Solve conflict

intel-2016.02/CMake-3.5.2-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'CMake'
+version = '3.5.2'
+
+homepage = 'http://www.cmake.org'
+description = """CMake, the cross-platform, open-source build system.
+ CMake is a family of tools designed to build, test and package software."""
+
+toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
+
+source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES'
+
+dependencies = [
+    ('ncurses', '6.0'),
+    # OS dependency should be preferred if the os version is more recent then this version,
+    # it's nice to have an up to date openssl for security reasons
+    # ('OpenSSL', '1.0.1s'),
+]
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

intel-2016.02/Doxygen-1.8.11-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,21 @@
+name = 'Doxygen'
+version = '1.8.11'
+
+homepage = 'http://www.doxygen.org'
+description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, 
+ IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D."""
+
+toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
+
+sources = ['%(namelower)s-%(version)s.src.tar.gz']
+source_urls = ['http://ftp.stack.nl/pub/users/dimitri/']
+
+builddependencies = [
+    ('CMake', '3.5.2'),
+    ('flex', '2.6.0'),
+    ('Bison', '3.0.4'),
+]
+
+parallel = 1
+
+moduleclass = 'devel'

intel-2016.02/HDF5-1.8.18-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,22 @@
+name = 'HDF5'
+version = '1.8.18'
+
+homepage = 'https://support.hdfgroup.org/HDF5/'
+description = """HDF5 is a data model, library, and file format for storing and managing data.
+ It supports an unlimited variety of datatypes, and is designed for flexible
+ and efficient I/O and for high volume and complex data."""
+
+toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
+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]
+checksums = ['dd2148b740713ca0295442ec683d7b1c']
+
+dependencies = [
+    ('zlib', '1.2.8'),
+    ('Szip', '2.1'),
+]
+
+moduleclass = 'data'

intel-2016.02/cURL-7.49.1-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'cURL'
+version = '7.49.1'
+
+homepage = 'http://curl.haxx.se'
+description = """libcurl is a free and easy-to-use client-side URL transfer library,
+ supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS,
+ POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports
+ SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload,
+ proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate,
+ Kerberos), file transfer resume, http proxy tunneling and more."""
+
+toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://curl.haxx.se/download/']
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+# dependencies = [('OpenSSL', '1.0.1t')]
+# configopts = "--with-ssl=$EBROOTOPENSSL"
+
+modextravars = {'CURL_INCLUDES': '%(installdir)s/include'}
+
+sanity_check_paths = {
+    'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'tools'

intel-2016.02/flex-2.6.0-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,21 @@
+name = 'flex'
+version = '2.6.0'
+
+homepage = 'http://flex.sourceforge.net/'
+description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, 
+ sometimes called a tokenizer, is a program which recognizes lexical patterns in text."""
+
+toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
+toolchainopts = {'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s']
+
+checksums = [
+    '5724bcffed4ebe39e9b55a9be80859ec',     # flex-2.6.0.tar.gz
+]
+
+dependencies = [('M4', '1.4.17')]
+builddependencies = [('Bison', '3.0.4')]
+
+moduleclass = 'lang'

intel-2016.02/icc-2016.2.181-GCC-4.9.3-2.25.eb

@@ -0,0 +1,33 @@
+# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/
+
+name = 'icc'
+version = '2016.2.181'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "C and C++ compiler from Intel"
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz']
+
+#checksums = ['d6f8529a44231e427219c8e025dec3b2']
+
+gccver = '4.9.3'
+binutilsver = '2.25'
+versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver)
+
+dependencies = [
+    ('GCCcore', gccver),
+    ('binutils', binutilsver, '', ('GCCcore', gccver)),
+]
+
+# list of regex for components to install
+# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources
+# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide
+components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_']
+
+dontcreateinstalldir = 'True'
+
+license_file = '/trinity/shared/licenses/intel/license.lic'
+
+moduleclass = 'compiler'

intel-2016.02/ifort-2016.2.181-GCC-4.9.3-2.25.eb

@@ -0,0 +1,36 @@
+# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/
+
+name = 'ifort'
+version = '2016.2.181'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "Fortran compiler from Intel"
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz']
+
+#checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f']
+
+# remove dependency on intel-mpi-rt-mic
+#patches = ['ifort_2016_no_mpi_mic_dependency.patch']
+
+gccver = '4.9.3'
+binutilsver = '2.25'
+versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver)
+
+dependencies = [
+    ('GCCcore', gccver),
+    ('binutils', binutilsver, '', ('GCCcore', gccver)),
+]
+
+# list of regex for components to install
+# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources
+# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide
+components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_']
+
+dontcreateinstalldir = 'True'
+
+license_file = '/opt/easybuild/easyconfigs/utils/license_intel_all.lic'
+
+moduleclass = 'compiler'

intel-2016.02/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb

@@ -0,0 +1,36 @@
+# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/
+
+name = 'imkl'
+version = '11.3.2.181'
+
+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': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.25'}
+
+sources = ['l_mkl_%(version)s.tgz']
+checksums = ['536dbd82896d6facc16de8f961d17d65']
+
+dontcreateinstalldir = 'True'
+
+#license_file = HOME + '/licenses/intel/license.lic'
+
+interfaces = True
+
+postinstallcmds = [
+    # extract the examples
+    'tar xvzf %(installdir)s/mkl/examples/examples_cluster.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.tgz -C %(installdir)s/mkl/examples/'
+]
+
+modextravars = {
+    'MKL_EXAMPLES': '%(installdir)s/mkl/examples/',
+}
+
+moduleclass = 'numlib'

intel-2016.02/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb

@@ -0,0 +1,33 @@
+# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/
+
+name = 'impi'
+version = '5.1.3.181'
+
+homepage = 'http://software.intel.com/en-us/intel-mpi-library/'
+description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message
+ passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for
+ Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification."""
+
+toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.25'}
+
+sources = ['l_mpi_p_%(version)s.tgz']
+
+checksums = ['1c14656859d48bf8b90c71dace2a977b']
+
+dontcreateinstalldir = 'True'
+
+#license_file = '/trinity/shared/licenses/intel/license.lic'
+
+# set up all the mpi commands to default to intel compilers
+# set_mpi_wrappers_all = 'True'
+
+postinstallcmds = [
+    'ln -s %(installdir)s/lib64/libmpi.so  %(installdir)s/lib64/libmpich.so',
+    'ln -s %(installdir)s/lib64/libmpigc4.so  %(installdir)s/lib64/libmpichcxx.so',
+    'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so',
+    'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so',
+    'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so',
+    'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so'
+]
+
+moduleclass = 'mpi'

intel-2016.02/netCDF-4.4.1.1-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,35 @@
+name = 'netCDF'
+version = '4.4.1.1'
+
+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': 'intel', 'version': '2016.02-GCC-4.9'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = [
+    'https://github.com/Unidata/netcdf-c/archive/'
+]
+
+dependencies = [
+    ('HDF5', '1.8.18'),
+    ('cURL', '7.49.1'),
+    ('Szip', '2.1'),
+]
+
+builddependencies = [
+    ('Autotools', '20150215'),
+    ('CMake', '3.5.2'),
+    ('Doxygen', '1.8.11'),
+]
+
+# make sure both static and shared libs are built
+configopts = [
+    "-DBUILD_SHARED_LIBS=OFF ",
+    "-DBUILD_SHARED_LIBS=ON ",
+]
+
+moduleclass = 'data'

intel-2016.02/netCDF-Fortran-4.4.4-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,17 @@
+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': 'intel', 'version': '2016.02-GCC-4.9'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/']
+sources = ['v%(version)s.tar.gz']
+
+dependencies = [('netCDF', '4.4.1.1')]
+
+moduleclass = 'data'

intel-2018/R-3.4.1-intel-2018.eb

@@ -47,6 +47,7 @@ dependencies = [
     ('HDF5', '1.8.18'),
     ('netCDF', '4.4.1.1'),
     ('netCDF-Fortran', '4.4.4'),
+    ('UDUNITS', '2.2.24'),
     ('GDAL', '2.2.0'),
     ('GEOS', '3.6.1'),
     # OS dependency should be preferred if the os version is more recent then this version,
@@ -652,6 +653,9 @@ exts_list = [
     ('ordinal', '2015.6-28', ext_options),
     ('classInt', '0.1-24', ext_options),
     ('pander', '0.6.1', ext_options),
+    ('rgeos', '0.3-26', ext_options),
+    ('sf', '0.5-5', ext_options),
+    ('velox', '0.2.0', ext_options),
 ]
 
 moduleclass = 'lang'

intel-2018/git-2.13.1-intel-2018.eb

@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'git'
+version = '2.13.1'
+
+homepage = 'http://git-scm.com/'
+description = """Git is a free and open source distributed version control system designed
+to handle everything from small to very large projects with speed and efficiency."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https://github.com/git/git/archive']
+checksums = ['c0e3fe359f715cb7dfc3ac63fa6e733a']
+
+builddependencies = [
+    ('Autoconf', '2.69'),
+]
+
+
+dependencies = [
+    ('cURL', '7.55.1'),
+    ('expat', '2.2.4'),
+    ('gettext', '0.19.8.1'),
+    ('Perl', '5.24.0'),
+]
+
+preconfigopts = 'make configure && '
+
+# Work around git build system bug.  If LIBS contains -lpthread, then configure
+# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS.
+configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'"
+
+sanity_check_paths = {
+    'files': ['bin/git'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

intel-2018/grib_api-1.16.0-intel-2018.eb

@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'grib_api'
+version = '1.16.0'
+
+homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home'
+description = """The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python
+ programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of
+ command line tools is also provided to give quick access to GRIB messages."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/']
+sources = ['grib_api-%(version)s-Source.tar.gz']
+
+dependencies = [
+    ('JasPer', '1.900.1'),
+]
+
+configopts = '--with-jasper=$EBROOTJASPER'
+
+parallel = 1
+
+moduleclass = 'data'

intel-2018/grib_api-1.26.1-intel-2018.eb

@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'grib_api'
+version = '1.26.1'
+
+homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home'
+description = """The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python
+ programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of
+ command line tools is also provided to give quick access to GRIB messages."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/']
+sources = ['grib_api-%(version)s-Source.tar.gz']
+
+dependencies = [
+    ('openjpeg', '1.5.2'),
+]
+
+configopts = '--with-openjpeg=$EBROOTOPENJPEG'
+
+parallel = 1
+
+moduleclass = 'data'

intel-2018/libgd-2.2.4-intel-2018.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'libgd'
+version = '2.2.4'
+
+homepage = 'https://libgd.github.io/'
+description = "GD is an open source code library for the dynamic creation of images by programmers."
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [
+    ('fontconfig', '2.12.4'),
+    ('libjpeg-turbo', '1.5.1'),
+    ('libpng', '1.6.32'),
+    ('zlib', '1.2.11'),
+]
+
+sanity_check_paths = {
+    'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT],
+    'dirs': ["bin", "include"],
+}
+
+moduleclass = 'lib'

intel-2018/openjpeg-1.5.2-intel-2018.eb

@@ -0,0 +1,35 @@
+easyblock = 'CMakeMake'
+
+name = 'openjpeg'
+version = '1.5.2'
+
+homepage = "http://www.openjpeg.org/"
+description = """OpenJPEG is an open-source JPEG 2000 codec written in C language. 
+ It has been developed in order to promote the use of JPEG 2000, a still-image 
+ compression standard from the Joint Photographic Experts Group (JPEG). 
+ Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 
+ Reference Software."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+source_urls = ["https://github.com/uclouvain/openjpeg/archive"]
+sources = ["version.%(version)s.tar.gz"]
+
+builddependencies = [
+    ('CMake', '3.9.1'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS:bool=on'
+
+sanity_check_paths = {
+    'files': ['bin/j2k_dump', 'bin/image_to_j2k'],
+    'dirs': [],
+}
+
+postinstallcmds = [
+    'ln -s %(installdir)s/include/openjpeg-1.5/openjpeg.h %(installdir)s/include/openjpeg.h'
+]
+
+separate_build_dir = True
+
+moduleclass = 'lib'

intel-2018/openjpeg-2.3.0-intel-2018.eb

@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'openjpeg'
+version = '2.3.0'
+
+homepage = "http://www.openjpeg.org/"
+description = """OpenJPEG is an open-source JPEG 2000 codec written in C language. 
+ It has been developed in order to promote the use of JPEG 2000, a still-image 
+ compression standard from the Joint Photographic Experts Group (JPEG). 
+ Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 
+ Reference Software."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+source_urls = ["https://github.com/uclouvain/openjpeg/archive"]
+sources = ["v%(version)s.tar.gz"]
+
+builddependencies = [
+    ('CMake', '3.9.1'),
+]
+
+configopts = '-DCMAKE_BUILD_TYPE=Release'
+
+sanity_check_paths = {
+    'files': ['bin/opj_compress', 'bin/opj_decompress'],
+    'dirs': [],
+}
+
+separate_build_dir = True
+
+moduleclass = 'lib'

utils/license_intel_2017.lic

@@ -0,0 +1,15 @@
+PACKAGE IF83F2F10 INTEL 2017.1221 4C05DD910FD7 COMPONENTS="AdvXEl \
+	ArBBL CCompL Comp-CL Comp-FL Comp-OpenMP Comp-PointerChecker \
+	DAAL-L DbgL FCompL MKernL PerfAnl PerfPrimL StaticAnlL \
+	ThreadAnlGui ThreadBB" OPTIONS=SUITE ck=117 SIGN=137EE472B4F4
+INCREMENT IF83F2F10 INTEL 2017.1221 21-dec-2017 uncounted \
+	6CA6357C502A VENDOR_STRING="SUPPORT=NCOM \
+	https://registrationcenter.intel.com" HOSTID="34028625bbfb \
+	9cebe82a6453" PLATFORMS="i86_r i86_re it64_lr it64_re amd64_re \
+	i86_mac x64_mac" ck=138 SN=SMSA6RM45M58 SIGN=02898FDAE456
+#
+# SerialNumber=3D83-6RM45M58
+#
+#
+# SerialNumber=3D83-6RM45M58
+#

utils/license_intel_all.lic

@@ -0,0 +1,5 @@
+SERVER intel-compiler-lic-one.sipr.ucl.ac.be 000000000000 27007
+SERVER intel-compiler-lic-two.sipr.ucl.ac.be 000000000000 27007
+SERVER intel-compiler-lic-three.sipr.ucl.ac.be 000000000000 27007
+USE_SERVER
+