Merge branch 'it4i-salomon'

a/alchemical-analysis/alchemical-analysis-1.0.1-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'PythonPackage'
+
+name = 'alchemical-analysis'
+version = '1.0.1'
+
+homepage = 'https://github.com/MobleyLab/alchemical-analysis'
+description = """An open tool implementing some recommended practices for analyzing alchemical free energy calculations"""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = ['https://github.com/MobleyLab/alchemical-analysis/archive/']
+sources = ['v%(version)s.tar.gz']
+
+dependencies = [
+    ('pymbar', '3.0.3'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/python2.7/site-packages/alchemical_analysis-%(version)s-py2.7.egg/'],
+}
+
+moduleclass = 'python'

a/alchemlyb/alchemlyb-0.1.0-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'PythonPackage'
+
+name = 'alchemlyb'
+version = '0.1.0'
+
+homepage = 'https://github.com/alchemistry/alchemlyb/'
+description = """alchemlyb is an attempt to make alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack"""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = ['https://github.com/alchemistry/alchemlyb/archive/']
+sources = ['%(version)s.tar.gz']
+
+dependencies = [
+    ('numpy', '1.13.3'),
+    ('scipy', '1.0.0'),
+    ('pandas', '0.23.4'),
+    ('pymbar', '3.0.3'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/python2.7/site-packages/'],
+}
+
+moduleclass = 'python'

g/gperftools/gperftools-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'gperftools'
+version = '2.7'
+
+homepage = 'http://github.com/gperftools/gperftools'
+description = """gperftools are for use by developers so that they can create more robust applications.
+ Especially of use to those developing multi-threaded applications in C++ with templates.
+ Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = [
+    'https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s']
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [('libunwind', '1.2.1', '', True)]
+
+configopts = '--enable-libunwind'
+
+sanity_check_paths = {
+    'files': [
+        'bin/pprof',
+        'lib/libprofiler.a',
+        'lib/libprofiler.%s' %
+        SHLIB_EXT,
+        'lib/libtcmalloc.a',
+        'lib/libtcmalloc.%s' %
+        SHLIB_EXT],
+    'dirs': []}
+
+modextrapaths = {'LD_PRELOAD': 'lib/libtcmalloc_minimal.so.4'}
+
+moduleclass = 'tools'

h/HDF5/HDF5-1.10.4-gompi-2019.02-parallel.eb

+# IT4Innovations 2019
+
+name = 'HDF5'
+version = '1.10.4'
+versionsuffix = '-parallel'
+
+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': 'gompi', 'version': '2019.02'}
+toolchainopts = {'pic': True}
+
+source_urls = [
+    'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = " --enable-parallel --enable-shared "
+configopts += " --enable-static --enable-fortran "
+configopts += " --enable-hl --with-zlib=$EBROOTZLIB"
+
+dependencies = [
+    ('zlib', '1.2.11', '', True),
+    ('Szip', '2.1', '', True),
+]
+
+moduleclass = 'data'

h/HDF5/HDF5-1.10.4-intel-2018a-parallel.eb

+# IT4Innovations 2019
+
+name = 'HDF5'
+version = '1.10.4'
+versionsuffix = '-parallel'
+
+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': 'intel', 'version': '2018a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = [
+    'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [
+    ('zlib', '1.2.11', '', True),
+    ('Szip', '2.1', '', True),
+]
+
+moduleclass = 'data'

h/h5py/h5py-2.9.0-intel-2018a-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'PythonPackage'
+
+name = 'h5py'
+version = '2.9.0'
+versionsuffix = '-Py-2.7'
+
+homepage = 'http://www.h5py.org/'
+description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
+ version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
+ amounts of data."""
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://files.pythonhosted.org/packages/43/27/a6e7dcb8ae20a4dbf3725321058923fec262b6f7835179d78ccc8d98deec/']
+sources = ['h5py-2.9.0.tar.gz']
+
+dependencies = [
+    ('HDF5', '1.10.4', '-parallel'),
+    ('numpy', '1.15.4', '-Py-2.7', True),
+    ('mpi4py', '3.0.0', '-Py-2.7'),  # required for MPI support
+    ('six', '1.11.0', '-Py-2.7', True),
+    ('pkgconfig', '1.3.1', '-Py-2.7'),
+    ('Cython', '0.27.3', '-Py-2.7', True),
+]
+
+prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && '
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python2.7/site-packages/h5py-2.9.0-py2.7-linux-x86_64.egg'],
+}
+moduleclass = 'python'

l/LAMMPS/LAMMPS-20181212-intel-2017c.eb

+# IT4Innovations 2017
+
+easyblock = 'CmdCp'
+
+name = 'LAMMPS'
+version = '20181212'
+
+homepage = 'http://lammps.sandia.gov'
+description = """LAMMPS is a classical molecular dynamics code,
+and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
+Has potentials for solid-state materials (metals, semiconductors) and soft
+matter (biomolecules, polymers) and coarse-grained or mesoscopic systems.
+It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic,
+meso, or continuum scale.
+"""
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+
+source_urls = ['https://github.com/lammps/lammps/archive']
+sources = ['patch_22Jun2018.tar.gz']
+
+dependencies = [
+    ('tbb', '2017.6.196', '', True),
+    ('gperftools', '2.7', '', True),
+]
+
+builddependencies = [
+    ('Python', '2.7.13', '-base', True),
+    ('CMake', '3.5.2', '', True),
+]
+
+commands = "cd src && make yes-kokkos && "
+commands += "make yes-user-phonon && make yes-misc && "
+commands += "make lib-reax args='-m ifort' && make yes-reax && "
+commands += "make yes-kspace && make yes-manybody && make yes-molecule && "
+commands += "make yes-qeq && make yes-rigid && make yes-user-misc && "
+commands += "make yes-user-reaxc && make yes-user-omp && "
+commands += "make -j 16 intel_cpu_intelmpi && mv lmp_intel_cpu_intelmpi lammps"
+
+cmds_map = [('.*', commands)]
+
+files_to_copy = [
+    (['src/lammps'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/lammps'],
+    'dirs': [''],
+}
+
+moduleclass = 'chem'

m/mpi4py/mpi4py-3.0.0-intel-2018a-Py-2.7.eb

+# IT4Innovations 2018
+
+easyblock = 'PythonPackage'
+
+name = 'mpi4py'
+version = '3.0.0'
+versionsuffix = '-Py-2.7'
+
+homepage = 'http://mpi4py.scipy.org/docs'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors."""
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('Py', '2.7', '', True),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python2.7/site-packages/mpi4py'],
+}
+
+moduleclass = 'python'

p/pandas/pandas-0.23.4-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = "PythonPackage"
+name = 'pandas'
+version = '0.23.4'
+
+homepage = 'https://pypi.python.org/pypi/pandas'
+description = 'Powerful data structures for data analysis, time series,and statistics.'
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('numpy', '1.13.3'),
+    ('pytz', '2018.9'),
+    ('python-dateutil', '2.6.1'),
+]
+
+sanity_check_paths = {
+    'files': [],
+     'dirs': ['lib/python2.7/site-packages/%(name)s-%(version)s-py2.7-linux-x86_64.egg'], }
+
+moduleclass = 'python'

p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'PythonPackage'
+
+name = 'pkgconfig'
+version = '1.3.1'
+versionsuffix = '-Py-2.7'
+
+homepage = 'http://github.com/matze/pkgconfig'
+description = """pkgconfig is a Python module to interface with the pkg-config command line tool"""
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+toolchainopts = {'usempi': True}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80']
+
+dependencies = [
+    ('Py', '2.7', '', True),
+    ('pkg-config', '0.29.2', '', True),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python2.7/site-packages/'],
+}
+
+moduleclass = 'devel'

p/pmx/pmx-20190115-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'PythonPackage'
+
+name = 'pmx'
+version = '20190115'
+
+homepage = 'https://github.com/alchemistry/alchemlyb/'
+description = """alchemlyb is an attempt to make alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack"""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = ['https://github.com/deGrootLab/pmx/archive/']
+sources = ['2016da08c4cea33bbca9ccd1f2094014110b7c6a.zip']
+
+dependencies = [
+    ('numpy', '1.13.3'),
+    ('scipy', '1.0.0'),
+    ('matplotlib', '2.1.1'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python2.7/site-packages/pmx'],
+}
+
+moduleclass = 'python'

p/pymbar/pymbar-3.0.3-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'PythonPackage'
+
+name = 'pymbar'
+version = '3.0.3'
+
+homepage = 'https://github.com/MobleyLab/alchemical-analysis'
+description = """An open tool implementing some recommended practices for analyzing alchemical free energy calculations"""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = ['https://github.com/choderalab/pymbar/archive/']
+sources = ['%(version)s.tar.gz']
+
+dependencies = [
+    ('numpy', '1.13.3'),
+    ('six' , '1.11.0'),
+    ('scipy', '1.0.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python2.7/site-packages/'],
+}
+
+moduleclass = 'python'

p/pytz/pytz-2018.9-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = "PythonPackage"
+name = 'pytz'
+version = '2018.9'
+
+homepage = 'http://pytz.sourceforge.net/'
+description = """pytz brings the Olson tz database into Python. This library allows
+  accurate and cross platform timezone calculations using Python 2.4 or higher."""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = ['https://files.pythonhosted.org/packages/af/be/6c59e30e208a5f28da85751b93ec7b97e4612268bb054d0dff396e758a90/']
+sources = ['%(name)s-%(version)s.tar.gz']
+
+sanity_check_paths = {
+    'files': ['lib/python2.7/site-packages/%(name)s-%(version)s-py2.7.egg'],
+    'dirs': [],
+}
+
+moduleclass = 'python'

q/QMCPACK/QMCPACK-3.6.0-intel-2018a.eb

@@ -19,13 +19,21 @@ dependencies = [
     ('CMake', '3.13.1', '', True),
     ('libxml2', '2.9.4', '', True),
     ('Boost', '1.68.0', '-serial'),
-    ('HDF5', '1.10.4', '-serial')
+    ('HDF5', '1.10.4', '-parallel'),
+    ('h5py', '2.9.0', '-Py-2.7'),
 ]
 
 separate_build_dir = True
 
 configopts = ' -DENABLE_SOA=1 '
 
+#preinstallopts = [
+#    #'cp %(builddir)s/easybuild_obj/ %(installdir)s/build -R',
+#    'cd %(builddir)s/easybuild_obj/ && ',
+#    'ctest -R deterministic -LE unstable && ',
+#    'ctest -R short -LE unstable && '
+#]
+
 sanity_check_paths = {
     'files': ['bin/qmcpack'],
     'dirs': ['bin'],

s/scikit-learn/scikit-learn-0.20.2-Py-2.7.eb

+# IT4Innovations 2019
+
+easyblock = 'PythonPackage'
+
+name = 'scikit-learn'
+version = '0.20.2'
+
+homepage = 'http://scikit-learn.org/stable/index.html'
+description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world,
+building upon numpy, scipy, and matplotlib. As a machine-learning module,
+it provides versatile tools for data mining and analysis in any field of science and engineering.
+It strives to be simple and efficient, accessible to everybody, and reusable in various contexts."""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('matplotlib', '2.1.1'),
+    ('numpy', '1.13.3'),
+    ('scipy', '1.0.0'),
+    ('scikit-image', '0.14.1'),
+    ('Tk', '8.6.6', '', True),
+]
+
+options = {'modulename': 'sklearn'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python3.6/site-packages/sklearn'],
+}
+
+moduleclass = 'python'

t/tbb/tbb-2018_U5-intel-2017c.eb

+# IT4Innovations 2019
+
+name = 'tbb'
+version = '2018_U5'
+
+homepage = 'https://01.org/tbb/'
+description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that
+ take full advantage of multicore performance, that are portable, composable and have future-proof scalability."""
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+
+source_urls = ['https://github.com/01org/tbb/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['c4c2896af527392496c5e01ef8579058a71b6eebbd695924cd138841c13f07be']
+
+builddependencies = [
+    ('binutils', '2.31.1', '', True)
+]
+
+moduleclass = 'lib'

x/X11/X11-20170314.eb

@@ -18,7 +18,7 @@ source_urls = [
 
 dependencies = [
     ('bzip2', '1.0.6'),
-    ('fontconfig', '2.13.0', '-libpng-1.6.34'),
+    ('fontconfig', '2.13.0'),
     ('freetype', '2.9.1', '-libpng-1.6.34'),
     ('zlib', '1.2.11'),
 ]