Conference call notes 20240117 - easybuilders/easybuild GitHub Wiki

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Notes on the 238th EasyBuild conference call, Wednesday 17 Jan 2024 (16:00 UTC)

Attendees

List of attendees (19):

Sebastian Achilles (JSC, Germany)
Simon Branford (Univ. of Birmingham, UK)
Alex Domingo (Vrije Universiteit Brussel, Belgium)
Markus Geimer (JSC, Germany)
Jasper Grimm (University of York, UK)
Stefan Harst (Univ. of Oldenburg)
Thomas Hayward-Schneider (Max Planck Institute for Plasma Physics, Germany)
Kenneth Hoste (HPC-UGent, Belgium)
Chia-Jung Hsu (Chalmers University of Technology, Sweden)
Adam Huffman (Big Data Institute, Oxford, UK)
Kurt Lust (UAntwerpen, Belgium + LUMI User Support Team)
Sam Moors (Vrije Universiteit Brussel, Belgium)
Sébastien Moretti (SIB, Switzerland)
Mikael Öhman (Chalmers University of Technology, Sweden)
Bart Oldeman (The Alliance, Canada)
Jure Pečar (EMBL, Heidelberg, Germany)
Jörg Saßmannshausen (Imperial College London, UK)
Alexandre Strube (JSC, Germany)
Lars Viklund (Umeå University, Sweden)

Agenda

overview of recent developments
quick status update on development for EasyBuild 5.0
Clang-based toolchains;
supporting OSs with OpenSSL 3.x (like RHEL9);
Q&A

Recent developments

latest EasyBuild release: 4.9.0 (30 Dec 2023)
- see release notes + highlights
next EasyBuild release: hopefully EasyBuild v5.0.0
- there will only be an EasyBuild v4.9.1 if there's a clear need for it, or if getting EasyBuild 5.0 is taking too long (way beyond 8 weeks v4.9.0 release)
ETA for EasyBuild 5.0 release: hopefully first EasyBuild release of 2024
- started doing short sprint meetings, each Monday at 15:00 CE(S)T to set next 5 goals to tackle that week
- monthly sync meetings every 1st Wed of the month at 14:00 CE(S)T: next today Wed 3 Jan'24 at 14:00 CET
- see also https://hackmd.io/tZtz6vMmRfGL6N9Rf__OEA
recent changes
- docs (merged PRs)
  - ...
- framework (merged PRs)
  - bug fixes
    - ...
  - enhancements
    - use --all option with EnvironmentModules v4.6+ to get available hidden modules (PR #4417)
    - add support for appending to path environment variables via modextrapaths_append (and add corresponding allow_append_abs_path) (PR #4436)
    - Add script for updating local git repos with develop branch (PR #4438)
  - changes
    - ...
  - code cleanup
    - ...
  - EasyBuild 5.0 (to 5.0.x branch)
    - bug fixes
      - ...
    - changes
      - switch to run_shell_cmd in scripts (PR #4422), in easybuild.* modules (PR #4430), and framework test suite (PRs #4427, #4428, #4431, #4432, )
      - bump minimum required Lmod to 8.0.0 (PR #4424)
    - enhancements
      - implement support for 'stream_output' option in run_shell_cmd (PR #4423)
      - detect Fortran .mod files in GCCcore installations (PR #4389)
- easyblocks (merged PRs)
  - bug fixes
    - set $BGW_TEST_MPI_NPROCS in BerkeleyGW test step (PR #2950)
    - fix ELPA preprocessor flag for QuantumESPRESSO >= 7 (PR #3063)
    - fix link order in PETSc easyblock for SCOTCH >= 7.x (PR #3069)
    - add Clang opt binary to RPATH wrapper dir (PR #3076)
  - enhancements
    - add pip_verbose option to PythonPackage and set it to True in PyTorch easyblock, to show build output when using pip (PR #3065)
  - updates
    - update WIEN2k easyblock for v23.2 (PR #3035)
  - changes
    - ...
  - new easyblocks
    - new easyblock for DualSPHysics (PR #3050)
  - EasyBuild 5.0 (to 5.0.x branch)
    - convert all generic easyblocks to run_shell_cmd (PR #3046)
    - disable check for .mod files in Clang, AOCC, AOMP, and CPLEX easyblocks (PR #3067)
    - remove custom easyblock for EggLib (no longer used) (PR #3066)
- easyconfigs (merged PRs)
  - ~over 125 easyconfig PRs were merged since last conf call
    - and over 175 old easyconfig PRs were closed as is, mostly because they were for easyconfigs using an unsupported or deprecated toolchains (see toolchain support policy)
  - bug fixes
    - add patch to fix flaky scipy build in SciPy-bundle v2023.11 (PR #19481)
    - fix LAPACK test failures in OpenBLAS 0.3.23/24 (PR #19495)
    - add patches for PyTorch v2.1.2 with foss/2022a to fix test failures on non-x86 platforms (PRs #19571, #19572, #19573)
    - use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 (PR #19584)
  - enhancements
    - ...
  - (noteworthy) new software
    - ...
  - noteworthy software updates
    - ...
  - changes
    - ...
  - EasyBuild 5.0 (to 5.0.x branch)
    - ...
work-in-progress
- docs (open PRs + issues)
  - project board to perform yearly review cycle of all documentation pages: https://github.com/orgs/easybuilders/projects/17/views/1
- framework (open PRs + issues)
  - reported bugs / bug fixes
    - Run unit tests on an updated version of Modules 4 (PR #4415)
    - don't hardcode /bin/bash in eb script, RPATH wrapper script, and run_shell_cmd (PR #4441)
      - use /usr/bin/env bash instead in eb + RPATH wrapper script
      - resolve path to bash via which in run_shell_cmd
      - Are there any use cases where you would want/need to not use the first bash in $PATH, but another bash?
        
        Do we need to also add a configuration option to specify the path to bash to use?
  - enhancements
    - improve output produced by --check-github (PR #4437)
    - show error when multiple PR options are passed (PR #4440)
  - changes
    - drop load storm safe guard for Environment Modules v4.2.4+ (PR #4373)
    - use more performant and concise dict construction (PR #4410)
    - clean up & speed up environment checks (PR #4409)
  - EasyBuild 5.0 (to 5.0.x branch)
    - deprecate failure to resolve a template value (PR #3285)
    - change tar command used in get_source_tarball_from_git to get reproducible tarballs (PR #4248)
    - replace parallel easyconfig parameter by maxparallel (PR #4398)
    - rename unclear run methods to install extensions (PR #4400)
      - needs more work, current approach of deprecating run methods & co is not working as intended...
    - bump minimum required Tmod (4.x) to 4.3.0 (PR #4425)
      - requires that PR #4415 is merged first
    - deprecate run_cmd and run_cmd_qa & co, move them to easybuild._deprecated module (WIP) (PR #4433)
      - requires that implementation of run_shell_cmd is complete, incl. support for asynchronously running commands and running interactive shell commands (WIP)
    - create lib/lib64 symlink before running postinstallcmds (PR #4435)
    - deprecate EnvironmentModulesC and EnvironmentModulesTcl (PR #4439)
    - support uninstalling software + module (issue #590)
    - clean up SLURM/Batchsystem environment before doing builds (issue #4434)
      - unset all $SLURM_* environment variables to avoid trouble with srun/MPI
- easyblocks (open PRs + issues)
  - bug reports/fixes
    - fix extension filter for Perl packages (PR #2699)
      - easyconfigs PR #18789 is a big step towards merging this, but there are other easyconfigs that needs to be tested first, like XML-LibXML, worker, GD, ...
    - implementation of CMake policy error for Python (PR #3055)
      - see also this issue comment
      - ready for testing
      - will only be included in EasyBuild v5.0, since it's a change in behaviour (but should be harmless, right CMake?)
    - pick Tcl/Tk lib directory correctly in R easyblock, may be either lib or lib64 (PR #3072)
    - use (=|:=) in regex because OpenFOAM rule files use := instead of = since v2212 (PR #3073)
    - update PyTorch easyblock to avoid configure warnings by disabling some options (PR #3070)
  - enhancements
    - update KOKKOS_CPU_MAPPING for AArch64 in LAMMPS (PR #3036)
    - refactor GAMESS-US easyblock to directly write install.info (v2) (PR #3047)
    - Support GROMACS builds with SYCL (AdaptiveCpp implementation) (PR #3077)
  - updates
    - update Clang-AOMP easyblock for ROCm 5.6 (PR #2958)
  - new easyblocks
    - ...
  - changes
    - ...
  - EasyBuild 5.0 (to 5.0.x branch)
    - enable download_dep_fail, use_pip, sanity_pip_check by default in PythonPackage easyblock (PR #3022)
      - needs some tests to make sure easyconfigs that are currently not setting use_pip yet are still working
        
        that includes PyTorch; see also PR #3079 to disable use_pip for PyTorch < v2.1)
      - testing easyconfig that currently do not set use_pip yet has revealed some problems
        
        any easyconfigs using CMakePythonPackage and using use_pip = True are broken, because PythonPackage changes installopts easyconfig parameter like it own's the place => being fixed in PR #3080
      - follow-up is needed in easyconfigs, to:
        
        clean up easyconfigs in 5.0.x branch that now set use_pip & co to True (see easyconfigs PR #19265)
        
        explicitly set use_pip & co to False in (non-archived) easyconfig that currently don't specify them at all and can't use pip for some reason (which should be a minimal set of easyconfigs)
    - update ConfigureMake easyblock to error out on unknown configure args (PR #3025 + #3026)
    - update PythonPackage easyblock to build wheel first when installing Python package with pip (PoC PR #3068](https://github.com/easybuilders/easybuild-easyblocks/pull/3068))
- easyconfigs (open PRs + issues)
  - bug fixes/reports
    - ...
  - enhancements
    - ...
  - new software
    - ...
  - noteworthy software updates
    - Qt5 v5.15.11 w/ GCCcore/13.2.0 (for foss/2023b) (PR #19320)
  - changes
    - ...
  - EasyBuild 5.0 (to 5.0.x branch)
    - clean up easyconfigs that explicitly set use_pip, sanity_pip_check and download_dep_fail (PR #19265)
  - closed PRs
    - ...

Clang-based toolchains

raised by Thomas, cfr. discussion in Slack
flang support in Clang makes it more interesting to have a Clang-based toolchain
two variants of Flang
- LLVM-based flang-new (previously F18)
  - this is what you get when installing Clang >= 15.x with EasyBuild (binary named flang-new)
- classic Fortran Clang compiler
  - based on PGI compilers
  - used by AMD (AOMP (CPU+GPU) + AOCC (CPU-only) + ROCm compilers (amd-clang, etc.)), Arm, etc. compiler suite
  - AOMP's Fortran compiler also included OpenMP offloading
  - current Clang-AOMP easyconfig PR produces flang binary (not flang-new)
- Fortran mod files produced by these are not compatible
- completely different compiler options
Fortran compiler in Intel oneAPI, NVHPC are a totally different frontend (with LLVM backend)
Markus has been playing with Clang-based toolchains for a while, but only for C/C++
current toolchains/compiler/clang.py can be updated to also support Fortran compiler (flang-new)
additional compiler support can be implemented in additional classes for AOMP, AOCC, etc so they can be used in EasyBuild toolchains
combining Clang (Fortran) compiler and Autotools/CMake can be a hassle...
battle plan
- foss/2023b -> replace with GCC with Clang with flang-new included
  - naming? cofbf
  - version: 2023b
- foss/2023b -> replace GCC with AOMP or ROCm compiler
  - aomp-ofbf
  - aocc-ofbf
  - rocm-ofbf
--include-toolchains is useful here, see http://docs.easybuild.io/including-additional-python-modules/#include_toolchains

Supporting OSs with OpenSSL 3.x

see also https://github.com/easybuilders/easybuild-easyconfigs/issues/19593
like RHEL9, Debian Bookworm (12.x), etc.
dealing with OpenSSL/1.1 wrapper
- wraps around system OpenSSL 1.1.x if available
- installs OpenSSL 1.1.x from source if not
- used as dependency for cURL, Python, Perl, Rust, R, TensorFlow, wget,
- we need to update openssl_wrapper.py easyblock to also support OpenSSL 3.0.x
  - so we can create an OpenSSL/3.0 wrapper
  - => already done by Sebastian a while ago, see also easyconfigs PR #15659
for which toolchains to we pick OpenSSL/3.0 instead of OpenSSL/1.1
OpenSSL/1.1 => OpenSSL/system
- OS openssl 1.1 => OpenSSL/1.1
- openssl 3 => OpenSSL/3.0 (or OpenSSL/3, cfr. their plan with using semantic versioning)
Jörg ran into trouble with recent Perl version when building on top of OpenSSL 3.x
```
undefined symbol: OSSL_PROVIDER_get0_name at
```
can test on jsc-zen3 that Sebastian has set up for testing easyconfig PRs
The Alliance is using OpenSSL 3.x in their new compat layer (with openssl-compat-1.1.1 also installed)
- EESSI ran into trouble with OpenSSL 3.x, cfr.
openssl3-devel package is available for RHEL8 & friends
for testing, we can use the container images provided via https://github.com/easybuilders/easybuild-containers

Q&A / others

EasyBuild User Meeting 2024
- Tue-Thu 23-25 April 2024 in Umeå (Sweden)
- https://easybuild.io/eum24
how to update list of Ruby gems?
- was probably done manually up until now...
- talk to rubygems.org
- could do update in a Ruby virtual environment
AFNI installing into $HOME/.local?!
- cfr. Jörg's PR #17309