diff --git a/b/Blender/Blender-3.1.0-GCC-10.3.0.eb b/b/Blender/Blender-3.1.0-GCC-10.3.0.eb index 944191f6..332f3194 100644 --- a/b/Blender/Blender-3.1.0-GCC-10.3.0.eb +++ b/b/Blender/Blender-3.1.0-GCC-10.3.0.eb @@ -14,11 +14,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender3.1/'] sources = ['blender-%(version)s-linux-x64.tar.xz'] -<<<<<<< HEAD -checksums = ['8cf60d0c2cbda2ad26d8ff65e54cce45'] -======= checksums = ['ced2aaabc75731c2ae0e29493d0d2db7803d2bbb70a11cd0e7f50546d465bd8c'] ->>>>>>> f9b20a6876de43df220c97513f83ee10c203bb30 postinstallcmds = [ 'ml CUDAcore;"nvcc" -arch=sm_80 --cubin "%(installdir)s/3.1/scripts/addons/cycles/source/kernel/device/cuda/kernel.cu" -o "%(installdir)s/3.1/scripts/addons/cycles/lib/kernel_sm_80.cubin" -m64 --ptxas-options="-v" --use_fast_math -DNVCC -I"%(installdir)s/3.1/scripts/addons/cycles/source" -DWITH_NANOVDB', diff --git a/b/Blender/Blender-3.2.2-GCC-10.3.0.eb b/b/Blender/Blender-3.2.2-GCC-10.3.0.eb new file mode 100644 index 00000000..0850d509 --- /dev/null +++ b/b/Blender/Blender-3.2.2-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +# IT4Innovations 2021 + +easyblock = 'Tarball' + +name = 'Blender' +version = '3.2.2' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender3.2/'] +sources = ['blender-%(version)s-linux-x64.tar.xz'] +checksums = ['1726560157d90cf2aaaeb6d25ded1783d66bff043814cd95b90fc0af1d9e018b'] + +postinstallcmds = [ + 'ml CUDAcore;"nvcc" -arch=sm_80 --cubin "%(installdir)s/3.2/scripts/addons/cycles/source/kernel/device/cuda/kernel.cu" -o "%(installdir)s/3.2/scripts/addons/cycles/lib/kernel_sm_80.cubin" -m64 --ptxas-options="-v" --use_fast_math -DNVCC -I"%(installdir)s/3.2/scripts/addons/cycles/source" -DWITH_NANOVDB', + 'find %(installdir)s -executable -exec chmod +x {} \;', +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["blender"], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb b/b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb new file mode 100644 index 00000000..cec51692 --- /dev/null +++ b/b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bwidget' +version = '1.9.15' + +homepage = 'https://core.tcl-lang.org/bwidget/home' +description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9c4dd648fdfd31de7cb5af44b392a1916f949dd195820684d940edcd8485ac13'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Tk', '8.6.12')] + +modextrapaths = {'TCLLIBPATH': '.'} + +sanity_check_paths = { + 'files': ['button.tcl'], + 'dirs': ['BWman', 'demo', 'images', 'lang', 'tests'], +} + +moduleclass = 'vis' diff --git a/c/CP2K/CP2K-2022.1-foss-2022a.eb b/c/CP2K/CP2K-2022.1-foss-2022a.eb new file mode 100644 index 00000000..854b39db --- /dev/null +++ b/c/CP2K/CP2K-2022.1-foss-2022a.eb @@ -0,0 +1,44 @@ +# IT4Innovations 2022 +# JK +#16007 + +## +# Author: Robert Mijakovic <robert.mijakovic@lxp.lu> +## +name = 'CP2K' +version = '2022.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b'] + +# https://github.com/cp2k/cp2k/releases/download/v2022.1/cp2k-2022.1.tar.bz2 +dependencies = [ + ('Libint', '2.7.2', '-lmax-6-cp2k'), + ('libxc', '5.2.3'), + ('libxsmm', '1.17'), + ('FFTW', '3.3.10'), + ('PLUMED', '2.8.0'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' 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/c/ctffind/ctffind-4.1.14-foss-2021a.eb b/c/ctffind/ctffind-4.1.14-foss-2021a.eb new file mode 100644 index 00000000..7ef5beaf --- /dev/null +++ b/c/ctffind/ctffind-4.1.14-foss-2021a.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('GSL', '2.7'), + ('wxWidgets', '3.1.5'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/f/FFTW.MPI/FFTW.MPI-3.3.8-NVHPC-22.2.eb b/f/FFTW.MPI/FFTW.MPI-3.3.8-NVHPC-22.2.eb new file mode 100644 index 00000000..6c827eef --- /dev/null +++ b/f/FFTW.MPI/FFTW.MPI-3.3.8-NVHPC-22.2.eb @@ -0,0 +1,25 @@ +# IT4Innovations 2022 +# JK + +name = 'FFTW.MPI' +version = '3.3.8' + +homepage = 'https://www.fftw.org' +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.""" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +dependencies = [ + ('FFTW', '3.3.8'), + ('OpenMPI', '4.1.2', '-CUDA-11.6.0'), +] + +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..bd31ea56 --- /dev/null +++ b/f/FFTW/FFTW-3.3.10-NVHPC-22.2-amd.eb @@ -0,0 +1,30 @@ +# 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'] + +builddependencies = [('binutils', '2.35')] + +configopts = '--enable-amd-opt' + +#runtest = 'check' + +moduleclass = 'numlib' diff --git a/f/FFTW/FFTW-3.3.8-NVHPC-22.2-amd.eb b/f/FFTW/FFTW-3.3.8-NVHPC-22.2-amd.eb new file mode 100644 index 00000000..88ada305 --- /dev/null +++ b/f/FFTW/FFTW-3.3.8-NVHPC-22.2-amd.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2022 +# JK + +name = 'FFTW' +version = '3.3.8' +local_amd_fftw_ver = '2.2' +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/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_amd_fftw_ver, + 'filename': 'amd-fftw-%s.tar.gz' % local_amd_fftw_ver, +}] +checksums = ['de9d777236fb290c335860b458131678f75aa0799c641490c644c843f0e246f8'] + +builddependencies = [('binutils', '2.35')] + +configopts = '--enable-amd-opt' + +#runtest = 'check' + +moduleclass = 'numlib' diff --git a/f/FFTW/FFTW-3.3.8-NVHPC-22.2.eb b/f/FFTW/FFTW-3.3.8-NVHPC-22.2.eb new file mode 100644 index 00000000..c8f0bae2 --- /dev/null +++ b/f/FFTW/FFTW-3.3.8-NVHPC-22.2.eb @@ -0,0 +1,28 @@ +# IT4Innovations 2022 +# JK + +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for local_computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and local_complex data.""" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# local_compilation fails when configuring with --enable-avx-128-fma, Intel local_compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/f/FoldX/FoldX-5.0.eb b/f/FoldX/FoldX-5.0.eb index 06d564f7..70f0041d 100644 --- a/f/FoldX/FoldX-5.0.eb +++ b/f/FoldX/FoldX-5.0.eb @@ -6,7 +6,7 @@ easyblock = 'Binary' name = 'FoldX' version = '5.0' -homepage = 'http://http://foldxsuite.crg.eu/' +homepage = 'https://foldxsuite.crg.eu/' description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.""" diff --git a/f/fio/fio-3.32-GCCcore-11.3.0.eb b/f/fio/fio-3.32-GCCcore-11.3.0.eb new file mode 100644 index 00000000..88c05298 --- /dev/null +++ b/f/fio/fio-3.32-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'ConfigureMake' + +name = 'fio' +version = '3.32' + +homepage = 'https://github.com/axboe/fio' + +description = 'Flexible I/O tester' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'axboe' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['409e459840912e68be487dbbda9a7a1b3f6ddf1478e3f456f278f957ce4f7b66'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['bin', 'man', 'share'], +} + +sanity_check_commands = ['fio -h'] + +moduleclass = 'tools' diff --git a/g/gh/gh-2.14.7.eb b/g/gh/gh-2.14.7.eb new file mode 100644 index 00000000..c9997ca6 --- /dev/null +++ b/g/gh/gh-2.14.7.eb @@ -0,0 +1,24 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'GoPackage' + +name = 'gh' +version = '2.14.7' + +homepage = 'https://github.com/cli/cli' +description = """gh is GitHub on the command line.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cli/cli/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a1a048714d7c7b237ea05f1fb51b3f3f4cdf90a16c60fa46f1df2eb5d96ce28d'] + +builddependencies = [ + ('Go', '1.18.1'), +] + +installopts = './cmd/%(namelower)s' + +moduleclass = 'tools' diff --git a/g/gpu_burn/gpu_burn-1.1-NVHPC-22.2-CUDA-11.6.0.eb b/g/gpu_burn/gpu_burn-1.1-NVHPC-22.2-CUDA-11.6.0.eb new file mode 100644 index 00000000..c2418d66 --- /dev/null +++ b/g/gpu_burn/gpu_burn-1.1-NVHPC-22.2-CUDA-11.6.0.eb @@ -0,0 +1,43 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'MakeCp' + +name = 'gpu_burn' +version = '1.1' +local_cudaversion = '11.6.0' +local_commit = 'c535b67' +versionsuffix = "-CUDA-%s" % local_cudaversion + +homepage = 'http://wili.cc/blog/gpu-burn.html' +description = """Multi-GPU CUDA stress test""" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} +toolchainopts = {'opt': False} + +source_urls = ['https://github.com/wilicc/gpu-burn/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = [ + '2dec738c935642395e15bd6ce71a14f8307c86661b3c8bc3826ff0272abf8f20', # gpu_burn-1.1.tar.gz +] + +dependencies = [('OpenMPI', '4.1.2', versionsuffix)] + +build_cmd = 'unset CFLAGS; make COMPUTE=8.0 CUDAPATH=${EBROOTCUDACORE}' + +files_to_copy = ['gpu_burn', 'gpu_burn-drv.o', 'compare.ptx', 'gpu_burn-drv.cpp', 'compare.cu'] + +sanity_check_paths = { + 'files': ['gpu_burn'], + 'dirs': [] +} + +modluafooter = """ +add_property('arch', 'gpu') +""" + +modextrapaths = {'PATH': '.'} + +parallel = 1 + +moduleclass = 'tools' 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..7beb7234 --- /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-unsupported --enable-shared' + +dependencies = [ + ('OpenMPI', '4.1.2', '-CUDA-11.6.0'), + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/h/HDF5/HDF5-1.13.1-gompi-2022a.eb b/h/HDF5/HDF5-1.12.2-gompi-2022a.eb similarity index 89% rename from h/HDF5/HDF5-1.13.1-gompi-2022a.eb rename to h/HDF5/HDF5-1.12.2-gompi-2022a.eb index 15bb656d..61907772 100644 --- a/h/HDF5/HDF5-1.13.1-gompi-2022a.eb +++ b/h/HDF5/HDF5-1.12.2-gompi-2022a.eb @@ -2,7 +2,7 @@ # JK name = 'HDF5' -version = '1.13.1' +version = '1.12.2' homepage = 'https://portal.hdfgroup.org/display/support' description = """HDF5 is a data model, library, and file format for storing and managing data. @@ -14,7 +14,7 @@ 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 = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] import os if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: diff --git a/h/HDF5/HDF5-1.13.1-iimpi-2022a.eb b/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb similarity index 84% rename from h/HDF5/HDF5-1.13.1-iimpi-2022a.eb rename to h/HDF5/HDF5-1.12.2-iimpi-2022a.eb index e1f9ba7f..2c68ad87 100644 --- a/h/HDF5/HDF5-1.13.1-iimpi-2022a.eb +++ b/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb @@ -2,7 +2,7 @@ # JK name = 'HDF5' -version = '1.13.1' +version = '1.12.2' homepage = 'https://portal.hdfgroup.org/display/support' description = """HDF5 is a data model, library, and file format for storing and managing data. @@ -14,9 +14,10 @@ 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 = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] import os +# core-avx2 is required due to a but in fortran compiler if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: toolchainopts = {'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'} else: diff --git a/h/HyperQueue/HyperQueue-0.12.0.eb b/h/HyperQueue/HyperQueue-0.12.0.eb new file mode 100644 index 00000000..0979ffc4 --- /dev/null +++ b/h/HyperQueue/HyperQueue-0.12.0.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'PackedBinary' + +name = 'HyperQueue' +version = '0.12.0' + +homepage = 'https://it4innovations.github.io/hyperqueue/' +description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks + and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs + and distributes them to fully utilize allocated notes. + You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/It4innovations/hyperqueue/releases/download/v%(version)s/'] +sources = ['hq-v%(version)s-linux-x64.tar.gz'] +checksums = ['43de90b23dae2ba1534f98e9aaed439fcf32cf3c5728790445894b487b49f7ec'] + +sanity_check_paths = { + 'files': ['hq'], + 'dirs': [], +} + + +moduleclass = 'devel' diff --git a/i/IMOD/IMOD-4.11.1-fosscuda-2020b.eb b/i/IMOD/IMOD-4.11.1-fosscuda-2020b.eb new file mode 100644 index 00000000..a25a7c15 --- /dev/null +++ b/i/IMOD/IMOD-4.11.1-fosscuda-2020b.eb @@ -0,0 +1,111 @@ +# IT4Innovations 2022 +# JK +# Had to fix some arch-specifying files in the source code! + +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'ConfigureMake' + +name = 'IMOD' +version = '4.11.1' + +homepage = 'https://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +# download manually from mercurial repository and create source tarball: +# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD +# get lunch ????? co to je +# cd IMOD +# hg update -r IMOD_4-11-1 +# cd .. +# tar czf IMOD-4.11.1.tar.gz IMOD +sources = [SOURCE_TAR_GZ] +patches = ['IMOD-4.11.5_fix-csvtohtml-py3.patch'] +checksums = [ + '4a2a51641a3169d1066faa8011caa90196fa1aef71da5d93cfafcf0703f8bcc6', # IMOD-4.11.1.tar.gz + '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch +] + +# can't include a valid checksum, since tarball has to be created manually +dependencies = [ + ('LibTIFF', '4.1.0'), + ('Qt5', '5.14.2'), + ('Java', '11', '', True), + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), +] + +# parallel build sometimes fails +parallel = 1 + +# replace hardcoded CUDA compute capabilitites in machines/rhlinux. +local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|' +local_cuda_replace += ' awk \'{' +local_cuda_replace += ' printf "-arch sm_"$1; ' +local_cuda_replace += ' for (i=1;i<=NF; i++){printf(" -gencode=arch=compute_%s,code=sm_%s",$i,$i) } ' +local_cuda_replace += ' }\'' +local_cudaarch_sed = 'sed -i "s/-arch sm_35/`' + local_cuda_replace + '`/g" machines/rhlinux &&' + +# modify all qmake pro files in order to pass CFLAGS +local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" + +# exports required for configure and build +local_exports = 'export QTDIR=$EBROOTQT5 &&' +local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&' +local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&' +local_exports += 'export CUDA_DIR=$CUDA_HOME &&' +# readw_or_imod.f and others with gfortran10: +# Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2)) +# => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0. +local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10 + +preconfigopts = local_exports +preconfigopts += local_cudaarch_sed +preconfigopts += local_qmake_pass_cflags + +preconfigopts += "mv pysrc/pip.py pysrc/imodpip.py &&" +preconfigopts += "sed -i 's/pip.py/imodpip.py/' pysrc/Makefile &&" +preconfigopts += "sed -i 's/from pip/from imodpip/' pysrc/* &&" + +# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. +# CFLAGs are passed with -flags. +configure_cmd = './setup ' +configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS +configure_cmd += '-i %(installdir)s ' # set installdir +configure_cmd += ' #' # avoid passing unknown arg --prefix + +prebuildopts = local_exports + +# create some missing directories required for installation process: +preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' + +# patch hardcoded /usr/bin/python to use Python included as dependency +preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " +preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " +preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && " + +modextravars = { + 'IMOD_DIR': "%(installdir)s", + 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', + 'IMOD_JAVADIR': '$JAVA_HOME', + 'FOR_DISABLE_STACK_TRACE': '1', +} +modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' +# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. +# modaliases = { +# 'subm': 'submfg $* &' +# } +sanity_check_paths = { + 'files': ['VERSION', 'bin/subm'], + 'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'], +} + +moduleclass = 'vis' diff --git a/i/IMOD/IMOD-4.11.1_RHEL7-64_CUDA8.0.eb b/i/IMOD/IMOD-4.11.1_RHEL7-64_CUDA8.0.eb new file mode 100644 index 00000000..e2ecf677 --- /dev/null +++ b/i/IMOD/IMOD-4.11.1_RHEL7-64_CUDA8.0.eb @@ -0,0 +1,28 @@ +# IT4Innovations 2022 +# JK +# --include-easyblock /apps/easybuild/it4i-easyblocks/easyblocks/i/imod.py !!! + +name = 'IMOD' +version = '4.11.1' +versionsuffix = '_RHEL7-64_CUDA8.0' + +homepage = 'http://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. +""" + +toolchain = SYSTEM + +source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/'] +sources = ['%(namelower)s_%(version)s%(versionsuffix)s.sh'] +checksums = ['8fefab2c85c85d8343005b2ac352c6b7de22e00847dc0975766b0312e44be0b8'] + +dependencies = [ + ('CUDA', '11.4.1'), + ('Java', '13.0.2'), +] + +moduleclass = 'vis' 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/l/libmad/libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch b/l/libmad/libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch deleted file mode 100644 index 0387456d..00000000 --- a/l/libmad/libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -Nru libmad-0.15.1b.orig/configure libmad-0.15.1b/configure ---- libmad-0.15.1b.orig/configure 2022-08-19 11:44:53.156998000 +0200 -+++ libmad-0.15.1b/configure 2022-08-19 11:45:31.855629909 +0200 -@@ -19099,7 +19099,6 @@ - case "$optimize" in - -O|"-O "*) - optimize="-O" -- optimize="$optimize -fforce-mem" - optimize="$optimize -fforce-addr" - : #x optimize="$optimize -finline-functions" - : #- optimize="$optimize -fstrength-reduce" -diff -Nru libmad-0.15.1b.orig/configure.ac libmad-0.15.1b/configure.ac ---- libmad-0.15.1b.orig/configure.ac 2022-08-19 11:44:53.172288000 +0200 -+++ libmad-0.15.1b/configure.ac 2022-08-19 11:45:43.617447388 +0200 -@@ -140,7 +140,6 @@ - case "$optimize" in - -O|"-O "*) - optimize="-O" -- optimize="$optimize -fforce-mem" - optimize="$optimize -fforce-addr" - : #x optimize="$optimize -finline-functions" - : #- optimize="$optimize -fstrength-reduce" diff --git a/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb b/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb index 02a6dce2..e5a93337 100644 --- a/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb +++ b/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb @@ -1,5 +1,7 @@ -# IT4Innovations 2022 -# JK +# Institution: IT4Innovations National Supercomputing Center, Czech Republic +# Author: Jakub Kropacek +# License: GPLv3 +# Year: 2022 easyblock = 'ConfigureMake' @@ -7,24 +9,24 @@ name = 'libmad' version = '0.15.1b' homepage = 'https://www.underbit.com/products/mad/' -description = """MAD is a high-quality MPEG audio decoder. It currently supports MPEG-1 and the MPEG-2 extension to lower sampling frequencies, as well as the de facto MPEG 2.5 format. All three audio layers — Layer I, Layer II, and Layer III (i.e. MP3) — are fully implemented.""" +description = """MAD is a high-quality MPEG audio decoder.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://sourceforge.net/projects/mad/files/libmad/%(version)s'] +source_urls = ['https://sourceforge.net/projects/mad/files/%(name)s/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch'] +patches = ['libmad-0.15.1b-remove-depreciated-gcc-option.patch'] checksums = [ 'bbfac3ed6bfbc2823d3775ebb931087371e142bb0e9bb1bee51a76a6e0078690', # libmad-0.15.1b.tar.gz - # libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch - 'c7dc07f0d502e31a09ddb82b30827a71d8dfacd39053ee2107d4fc4b0470d2c3', + # libmad-0.15.1b-remove-depreciated-gcc-option.patch + '8f96a23a22ba66e62f32e20064d01f4c7f6a18ba0aab85d3be9ce63794b2c678', ] builddependencies = [('binutils', '2.38')] sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['include/mad.h', 'lib/libmad.a', 'lib/libmad.la', 'lib/libmad.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib', 'lib64'] } moduleclass = 'lib' diff --git a/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb b/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb new file mode 100644 index 00000000..3ed0a87c --- /dev/null +++ b/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +# IT4Innovations 2022 +# JK +#16007 + +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.17' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb b/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb new file mode 100644 index 00000000..2bf90cc7 --- /dev/null +++ b/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('cppy', '1.2.1') +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '9.1.1'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': SOURCE_ZIP, + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('kiwisolver', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['48cf850ce14fa18067f2d9e0d646763681948487a8080ec0af2686468b4607a2'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/n/nano/nano-6.3.eb b/n/nano/nano-6.3.eb deleted file mode 100644 index ddc01bbe..00000000 --- a/n/nano/nano-6.3.eb +++ /dev/null @@ -1,25 +0,0 @@ -# IT4Innovations 2022 -# JK LK - -easyblock = 'ConfigureMake' - -name = 'nano' -version = '6.3' - -homepage = 'http://www.nano-editor.org/' -description = """Small and friendly text editor""" - -toolchain = SYSTEM - -source_urls = ['https://www.nano-editor.org/dist/v6/'] -sources = [SOURCE_TAR_GZ] -checksums = ['24c51bb2bddc682f95ae745c743cbceebd836549de66bdfd6af80a40333cc6a7'] - -dependencies = [('ncurses', '6.2')] - -sanity_check_paths = { - 'files': ['bin/nano'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/n/nano/nano-6.4-GCCcore-11.3.0.eb b/n/nano/nano-6.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000..cbfc8cfb --- /dev/null +++ b/n/nano/nano-6.4-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'ConfigureMake' + +name = 'nano' +version = '6.4' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v6/'] +sources = [SOURCE_TAR_GZ] +checksums = ['85ebd9b4dba49839821d529bea16ac1acae0c9b9db2157531e40c9dffeb1b656'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' diff --git a/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb b/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb new file mode 100644 index 00000000..77a30fa8 --- /dev/null +++ b/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb @@ -0,0 +1,64 @@ +# IT4Innovations 2022 +# JK +#16007 + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.8.0' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82'] + +builddependencies = [ + ('xxd', '8.2.4220'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GSL', '2.7'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/q/QD/QD-2.3.17-NVHPC-22.2.eb b/q/QD/QD-2.3.17-NVHPC-22.2.eb new file mode 100644 index 00000000..e1650917 --- /dev/null +++ b/q/QD/QD-2.3.17-NVHPC-22.2.eb @@ -0,0 +1,24 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'ConfigureMake' + +name = 'QD' +version = '2.3.17' +local_gitcommit = 'a5dbb61' + +homepage = 'https://github.com/scibuilder/QD' +description = "Quad Double computation package" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} + +source_urls = ['https://github.com/scibuilder/QD/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_gitcommit, 'filename': SOURCE_TAR_GZ}] +checksums = ['1e5949b7d20434193d496c28070d8f2fb6406a7688a86080dfdac57fbe730624'] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['qdmod', 'qd']], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index a2411df1..cca69df0 100644 --- a/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -40,7 +40,7 @@ checksums = [ builddependencies = [('M4', '1.4.19')] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('ELPA', '2021.11.001'), ('libxc', '5.2.3'), ] diff --git a/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index 1a9a4492..6f0919c4 100644 --- a/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -15,7 +15,6 @@ toolchain = {'name': 'intel', 'version': '2022a'} import os if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: toolchainopts = {'usempi': True, 'openmp': True, 'optarch': 'march=core-avx2', 'opt': 'O3'} -# 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 = {'usempi': True, 'openmp': True, 'opt': 'O3'} @@ -41,7 +40,7 @@ checksums = [ builddependencies = [('M4', '1.4.19')] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('ELPA', '2021.11.001'), ('libxc', '5.2.3'), ] diff --git a/r/RELION/RELION-4.0-beta-foss-2021a.eb b/r/RELION/RELION-4.0-beta-foss-2021a.eb new file mode 100644 index 00000000..7d989de7 --- /dev/null +++ b/r/RELION/RELION-4.0-beta-foss-2021a.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '4.0_beta.2022.04.20' +_commit = '9b23e50' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM). + """ + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +sources = [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCELOWER_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/3dem', + 'repo_name': '%(namelower)s', + 'commit': _commit, + 'keep_git_dir': True, + }, +}] +checksums = ['98b053a11c9ccdd144bcee5296e29cc08a05094094b27ad34536175b5a8405c2'] + +# Note: no checksum(s), due to use of `git_config` + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('ctffind', '4.1.14'), # required for most workloads + ('tbb', '2020.3'), + # optional graphics libraries: + ('Ghostscript', '9.54.0'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.2.0'), + # GUI-specific dependencies: + ('FLTK', '1.3.6'), + ('X11', '20210518'), +] + +local_disable_gui = False + +# Useful information for non-release builds +_version_maj = version.split('_')[0] +modloadmsg = "Current version pulled from commit %s from https://github.com/3dem/relion ver%s branch" % (_commit, _version_maj) + +skipsteps = ['sanitycheck'] + +moduleclass = 'bio' diff --git a/s/ScaLAPACK/ScaLAPACK-3.0-NVHPC-22.2.eb b/s/ScaLAPACK/ScaLAPACK-3.0-NVHPC-22.2.eb new file mode 100644 index 00000000..85cf67bd --- /dev/null +++ b/s/ScaLAPACK/ScaLAPACK-3.0-NVHPC-22.2.eb @@ -0,0 +1,49 @@ +# IT4Innovations 2022 +# LK JK + +easyblock = 'CMakeMake' + +name = 'ScaLAPACK' +version = '3.0' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines +redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'NVHPC', 'version': '22.2'} +toolchainopts = {'pic': True} + +# https://github.com/amd/scalapack/archive/3.0.tar.gz +source_urls = ['https://github.com/amd/scalapack/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6e6f3578f44a8e64518d276e7580530599ecfa8729f568303ed2590688e7096f'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('OpenMPI', '4.1.2', '-CUDA-11.6.0'), + ('BLIS', '3.0.1'), + ('libFLAME', '5.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis-mt.a" ' +configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DUSE_OPTIMIZED_LAPACK_BLAS=ON ' +configopts += '-DUSE_F2C=ON ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + + +moduleclass = 'numlib' diff --git a/t/Togl/Togl-2.0-GCCcore-10.2.0.eb b/t/Togl/Togl-2.0-GCCcore-11.3.0.eb similarity index 63% rename from t/Togl/Togl-2.0-GCCcore-10.2.0.eb rename to t/Togl/Togl-2.0-GCCcore-11.3.0.eb index aa385116..1a55a016 100644 --- a/t/Togl/Togl-2.0-GCCcore-10.2.0.eb +++ b/t/Togl/Togl-2.0-GCCcore-11.3.0.eb @@ -1,5 +1,5 @@ -# IT4Innovations 2021 -# JK, LK +# Last contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 easyblock = 'ConfigureMake' @@ -9,9 +9,9 @@ version = '2.0' homepage = 'https://sourceforge.net/projects/togl/' description = """A Tcl/Tk widget for OpenGL rendering.""" -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://downloads.sourceforge.net/project/togl/Togl/2.0/'] +source_urls = ['https://downloads.sourceforge.net/project/%(namelower)s/%(name)s/%(version)s/'] sources = ['%(name)s%(version)s-src.tar.gz'] patches = [ 'Togl-2.0_configure.patch', @@ -23,12 +23,12 @@ checksums = [ '05db6b3ca5139f60616d074903883a3070fcfb1eb8c965b0938779b4f9a6ec6a', # Togl-2.0_decl.patch ] -builddependencies = [('binutils', '2.35')] +builddependencies = [('binutils', '2.38')] dependencies = [ - ('Mesa', '20.2.1'), - ('Tk', '8.6.11'), - ('Tcl', '8.6.11'), + ('Mesa', '22.0.3'), + ('Tk', '8.6.12'), + ('Tcl', '8.6.12'), ] preconfigopts = 'export CFLAGS="$CFLAGS -DTOGL_USE_FONTS=0" && ' @@ -38,12 +38,12 @@ configopts += "--with-tcl=$EBROOTTCL/lib --with-tk=$EBROOTTK/lib" sanity_check_paths = { 'files': [], - 'dirs': ['include', 'lib'], + 'dirs': ['include', 'lib', 'lib/%(name)s%(version)s'], } modextrapaths = { - 'LD_LIBRARY_PATH': 'lib/Togl2.0', - 'LIBRARY_PATH': 'lib/Togl2.0', + 'LD_LIBRARY_PATH': 'lib/%(name)s%(version)s', + 'LIBRARY_PATH': 'lib/%(name)s%(version)s', } moduleclass = 'vis' diff --git a/v/VASP/VASP-5.4.1-24Jun15-intel-2020b.eb b/v/VASP/VASP-5.4.1-24Jun15-intel-2020b.eb index 5dddd20d..9ff3e23f 100644 --- a/v/VASP/VASP-5.4.1-24Jun15-intel-2020b.eb +++ b/v/VASP/VASP-5.4.1-24Jun15-intel-2020b.eb @@ -60,4 +60,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF-karolina.eb b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF-karolina.eb index 3782f463..8ac5890b 100644 --- a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF-karolina.eb +++ b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF-karolina.eb @@ -67,4 +67,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF.eb b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF.eb index 2a63da4e..1cfde837 100644 --- a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF.eb +++ b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF.eb @@ -72,4 +72,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-VASPsol-karolina.eb b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-VASPsol-karolina.eb index d2d594f3..52d1950e 100644 --- a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-VASPsol-karolina.eb +++ b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-VASPsol-karolina.eb @@ -66,4 +66,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-karolina.eb b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-karolina.eb index a59ce032..5273dcdd 100644 --- a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-karolina.eb +++ b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-karolina.eb @@ -68,4 +68,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-vtst-karolina.eb b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-vtst-karolina.eb index 92b2d92c..5a8beb9a 100644 --- a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-vtst-karolina.eb +++ b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-vtst-karolina.eb @@ -69,4 +69,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential.eb b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential.eb index 53dc2584..f1bfb396 100644 --- a/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential.eb +++ b/v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential.eb @@ -63,4 +63,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-5.4.4-intel-2020a.eb b/v/VASP/VASP-5.4.4-intel-2020a.eb index d9fd327b..1fa06228 100644 --- a/v/VASP/VASP-5.4.4-intel-2020a.eb +++ b/v/VASP/VASP-5.4.4-intel-2020a.eb @@ -60,4 +60,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential-BEEF.eb b/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential-BEEF.eb index 006764c6..2471a719 100644 --- a/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential-BEEF.eb +++ b/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential-BEEF.eb @@ -66,4 +66,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential.eb b/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential.eb index 44529135..5a883ae2 100644 --- a/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential.eb +++ b/v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential.eb @@ -59,4 +59,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential-karolina.eb b/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential-karolina.eb index f2f4e8eb..7de6c2e6 100644 --- a/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential-karolina.eb +++ b/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential-karolina.eb @@ -64,4 +64,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential.eb b/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential.eb index dfd798d1..86183a18 100644 --- a/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential.eb +++ b/v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential.eb @@ -59,4 +59,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.2.0-intel-2020b.eb b/v/VASP/VASP-6.2.0-intel-2020b.eb index 3bde1b7a..e8b9f879 100644 --- a/v/VASP/VASP-6.2.0-intel-2020b.eb +++ b/v/VASP/VASP-6.2.0-intel-2020b.eb @@ -49,4 +49,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-VASPsol-karolina.eb b/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-VASPsol-karolina.eb index 670371e0..e233da89 100644 --- a/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-VASPsol-karolina.eb +++ b/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-VASPsol-karolina.eb @@ -64,4 +64,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-karolina.eb b/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-karolina.eb index 21f92140..9cc2a3e7 100644 --- a/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-karolina.eb +++ b/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-karolina.eb @@ -64,4 +64,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential.eb b/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential.eb index b93a1ccc..e289ff12 100644 --- a/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential.eb +++ b/v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential.eb @@ -60,4 +60,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-vtst-karolina.eb b/v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-vtst-karolina.eb index 905b9b43..4540f525 100644 --- a/v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-vtst-karolina.eb +++ b/v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-vtst-karolina.eb @@ -68,4 +68,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb b/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb index 4d09619f..84b8e617 100644 --- a/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb +++ b/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb @@ -64,4 +64,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' 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 index cdc76e33..931815d2 100644 --- a/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential.eb +++ b/v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential.eb @@ -63,4 +63,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.3.1-foss-2022a.eb b/v/VASP/VASP-6.3.1-foss-2022a.eb index 615d2a7a..01839b4e 100644 --- a/v/VASP/VASP-6.3.1-foss-2022a.eb +++ b/v/VASP/VASP-6.3.1-foss-2022a.eb @@ -77,4 +77,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.3.1-intel-2021b.eb b/v/VASP/VASP-6.3.1-intel-2021b.eb index 2030fcb9..388200d4 100644 --- a/v/VASP/VASP-6.3.1-intel-2021b.eb +++ b/v/VASP/VASP-6.3.1-intel-2021b.eb @@ -75,4 +75,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch b/v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch new file mode 100644 index 00000000..e4dec17b --- /dev/null +++ b/v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch @@ -0,0 +1,65 @@ +# IT4Innovations 2022 +# JK +# +# Adjusts makefile.include for use within the EasyBuild environment. +--- arch/makefile.include.nvhpc_acc.orig 2022-09-02 21:28:42.393086358 +0200 ++++ arch/makefile.include.nvhpc_acc 2022-09-02 21:28:48.142969028 +0200 +@@ -16,8 +16,8 @@ + + # N.B.: you might need to change the cuda-version here + # to one that comes with your NVIDIA-HPC SDK +-FC = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.0 +-FCL = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.0 -c++libs ++FC = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.6 ++FCL = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.6 -c++libs + + FREE = -Mfree + +@@ -60,19 +60,19 @@ + + # Specify your NV HPC-SDK installation (mandatory) + #... first try to set it automatically +-NVROOT =$(shell which nvfortran | awk -F /compilers/bin/nvfortran '{ print $$1 }') ++#NVROOT =$(shell which nvfortran | awk -F /compilers/bin/nvfortran '{ print $$1 }') + + # If the above fails, then NVROOT needs to be set manually +-#NVHPC ?= /opt/nvidia/hpc_sdk +-#NVVERSION = 21.11 +-#NVROOT = $(NVHPC)/Linux_x86_64/$(NVVERSION) ++NVHPC ?= ${EBROOTNVHPC} ++NVVERSION = ${EBVERSIONNVHPC} ++NVROOT = $(NVHPC)/Linux_x86_64/$(NVVERSION) + + ## Improves performance when using NV HPC-SDK >=21.11 and CUDA >11.2 +-#OFLAG_IN = -fast -Mwarperf +-#SOURCE_IN := nonlr.o ++OFLAG_IN = -fast -Mwarperf ++SOURCE_IN := nonlr.o + + # Software emulation of quadruple precsion (mandatory) +-QD ?= $(NVROOT)/compilers/extras/qd ++QD ?= ${EBROOTQD} + LLIBS += -L$(QD)/lib -lqdmod -lqd + INCS += -I$(QD)/include/qd + +@@ -88,15 +88,15 @@ + LLIBS += $(SCALAPACK) $(LAPACK) $(BLAS) + + # FFTW (mandatory) +-FFTW_ROOT ?= /path/to/your/fftw/installation ++FFTW_ROOT ?= ${EBROOTFFTWMPI} + LLIBS += -L$(FFTW_ROOT)/lib -lfftw3 + INCS += -I$(FFTW_ROOT)/include + + # HDF5-support (optional but strongly recommended) +-#CPP_OPTIONS+= -DVASP_HDF5 +-#HDF5_ROOT ?= /path/to/your/hdf5/installation +-#LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran +-#INCS += -I$(HDF5_ROOT)/include ++CPP_OPTIONS+= -DVASP_HDF5 ++HDF5_ROOT ?= ${EBROOTHDF5} ++LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran ++INCS += -I$(HDF5_ROOT)/include + + # For the VASP-2-Wannier90 interface (optional) + #CPP_OPTIONS += -DVASP2WANNIER90 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..8e368966 --- /dev/null +++ b/v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0.eb @@ -0,0 +1,72 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'MakeCp' + +name = 'VASP' +version = '6.3.2' +local_cudaversion = '11.6.0' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'https://www.vasp.at' +docurls = 'https://www.vasp.at/wiki/index.php/The_VASP_Manual' +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. + +This is a GPU-enabled build. + +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 the ID of your VASP license, list of authorized users for whom you require access, +and their email which is associated with your license (use only https://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'] +patches = ['VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch'] +checksums = [ + 'f7595221b0f9236a324ea8afe170637a578cdd5a837cc7679e7f7812f6edf25a', # vasp.6.3.2.tgz + # VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch + 'ba944e61219684af0313fc32fd64c31a0b61919b8c3829ed4651c40d60675ed3', +] + +dependencies = [ + ('OpenMPI', '4.1.2', versionsuffix), + ('FFTW.MPI', '3.3.8'), + ('imkl', '2022.1.0', '', True), + ('ScaLAPACK', '3.0'), + ('HDF5', '1.12.1'), + ('QD', '2.3.17'), +] + +prebuildopts = 'cp arch/makefile.include.nvhpc_acc ./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 = 'chem' diff --git a/v/VASP/VASP-6.3.2-intel-2021b-SCPC.eb b/v/VASP/VASP-6.3.2-intel-2021b-SCPC.eb index 57f467cf..52b931d2 100644 --- a/v/VASP/VASP-6.3.2-intel-2021b-SCPC.eb +++ b/v/VASP/VASP-6.3.2-intel-2021b-SCPC.eb @@ -93,4 +93,4 @@ sanity_check_paths = { modluafooter = 'add_property("state","license")' -moduleclass = 'phys' +moduleclass = 'chem' diff --git a/v/vaspkit/vaspkit-1.3.5-foss-2022a-WIP.eb b/v/vaspkit/vaspkit-1.3.5-foss-2022a-WIP.eb new file mode 100644 index 00000000..d5bc633e --- /dev/null +++ b/v/vaspkit/vaspkit-1.3.5-foss-2022a-WIP.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'Tarball' + +name = 'vaspkit' +version = '1.3.5' + +homepage = 'https://vaspkit.com/' +docurls = 'https://vaspkit.com/' +description = """VASPKIT aims at providing a powerful and user-friendly interface to perform high + throughput analysis of various material properties from the raw calculated data using the widely-used + VASP code.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s.%(version)s.linux.x64.tar.gz'] +patches = ['vaspkit-1.3.5-fix-install.patch'] + +dependencies = [('matplotlib', '3.5.2')] + +sanity_check_paths = { + 'files': ["bin/vaspkit", "how_to_set_environment_variables"], + 'dirs': ["bin", "utilities", "examples"], +} + +modloadmsg = "Vaspkit configuration template is available at $EBROOTVASPKIT/how_to_set_environment_variables." + +moduleclass = 'tools' diff --git a/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb b/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb new file mode 100644 index 00000000..14a83465 --- /dev/null +++ b/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb @@ -0,0 +1,42 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +name = 'XCrySDen' +version = '1.6.2' + +homepage = "http://www.xcrysden.org/" +description = """ +XCrySDen is a crystalline and molecular structure visualisation program aiming +at display of isosurfaces and contours, which can be superimposed on +crystalline structures and interactively rotated and manipulated. +""" +docurls = "http://www.xcrysden.org/Documentation.html" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ["http://www.xcrysden.org/download/"] +sources = [SOURCELOWER_TAR_GZ] +patches = ['XCrySDen-1.6.2-no-bwidget-tcl-download.patch'] +checksums = [ + '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f', # xcrysden-1.6.2.tar.gz + 'e5f79c77116c6faf441d63f62bb3d22c5520163995b28e505d2168424a587bac', # XCrySDen-1.6.2-no-bwidget-tcl-download.patch +] + +dependencies = [ + ('Togl', '2.0'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('bwidget', '1.9.15'), +] + +# gcc fix by Jakob Schiotz, commit 7433b19bd05d1d511ee135a92b3ba845c89814d7 +prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" + +sanity_check_commands = [ + 'xcrysden --help', + # requires DISPLAY + #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ + # && rm output.png', +] + +moduleclass = 'vis' diff --git a/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb b/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb new file mode 100644 index 00000000..0a89de90 --- /dev/null +++ b/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb @@ -0,0 +1,40 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +name = 'XCrySDen' +version = '1.6.2' + +homepage = "http://www.xcrysden.org/" +docurls = "http://www.xcrysden.org/Documentation.html" +description = """ +XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces +and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. +It also possesses some tools for analysis of properties in reciprocal space such as interactive selection +of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ["http://www.xcrysden.org/download/"] +sources = [SOURCELOWER_TAR_GZ] +patches = ['XCrySDen-1.6.2-no-bwidget-tcl-download.patch'] +checksums = [ + '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f', # xcrysden-1.6.2.tar.gz + 'e5f79c77116c6faf441d63f62bb3d22c5520163995b28e505d2168424a587bac', # XCrySDen-1.6.2-no-bwidget-tcl-download.patch +] + +dependencies = [ + ('Togl', '2.0'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('bwidget', '1.9.15'), +] + +sanity_check_commands = [ + 'xcrysden --help', + # requires DISPLAY + #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ + # && rm output.png', +] + +moduleclass = 'vis' diff --git a/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb b/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb new file mode 100644 index 00000000..b099bb09 --- /dev/null +++ b/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +# IT4Innovations 2022 +# JK +#16007 + +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '8.2.4220' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + +moduleclass = 'tools'