Commit 9c8b6da6 authored by Lukáš Krupčík's avatar Lukáš Krupčík

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

	new file:   g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb
	new file:   g/GDAL/GDAL-2.4.0-intel-2017a-Py-2.7.eb
	new file:   g/grace/grace-5.1.25-intel-2017c.eb
	new file:   m/motif/motif-2.3.8.eb
	new file:   n/netCDF/netCDF-4.6.3-intel-2017a.eb
	new file:   r/R/Makevars
	modified:   r/R/R-3.5.3-intel-2017a.eb
	new file:   s/SAMtools/SAMtools-1.9-intel-2017a.eb
	new file:   s/SWIG/SWIG-3.0.8-Py-2.7.eb
	new file:   s/SuiteSparse/SuiteSparse-5.4.0-intel-2017c-ParMETIS-4.0.3.eb
	modified:   t/Trilinos/Trilinos-12.12.1-intel-2017c-Py-2.7.eb
	new file:   t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb
parent 555aee78
Pipeline #7618 failed with stage
in 15 seconds
# 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=$EBROOTPYTHON/bin/python'
modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
sanity_check_paths = {
'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages']
}
moduleclass = 'data'
easyblock = 'ConfigureMake'
name = 'GDAL'
version = '2.2.3'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.gdal.org/'
description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
data translation and processing."""
toolchain = {'name': 'intel', 'version': '2018b'}
toolchainopts = {'usempi': True}
source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
sources = [SOURCELOWER_TAR_XZ]
checksums = ['a328d63d476b3653f5a25b5f7971e87a15cdf8860ab0729d4b1157ba988b8d0b']
dependencies = [
('Python', '3.6.6'),
('netCDF', '4.6.1'),
('expat', '2.2.5'),
('GEOS', '3.6.2', '-Python-%(pyver)s'),
('SQLite', '3.24.0'),
('libxml2', '2.9.8'),
('libpng', '1.6.34'),
('libjpeg-turbo', '2.0.0'),
('JasPer', '2.0.14'),
('LibTIFF', '4.0.9'),
('zlib', '1.2.11'),
('cURL', '7.60.0'),
('PCRE', '8.41'),
('PROJ', '5.0.0'),
('libgeotiff', '1.4.2'),
]
configopts = '--with-expat=$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=$EBROOTLIBGEOTIFF'
modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
sanity_check_paths = {
'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages']
}
moduleclass = 'data'
# ITInnovations 2018
#
# Error in SWIG build, finished by hand
easyblock = 'ConfigureMake'
name = 'GDAL'
version = '2.4.0'
versionsuffix = '-Py-2.7'
homepage = 'http://www.gdal.org/'
description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
data translation and processing."""
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'usempi': True}
source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
sources = [SOURCELOWER_TAR_XZ]
dependencies = [
('Py', '2.7', '', True),
('netCDF', '4.6.3'),
('expat', '2.2.6', '', True),
('GEOS', '3.7.1', '', ('Py', '2.7')),
('SQLite', '3.17.0', '', True),
('libxml2', '2.9.9', '', True),
('libpng', '1.6.34', '', True),
('libjpeg-turbo', '1.5.3', '', True),
('JasPer', '2.0.14', '', True),
('LibTIFF', '4.0.7', '', True),
('zlib', '1.2.11', '', True),
('cURL', '7.56.1', '', True),
('PCRE', '8.42','', True),
('PROJ', '5.0.0'),
]
configopts = '--with-expat=$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'
# 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'
# 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'
# 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'
# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex<double>::_M_value" is inaccessible'
PKG_CXXFLAGS = -wd308
......@@ -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'],
......
# 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'
# 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'
# 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'
......@@ -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')),
......
# 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'
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment