Merge branch 'it4i-karolina'

i/irodsfs/irodsfs-0.7.6.eb

@@ -23,8 +23,7 @@ sanity_check_paths = {
 
 postinstallcmds = [
     'cp /mnt/proj3/easybuild/scripts/irods-startup.sh %(installdir)s/',
-    'cp /mnt/proj3/easybuild/scripts/irods.it4i.cz.crt %(installdir)s/',
-#    'curl -L https://docs.it4i.cz/irods1.it4i.cz.crt -o %(installdir)s/irods1.it4i.cz.crt',
+    'cp /mnt/proj3/easybuild/scripts/chain_geant_ov_rsa_ca_4_full.* %(installdir)s/',
 ]
 
 modluafooter = 'execute{cmd="bash $EBROOTIRODSFS/irods-startup.sh", modeA={"load"}}'

j/JUnit/JUnit-4.13.2-Java-13.eb

@@ -0,0 +1,26 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'JAR'
+
+name = 'JUnit'
+version = '4.13.2'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://sourceforge.net/projects/junit'
+description = """A programmer-oriented testing framework for Java."""
+
+toolchain = SYSTEM
+
+source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/']
+sources = ['%(namelower)s-%(version)s.jar']
+checksums = ['8e495b634469d64fb8acfa3495a065cbacc8a0fff55ce1e31007be4c16dc57d3']
+
+dependencies = [('Java', '13', '', True)]
+
+sanity_check_paths = {
+    'files': sources,
+    'dirs': [],
+}
+
+moduleclass = 'devel'

l/LAPACK/LAPACK-3.10.0-gompi-2021a.eb

@@ -0,0 +1,16 @@
+name = 'LAPACK'
+version = '3.10.0'
+
+homepage = 'https://www.netlib.org/lapack/'
+description = """LAPACK is written in Fortran90 and provides routines for solving systems of
+ simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue
+ problems, and singular value problems."""
+
+toolchain = {'name': 'gompi', 'version': '2021a'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19']
+
+moduleclass = 'numlib'

l/libreoffice/libreoffice-7.4.1.1-GCCcore-11.3.0.eb

@@ -0,0 +1,50 @@
+# Contribution from IT4Innovations National Supercomputing Center, Czech Republic
+# JK
+
+easyblock = 'ConfigureMake'
+
+name = 'libreoffice'
+version = '7.4.1.1'
+local_javasuffix = '-Java-13'
+
+homepage = 'https://libreoffice.org'
+description = """
+LibreOffice is a free and powerful office suite, and a successor to OpenOffice.org (commonly known as OpenOffice).
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['http://download.documentfoundation.org/libreoffice/src/7.4.1/']
+sources = ['%(name)s-%(version)s.tar.xz']
+checksums = ['2c5c219c538776b4ec3815fe74c1915024cbe17dd0950e725e544ff49b20a28c']
+
+builddependencies = [('Doxygen', '1.9.4')]
+
+dependencies = [
+    ('libxslt', '1.1.34'),
+    ('Qt5', '5.15.5'),
+    ('flex', '2.6.4'),
+#    ('GStreamer', '1.20.2'), # GCC, --disable-gstreamer
+    ('NSS', '3.79'), # --disable-nss, experimental, will use OpenSSL instead
+#    ('NSPR', '4.34'), # fix for failed to initialize NSS library?
+    ('GTK3', '3.24.33'),
+    ('Python', '3.10.4'),
+#    ('Java', ''), # --without-java
+    ('gperf', '3.1'),
+# Java dependencies, or --without-java
+    ('ant', '1.10.11', local_javasuffix, True),
+#    ('JUnit', '4.13.2', local_javasuffix, True), # --with-junit=${EBROOTJUNIT}
+]
+
+configure_cmd = "./autogen.sh"
+configopts = '--disable-cups --disable-gstreamer-1.0 --disable-postgresql-sdbc --without-junit --disable-mariadb-sdbc'
+buildopts = "verbose=t"
+
+runtest = "check"
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ["."]
+}
+
+moduleclass = 'tools'

m/Mmg/Mmg-5.6.0-gompi-2021a.eb

@@ -0,0 +1,49 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'CMakeMake'
+
+name = 'Mmg'
+version = '5.6.0'
+
+homepage = 'https://www.mmgtools.org/'
+description = """
+Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries:
+the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation
+and generation of a triangulation from a set of points or from given boundary edges
+the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation
+and isovalue discretization
+the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh
+and implicit domain meshing
+the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries
+"""
+
+toolchain = {'name': 'gompi', 'version': '2021a'}
+
+source_urls = ['https://github.com/MmgTools/mmg/archive']
+sources = ['v%(version)s.tar.gz']
+patches = ['mmg-%(version)s_remove_ci_tests.patch']
+checksums = [
+    'bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437',  # v5.6.0.tar.gz
+    '99de7437fb9d036c786b7f1526da93d4aa1d28e728fe7279f4c9204bbbb9f734',  # mmg-5.6.0_remove_ci_tests.patch
+]
+
+builddependencies = [('CMake', '3.20.1')]
+
+dependencies = [('SCOTCH', '6.1.0')]
+
+# CI tests require downloading of data that might not be available in the future.
+# Sticking to tests included in the source with help of patch
+configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON '
+configopts += '-DTEST_LIBMMG2D=ON -DTEST_LIBMMG3D=ON -DTEST_LIBMMGS=ON '
+configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON '
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/%s_O3' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] +
+             ['lib/lib%s.%s' % (x, y) for x in ['mmg2d', 'mmg3d', 'mmgs', 'mmg'] for y in ['a', SHLIB_EXT]],
+    'dirs': ['include/mmg/%s' % x for x in ['mmg2d', 'mmg3d', 'mmgs']]
+}
+
+moduleclass = 'math'

m/mpi4py/mpi4py-3.1.3-foss-2021a.eb

@@ -0,0 +1,27 @@
+# IT4Innovations
+# JK 2022
+
+easyblock = 'PythonPackage'
+
+name = 'mpi4py'
+version = '3.1.3'
+
+homepage = 'http://mpi4py.scipy.org/docs'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('Python', '3.9.5'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python3.9/site-packages/mpi4py'],
+}
+
+moduleclass = 'mpi'

p/PETSc/PETSc-3.17.2-foss-2021a.eb

@@ -1,59 +0,0 @@
-# IT4Innovations
-# LK JK
-
-name = 'PETSc'
-version = '3.17.2'
-
-homepage = 'https://www.mcs.anl.gov/petsc'
-description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
- scalable (parallel) solution of scientific applications modeled by partial differential equations."""
-
-toolchain = {'name': 'foss', 'version': '2021a'}
-import os
-if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
-   toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2', 'pic': True}
-else:
-   toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
-
-source_urls = [
-    'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
-    'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
-]
-sources = [SOURCELOWER_TAR_GZ]
-patches = [
-    'PETSc_ranlib-fix.patch',
-]
-checksums = [
-    '2313dd1ca41bf0ace68671ea6f8d4abf90011ed899f5e1e08658d3f18478359d',  # petsc-3.17.2.tar.gz
-    '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297',  # PETSc_ranlib-fix.patch
-]
-
-builddependencies = [('CMake', '3.20.1')]
-
-dependencies = [
-    ('Python', '3.9.5'),
-    ('SciPy-bundle', '2021.05'),
-    ('Boost', '1.76.0'),
-    ('METIS', '5.1.0'),
-    ('SCOTCH', '6.1.0'),
-    ('MUMPS', '5.4.0', '-metis'),
-#    ('SuiteSparse', '5.10.1', '-METIS-5.1.0'),
-    ('Hypre', '2.24.0'),
-]
-
-# enabling --with-mpi4py seems to be totally broken, leads to make errors like:
-# No rule to make target 'mpi4py-build'
-configopts = ' CC=$CC CXX=$CXX FC=$FC F77=$F77 F90=$F90 '
-configopts += ' CFLAGS=$CFLAGS CXXFLAGS=$CXXFLAGS FFLAGS=$FFLAGS F90FLAGS=$F90FLAGS '
-configopts += ' CPPFLAGS=$CPPFLAGS LDFLAGS=$LDFLAGS '
-configopts += ' --LIBS="$LIBS -lrt" --with-mpi4py=0 '
-#configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 --with-fortran=1 --download-scalapack '
-#configopts += '--download-parmetis --download-metis --download-mumps=yes'
-
-shared_libs = 1
-
-# only required when building PETSc in a SLURM job environment
-# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 '
-# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && "
-
-moduleclass = 'numlib'

p/PETSc/PETSc-3.17.4-foss-2021a.eb

@@ -0,0 +1,86 @@
+# Updated to version 3.17.0 with significantly more modules added
+# J. Sassmannshausen ICL/UK 
+
+easyblock = 'ConfigureMake'
+
+name = 'PETSc'
+version = '3.17.4'
+
+homepage = 'https://www.mcs.anl.gov/petsc'
+description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
+ scalable (parallel) solution of scientific applications modeled by partial differential equations.
+
+This installation is build with significant amounts of modules in it compared to previous versions."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
+
+source_urls = [
+    'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+    'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'webclient-3.17.0.patch',
+]
+checksums = [
+    '99c127486722a3ffd95a268b4ceb0976cbf217926c681a9631bd7246eab8cb2a',  # petsc-3.17.4.tar.gz
+    '2ba253df42853385e2683dbc87dfcb66d4ce4bcd84e054efa8f466274f49bc81',  # webclient-3.17.0.patch
+]
+
+builddependencies = [
+    ('Eigen', '3.3.9'),
+    ('CMake', '3.20.1')
+]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('Boost', '1.76.0'),
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '6.1.0'),
+    ('MUMPS', '5.4.0', '-metis'),
+    ('SuiteSparse', '5.10.1', '-METIS-5.1.0'),
+    ('Hypre', '2.21.0'),
+    ('zlib', '1.2.11'),
+    ('BLIS', '0.8.1'),
+    ('Szip', '2.1.1'),
+    ('HDF5', '1.12.1'),
+    ('GMP', '6.2.1'),
+    ('GSL', '2.7'),
+    ('libjpeg-turbo', '2.0.6'),
+    ('libpng', '1.6.37'),
+    ('giflib', '5.2.1'),
+    ('OpenSSL', '1.1', '', True),
+    ('libyaml', '0.2.5'),
+    ('zstd', '1.4.9'),
+    ('Mmg', '5.6.0'),
+    ('MPFR', '4.1.0'),
+    ('googletest', '1.11.0'),
+    ('muParser', '2.3.3'),
+    ('ParMETIS', '4.0.3'),
+]
+
+# enabling --with-mpi4py seems to be totally broken, leads to make errors like:
+# No rule to make target 'mpi4py-build'
+configopts = '--configModules=PETSc.Configure --optionsModule=config.compilerOptions '
+configopts += '--LIBS="$LIBS -lrt" --download-mpi4py --with-mpi4py=1 --download-petsc4py --CXXFLAGS="$CXXFLAGS '
+configopts += '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --with-mpi=1 --with-build-step-np=4 '
+configopts += '--CPPFLAGS="$CPPFLAGS" --F90FLAGS="$F90FLAGS" --FFLAGS="$FFLAGS" --FCFLAGS="$FCFLAGS" '
+configopts += '--with-blaslapack-lib=" -lflexiblas -lgfortran" '
+configopts += '--with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 '
+configopts += '--with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-scalapack=1 '
+configopts += '--with-python=1 --with-boost=1 --with-metis=1 -with-ptscotch=1 --with-mumps=1 '
+configopts += '--with-hypre=1  --with-suitesparse=1 --with-hwloc=1 --with-openmp=1 --with-zlib=1 --with-blis=1 '
+configopts += '--with-hdf5=1 --with-eigen=1 --with-parmetis=1 --with-gmp=1 --with-gsl=1 --with-libjpeg=1 '
+configopts += '--with-libpng=1 --with-yaml=1 --with-zstd=1 --with-ssl=1 --with-triangle=0 --with-giflib=1 '
+
+sanity_check_paths = {
+    'files': ['lib/libpetsc.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share']
+}
+
+modextrapaths = {'PYTHONPATH': 'lib'}
+
+moduleclass = 'numlib'
+

p/PETSc/webclient-3.17.0.patch

@@ -0,0 +1,69 @@
+Based on https://gitlab.com/petsc/petsc/-/merge_requests/5257
+Author: J. Sassmannshausen / ICL (UK)
+diff --git a/petsc-3.17.0.orig/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py b/petsc-3.17.0/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py
+index ecc3b03..6c6c354 100755
+--- a/petsc-3.17.0.orig/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py
++++ b/petsc-3.17.0/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py
+@@ -36,6 +36,7 @@ configure_options = [
+   '--with-mpi-f90module-visibility=0',
+   '--download-kokkos=1',
+   '--download-kokkos-kernels=1',
++  '--with-ssl=1',
+   ]
+ 
+ if __name__ == '__main__':
+diff --git a/petsc-3.17.0.orig/config/examples/arch-ci-linux-gcc-pkgs-opt.py b/petsc-3.17.0/config/examples/arch-ci-linux-gcc-pkgs-opt.py
+index 8828156..132e3d6 100755
+--- a/petsc-3.17.0.orig/config/examples/arch-ci-linux-gcc-pkgs-opt.py
++++ b/petsc-3.17.0/config/examples/arch-ci-linux-gcc-pkgs-opt.py
+@@ -28,6 +28,7 @@ configure_options = [
+   '--download-amrex',
+   '--download-hypre',
+   '--download-ks',
++  '--with-ssl=1',
+ ]
+ 
+ if __name__ == '__main__':
+diff --git a/petsc-3.17.0.orig/src/sys/webclient/box.c b/petsc-3.17.0/src/sys/webclient/box.c
+index d306966..eb2fac7 100644
+--- a/petsc-3.17.0.orig/src/sys/webclient/box.c
++++ b/petsc-3.17.0/src/sys/webclient/box.c
+@@ -304,9 +304,9 @@ PetscErrorCode PetscBoxUpload(MPI_Comm comm,const char access_token[],const char
+     PetscCall(PetscPushJSONValue(body,"mimeType","text.html",len));
+     PetscCall(PetscStrcat(body,","));
+     PetscCall(PetscPushJSONValue(body,"description","a file",len));
+-    ierr = PetscStrcat(body, "}\r\n\r\n"
+-                             "--foo_bar_baz\r\n"
+-                             "Content-Type: text/html\r\n\r\n");PetscCall(ierr);
++    PetscCall(PetscStrcat(body, "}\r\n\r\n"
++                                "--foo_bar_baz\r\n"
++                                "Content-Type: text/html\r\n\r\n"));
+     PetscCall(PetscStrlen(body,&blen));
+     fd = fopen (filename, "r");
+     PetscCheck(fd,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to open file: %s",filename);
+diff --git a/petsc-3.17.0.orig/src/sys/webclient/client.c b/petsc-3.17.0/src/sys/webclient/client.c
+index dfe6b12..350cac9 100644
+--- a/petsc-3.17.0.orig/src/sys/webclient/client.c
++++ b/petsc-3.17.0/src/sys/webclient/client.c
+@@ -123,7 +123,7 @@ static PetscErrorCode PetscHTTPBuildRequest(const char type[],const char url[],c
+ 
+   if (header) {
+     PetscCall(PetscStrendswith(header,"\r\n",&flg));
+-    PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"header must end with \\r\");
++    PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"header must end with \\r\\n");
+   }
+ 
+   PetscCall(PetscStrlen(type,&typelen));
+diff --git a/petsc-3.17.0.orig/src/sys/webclient/google.c b/petsc-3.17.0/src/sys/webclient/google.c
+index 8626b7c..c66f8cc 100644
+--- a/petsc-3.17.0.orig/src/sys/webclient/google.c
++++ b/petsc-3.17.0/src/sys/webclient/google.c
+@@ -158,7 +158,7 @@ PetscErrorCode PetscGoogleDriveUpload(MPI_Comm comm,const char access_token[],co
+     fd = fopen (filename, "r");
+     PetscCheck(fd,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to open file: %s",filename);
+     rd = fread (body+blen, sizeof (unsigned char), sb.st_size, fd);
+-    PetscCheckFalse(rd != (size_t) sb.st_size,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to read entire file: %s %d %d",filename,(int)rd,sb.st_size);
++    PetscCheckFalse(rd != (size_t) sb.st_size,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to read entire file: %s %d %d",filename,(int)rd,(int)sb.st_size);
+     fclose(fd);
+     body[blen + rd] = 0;
+     ierr = PetscStrcat(body,"\r\n\r\n"

s/SuiteSparse/SuiteSparse-5.13.0-foss-2021a-METIS-5.1.0.eb

@@ -0,0 +1,34 @@
+# IT4Innovations 2022
+# JK
+
+name = 'SuiteSparse'
+version = '5.13.0'
+local_metis_ver = '5.1.0'
+versionsuffix = '-METIS-%s' % local_metis_ver
+
+homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries manipulate sparse matrices."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['59c6ca2959623f0c69226cf9afb9a018d12a37fab3a8869db5f6d7f83b6b147d']
+
+builddependencies = [
+    ('CMake', '3.20.1'),
+    ('M4', '1.4.18'),
+]
+
+dependencies = [
+    ('METIS', local_metis_ver),
+    ('MPFR', '4.1.0'),
+]
+
+# make sure that bin/demo can find libsuitesparseconfig.so.5 during build
+prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
+# remove broken symlink
+prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && "
+
+moduleclass = 'numlib'

x/XMLSec/XMLSec-1.2.34-GCCcore-11.3.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'XMLSec'
+version = '1.2.34'
+
+homepage = 'https://www.aleksey.com/xmlsec/index.html'
+
+description = """XML Security Library is a C library based on LibXML2,
+ supporting major XML security standards."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['http://www.aleksey.com/xmlsec/download/']
+sources = ['%(namelower)s%(version_major)s-%(version)s.tar.gz']
+checksums = ['52ced4943f35bd7d0818a38298c1528ca4ac8a54440fd71134a07d2d1370a262']
+
+builddependencies = [
+    ('binutils', '2.38')
+]
+
+dependencies = [
+    ('libtool', '2.4.7'),
+    ('libxml2', '2.9.13'),
+    ('OpenSSL', '1.1', '', True),
+]
+
+sanity_check_paths = {
+    'files': ['bin/xmlsec1', 'bin/xmlsec1-config',
+              'lib/libxmlsec1.a', 'lib/libxmlsec1-openssl.a',
+              'lib/libxmlsec1.%s.%s' % (SHLIB_EXT, version),
+              'lib/libxmlsec1-openssl.%s.%s' % (SHLIB_EXT, version)],
+    'dirs': ['include/xmlsec%(version_major)s/xmlsec', 'share'],
+}
+
+moduleclass = 'lib'