new file: a/Amber/Amber-18-iomkl-2017b-AmberTools-18-serial.eb

new file:   h/HDF5/HDF5-1.10.1-iomkl-2017b.eb
	new file:   i/imkl/imkl-2017.4.239-iompi-2017b.eb
	new file:   i/iomkl/iomkl-2017b.eb
	new file:   i/iompi/iompi-2017b.eb
	new file:   n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2017b.eb
	new file:   n/netCDF/netCDF-4.6.1-iomkl-2017b.eb


Former-commit-id: 56909937a645128d160f538f049f23af47a25212

a/Amber/Amber-18-iomkl-2017b-AmberTools-18-serial.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2018
+
+name = 'Amber'
+version = '18'
+ambertools_ver = '18'
+# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
+#patchlevels = (5, 14)  # (AmberTools, Amber)
+versionsuffix = '-AmberTools-%s-serial' %(ambertools_ver)
+
+homepage = 'http://ambermd.org/amber.html'
+description = """Amber (originally Assisted Model Building with Energy
+ Refinement) is software for performing molecular dynamics and structure
+ prediction."""
+
+toolchain = {'name': 'iomkl', 'version': '2017b'}
+toolchainopts = {'usempi': False}
+
+sources = [
+    'Amber%(version)s.tar.bz2',
+    'AmberTools%s.tar.bz2' % ambertools_ver,
+]
+
+#patches = ['Amber-%(version)s_fix-hardcoding.patch']
+
+dependencies = [
+    ('netCDF', '4.6.1'),
+    ('netCDF-Fortran', '4.4.4'),
+    ('Py', '2.7', '', True),
+]
+
+moduleclass = 'chem'

h/HDF5/HDF5-1.10.1-iomkl-2017b.eb

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+# IT4Innovations 2018
+
+name = 'HDF5'
+version = '1.10.1'
+
+homepage = 'http://www.hdfgroup.org/HDF5/'
+description = """HDF5 is a unique technology suite that makes possible the management of
+ extremely large and complex data collections."""
+
+toolchain = {'name': 'iomkl', 'version': '2017b'}
+toolchainopts = {'pic': True, 'usempi': False}
+
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+
+sources = [SOURCELOWER_TAR_GZ]
+
+buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"'
+
+dependencies = [
+    ('zlib', '1.2.11', '', True),
+    ('Szip', '2.1', '', True),
+]
+
+moduleclass = 'data'

i/imkl/imkl-2017.4.239-iompi-2017b.eb

@@ -0,0 +1,37 @@
+# IT4Innovations 2018
+
+name = 'imkl'
+version = '2017.4.239'
+
+homepage = 'http://software.intel.com/en-us/intel-mkl/'
+description = """Intel Math Kernel Library is a library of highly optimized,
+ extensively threaded math routines for science, engineering, and financial
+ applications that require maximum performance. Core math functions include
+ BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more."""
+
+toolchain = {'name': 'iompi', 'version': '2017b'}
+
+sources = ['l_mkl_%(version)s.tgz']
+
+dontcreateinstalldir = 'True'
+
+license_file = '/apps/licenses/intel/license.lic'
+
+interfaces = True
+
+postinstallcmds = [
+    # extract the examples
+    'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/',
+]
+
+modextravars = {
+    'MKL_EXAMPLES': '%(installdir)s/mkl/examples/',
+}
+
+moduleclass = 'numlib'

i/iomkl/iomkl-2017b.eb

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+# IT4Innovations 2018
+
+easyblock = "Toolchain"
+
+name = 'iomkl'
+version = '2017b'
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL &
+ OpenMPI."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+compver = '2017.5.239'
+gccsuff = '-GCC-6.3.0-2.27'
+
+dependencies = [
+    ('icc', compver, gccsuff),
+    ('ifort', compver, gccsuff),
+    ('OpenMPI', '1.10.7', gccsuff, True),
+    ('imkl', '2017.4.239', '', ('iompi', version)),
+]
+
+moduleclass = 'toolchain'

i/iompi/iompi-2017b.eb

@@ -0,0 +1,22 @@
+# IT4Innovations 2018
+
+easyblock = "Toolchain"
+
+name = 'iompi'
+version = '2017b'
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel C/C++ and Fortran compilers, alongside Open MPI."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+compver = '2017.5.239'
+compversuff = '-GCC-6.3.0-2.27'
+
+dependencies = [
+    ('icc', compver, compversuff),
+    ('ifort', compver, compversuff),
+    ('OpenMPI', '1.10.7', compversuff, True),
+]
+
+moduleclass = 'toolchain'

n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2017b.eb

@@ -0,0 +1,19 @@
+# IT4Innovations 2018
+
+name = 'netCDF-Fortran'
+version = '4.4.4'
+
+homepage = 'http://www.unidata.ucar.edu/software/netcdf/'
+description = """NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data."""
+
+toolchain = {'name': 'iomkl', 'version': '2017b'}
+toolchainopts = {'pic': True}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https://github.com/Unidata/netcdf-fortran/archive']
+
+dependencies = [('netCDF', '4.6.1')]
+
+moduleclass = 'data'

n/netCDF/netCDF-4.6.1-iomkl-2017b.eb

@@ -0,0 +1,35 @@
+# IT4Innovations 2018
+
+name = 'netCDF'
+version = '4.6.1'
+
+homepage = 'http://www.unidata.ucar.edu/software/netcdf/'
+description = """NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data."""
+
+toolchain = {'name': 'iomkl', 'version': '2017b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https://github.com/Unidata/netcdf-c/archive/']
+
+dependencies = [
+    ('HDF5', '1.10.1'),
+    ('cURL', '7.56.1', '', True),
+    ('Szip', '2.1', '', True),
+]
+
+builddependencies = [
+    ('Autotools', '20180311', '', True),
+    ('CMake', '3.11.4', '' , ('GCC', '6.3.0-2.27')),
+    ('Doxygen', '1.8.11', '', True),
+]
+
+# make sure both static and shared libs are built
+configopts = [
+    "-DBUILD_SHARED_LIBS=OFF ",
+    "-DBUILD_SHARED_LIBS=ON ",
+]
+
+moduleclass = 'data'