use --from-commit instead of --from-pr for installations done with EasyBuild v4.9.1

[boegel]

This doesn't affect the ingested installations at all, but going forward we should use --from-commit instead of --from-pr, and simply use the last commit in the (merged) PR

[eessi-bot]

Instance eessi-bot-mc-aws is configured to build:

• arch x86_64/generic for repo eessi-hpc.org-2023.06-compat
• arch x86_64/generic for repo eessi-hpc.org-2023.06-software
• arch x86_64/generic for repo eessi.io-2023.06-compat
• arch x86_64/generic for repo eessi.io-2023.06-software
• arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-compat
• arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-software
• arch x86_64/intel/haswell for repo eessi.io-2023.06-compat
• arch x86_64/intel/haswell for repo eessi.io-2023.06-software
• arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-compat
• arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-software
• arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-compat
• arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-software
• arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-compat
• arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-software
• arch x86_64/amd/zen2 for repo eessi.io-2023.06-compat
• arch x86_64/amd/zen2 for repo eessi.io-2023.06-software
• arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-compat
• arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-software
• arch x86_64/amd/zen3 for repo eessi.io-2023.06-compat
• arch x86_64/amd/zen3 for repo eessi.io-2023.06-software
• arch aarch64/generic for repo eessi-hpc.org-2023.06-compat
• arch aarch64/generic for repo eessi-hpc.org-2023.06-software
• arch aarch64/generic for repo eessi.io-2023.06-compat
• arch aarch64/generic for repo eessi.io-2023.06-software
• arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-compat
• arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-software
• arch aarch64/neoverse_n1 for repo eessi.io-2023.06-compat
• arch aarch64/neoverse_n1 for repo eessi.io-2023.06-software
• arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-compat
• arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-software
• arch aarch64/neoverse_v1 for repo eessi.io-2023.06-compat
• arch aarch64/neoverse_v1 for repo eessi.io-2023.06-software

[eessi-bot]

Instance eessi-bot-mc-azure is configured to build:

• arch x86_64/amd/zen4 for repo eessi-hpc.org-2023.06-compat
• arch x86_64/amd/zen4 for repo eessi-hpc.org-2023.06-software
• arch x86_64/amd/zen4 for repo eessi.io-2023.06-compat
• arch x86_64/amd/zen4 for repo eessi.io-2023.06-software

[bedroge]

@boegel I'm not entirely sure how this works, but I'm wondering if we shouldn't use the merge commit itself instead of the last commit in the PR? For instance, with the one for Bioconductor you're now using the last commit which actually synced with develop, and using --copy-ec results in downloading the following files:

AMGX-2.4.0_external-thrust.patch
AMGX-2.4.0_fix-openmp-linking.patch
AMGX-2.4.0-foss-2023a-CUDA-12.1.1.eb
arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb
arrow-R-14.0.1-foss-2023a-R-4.3.2.eb
astropy-5.1.1-intel-2022a.eb
attrdict3-2.0.2-GCCcore-12.3.0.eb
BCFtools-1.19-GCC-13.2.0.eb
CCCL-2.3.0-GCCcore-12.3.0-CUDA-12.1.1.eb
CGAL-5.6.1-GCCcore-13.2.0.eb
cmph-2.0-GCCcore-12.3.0.eb
dm-haiku-0.0.9-foss-2022a-CUDA-11.7.0.eb
dotNET-Core-6.0.420.eb
dotNET-Core-6.0.eb
dotNET-Core-8.0.203.eb
dotNET-Core-8.0.eb
easyconfigs.py
FDMNES-2024-02-29-gomkl-2023a.eb
Giza-1.4.1-GCCcore-13.2.0.eb
gmsh-4.12.2-foss-2023a.eb
h5py-3.11.0-foss-2023b.eb
HTSlib-1.19.1-GCC-13.2.0.eb
ICON-2024.01-foss-2023a.eb
ICON-2024.01_lzacc-undefined.patch
LAPACK-3.12.0-GCC-13.2.0.eb
libfyaml-0.9-GCCcore-12.3.0.eb
libmad-0.15.1b-GCCcore-12.3.0.eb
MATSim-15.0-GCCcore-12.3.0-Java-17.eb
MATSim-15.0-Java-17.eb
MetaMorpheus-1.0.5.eb
METIS-5.1.0-GCCcore-13.2.0.eb
MUMPS-5.6.1-gomkl-2023a-metis-seq.eb
MUMPS-5.6.2_shared-pord.patch
nanomath-1.3.0-foss-2022b.eb
Optax-0.1.7-foss-2022a-CUDA-11.7.0.eb
orthAgogue-20141105-gompi-2023a.eb
PhyML-3.3.20220408-foss-2023a.eb
PhyML-3.3.20220408_mcmc.c-fix.patch
plc-3.10-intel-2022a.eb
plyfile-1.0.3_use_pdm_backend.patch
PnetCDF-1.13.0-iimpi-2023a.eb
POV-Ray-3.7.0.10-GCC-12.3.0.eb
Pysam-0.22.0-GCC-13.2.0.eb
PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb
PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb
R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb
Rhdf5lib-1.20.0_fix_hardcoded_path_to_mv.patch
SAMtools-1.19.2-GCC-13.2.0.eb
SCOTCH-7.0.4-gompi-2023b.eb
SentencePiece-0.2.0-GCC-12.3.0.eb
SoX-14.4.2-GCCcore-12.3.0.eb
Spack-0.21.2.eb
STAR-2.7.11b-GCC-13.2.0.eb
tbb-2020.3-GCCcore-12.3.0.eb
tiktoken-0.6.0-GCCcore-12.3.0.eb
torchaudio-2.1.2_transform_test_tol.patch
torchaudio-2.1.2_use-external-sox.patch
torch-ignite-0.4.13_dont_destroy_python_path_in_test_launcher.patch
torchtext-0.16.2_download-to-project-root.patch
torchvision-0.16.2_ffmpeg-6.0-fix.patch
torchvision-0.16.2_quantized_tol.patch
VAMPIRE-ASM-6.0-foss-2022b.eb
WGDgc-1.3-foss-2023a-R-4.3.2.eb
xxd-9.1.0307-GCCcore-13.2.0.eb
YACS-0.1.8-GCCcore-12.3.0.eb

The older Bioconductor easyconfigs, which are also updated by that same PR, are not included, is that expected? In other words, what would have happened if our software layer PR would have needed one of those?

The merge commit itself (f8fa6c791dc009696b6cd0280d549163c5b65e38) does return the following files (which is mor ein line with what I expected):

R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb
R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb
R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb
R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb

If it does not really matter for the builds themselves, I'm fine with either approach, just wondering how this works.

[trz42]

In NorESSI#344, I first used the merge commit in easybuilders/easybuild-easyconfigs#20379. This failed, because some easyconfig was not available. I then used the last commit before the merge commit. Still the builds failed (maybe for another reason ... have to check).

Edit: Now it fails building the extension Rhdf5lib so probably unrelated to which commit is used.

[boegel]

• easyconfig files for dependencies not found when using --from-commit easybuilders/easybuild-framework#4540

[ocaisa]

I think we have to just enforce this going forward right? We can't really tweak older easystack files as, for reproducibility, they are tied to an EasyBuild release...and --from-commit didn't work properly until 4.9.2 .

We can easily add a CI check to ensure that from-pr is not used going forward (empty the yaml file of comments and then just grep the remainder for the from-pr string)