toolchainopts = {'usempi': 'True'}
+
+source_urls = ['https://github.com/plumed/plumed2/archive/']
+sources = ['v%(version)s.tar.gz']
+
+dependencies = [
+    ('zlib', '1.2.11', '', True),
+    ('GSL', '2.3'),
+    ('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'