{bio,lib}[foss/2022a] AlphaPulldown v0.30.7, cctbx-base v2023.5

[boegel]

(created using eb --new-pr)
requires:

• {lib}[foss/2022a] Boost.Python-NumPy v1.79.0 #18505

[boegel]

@boegelbot please test @ generoso

[boegelbot]

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=18506 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18506 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 11406

Test results coming soon (I hope)...

- notification for comment with ID 1670208467 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegel]

@boegelbot please test @ jsc-zen2

[boegelbot]

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18506 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18506 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

• exit code: 0
• output:

Submitted batch job 3105

Test results coming soon (I hope)...

- notification for comment with ID 1670219991 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/e2599cbb312fa0f516f121b4cd956013 for a full test report.

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/a8a284098a526c00e0918fad2b85b30c for a full test report.

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3116.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/f7c0b0675775fa03036dff26ffabf48e for a full test report.

[ThomasHoffmann77]

@boegel

• The bootstrap script downloads plenty of sources on the fly. cctbx_dnl_sources_2023.6.txt.gz
  To avoid this, the libtbx/configure.py could be used with the ConfigureMake easyblock. It would require a patch in order to handle "--prefix". cctbx-2023.6_configure_prefix.patch.gz
• The test step or sanity check step could contain
  cd $(mktemp -d) && libtbx.run_tests_parallel module=modulename with modulename=cctbx (and mmtbx, libtbx, smtbx, iotbx, ... if installed). Some of these tests will fail due to expecting data in modules/chem_data. Others require regression data only available in the phenix-release sources.
• As far as I understand cctbx requires the build directory at runtime (?) (see site-packages/libtbx/env_config.py line 2993)
  -> buildininstalldir = True ? or modify libtbx_env pickle
  I still cannot python -c "import cctbx" after loading the cctbx-base module.

[verdurin]

Test report by @verdurin
FAILED
Build succeeded for 10 out of 11 (2 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/fd35081c179af46081d99d3d192569e8 for a full test report.

[boegel]

@ThomasHoffmann77 Thanks a lot for the feedback, I clearly overlooked some important details...

Can you share your easyconfig file, even if it's not clean/finished, so we can look into a better approach based on both initial attempts?

[ThomasHoffmann77]

cctbx dependency is planned to be replaced by biopython: KosinskiLab/AlphaPulldown#343

[ThomasHoffmann77]

cctbx dependency is planned to be replaced by biopython: KosinskiLab/AlphaPulldown#343

see: KosinskiLab/AlphaPulldown@525feb8

[boegel]

Superseded by new PR for latest AlphaPulldown version that doesn't depend on cctbx-base anymore:

• {bio}[foss/2022a] AlphaPulldown v2.0.0b4, Uni-Core v0.0.3 #21179