Conference call notes 20221012 - easybuilders/easybuild GitHub Wiki

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Notes on the 207th EasyBuild conference call, Wednesday 12 October 2022 (08:00 UTC)

Attendees

List of attendees (11):

  • Simon Branford (Univ. of Birmingham, UK)
  • Jasper Grimm (University of York, UK)
  • Kenneth Hoste (HPC-UGent)
  • Adam Huffman (Big Data Institute, Oxford, UK)
  • Kurt Lust (UAntwerpen & LUST)
  • Sebastien Moretti (SIB, Switzerland)
  • Mikael Öhman (Chalmers University of Technology, Sweden)
  • Jurij Pečar (EMBL, Germany)
  • Jörg Saßmannshausen (Imperial College London, UK)
  • Åke Sandgren (Umeå University, Sweden)
  • Caspar van Leeuwen (SURF, Netherlands)

Agenda

  • overview of recent developments + outlook to next EasyBuild release
  • failing LAPACK tests with OpenBLAS-0.3.20 and GCC-11.3.0 (issue #16380)
  • Q&A

Recent developments

  • release timeline
    • latest release: EasyBuild v4.6.1 (12 Sept 2022)
    • ETA next release (EasyBuild v4.6.2?): by end of Oct?
  • recent changes
    • framework
      • bug fixes
        • replace use of symlink with copied files in alt_location tests (PR #4083)
          • fixes problem with installing EasyBuild on BeeGFS (see issue #4060)
        • make sure that GitPython version is a proper version before checking minimal required version (PR #4090 + PR #4091)
          • fixes hard crash with eb --check-github if GitPython==3.1.28 was installed (which has 'git' as version)
      • enhancements
        • add GITHUB_RELEASE and GITHUB_LOWER_RELEASE template constants (PR #4084)
        • make --inject-checksums inject dictionary value for checksums which maps filename to SHA256 checksum (PR #4085)
          • example diff: 
            --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.3.0.eb
@@ -16,8 +16,8 @@ source_urls = ['https://sourceware.org/pub/%(name)s/']
 sources = [SOURCE_TAR_GZ]
 patches = ['bzip2-%(version)s-pkgconfig.patch']
 checksums = [
-    'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269',  # bzip2-1.0.8.tar.gz
-    '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1',  # bzip2-1.0.8-pkgconfig.patch
+    {'bzip2-1.0.8.tar.gz': 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269'},
+    {'bzip2-1.0.8-pkgconfig.patch': '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1'},
 ]
        • add %(cuda_cc_cmake)s template (PR #4087)
      • changes
        • update to v3 of actions/checkout and actions/setup-python in CI workflows (PR #4089)
          • required because v2 of these actions use Node.js v12, which is being deprecated
    • easyblocks
      • bug fixes
        • don't install docs (to avoid trouble with Java) + add Rocky support for ABAQUS (PR #2792)
        • handle iterative builds with MakeCp easyblock (PR #2798)
        • correctly count the number of failing tests (not failing test suites) in PyTorch builds (PR #2794)
      • enhancements
        • ...
      • updates
        • update OpenFOAM easyblock to support OpenFOAM 10 + clean up variant/version checks (PR #2766)
      • changes
        • make the test output from PythonPackage less verbose by disabling default search for error patterns done by run_cmd (PR #2797)
      • new software
        • ...
    • easyconfigs
      • ~50 easyconfig PRs were merged since last conf call
      • bug fixes
        • replace HDF5 v1.13.1 with v1.12.2 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (PR #16153)
        • skip flaky test in PyTorch 1.9.0 (PR #16258)
        • add --with-versioned-syms to ncurses 6.2 and 6.3 (PR #16270)
        • fix execution permissions for bin/ngm* for NextGenMap v0.5.5 (PR #16383)
      • enhancements
        • ...
      • (noteworthy) new software
      • noteworthy software updates
        • ...
      • changes
        • update easyconfigs to use SYSTEM template constant instead of True in dependencies (PR #16386)
          • enhancement for test suite to avoid that True is introduced in PRs (PR #16384)
  • work in progress
    • framework
      • reported bugs / bug fixes
        • NameError: name 'Group' is not defined (because Rich version installed is too old) (PR #4045)
        • fix trying to generate RPATH wrappers for Clang (PR #4088)
      • enhancements
        • add support for easystack file that contains easyconfig filenames + implement parsing of configuration options (PR #4021)
        • adding support for the use of --from-pr _and other options) in easystack files (WIP PR #4057)
        • add support for --sources-url to fetch sources from additional URLs (PR #4079)
        • we should set $CUDAARCHS environment variable (plus additional cuda_cc_ template) (issue #4086)
      • changes
        • replaced distutils LooseVersion with packaging.version.parse (PR #4074)
          • alternative to PR #3794 which "vendors" LooseVersion into EasyBuild (and avoids introducing a dependency on a Python package outside of the Python standard library)
          • this change should only be done for EasyBuild v5.0 (in a dedicated 5.x branch)?
    • easyblocks
      • bug reports/fixes
        • fix installing of Clang with RPATH linking [WIP] (PR #2799)
      • enhancements
        • add support for CP2K QM/MM in GROMACS easyblock (PR #2750)
        • enhance psmpi easyblock to activate CUDA support when it is a dependency + make check for static libs in MPICH easyblock optional (PR #2787)
      • updates
        • update GAMESS-US easyblock for newer versions (PR #2791)
        • update PETSc easyblock for newer versions (PR #2796)
      • new software
        • add easyblock for CUDA compatibility libraries (PR #2764)
      • changes
        • make the check for mpirun optional in OpenMPI easyblock (PR #2788)
    • easyconfigs
      • still over 700 open easyconfig PRs...
      • bug fixes/reports
        • LAPACK tests are failing with OpenBLAS-0.3.20 and GCC-11.3.0 (issue #16380)
          • OpenBLAS easyblock should be enhanced so the test step fails if any serious problems are found
          • OpenBLAS-0.3.20-GCCcore-11.3.0.eb should be changed to disable use of -ftree-vectorize
          • are more changes required short-term?
          • should we stop trying to control the compiler options used for OpenBLAS?
          • we should also revist the ignored scipy failing tests (cfr. issue #2237)
        • FlexiBLAS cause core dump (simple test example) (issue #16387)
      • new software
      • noteworthy software updates
      • changes
        • ...

Failing LAPACK tests with OpenBLAS-0.3.20 and GCC-11.3.0

Q&A