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Merge branch '2023.06-software.eessi.io' of github-trz:EESSI/software-layer into 2023.06-grace-hopper-eb494-2023b-GROMACS-CUDA
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‎easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.0.0-2023a.yml‎

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easyconfigs:
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- Siesta-5.2.2-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/22292
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# and https://github.com/easybuilders/easybuild-easyconfigs/pull/22646
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from-commit: b212c00fdc3983678037429719f1b210cb978b42

‎easystacks/software.eessi.io/2023.06/grace/eessi-2023.06-eb-4.8.2-2022b.yml‎

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easyconfigs:
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# from here on built originally with EB 4.8.2
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# need to keep building Qt5 with 4.8.2 because more recent versions include an
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# updated easyblock for python which doesn't work correctly for Python-2.7.18
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- Qt5-5.15.7-GCCcore-12.2.0.eb
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# try to also build QE with EB 4.8.2 --> worked but it looks like we may not have
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# used the FoX library, see https://github.com/easybuilders/easybuild-easyconfigs/pull/20070/files#diff-b5e488fd7d21901d2307ed7994868853061fb5c60080e91cb186e2f937e45522
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# so we move building QE 7.2 with EB 4.9.4; that failed plus QE was not built
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# with the FoX library for any other of the supported CPU microarchitectures,
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# hence we keep building it with EB 4.8.2 (here in this easystack file)
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- QuantumESPRESSO-7.2-foss-2022b.eb

‎easystacks/software.eessi.io/2023.06/grace/eessi-2023.06-eb-4.9.4-2022b.yml‎

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easyconfigs:
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# from here on built originally with EB 4.8.2
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# make sure Python-3.10.8-GCCcore-12.2.0-bare.eb is built from correct PR/commit
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# commit 1ee17c0f7726c69e97442f53c65c5f041d65c94f from
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# https://github.com/easybuilders/easybuild-easyblocks/pull/3352 was included
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# since EB 4.9.3 --> no special treating needed
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# same applies to Python-3.10.8-GCCcore-12.2.0
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#
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# originally built with EB 4.8.2, PR 19159 was included since EB 4.9.0, PR 3492
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# was included in EB 5.0.0 -> need to keep commit for easyblock
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# - OpenBLAS-0.3.21-GCC-12.2.0.eb:
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# options:
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# # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19159
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# # required for Sapphire Rapids support
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# from-pr: 19159
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# # see https://github.com/easybuilders/easybuild-easyblocks/pull/3492
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# include-easyblocks-from-pr: 3492
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- OpenBLAS-0.3.21-GCC-12.2.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyblocks/pull/3492
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include-easyblocks-from-commit: 4cef6cea5badad0846be3f536d2af70433ff8c51
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# originally built with EB 4.8.2, PR 19940 was included since EB 4.9.1
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# - OpenMPI-4.1.4-GCC-12.2.0.eb:
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# options:
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# from-pr: 19940
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- OpenMPI-4.1.4-GCC-12.2.0.eb
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- foss-2022b.eb
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# originally built with EB 4.8.2, PR 19339 was included since EB 4.9.0
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# - HarfBuzz-5.3.1-GCCcore-12.2.0.eb:
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# options:
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# from-pr: 19339
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- HarfBuzz-5.3.1-GCCcore-12.2.0.eb
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# moved Qt5 to easystack file used with EB 4.8.2 because it needs an older
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# version of the python easyblock
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# - Qt5-5.15.7-GCCcore-12.2.0.eb
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# we try to build QE with EB 4.8.2 too, that worked; building with updated
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# easyconfigs (via EB 4.9.4) didn't work, and wasn't done for any of the other
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# supported CPU microarchitectures. Hence, we build QE with 4.8.2
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# - QuantumESPRESSO-7.2-foss-2022b.eb

‎easystacks/software.eessi.io/2023.06/grace/eessi-2023.06-eb-4.9.4-2023a.yml‎

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- PostgreSQL-16.1-GCCcore-12.3.0.eb
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- ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
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- GDAL-3.7.1-foss-2023a.eb
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- ncdu-1.18-GCC-12.3.0.eb
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- SAMtools-1.18-GCC-12.3.0.eb
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- R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
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options:
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# (additional extensions have been added)
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21948
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from-commit: f9cfe6ac7d9019970c2be3e8b09db4d846cf005a
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- ipympl-0.9.3-gfbf-2023a.eb
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- ESPResSo-4.2.2-foss-2023a.eb
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- GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
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- WhatsHap-2.2-foss-2023a.eb
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- BLAST+-2.14.1-gompi-2023a.eb
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- Valgrind-3.21.0-gompi-2023a.eb
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- OrthoFinder-2.5.5-foss-2023a.eb
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- OpenFOAM-10-foss-2023a.eb
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- OpenFOAM-11-foss-2023a.eb
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- BCFtools-1.18-GCC-12.3.0.eb
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- BWA-0.7.18-GCCcore-12.3.0.eb
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- CapnProto-1.0.1-GCCcore-12.3.0.eb
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- DendroPy-4.6.1-GCCcore-12.3.0.eb
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- DIAMOND-2.1.8-GCC-12.3.0.eb
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- FastME-2.1.6.3-GCC-12.3.0.eb
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- fastp-0.23.4-GCC-12.3.0.eb
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- HMMER-3.4-gompi-2023a.eb
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- IQ-TREE-2.3.5-gompi-2023a.eb
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- KronaTools-2.8.1-GCCcore-12.3.0.eb
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- LSD2-2.4.1-GCCcore-12.3.0.eb
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- MAFFT-7.520-GCC-12.3.0-with-extensions.eb
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- ncbi-vdb-3.0.10-gompi-2023a.eb
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- MetalWalls-21.06.1-foss-2023a.eb
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- QuantumESPRESSO-7.3.1-foss-2023a.eb
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- CP2K-2023.1-foss-2023a.eb
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- amdahl-0.3.1-gompi-2023a.eb
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- LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb
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- numba-0.58.1-foss-2023a.eb
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- librosa-0.10.1-foss-2023a.eb
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- xarray-2023.9.0-gfbf-2023a.eb
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- SciTools-Iris-3.9.0-foss-2023a.eb
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- OpenFOAM-v2312-foss-2023a.eb
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- BioPerl-1.7.8-GCCcore-12.3.0.eb
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- grpcio-1.57.0-GCCcore-12.3.0.eb
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- orjson-3.9.15-GCCcore-12.3.0.eb
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- wradlib-2.0.3-foss-2023a.eb
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- MBX-1.1.0-foss-2023a.eb
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- Transrate-1.0.3-GCC-12.3.0.eb
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- Critic2-1.2-foss-2023a.eb
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- LRBinner-0.1-foss-2023a.eb
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- Redland-1.0.17-GCC-12.3.0.eb
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- ccache-4.9-GCCcore-12.3.0.eb
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- GDB-13.2-GCCcore-12.3.0.eb
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- tmux-3.3a-GCCcore-12.3.0.eb
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- Vim-9.1.0004-GCCcore-12.3.0.eb
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- gmsh-4.12.2-foss-2023a.eb
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- basemap-1.3.9-foss-2023a.eb
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- geopandas-0.14.2-foss-2023a.eb
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- R-bundle-CRAN-2023.12-foss-2023a.eb
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- archspec-0.2.1-GCCcore-12.3.0.eb
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- ROOT-6.30.06-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21526
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from-commit: 6cbfbd7d7a55dc7243f46d0beea510278f4718df
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# see https://github.com/easybuilders/easybuild-easyblocks/pull/3467
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include-easyblocks-from-commit: c3aebe1f133d064a228c5d6c282e898b83d74601
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- waLBerla-6.1-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21600
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from-commit: 9b12318bcff1749781d9eb71c23e21bc3a79ed01
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- mpl-ascii-0.10.0-gfbf-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21679
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from-commit: 7106f63160b1418d605882dd02ba151d099300bd
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- jedi-0.19.0-GCCcore-12.3.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21650
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from-commit: 109998f6adcda7efb4174b1e5f73b41ee82d1f13
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- Solids4foam-2.1-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21606
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from-commit: 63562c58acf1be64407192b6862c3bd80253d2e0
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- Cassiopeia-2.0.0-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21657
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from-commit: 7f1f0e60487e7e1fcb5c4e6bc4fbc4f89994e3fd
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- LightGBM-4.5.0-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21699
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from-commit: e3407bd127d248c08960f6b09c973da0fdecc2c3
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- OpenFOAM-v2406-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyblocks/pull/3519
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include-easyblocks-from-commit: e4a3ff1932350d575dffc7597435609fad6dd691
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- Paraver-4.11.4-GCC-12.3.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/20230
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from-commit: 91c8df6b4c0810061e9f325427c9c79e961bc4b0
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- Tombo-1.5.1-foss-2023a.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21925
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from-commit: 522ca010ab11949ab9594037f72b975cf1cd0d33
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- elfx86exts-0.6.2-GCC-12.3.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/22145
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from-commit: 31478e5c9869de3add74d0a02dd5df01ea65b21e
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- archspec-0.2.5-GCCcore-12.3.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/22235
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from-commit: 01dd97ea62fe4d7d0df040ede3af03eb2f1b8641

‎install_apptainer_ubuntu.sh‎

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set -e
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# see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
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sudo apt-get install alien
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alien --version
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epel_subdir="pub/epel/8"
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apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
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curl -OL https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/${apptainer_rpm}
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sudo alien -d ${apptainer_rpm}
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sudo apt install ./apptainer*.deb
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# No unpriviledged user name spaces in Ubuntu 23.10+
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ubuntu_version=$(lsb_release -r | awk '{print $2}')
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if [[ $(echo -e "$ubuntu_version\n23.10" | sort -V | head -n 1) == "23.10" ]]; then
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sudo tee /etc/apparmor.d/apptainer << 'EOF'
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# Permit unprivileged user namespace creation for apptainer starter
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abi <abi/4.0>,
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include <tunables/global>
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profile apptainer /usr/libexec/apptainer/bin/starter{,-suid}
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flags=(unconfined) {
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userns,
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# Site-specific additions and overrides. See local/README for details.
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include if exists <local/apptainer>
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}
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EOF
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sudo systemctl reload apparmor
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fi
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sudo apt update
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sudo apt install -y software-properties-common
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sudo add-apt-repository -y ppa:apptainer/ppa
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sudo apt update
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sudo apt install -y apptainer-suid
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apptainer --version
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# also check whether 'singularity' command is still provided by Apptainer installation
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singularity --version

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