diff --git a/g/GDAL/GDAL-2.2.3-intel-2017a-Py-2.7.eb b/g/GDAL/GDAL-2.2.3-intel-2017a-Py-2.7.eb new file mode 100644 index 00000000..227a7942 --- /dev/null +++ b/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=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb b/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000..2523cf04 --- /dev/null +++ b/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a328d63d476b3653f5a25b5f7971e87a15cdf8860ab0729d4b1157ba988b8d0b'] + +dependencies = [ + ('Python', '3.6.6'), + ('netCDF', '4.6.1'), + ('expat', '2.2.5'), + ('GEOS', '3.6.2', '-Python-%(pyver)s'), + ('SQLite', '3.24.0'), + ('libxml2', '2.9.8'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.0.9'), + ('zlib', '1.2.11'), + ('cURL', '7.60.0'), + ('PCRE', '8.41'), + ('PROJ', '5.0.0'), + ('libgeotiff', '1.4.2'), +] + +configopts = '--with-expat=$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=$EBROOTLIBGEOTIFF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/g/GDAL/GDAL-2.4.0-intel-2017a-Py-2.7.eb b/g/GDAL/GDAL-2.4.0-intel-2017a-Py-2.7.eb new file mode 100644 index 00000000..2c099cfa --- /dev/null +++ b/g/GDAL/GDAL-2.4.0-intel-2017a-Py-2.7.eb @@ -0,0 +1,51 @@ +# ITInnovations 2018 +# +# Error in SWIG build, finished by hand +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.4.0' +versionsuffix = '-Py-2.7' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Py', '2.7', '', True), + ('netCDF', '4.6.3'), + ('expat', '2.2.6', '', True), + ('GEOS', '3.7.1', '', ('Py', '2.7')), + ('SQLite', '3.17.0', '', True), + ('libxml2', '2.9.9', '', True), + ('libpng', '1.6.34', '', True), + ('libjpeg-turbo', '1.5.3', '', True), + ('JasPer', '2.0.14', '', True), + ('LibTIFF', '4.0.7', '', True), + ('zlib', '1.2.11', '', True), + ('cURL', '7.56.1', '', True), + ('PCRE', '8.42','', True), + ('PROJ', '5.0.0'), +] + +configopts = '--with-expat=$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' diff --git a/g/grace/grace-5.1.25-intel-2017c.eb b/g/grace/grace-5.1.25-intel-2017c.eb new file mode 100644 index 00000000..087b8728 --- /dev/null +++ b/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' diff --git a/m/motif/motif-2.3.8.eb b/m/motif/motif-2.3.8.eb new file mode 100644 index 00000000..5f5f9ddc --- /dev/null +++ b/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' diff --git a/n/netCDF/netCDF-4.6.3-intel-2017a.eb b/n/netCDF/netCDF-4.6.3-intel-2017a.eb new file mode 100644 index 00000000..2869530d --- /dev/null +++ b/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' diff --git a/r/R/Makevars b/r/R/Makevars new file mode 100644 index 00000000..12172cf4 --- /dev/null +++ b/r/R/Makevars @@ -0,0 +1,2 @@ +# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' +PKG_CXXFLAGS = -wd308 diff --git a/r/R/R-3.5.3-intel-2017a.eb b/r/R/R-3.5.3-intel-2017a.eb index 1a436129..d2e0b832 100644 --- a/r/R/R-3.5.3-intel-2017a.eb +++ b/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'], diff --git a/s/SAMtools/SAMtools-1.9-intel-2017a.eb b/s/SAMtools/SAMtools-1.9-intel-2017a.eb new file mode 100644 index 00000000..a994db35 --- /dev/null +++ b/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' diff --git a/s/SWIG/SWIG-3.0.8-Py-2.7.eb b/s/SWIG/SWIG-3.0.8-Py-2.7.eb new file mode 100644 index 00000000..68f97784 --- /dev/null +++ b/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' diff --git a/s/SuiteSparse/SuiteSparse-5.4.0-intel-2017c-ParMETIS-4.0.3.eb b/s/SuiteSparse/SuiteSparse-5.4.0-intel-2017c-ParMETIS-4.0.3.eb new file mode 100644 index 00000000..9dc8375e --- /dev/null +++ b/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' diff --git a/t/Trilinos/Trilinos-12.12.1-intel-2017c-Py-2.7.eb b/t/Trilinos/Trilinos-12.12.1-intel-2017c-Py-2.7.eb index e016a78c..249dc0e4 100644 --- a/t/Trilinos/Trilinos-12.12.1-intel-2017c-Py-2.7.eb +++ b/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')), diff --git a/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb b/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb new file mode 100644 index 00000000..a5bd8719 --- /dev/null +++ b/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'