diff --git a/g/grace/grace-5.1.25-intel-2020b.eb b/g/grace/grace-5.1.25-intel-2020b.eb index 6d8de3be..b076c50e 100644 --- a/g/grace/grace-5.1.25-intel-2020b.eb +++ b/g/grace/grace-5.1.25-intel-2020b.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'intel', 'version': '2020b'} # ('netCDF', '4.6.1'), #] -#runtest = 'tests' +runtest = 'tests' # we also need to run make links right before or after make install. installopts = 'links' diff --git a/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb b/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000..95ec77fa --- /dev/null +++ b/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb @@ -0,0 +1,29 @@ +# IT4Innovatios 2022 +# LK JK + +name = 'impi' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/'] +sources = ['l_mpi_oneapi_p_%(version)s.441_offline.sh'] +checksums = ['cc4b7072c61d0bd02b1c431b22d2ea3b84b967b59d2e587e77a9e7b2c24f2a29'] + +dependencies = [('UCX', '1.11.2')] + +modextravars = { + 'I_MPI_OFI_PROVIDER': 'MLX', + 'FI_PROVIDER': 'verbs', + 'I_MPI_CC' : 'icc', + 'I_MPI_CXX': 'icpc', + 'I_MPI_F77': 'ifort', + 'I_MPI_F90': 'ifort', + 'I_MPI_FC': 'ifort', +} + +moduleclass = 'mpi' diff --git a/m/mpi4py/mpi4py-3.1.3-foss-2021a-Python-3.9.5.eb b/m/mpi4py/mpi4py-3.1.3-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000..f3e087ab --- /dev/null +++ b/m/mpi4py/mpi4py-3.1.3-foss-2021a-Python-3.9.5.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' diff --git a/m/mpi4pyscf/mpi4pyscf-0.3.1-foss-2021a-Python-3.9.5.eb b/m/mpi4pyscf/mpi4pyscf-0.3.1-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000..d1dc3b3b --- /dev/null +++ b/m/mpi4pyscf/mpi4pyscf-0.3.1-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,28 @@ +# IT4Innovations +# JK 2022 + +easyblock = 'PackedBinary' + +name = 'mpi4pyscf' +version = '0.3.1' + +homepage = 'https://github.com/pyscf/mpi4pyscf' +description = """mpi4pyscf is a plugin for PySCF which enables MPI (Message Passing Interface) parallelism.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# clone from github and create an archive +# instalace akorat prekopiruje f2py binarky :D +sources = [SOURCE_TAR_GZ] +extract_sources = True + +dependencies = [ + ('Python', '3.9.5'), + ('mpi4py', '3.1.3'), + ('PySCF', '2.0.1'), +] + +skipsteps = ['sanitycheck'] +modextrapaths = {'PYTHONPATH': 'mpi4pyscf'} + +moduleclass = 'mpi' diff --git a/m/mpi4pyscf/mpi4pyscf-0.3.1.tar.gz b/m/mpi4pyscf/mpi4pyscf-0.3.1.tar.gz new file mode 100644 index 00000000..af1d7468 Binary files /dev/null and b/m/mpi4pyscf/mpi4pyscf-0.3.1.tar.gz differ diff --git a/p/Paraver/Paraver-4.10.0-foss-2021a.eb b/p/Paraver/Paraver-4.10.0-foss-2021a.eb new file mode 100644 index 00000000..a5e955d2 --- /dev/null +++ b/p/Paraver/Paraver-4.10.0-foss-2021a.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.10.0' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['83289584040bcedf8cab1b2ae3545191c8bdef0e11ab62b06e54cbf111f2127a'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('wxWidgets', '3.1.5'), +] + +moduleclass = 'perf' diff --git a/p/PySCF/PySCF-2.0.1-foss-2021a.eb b/p/PySCF/PySCF-2.0.1-foss-2021a.eb new file mode 100644 index 00000000..4d5bb4dd --- /dev/null +++ b/p/PySCF/PySCF-2.0.1-foss-2021a.eb @@ -0,0 +1,48 @@ +# IT4Innovations +# JK 2022 + +easyblock = 'CMakeMakeCp' + +name = 'PySCF' +version = '2.0.1' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6a152860787351aae52dc1ef2399bd9564fa314dca070312cfc0f2c3fc7412cf'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, scipy + ('h5py', '3.2.1'), + ('libcint', '4.4.0'), + ('libxc', '5.1.5'), + ('XCFun', '2.1.1'), +] + +start_dir = 'pyscf/lib' + +separate_build_dir = True + +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" + +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' diff --git a/q/QEMU/QEMU-5.1.0-VDE2.eb b/q/QEMU/QEMU-5.1.0.eb similarity index 93% rename from q/QEMU/QEMU-5.1.0-VDE2.eb rename to q/QEMU/QEMU-5.1.0.eb index c6d369d5..c1f88535 100644 --- a/q/QEMU/QEMU-5.1.0-VDE2.eb +++ b/q/QEMU/QEMU-5.1.0.eb @@ -5,7 +5,6 @@ easyblock = 'ConfigureMake' name = "QEMU" version = "5.1.0" -versionsuffix = "-VDE2" homepage = 'http://wiki.qemu.org/Main_Page' description = """QEMU is a generic and open source machine emulator and @@ -21,7 +20,6 @@ source_urls = ['http://wiki.qemu-project.org/download/'] patches = ['qemu-slirp-smb-2.9.0.patch'] dependencies = [ - ('VDE2', '2.3.2'), ('Python', '3.8.2', '', ('GCCcore', '9.3.0')), ('pixman', '0.34.0'), ] diff --git a/q/QEMU/QEMU-6.2.0-VDE2.eb b/q/QEMU/QEMU-6.2.0-GCC-10.2.0.eb similarity index 77% rename from q/QEMU/QEMU-6.2.0-VDE2.eb rename to q/QEMU/QEMU-6.2.0-GCC-10.2.0.eb index 9091fe32..bc72c428 100644 --- a/q/QEMU/QEMU-6.2.0-VDE2.eb +++ b/q/QEMU/QEMU-6.2.0-GCC-10.2.0.eb @@ -5,7 +5,6 @@ easyblock = 'ConfigureMake' name = "QEMU" version = "6.2.0" -versionsuffix = "-VDE2" homepage = 'http://wiki.qemu.org/Main_Page' description = """QEMU is a generic and open source machine emulator and @@ -13,7 +12,7 @@ virtualizer.""" configopts = "--target-list=x86_64-softmmu,x86_64-linux-user,i386-softmmu,i386-linux-user" -toolchain = SYSTEM +toolchain = {'name': 'GCC', 'version': '10.2.0'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://wiki.qemu-project.org/download/'] @@ -21,9 +20,10 @@ source_urls = ['http://wiki.qemu-project.org/download/'] patches = ['qemu-slirp-smb-2.9.0.patch'] dependencies = [ - ('VDE2', '2.3.2'), - ('Python', '3.8.6', '', ('GCCcore', '10.2.0')), - ('pixman', '0.40.0', '', ('GCCcore', '10.2.0')), + ('Python', '3.8.6'), + ('pixman', '0.40.0'), + ('Ninja', '1.10.1'), + ('GLib', '2.66.1'), ] sanity_check_paths = { diff --git a/q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb b/q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb index c7257254..2e60a9d8 100644 --- a/q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb +++ b/q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb @@ -32,6 +32,8 @@ dependencies = [ ('Python', '3.8.6'), ('h5py', '3.1.0'), ('SciPy-bundle', '2020.11'), + ('FFTW', '3.3.8'), +# ('PySCF', '2.0.1'), # does not work with intel toolchain ('GCC', '9.3.0', '', True), ] @@ -43,15 +45,22 @@ configopts += ' -DHDF5_PREFER_PARALLEL=1 -DENABLE_PHDF5=1 ' configopts += ' -DQMC_SYMLINK_TEST_FILES=0 ' configopts += ' -DCMAKE_BUILD_TYPE=Release ' configopts += ' -DQMC_OMP=ON ' +configopts += ' -DCMAKE_INSTALL_PREFIX=%(installdir)s' +configopts += ' -DINSTALL_NEXUS=ON ' +configopts += ' -DBUILD_UNIT_TESTS=ON -DBUILD_MICRO_BENCHMARKS=ON ' +configopts += ' -DBUILD_AFQMC=ON ' # FCIQMC fails # prekopiruje nexus knihovny o kterych install file tvrdi, ze nejsou potreba # ale evidentne to bez nich nejede + preinstallopts = [ - ' mkdir -p %(installdir)s/nexus && ', - ' cp -r %(builddir)s/qmcpack-%(version)s/nexus/lib %(installdir)s/nexus/lib && ', + ' mkdir -p %(installdir)s/nexus && ', + ' mkdir -p %(installdir)s/QMCTools && ', + ' cp -r %(builddir)s/qmcpack-%(version)s/nexus %(installdir)s/ && ', + ' cp %(builddir)s/qmcpack-%(version)s/src/QMCTools/*.py %(installdir)s/QMCTools/ && ', ] -modextrapaths = {'PYTHONPATH': 'nexus/lib'} +modextrapaths = {'PYTHONPATH': ['nexus/lib', 'QMCTools']} sanity_check_paths = { 'files': ['bin/qmcpack'], diff --git a/q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb.old b/q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb.old new file mode 100644 index 00000000..c7257254 --- /dev/null +++ b/q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb.old @@ -0,0 +1,61 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'CMakeMake' + +name = 'QMCPACK' +version = '3.13.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = "https://qmcpack.org/" +description = """QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code. Its main applications are electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. Orbital space auxiliary field QMC (AFQMC) has recently been added. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater local_computational expense. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} +import os +if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: + toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'} + prebuildopts = "echo %(builddir)s && while read i; do echo $i; sed 's|-xHost|-march=core-avx2|g' -i $i; done < <(grep xHost %(builddir)s -R | cut -d ':' -f 1 | sort -u) &&" +else: + toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/QMCPACK/qmcpack/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.20.1', '', True),] + +# odstran z module file GCC 9.3.0 - rovnak na intel +dependencies = [ + ('libxml2', '2.9.10'), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7', '', ('iimpi', '2020b')), + ('Python', '3.8.6'), + ('h5py', '3.1.0'), + ('SciPy-bundle', '2020.11'), + ('GCC', '9.3.0', '', True), +] + +separate_build_dir = True + +configopts = ' -DENABLE_SOA=1 ' +configopts += ' -DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc ' +configopts += ' -DHDF5_PREFER_PARALLEL=1 -DENABLE_PHDF5=1 ' +configopts += ' -DQMC_SYMLINK_TEST_FILES=0 ' +configopts += ' -DCMAKE_BUILD_TYPE=Release ' +configopts += ' -DQMC_OMP=ON ' + +# prekopiruje nexus knihovny o kterych install file tvrdi, ze nejsou potreba +# ale evidentne to bez nich nejede +preinstallopts = [ + ' mkdir -p %(installdir)s/nexus && ', + ' cp -r %(builddir)s/qmcpack-%(version)s/nexus/lib %(installdir)s/nexus/lib && ', +] + +modextrapaths = {'PYTHONPATH': 'nexus/lib'} + +sanity_check_paths = { + 'files': ['bin/qmcpack'], + 'dirs': ['bin'], +} + +moduleclass = 'phys' diff --git a/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021a.eb b/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021a.eb new file mode 100644 index 00000000..579609ab --- /dev/null +++ b/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021a.eb @@ -0,0 +1,54 @@ +# JK 2022 + +name = 'QuantumESPRESSO' +version = '7.0' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +import os +if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: + toolchainopts = {'usempi': True, 'openmp': True, 'optarch': 'march=core-avx2'} +else: + toolchainopts = {'usempi': True, 'openmp': True} + +if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: + prebuildopts = "echo %(builddir)s && while read i; do echo $i; sed 's|-xHost|-march=core-avx2|g' -i $i; done < <(grep xHost %(builddir)s -R | cut -d ':' -f 1 | sort -u) && " + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s.0/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + '268ec506f88c56ba4e9b691c1e81e33a6ad7949f857f1c6c32197f9c2af2a957', # qe-%(version)s-ReleasePack.tgz + '71b83c7ffaf98e111e2cb0b3fe6da0084c07f0f4f9e641046142924568e96802', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.5'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/r/R/R-4.1.0-foss-2021a.eb b/r/R/R-4.1.0-foss-2021a.eb index 0be5a6e4..2e56d8e4 100644 --- a/r/R/R-4.1.0-foss-2021a.eb +++ b/r/R/R-4.1.0-foss-2021a.eb @@ -1548,7 +1548,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], #['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-march=znver3-karolina.eb b/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb similarity index 99% rename from v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-march=znver3-karolina.eb rename to v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb index 656da0d2..5dce9d3f 100644 --- a/v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-march=znver3-karolina.eb +++ b/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb @@ -1,5 +1,5 @@ # IT4Innovations 2021 -# LK +# LK JK easyblock = 'MakeCp' diff --git a/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential.eb b/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential.eb new file mode 100644 index 00000000..ff76f502 --- /dev/null +++ b/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential.eb @@ -0,0 +1,67 @@ +# IT4Innovations 2021 +# LK JK + +easyblock = 'MakeCp' + +name = 'VASP' +version = '6.3.0' +versionsuffix = '-mkl=sequential' + +homepage = 'http://www.vasp.at' +description = """The Vienna Ab initio Simulation Package (VASP) is a local_computer program for atomic scale +materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +# Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on +# how to get access to the code +sources = ['%(namelower)s.%(version)s.tgz'] + +prebuildopts = 'cp arch/makefile.include.intel ./makefile.include && ' + +# AMD/intel cpu +import os +if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: + prebuildopts += 'sed -i "s|-xHOST|-march=core-avx2|" makefile.include && ' + +# path to libfftw3xf_intel.a is hardcoded in makefile.include +prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && ' + +# remove mkl flag to prevent mixing dynamic libs with the static libs in +# LIBBLACS/SCALAPACK +prebuildopts += 'sed -i "s|-mkl=sequential ||" makefile.include && ' + +# OFLAG = -O2 -xAVX +prebuildopts += 'sed -i "s|OFLAG = -O2|OFLAG = -O3 -ip -march=xHost|" makefile.include && ' + +# objects add MKLROOT +prebuildopts += 'sed -i "s|OBJECTS = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o|OBJECTS = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o \$(MKLROOT)/lib/intel64_lin/libfftw3xf_intel.a|" makefile.include && ' + +prebuildopts += 'sed -i "s|FFLAGS = -assume byterecl -w|FFLAGS = -FR -assume byterecl|" makefile.include && ' +prebuildopts += 'sed -i "s|BLAS =|BLAS = -mkl=sequential|" makefile.include && ' + +# VASP uses LIBS as a list of folders +prebuildopts += 'unset LIBS && ' + +#prebuildopts += 'exit 1' + +buildopts = 'std gam ncl ' # 'BLACS="$LIBBLACS" SCALAPACK="$LIBSCALAPACK" ' + +parallel = 1 + +files_to_copy = [(['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], + 'dirs': [] +} + +modluafooter = 'add_property("state","license")' + +moduleclass = 'phys'