Merge branch 'it4i-salomon'

g/GDAL/GDAL-2.2.3-intel-2017a-Py-2.7.eb

@@ -0,0 +1,51 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'GDAL'
+version = '2.2.3'
+versionsuffix = '-Py-2.7'
+
+homepage = 'http://www.gdal.org/'
+description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
+ Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
+ to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
+ data translation and processing."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['a328d63d476b3653f5a25b5f7971e87a15cdf8860ab0729d4b1157ba988b8d0b']
+
+dependencies = [
+    ('Py', '2.7', '', True),
+    ('netCDF', '4.6.3'),
+    ('expat', '2.2.6', '', True),
+    ('GEOS', '3.7.1', '', ('Py', '2.7')),
+    ('SQLite', '3.27.1', '', True),
+    ('libxml2', '2.9.9', '', True),
+    ('libpng', '1.6.34', '', True),
+    ('libjpeg-turbo', '1.5.3', '', True),
+    ('JasPer', '2.0.14', '', True),
+    ('LibTIFF', '4.0.7', '', True),
+    ('zlib', '1.2.11', '', True),
+    ('cURL', '7.56.1', '', True),
+    ('PCRE', '8.42', '', True),
+    ('PROJ', '5.0.0'),
+]
+
+configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF'
+configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO'
+configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER'
+configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python'
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'data'

g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb

@@ -0,0 +1,51 @@
+easyblock = 'ConfigureMake'
+
+name = 'GDAL'
+version = '2.2.3'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.gdal.org/'
+description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
+ Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
+ to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
+ data translation and processing."""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['a328d63d476b3653f5a25b5f7971e87a15cdf8860ab0729d4b1157ba988b8d0b']
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('netCDF', '4.6.1'),
+    ('expat', '2.2.5'),
+    ('GEOS', '3.6.2', '-Python-%(pyver)s'),
+    ('SQLite', '3.24.0'),
+    ('libxml2', '2.9.8'),
+    ('libpng', '1.6.34'),
+    ('libjpeg-turbo', '2.0.0'),
+    ('JasPer', '2.0.14'),
+    ('LibTIFF', '4.0.9'),
+    ('zlib', '1.2.11'),
+    ('cURL', '7.60.0'),
+    ('PCRE', '8.41'),
+    ('PROJ', '5.0.0'),
+    ('libgeotiff', '1.4.2'),
+]
+
+configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF'
+configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO'
+configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER'
+configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python'
+configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF'
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'data'

g/GDAL/GDAL-2.4.0-intel-2017a-Py-2.7.eb

@@ -0,0 +1,51 @@
+# ITInnovations 2018
+#
+# Error in SWIG build, finished by hand
+easyblock = 'ConfigureMake'
+
+name = 'GDAL'
+version = '2.4.0'
+versionsuffix = '-Py-2.7'
+
+homepage = 'http://www.gdal.org/'
+description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
+ Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
+ to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
+ data translation and processing."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+
+dependencies = [
+    ('Py', '2.7', '', True),
+    ('netCDF', '4.6.3'),
+    ('expat', '2.2.6', '', True),
+    ('GEOS', '3.7.1', '', ('Py', '2.7')),
+    ('SQLite', '3.17.0', '', True),
+    ('libxml2', '2.9.9', '', True),
+    ('libpng', '1.6.34', '', True),
+    ('libjpeg-turbo', '1.5.3', '', True),
+    ('JasPer', '2.0.14', '', True),
+    ('LibTIFF', '4.0.7', '', True),
+    ('zlib', '1.2.11', '', True),
+    ('cURL', '7.56.1', '', True),
+    ('PCRE', '8.42','', True),
+    ('PROJ', '5.0.0'),
+]
+
+configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF'
+configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO'
+configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER'
+configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python'
+
+modextrapaths = {'PYTHONPATH': 'lib/python2.7/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include', 'lib/python2.7/site-packages']
+}
+
+moduleclass = 'data'

g/grace/grace-5.1.25-intel-2017c.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'grace'
+version = '5.1.25'
+
+homepage = 'http://freecode.com/projects/grace'
+description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif."""
+
+source_urls = ['https://fossies.org/linux/misc/']
+sources = [SOURCE_TAR_GZ]
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+
+dependencies = [
+    ('motif', '2.3.8', '', True),
+    ('netCDF', '4.6.1'),
+]
+
+runtest = 'tests'
+
+# we also need to run make links right before or after make install.
+installopts = 'links'
+
+sanity_check_paths = {
+    'files': ['bin/xmgrace'],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

m/motif/motif-2.3.8.eb

@@ -0,0 +1,51 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'motif'
+version = '2.3.8'
+
+homepage = 'http://motif.ics.com/'
+description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building
+ applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems.
+ It was the standard toolkit for the Common Desktop Environment and thus for Unix."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['%(name)s-%(version)s.tar.gz']
+source_urls = [SOURCEFORGE_SOURCE]
+
+dependencies = [
+    ('X11', '20180604'),
+    ('libpng', '1.6.34'),
+    ('xbitmaps', '1.1.1'),
+    ('freetype', '2.9.1'),
+    ('libjpeg-turbo', '2.0.2'),
+    ('bzip2', '1.0.6'),
+]
+builddependencies = [
+    ('Autotools', '20180311'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.0.5'),
+    ('util-linux', '2.33.1'),
+]
+
+# makefile is not parallel safe
+parallel = 1
+
+sanity_check_paths = {
+    'files': [
+        'lib/libMrm.a',
+        'lib/libUil.a',
+        'lib/libXm.a',
+        'bin/mwm',
+        'bin/uil',
+        'bin/xmbind'],
+    'dirs': [
+        'include/Mrm',
+        'include/uil',
+        'include/X11',
+        'include/Xm'],
+}
+
+moduleclass = 'vis'

n/netCDF/netCDF-4.6.3-intel-2017a.eb

@@ -0,0 +1,36 @@
+# IT4Innovations 2019
+
+name = 'netCDF'
+version = '4.6.3'
+
+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': 'intel', 'version': '2017a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = [
+    'https://github.com/Unidata/netcdf-c/archive/'
+]
+
+dependencies = [
+    ('HDF5', '1.10.2'),
+    ('cURL', '7.56.1', '', True),
+    ('Szip', '2.1', '', True),
+]
+
+builddependencies = [
+    ('CMake', '3.13.1', '', True),
+    ('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'

r/R/Makevars

@@ -0,0 +1,2 @@
+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex<double>::_M_value" is inaccessible'
+PKG_CXXFLAGS = -wd308

r/R/R-3.5.3-intel-2017a.eb

@@ -35,7 +35,7 @@ dependencies = [
     ('Tk', '8.6.9', '', True),  # for tcltk
     ('cURL', '7.56.1', '', True),  # for RCurl
     ('libxml2', '2.9.9', '', True),  # for XML
-    ('GDAL', '2.1.3', '-Python-2.7.13' , True),  # for rgdal
+    ('GDAL', '2.4.0', '-Py-2.7'),  # for rgdal
     ('PROJ', '5.0.0'),  # for rgdal
     ('GMP', '6.1.2', '', True),  # for igraph
     ('NLopt', '2.4.2', '', True),  # for nloptr
@@ -1465,6 +1465,7 @@ exts_list = [
     }),
     ('multicool', '0.1-10', {
         'checksums': ['5bb0cb0d9eb64420c862877247a79bb0afadacfe23262ec8c3fa26e5e34d6ff9'],
+        'patches'  : [('multicool-0.1-10_icpc-wd308.patch', '1')],
     }),
     ('plot3D', '1.1.1', {
         'checksums': ['f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632'],
@@ -1606,6 +1607,7 @@ exts_list = [
     }),
     ('imager', '0.41.1', {
         'checksums': ['afb42fdd3f62c41007eafa205f671cc4af6d165dc813a7cac194124251bc4849'],
+        'patches':   ['imager-0.41.1_icpc-wd308.patch'],
     }),
     ('signal', '0.7-6', {
         'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'],
@@ -1657,6 +1659,7 @@ exts_list = [
     }),
     ('Rtsne', '0.13', {
         'checksums': ['1c3bffe3bd11733ee4fe01749c293669daafda1af2ec74f9158f6080625b999d'],
+        'patches'  : ['Rtsne-0.13_icpc-wd308.patch'],
     }),
     ('cowplot', '0.9.3', {
         'checksums': ['3e10475fd7506ea9297ed72eb1a3acf858c6fa99d26e46fc39654eba000c3dcb'],
@@ -1888,6 +1891,7 @@ exts_list = [
     }),
     ('optmatch', '0.9-10', {
         'checksums': ['e1fcc23ab969a4018ef33ca22a210c14f8ca81840bee8e5e2e1c3179729adbca'],
+        'patches'  : ['optmatch-0.9-10_icpc-wd308.patch'],
     }),
     ('SKAT', '1.3.2.1', {
         'checksums': ['7442408ccd1b9d2abb3f3dbd27e1b46e50b87042195bc46ce25fe0d887f98e7a'],

s/SAMtools/SAMtools-1.9-intel-2017a.eb

@@ -0,0 +1,24 @@
+# IT4Innovations 2019
+
+name = 'SAMtools'
+version = '1.9'
+
+homepage = 'http://www.htslib.org/'
+description = """SAM Tools provide various utilities for manipulating alignments in the SAM format,
+ including sorting, merging, indexing and generating alignments in a per-position format."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = [
+    'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+
+dependencies = [
+    ('ncurses', '6.0', '', True),
+    ('zlib', '1.2.11', '', True),
+    ('XZ', '5.2.3', '', True),
+    ('bzip2', '1.0.6', '', True),
+]
+
+moduleclass = 'bio'

s/SWIG/SWIG-3.0.8-Py-2.7.eb

@@ -0,0 +1,20 @@
+# IT4Innovations
+
+name = 'SWIG'
+version = '3.0.8'
+
+homepage = 'http://www.swig.org/'
+description = """SWIG is a software development tool that connects programs written in C and C++ with
+ a variety of high-level programming languages."""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+toolchainopts = {'pic': True, 'opt': True, 'optarch': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [
+    ('PCRE', '8.42', '', True),
+]
+
+moduleclass = 'devel'

s/SuiteSparse/SuiteSparse-5.4.0-intel-2017c-ParMETIS-4.0.3.eb

@@ -0,0 +1,24 @@
+# IT4Innovations 2019
+
+name = 'SuiteSparse'
+version = '5.4.0'
+versionsuffix = '-ParMETIS-4.0.3'
+
+homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries manipulate sparse matrices."""
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse']
+sources = [SOURCE_TAR_GZ]
+
+builddependencies = [('CMake', '3.13.1', '', True)]
+
+dependencies = [('ParMETIS', '4.0.3')]
+
+prebuildopts = "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:%(builddir)s/SuiteSparse/lib && "
+
+parallel = 1
+
+moduleclass = 'numlib'

t/Trilinos/Trilinos-12.12.1-intel-2017c-Py-2.7.eb

@@ -39,7 +39,7 @@ dependencies = [
     ('Py', '2.7', '', True),
     ('Boost', '1.68.0', versionsuffix),
     ('SCOTCH', '6.0.6'),
-    ('SuiteSparse', '5.4.0', '-METIS-5.1.0'),
+    ('SuiteSparse', '5.4.0', '-ParMETIS-4.0.3'),
     ('ParMETIS', '4.0.3'),
     ('netCDF', '4.6.1'),
     ('MATIO', '1.5.12', '', ('GCCcore', '6.3.0')),

t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb

@@ -0,0 +1,55 @@
+# IT4Innovations 2019
+
+name = 'Trilinos'
+version = '12.14.1'
+versionsuffix = '-Py-2.7'
+
+homepage = 'https://trilinos.org'
+description = """The Trilinos Project is an effort to develop algorithms and enabling technologies
+ within an object-oriented software framework for the solution of large-scale, complex multi-physics
+ engineering and scientific problems. A unique design feature of Trilinos is its focus on packages."""
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+toolchainopts = {'usempi': True, 'pic': True, 'strict': True}
+
+source_urls = ['https://github.com/trilinos/Trilinos/archive/']
+sources = ['%(namelower)s-release-12-14-1.tar.gz']
+#patches = [
+#    ('Trilinos-12.12.1_fix-CEpetra-LAPACK.patch', 'packages/CTrilinos'),
+#    'Trilinos-12.12.1_muelu-fix-function-signature.patch',
+#    'Trilinos-12.12.1_fix-Sundance.patch',
+#]
+
+#configopts = '-D EpetraExt_inout_hdf5_test_MPI_4_DISABLE=ON'
+configopts = '-DEpetraExt_ENABLE_HDF5=OFF'
+
+builddependencies = [
+    ('CMake', '3.13.1', '', True),
+    ('SWIG', '3.0.12', versionsuffix, True),
+]
+
+dependencies = [
+    ('Py', '2.7', '', True),
+    ('Boost', '1.68.0', versionsuffix),
+    ('SCOTCH', '6.0.6'),
+    ('SuiteSparse', '5.4.0', '-ParMETIS-4.0.3'),
+    ('ParMETIS', '4.0.3'),
+    ('netCDF', '4.6.1'),
+    ('MATIO', '1.5.12', '', ('GCCcore', '6.3.0')),
+    ('GLM', '0.9.9.0', '', ('GCCcore', '6.3.0')),
+    ('X11', '20180604', '', True),
+]
+
+# disable TrilinosCouplings package, doesn't build correctly (examples fail to compile)
+skip_exts = ['TrilinosCouplings']
+
+# workaround for Teuchos.pyc not being found during "make install"
+# see https://github.com/trilinos/Trilinos/issues/1749
+preinstallopts = "cd %(builddir)s/trilinos-%(version)s-Source/packages/PyTrilinos/src/PyTrilinos && "
+preinstallopts += "python -m compileall -l -f . && cd - && "
+
+# too parallel is too slow because of memory requirements (results in swapping), and may cause build/tests to fail
+# building with 20 cores seems to require about 100GB of memory (peak usage)
+maxparallel = 10
+
+moduleclass = 'numlib'