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Merge pull request #13343 from easybuilders/4.4.x
release EasyBuild v4.4.1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| easyblock = 'ConfigureMake' | ||
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| name = 'ABINIT' | ||
| version = '9.4.1' | ||
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| homepage = 'https://www.abinit.org/' | ||
| description = """ABINIT is a package whose main program allows one to find the total energy, | ||
| charge density and electronic structure of systems made of electrons and nuclei (molecules | ||
| and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a | ||
| planewave or wavelet basis.""" | ||
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| toolchain = {'name': 'foss', 'version': '2020b'} | ||
| toolchainopts = {'usempi': True, 'pic': True} | ||
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| source_urls = ['https://www.abinit.org/sites/default/files/packages/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['ec74133ef9d247cb6ad44c205675694919cf36d7f1682a9b85cae8bdecdc22a8'] | ||
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| builddependencies = [ | ||
| ('Python', '3.8.6'), | ||
| ] | ||
| dependencies = [ | ||
| ('libxc', '4.3.4'), | ||
| ('netCDF', '4.7.4'), | ||
| ('netCDF-Fortran', '4.5.3'), | ||
| ('HDF5', '1.10.7'), | ||
| ('Wannier90', '3.1.0'), | ||
| ] | ||
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| # Needed due to changes in GCC10. | ||
| configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' | ||
| configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' | ||
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| # Ensure MPI | ||
| configopts += '--with-mpi="yes" --enable-openmp="no" ' | ||
| # configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' | ||
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| # BLAS/Lapack from OpenBLAS | ||
| configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' | ||
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| # FFTW | ||
| configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' | ||
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| # libxc support | ||
| configopts += '--with-libxc=${EBROOTLIBXC} ' | ||
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| # hdf5/netcdf4 support | ||
| configopts += '--with-netcdf="${EBROOTNETCDF}" ' | ||
| configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' | ||
| configopts += '--with-hdf5="${EBROOTHDF5}" ' | ||
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| # Wannier90 | ||
| configopts += '--with-wannier90="${EBROOTWANNIER90}" ' | ||
| preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' | ||
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| # 'make check' is just executing some basic unit tests. | ||
| # Also running 'make tests_v1' to have some basic validation | ||
| runtest = "check && make test_v1" | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], | ||
| 'dirs': ['lib/pkgconfig'], | ||
| } | ||
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| moduleclass = 'chem' |
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51 changes: 51 additions & 0 deletions
51
easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| # Author: Jasper Grimm (UoY) | ||
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| easyblock = 'Tarball' | ||
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| name = 'AMPHORA2' | ||
| version = '20190730' | ||
| local_commit = '9fb9ce8' | ||
| local_raxmlsuffix = '-pthreads-avx2' | ||
| local_javasuffix = '-Java-%(javaver)s' | ||
| versionsuffix = local_javasuffix + local_raxmlsuffix | ||
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| homepage = 'https://github.com/wu-lab-uva/AMPHORA2' | ||
| description = "An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences." | ||
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| toolchain = {'name': 'gompi', 'version': '2020b'} | ||
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| github_account = 'wu-lab-uva' | ||
| source_urls = [GITHUB_SOURCE] | ||
| sources = ['%s.tar.gz' % local_commit] | ||
| checksums = ['2d361fcc2b800c3daaf25692988af6105669cba2ff513aba82f36089beb2839f'] | ||
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| dependencies = [ | ||
| ('Perl', '5.32.0'), | ||
| ('Java', '13', '', True), | ||
| ('BioPerl', '1.7.8'), | ||
| ('HMMER', '3.3.2'), | ||
| ('EMBOSS', '6.6.0', local_javasuffix), | ||
| ('RAxML', '8.2.12', local_raxmlsuffix), | ||
| ] | ||
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| local_scripts = ['%s.pl' % x for x in ['MarkerAlignTrim', 'MarkerScanner', 'Phylotyping']] | ||
| fix_perl_shebang_for = ['Scripts/*.pl'] | ||
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| # Exit with code 0 when running -Help | ||
| preinstall_cmd = "sed -i 's|die $usage if $help|if ($help) {print $usage; exit 0}|g' Scripts/*.pl && " | ||
| # Fix RAxML binary name | ||
| preinstall_cmd += "sed -i 's|raxmlHPC-PTHREADS|raxmlHPC%s|g' Scripts/Phylotyping.pl" % local_raxmlsuffix.upper() | ||
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| sanity_check_paths = { | ||
| 'files': ['Scripts/%s' % x for x in local_scripts], | ||
| 'dirs': [], | ||
| } | ||
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| sanity_check_commands = ["%s -Help" % x for x in local_scripts] | ||
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| modextrapaths = { | ||
| 'AMPHORA2_home': '', | ||
| 'PATH': 'Scripts', | ||
| } | ||
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| moduleclass = 'bio' |
42 changes: 42 additions & 0 deletions
42
easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| ## | ||
| # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild | ||
| # | ||
| # Authors:: Jorgen Nordmoen <jorgen.nordmoen@usit.uio.no> | ||
| # License:: GPLv2 or later, MIT, three-clause BSD. | ||
| # $Id$ | ||
| ## | ||
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| name = 'AOMP' | ||
| version = '13.0-2' | ||
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| homepage = 'https://github.com/ROCm-Developer-Tools/aomp' | ||
| description = "AMD fork of LLVM, setup for OpenMP offloading to Accelerators" | ||
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| toolchain = {'name': 'GCCcore', 'version': '10.2.0'} | ||
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| source_urls = ['https://github.com/ROCm-Developer-Tools/aomp/releases/download/rel_%(version)s/'] | ||
| sources = ['aomp-%(version)s.tar.gz'] | ||
| patches = ['AOMP-%(version)s_remove_hardcoded_paths.patch'] | ||
| checksums = [ | ||
| # aomp-13.0-2.tar.gz: | ||
| '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', | ||
| # AOMP-13.0-2_remove_hardcoded_paths.patch: | ||
| 'ec41ffcec63d079b6a73c93bea29e0b8d77ca7b059725aa1d47c334f7e476ff0', | ||
| ] | ||
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| builddependencies = [ | ||
| ('CMake', '3.18.4'), | ||
| ('Perl', '5.32.0'), | ||
| ('Python', '3.8.6'), | ||
| ('elfutils', '0.183'), | ||
| ('pkg-config', '0.29.2'), | ||
| ] | ||
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| dependencies = [ | ||
| ('binutils', '2.35'), | ||
| ('libffi', '3.3'), | ||
| ('ncurses', '6.2'), | ||
| ('numactl', '2.0.13'), | ||
| ] | ||
|
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| moduleclass = 'compiler' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| ## | ||
| # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild | ||
| # | ||
| # Authors:: Jorgen Nordmoen <jorgen.nordmoen@usit.uio.no> | ||
| # License:: GPLv2 or later, MIT, three-clause BSD. | ||
| # $Id$ | ||
| ## | ||
|
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| name = 'AOMP' | ||
| version = '13.0-2' | ||
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| homepage = 'https://github.com/ROCm-Developer-Tools/aomp' | ||
| description = "AMD fork of LLVM, setup for OpenMP offloading to Accelerators" | ||
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| toolchain = {'name': 'gcccuda', 'version': '2020a'} | ||
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| source_urls = ['https://github.com/ROCm-Developer-Tools/aomp/releases/download/rel_%(version)s/'] | ||
| sources = ['aomp-%(version)s.tar.gz'] | ||
| patches = ['AOMP-%(version)s_remove_hardcoded_paths.patch'] | ||
| checksums = [ | ||
| # aomp-13.0-2.tar.gz: | ||
| '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', | ||
| # AOMP-13.0-2_remove_hardcoded_paths.patch: | ||
| 'ec41ffcec63d079b6a73c93bea29e0b8d77ca7b059725aa1d47c334f7e476ff0', | ||
| ] | ||
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| builddependencies = [ | ||
| ('CMake', '3.16.4'), | ||
| ('Perl', '5.30.2'), | ||
| ('Python', '3.8.2'), | ||
| ('elfutils', '0.182'), | ||
| ('pkg-config', '0.29.2'), | ||
| ] | ||
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| dependencies = [ | ||
| ('binutils', '2.34'), | ||
| ('libffi', '3.3'), | ||
| ('ncurses', '6.2'), | ||
| ('numactl', '2.0.13'), | ||
| ] | ||
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| moduleclass = 'compiler' |
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