Merge branch 'it4i-salomon'

3ee06e70 · Lukáš Krupčík · 5274ab3c · f36c3efb · 3ee06e70 · 3ee06e70
Commit 3ee06e70 authored Jan 12, 2018 by Lukáš Krupčík
--- a/a/APR-util/APR-util-1.5.4.eb
+++ b/a/APR-util/APR-util-1.5.4.eb
+easyblock = 'ConfigureMake'
+
+name = 'APR-util'
+version = '1.5.4'
+
+homepage = 'http://apr.apache.org/'
+description = "Apache Portable Runtime (APR) util libraries."
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://archive.apache.org/dist/apr/']
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [
+    ('APR', '1.5.2'),
+    ('SQLite', '3.17.0'),
+    ('expat', '2.2.0'),
+]
+
+configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT "
+
+sanity_check_paths = {
+    'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"],
+    'dirs': ["include/apr-1"],
+}
+
+parallel = 1
+
+moduleclass = 'tools'
--- a/a/APR/APR-1.5.2.eb
+++ b/a/APR/APR-1.5.2.eb
+easyblock = 'ConfigureMake'
+
+name = 'APR'
+version = '1.5.2'
+
+homepage = 'http://apr.apache.org/'
+description = "Apache Portable Runtime (APR) libraries."
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://archive.apache.org/dist/apr/']
+sources = [SOURCELOWER_TAR_GZ]
+
+sanity_check_paths = {
+    'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"],
+    'dirs': ["include/apr-1"],
+}
+
+moduleclass = 'tools'
--- a/a/attrs/attrs-14.4.0-Py-2.7.eb
+++ b/a/attrs/attrs-14.4.0-Py-2.7.eb
+# IT4Innovations 2018
+
+easyblock = 'PythonPackage'
+
+name = 'attrs'
+version = '17.4.0'
+
+homepage = 'http://www.attrs.org/'
+description = 'Classes Without Boilerplate'
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+options = {'modulename': 'attr'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python2.7/site-packages/%(name)s-%(version)s-py2.7.egg'],
+}
+
+moduleclass = 'python'
--- a/c/cereal/cereal-1.2.1.eb
+++ b/c/cereal/cereal-1.2.1.eb
+# IT4Innovations 2018
+
+easyblock = 'Tarball'
+
+name = 'cereal'
+version = '1.2.1'
+
+homepage = 'http://uscilab.github.io/cereal/'
+description = 'cereal is a header-only C++11 serialization library.'
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['https://github.com/USCiLab/cereal/archive/']
+sources = ['v%(version)s.tar.gz']
+
+skipsteps = ['configure', 'build']
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['include/cereal'],
+}
+
+moduleclass = 'lib'
--- a/f/fontconfig/fontconfig-2.11.1.eb
+++ b/f/fontconfig/fontconfig-2.11.1.eb
@@ -2,7 +2,7 @@ easyblock = 'ConfigureMake'

 name = "fontconfig"
 version = '2.11.1'
-versionsuffix = '-upgrade'
+#versionsuffix = '-upgrade'

 homepage = 'http://www.freedesktop.org/software/fontconfig'
 description = """Fontconfig is a library designed to provide system-wide font configuration, customization and

--- a/h/HDF5/HDF5-1.10.1-serial.eb
+++ b/h/HDF5/HDF5-1.10.1-serial.eb
+# IT4Innovations 2017
+
+name = 'HDF5'
+version = '1.10.1'
+versionsuffix= '-serial'
+
+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': 'GCC', 'version': '6.3.0-2.27'}
+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]
+
+dependencies = [
+    ('zlib', '1.2.11', '', True),
+    ('Szip', '2.1', '', True),
+]
+
+moduleclass = 'data'
--- a/h/h5py/h5py-2.7.1-Py-2.7.eb
+++ b/h/h5py/h5py-2.7.1-Py-2.7.eb
+# IT4Innovations 2018
+
+easyblock = 'PythonPackage'
+
+name = 'h5py'
+version = '2.7.1'
+
+homepage = 'https://github.com/jupyter/testpath'
+description = """Test utilities for code working with files and commands"""
+
+toolchain = {'name': 'Py', 'version': '2.7'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('HDF5', '1.10.1', '-serial', ('GCC', '6.3.0-2.27')),
+    ('numpy', '1.13.3'),
+    ('mpi4py', '3.0.0'),  # required for MPI support
+    ('six', '1.11.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg'],
+}
+moduleclass = 'python'
--- a/i/icc/icc-2017.5.239-GCC-6.3.0-2.27.eb
+++ b/i/icc/icc-2017.5.239-GCC-6.3.0-2.27.eb
+name = 'icc'
+version = '2017.5.239'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "Intel C and C++ compilers"
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz']
+
+checksums = ['b31c6a83653cbc94123f75ce1781e01f']
+
+gccver = '6.3.0'
+binutilsver = '2.27'
+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?_', 'intel-gdb', 'intel-gdb(?!.*mic)']
+
+dontcreateinstalldir = 'True'
+
+license_file = '/apps/licenses/intel/license.lic'
+
+moduleclass = 'compiler'
--- a/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb
+++ b/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb
 name = 'icc'
-version = '2018.0.128'
+version = '2018.1.163'

 homepage = 'http://software.intel.com/en-us/intel-compilers/'
 description = "Intel C and C++ compilers"

 toolchain = {'name': 'dummy', 'version': ''}

-sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz']
+sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz']

-checksums = ['5bd22f0b1d2f01dfdee755aeae4c89fa']
+checksums = ['ddbfdf88eed095817650ec0a226ef3b9c07c41c855d258e80eaade5173fedb6e']

 gccver = '6.4.0'
 binutilsver = '2.28'
@@ -28,8 +28,4 @@ dontcreateinstalldir = 'True'

 license_file = '/apps/licenses/intel/license.lic'

-postinstallcmds = [
-    'rm /tmp/easybuild/easybuild_intel/* -rf',
-]
-
 moduleclass = 'compiler'
--- a/i/iccifort/iccifort-2017.5.239-GCC-6.3.0-2.27.eb
+++ b/i/iccifort/iccifort-2017.5.239-GCC-6.3.0-2.27.eb
+easyblock = 'Toolchain'
+
+name = 'iccifort'
+version = '2017.5.239'
+versionsuffix = '-GCC-6.3.0-2.27'
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = "Intel C, C++ & Fortran compilers"
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+dependencies = [
+    ('icc', version, versionsuffix),
+    ('ifort', version, versionsuffix),
+]
+
+moduleclass = 'toolchain'
--- a/i/iccifort/iccifort-2018.0.128-GCC-6.4.0-2.28.eb
+++ b/i/iccifort/iccifort-2018.0.128-GCC-6.4.0-2.28.eb
 easyblock = 'Toolchain'

 name = 'iccifort'
-version = '2018.0.128'
+version = '2018.1.163'
 versionsuffix = '-GCC-6.4.0-2.28'

 homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
 description = "Intel C, C++ & Fortran compilers"

-toolchain = {'name': 'dummy', 'version': 'dummy'}
+toolchain = {'name': 'dummy', 'version': ''}

 dependencies = [
    ('icc', version, versionsuffix),

--- a/i/ifort/ifort-2017.5.239-GCC-6.3.0-2.27.eb
+++ b/i/ifort/ifort-2017.5.239-GCC-6.3.0-2.27.eb
+name = 'ifort'
+version = '2017.5.239'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "Intel Fortran compiler"
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz']
+
+checksums = ['66968fb808eee91b6ee7dbd1c76d337f']
+
+# remove dependency on intel-mpi-rt-mic
+patches = ['ifort_2017_no_mpi_mic_dependency.patch']
+
+gccver = '6.3.0'
+binutilsver = '2.27'
+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?_', 'intel-gdb']
+
+dontcreateinstalldir = 'True'
+
+license_file = '/apps/licenses/intel/license.lic'
+
+moduleclass = 'compiler'
--- a/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb
+++ b/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb
 name = 'ifort'
-version = '2018.0.128'
+version = '2018.1.163'

 homepage = 'http://software.intel.com/en-us/intel-compilers/'
 description = "Intel Fortran compiler"

 toolchain = {'name': 'dummy', 'version': ''}

-sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz']
-
+sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz']
+patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch']
 checksums = [
-    '05d04873d47043ef6fd55a85ce501e6d',  # parallel_studio_xe_2018_composer_edition_for_fortran.tgz
-    '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325',  # ifort_2017_no_mpi_mic_dependency.patch
+    # parallel_studio_xe_2018_update1_composer_edition_for_fortran.tgz
+    'c9e7a3ecd89632e4a2babf3a483542edcfd7bc8646ee616f035a0caaf936dcd0',
+    'fdc818390643e77b3dc7ae1d9ba4547e1f1792da8674ff47747c56d97be6fb99',   # ifort_2018.1.163_no_mpi_mic_dependency.patch
 ]

-# remove dependency on intel-mpi-rt-mic
-#patches = ['ifort_2017_no_mpi_mic_dependency.patch']
-
 gccver = '6.4.0'
 binutilsver = '2.28'
 versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver)
@@ -34,8 +32,4 @@ dontcreateinstalldir = 'True'

 license_file = '/apps/licenses/intel/license.lic'

-postinstallcmds = [
-    'rm /tmp/easybuild/easybuild_intel/* -rf',
-]
-
 moduleclass = 'compiler'
--- a/i/ifort/ifort_2018.1.163_no_mpi_mic_dependency.patch
+++ b/i/ifort/ifort_2018.1.163_no_mpi_mic_dependency.patch
+--- parallel_studio_xe_2018_update1_composer_edition_for_fortran/pset/mediaconfig.xml.orig	2017-11-15 14:33:21.020900575 +0100
+++ parallel_studio_xe_2018_update1_composer_edition_for_fortran/pset/mediaconfig.xml	2017-11-15 14:33:25.910946330 +0100
+@@ -962,7 +962,7 @@
+     </Layers>
+     <InstallDir>${COMPLIB_ROOT}</InstallDir>
+     <GUID>1510147141733</GUID>
+-    <Component depend="35.3;1.1;1.3;1.91;1.11;1.12;1.14;1.16;1.7;1.27;1.24;142.2" id="1" invisible="0" mandatory="0" platform="INTEL64">
+    <Component depend="35.3;1.1;1.3;1.91;1.11;1.12;1.14;1.16;1.7;1.27;1.24" id="1" invisible="0" mandatory="0" platform="INTEL64">
+       <Name>Intel Fortran Compiler for Intel(R) 64</Name>
+       <Description>Intel Fortran Compiler 18.0 Update 1</Description>
+       <Name locale="ja_JP.UTF-8">インテル(R) Fortran コンパイラー (インテル(R) 64)</Name>
--- a/i/iimpi/iimpi-2017b.eb
+++ b/i/iimpi/iimpi-2017b.eb
@@ -8,12 +8,12 @@ description = """Intel C/C++ and Fortran compilers, alongside Intel MPI."""

 toolchain = {'name': 'dummy', 'version': ''}

-compver = '2017.4.196'
+compver = '2017.5.239'
 suff = '-GCC-6.3.0-2.27'
 dependencies = [
    ('icc', compver, suff),
    ('ifort', compver, suff),
-    ('impi', '2017.3.196', '', ('iccifort', '%s%s' % (compver, suff))),
+    ('impi', '2017.4.239', '', ('iccifort', '%s%s' % (compver, suff))),
 ]

 moduleclass = 'toolchain'
--- a/i/iimpi/iimpi-2018.00.eb
+++ b/i/iimpi/iimpi-2018.00.eb
-easyblock = "Toolchain"
+easyblock = 'Toolchain'

 name = 'iimpi'
-version = '2018.00'
+version = '2018a'

 homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
 description = """Intel C/C++ and Fortran compilers, alongside Intel MPI."""

-toolchain = {'name': 'dummy', 'version': 'dummy'}
+toolchain = {'name': 'dummy', 'version': ''}

-compver = '2018.0.128'
+compver = '2018.1.163'
 suff = '-GCC-6.4.0-2.28'
 dependencies = [
    ('icc', compver, suff),

--- a/i/imkl/imkl-2017.4.239-iimpi-2017b.eb
+++ b/i/imkl/imkl-2017.4.239-iimpi-2017b.eb
+name = 'imkl'
+version = '2017.4.239'
+
+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': '2017b'}
+
+sources = ['l_mkl_%(version)s.tgz']
+checksums = ['3066272dd0ad3da7961b3d782e1fab3b']
+
+dontcreateinstalldir = 'True'
+
+interfaces = True
+
+postinstallcmds = [
+    # extract the examples
+    'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.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_f.tgz -C %(installdir)s/mkl/examples/',
+    'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/',
+]
+
+modextravars = {
+    'MKL_EXAMPLES': '%(installdir)s/mkl/examples/',
+}
+
+moduleclass = 'numlib'
--- a/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb
+++ b/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb
 name = 'imkl'
-version = '2018.0.128'
+version = '2018.1.163'

 homepage = 'http://software.intel.com/en-us/intel-mkl/'
 description = """Intel Math Kernel Library is a library of highly optimized,
@@ -7,10 +7,10 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 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': '2018.00'}
+toolchain = {'name': 'iimpi', 'version': '2018a'}

 sources = ['l_mkl_%(version)s.tgz']
-checksums = ['0fa23779816a0f2ee23a396fc1af9978']
+checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca']

 dontcreateinstalldir = 'True'


--- a/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.3.0-2.27.eb
+++ b/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.3.0-2.27.eb
+name = 'impi'
+version = '2017.4.239'
+
+homepage = 'http://software.intel.com/en-us/intel-mpi-library/'
+description = "Intel MPI Library, compatible with MPICH ABI"
+
+toolchain = {'name': 'iccifort', 'version': '2017.5.239-GCC-6.3.0-2.27'}
+
+sources = ['l_mpi_%(version)s.tgz']
+
+checksums = ['460a9ef1b3599d60b4d696e3f0f2a14d']
+
+dontcreateinstalldir = 'True'
+
+components = ['intel-mpi', 'intel-psxe', 'intel-imb']
+
+# 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'
--- a/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb
+++ b/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb
 name = 'impi'
-version = '2018.0.128'
+version = '2018.1.163'

 homepage = 'http://software.intel.com/en-us/intel-mpi-library/'
 description = "Intel MPI Library, compatible with MPICH ABI"

-toolchain = {'name': 'iccifort', 'version': '2018.0.128-GCC-6.4.0-2.28'}
+toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'}

 sources = ['l_mpi_%(version)s.tgz']

-checksums = ['15b46fc6a3014595de897aa48d3a658b']
+checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c']

 dontcreateinstalldir = 'True'

@@ -26,8 +26,4 @@ postinstallcmds = [
    'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so'
 ]

-postinstallcmds = [
-    'rm /tmp/easybuild/easybuild_intel/* -rf',
-]
-
 moduleclass = 'mpi'