diff --git a/c/Cordax/Cordax-1.0-Python-2.7.18.eb b/c/Cordax/Cordax-1.0-Python-2.7.18.eb deleted file mode 100644 index 2172fa73..00000000 --- a/c/Cordax/Cordax-1.0-Python-2.7.18.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'Binary' - -name = 'Cordax' -version = '1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'N/A' -description = """CORDAX is an aggregation propensity predictor based on predicted packing energies.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -sources = ['%(namelower)s-%(version)s.tar.gz'] - -dependencies = [ - ('Python', '2.7.18'), - ('matplotlib', '2.2.5', '-Python-%(pyver)s'), - ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), - ('scikit-learn', '0.20.4', '-Python-%(pyver)s'), - ('Biopython', '1.72', '-Python-%(pyver)s'), - ('FoldX', '5.0', '', True), -] - -extract_sources = True -skipsteps = ['sanitycheck'] - -moduleclass = 'bio' diff --git a/c/Cordax/Cordax-20220830-foss-2020b.eb b/c/Cordax/Cordax-20220830-foss-2020b.eb new file mode 100644 index 00000000..dac13ff8 --- /dev/null +++ b/c/Cordax/Cordax-20220830-foss-2020b.eb @@ -0,0 +1,40 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'Tarball' + +name = 'Cordax' +version = '20220830' + +homepage = 'https://cordax.switchlab.org/' +description = """CORDAX is an aggregation propensity predictor based on predicted packing energies.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = ['Cordax-20220830-set-proper-paths.patch'] +checksums = [ + 'bc2b2e84f3df84c1ecabc774fed247998d1aeb38bade04127e47cd585130160d', # cordax-20220830.tar.gz + 'df8261e08da5d4e698f8621284d22bab99a0064f27d7735933c0d15c9ed730ff', # Cordax-20220830-set-proper-paths.patch +] + +dependencies = [ + ('Python', '2.7.18'), + ('matplotlib', '2.2.5', '-Python-%(pyver)s'), + ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), + ('scikit-learn', '0.20.4', '-Python-%(pyver)s'), + ('Biopython', '1.72', '-Python-%(pyver)s'), + ('FoldX', '5.0', '', True), +] + +sanity_check_paths = { + 'files': ['parser.py', 'precomputed_dg.py', 'predictor.py', 'propensity.py', 'run_foldx.py', + 'standalone.py', 'utils.py'], + 'dirs': ['dataset', 'foldx', 'test', 'DATADIR'], +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "Precalculated models are available at $EBROOTCORDAX/DATADIR" + +moduleclass = 'bio' diff --git a/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb b/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb new file mode 100644 index 00000000..f50c805d --- /dev/null +++ b/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb @@ -0,0 +1,34 @@ +# IT4Innovations 2022 +# JK + +name = 'FFTW.MPI' +version = '3.3.10' +local_amd_fftw_ver = '3.2' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-aocl/fftw/' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data. +AMD FFTW includes selective kernels and routines optimized for the AMD EPYC™ processor family.""" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/amd/amd-fftw/archive/refs/tags/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_amd_fftw_ver, + 'filename': 'amd-fftw-%s.tar.gz' % local_amd_fftw_ver, +}] +checksums = ['31cab17a93e03b5b606e88dd6116a1055b8f49542d7d0890dbfcca057087b8d0'] + +dependencies = [ + ('FFTW', '3.3.10', '-amd'), + ('OpenMPI', '4.1.2', '-CUDA-11.6.0-v2'), +] + + +configopts = '--enable-amd-opt' + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/f/FFTW/FFTW-3.3.10-NVHPC-22.2-amd.eb b/f/FFTW/FFTW-3.3.10-NVHPC-22.2-amd.eb new file mode 100644 index 00000000..3b822f7b --- /dev/null +++ b/f/FFTW/FFTW-3.3.10-NVHPC-22.2-amd.eb @@ -0,0 +1,28 @@ +# IT4Innovations 2022 +# JK + +name = 'FFTW' +version = '3.3.10' +local_amd_fftw_ver = '3.2' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-aocl/fftw/' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data. +AMD FFTW includes selective kernels and routines optimized for the AMD EPYC™ processor family.""" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/amd/amd-fftw/archive/refs/tags/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_amd_fftw_ver, + 'filename': 'amd-fftw-%s.tar.gz' % local_amd_fftw_ver, +}] +checksums = ['31cab17a93e03b5b606e88dd6116a1055b8f49542d7d0890dbfcca057087b8d0'] + +configopts = '--enable-amd-opt' + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/h/HDF5/HDF5-1.12.1-NVHPC-22.2.eb b/h/HDF5/HDF5-1.12.1-NVHPC-22.2.eb new file mode 100644 index 00000000..649bca0d --- /dev/null +++ b/h/HDF5/HDF5-1.12.1-NVHPC-22.2.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2022 +# LK JK + +name = 'HDF5' +version = '1.12.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +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': 'NVHPC', 'version': '22.2'} +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] +checksums = ['79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca'] + +configopts = '--enable-fortran --enable-fortran 2003 --enable-cxx --enable-parallel --enable-shared' + +dependencies = [ + ('OpenMPI', '4.1.2', '-CUDA-11.6.0-v2'), + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/i/irodsfs/irodsfs-0.7.6.eb b/i/irodsfs/irodsfs-0.7.6.eb index 6b2f8e11..d7b5ac7a 100644 --- a/i/irodsfs/irodsfs-0.7.6.eb +++ b/i/irodsfs/irodsfs-0.7.6.eb @@ -23,7 +23,8 @@ sanity_check_paths = { postinstallcmds = [ 'cp /mnt/proj3/easybuild/scripts/irods-startup.sh %(installdir)s/', - 'curl -L https://docs.it4i.cz/irods1.it4i.cz.crt -o %(installdir)s/irods1.it4i.cz.crt', + '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', ] modluafooter = 'execute{cmd="bash $EBROOTIRODSFS/irods-startup.sh", modeA={"load"}}' diff --git a/v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0.eb b/v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0.eb new file mode 100644 index 00000000..87a2f3a4 --- /dev/null +++ b/v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0.eb @@ -0,0 +1,95 @@ +# IT4Innovations 2022 +# JK LK + +easyblock = 'MakeCp' + +name = 'VASP' +version = '6.3.2' + +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 an academic license from University of Vienna. Follow the instructions at https://www.vasp.at/index.php/faqs. + +Please send us a list of authorized users and their IDs for which you need access (use only http://support.it4i.cz/rt). We are responsible for verifying your licenses.""" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} +toolchainopts = {'pic': 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'] +checksums = ['f7595221b0f9236a324ea8afe170637a578cdd5a837cc7679e7f7812f6edf25a'] + +# use serial compilation of W90, see https://www.vasp.at/wiki/index.php/Makefile.include#Wannier90_.28optional.29 +# Important: In case of Wannier90 3.x, you should compile a serial version by removing COMMS=mpi in the make.inc of Wannier90. +dependencies = [ + ('HDF5', '1.12.1'), + ('FFTW', '3.3.8', '', True), +# ('Wannier90', '3.1.0', '-serial'), +] + +prebuildopts = 'cp arch/makefile.include.nvhpc_acc ./makefile.include && ' + +# OFLAG '-fast' is the VASP default, no need to change it + +# SCALAPACK and FFTW +#prebuildopts += 'sed -i "s|\(SCALAPACK_ROOT\s\+?=\) /path/to/your/scalapack/installation|\\1 ${EBROOTSCALAPACK}|" makefile.include && ' +prebuildopts += 'sed -i "s|\(FFTW_ROOT\s\+?=\) /path/to/your/fftw/installation|\\1 ${EBROOTFFTW}|" makefile.include && ' + +# FLexiBLAS shadows OpenBLAS, for more info see FlexiBLAS description +#prebuildopts += 'sed -i "s|\(OPENBLAS_ROOT\s\+?=\) /path/to/your/openblas/installation|\\1 ${EBROOTFLEXIBLAS}|" makefile.include && ' +#prebuildopts += 'sed -i "s|\(L\$(OPENBLAS_ROOT)\/lib\) -lopenblas|\\1 -lflexiblas|" makefile.include && ' + +# CUDA version +prebuildopts += 'sed -i "s|cuda11.0|cuda11.6|g" makefile.include && ' + +# NVHPC settings +prebuildopts += 'sed -i "/NVHPC/,+s|^#||" makefile.include && ' +prebuildopts += 'sed -i "s|#\(NVVERSION\s\+=\) 21.11|\\1 ${EBVERSIONNVHPC}|" makefile.include && ' +prebuildopts += 'sed -i "/NVROOT\s\+=/,+s|^#||" makefile.include && ' + +# Improves performance when using NV HPC-SDK >=21.11 and CUDA >11.2 +prebuildopts += 'sed -i "/OFLAG_IN/,+s|^#||" makefile.include && ' +prebuildopts += 'sed -i "/SOURCE_IN/,+s|^#||" makefile.include && ' + +# HDF5 support +prebuildopts += 'sed -i "/DVASP_HDF5/,+s|^#||" makefile.include && ' +prebuildopts += 'sed -i "s|#\(HDF5_ROOT\s\+?=\) /path/to/your/hdf5/installation|\\1 ${EBROOTHDF5}|" makefile.include && ' +prebuildopts += 'sed -i "/L\$(HDF5_ROOT)\/lib -lhdf5_fortran/,+s|^#||" makefile.include && ' +prebuildopts += 'sed -i "/I\$(HDF5_ROOT)\/include/,+s|^#||" makefile.include && ' + +# Wannier90 interface +# nejde zatim zkompilovat +#prebuildopts += 'sed -i "/DVASP2WANNIER90/,+s|^#||" makefile.include && ' +#prebuildopts += 'sed -i "s|#\(WANNIER90_ROOT\s\+?=\) /path/to/your/wannier90/installation|\\1 ${EBROOTWANNIER90}|" makefile.include && ' +#prebuildopts += 'sed -i "/L\$(WANNIER90_ROOT)\/lib -lwannier/,+s|^#||" makefile.include && ' + +# scaLAPACK +# crashes on /apps/all/binutils/2.35-GCCcore-10.2.0/bin/ld: cannot find -lscalapack +prebuildopts += 'sed -i "s/\$(SCALAPACK)//" makefile.include && ' +prebuildopts += '{ echo ""; echo "# scaLAPACK"; echo SCALAPACK_ROOT ?= \$\(NVROOT\)/comm_libs/mpi/lib; } >> makefile.include && ' +prebuildopts += 'echo "LLIBS += -L\$(NVHPC)/comm_libs/mpi/lib -Mscalapack" >> makefile.include && ' + +# VASP uses LIBS as a list of folders +prebuildopts += 'unset LIBS && ' + +buildopts = 'std gam ncl ' + +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"), + add_property("arch", "gpu"), +""" + +moduleclass = 'phys'