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Conference call notes 20200513
Kenneth Hoste edited this page May 13, 2020
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Notes on the 147th EasyBuild conference call, Wednesday May 13th 2020 (8:00 UTC - 10:00 CEST)
Alphabetical list of attendees (XXX):
-
Kenneth Hoste (HPC-UGent, Belgium)
-
Ake
-
Mikael
-
Henrik Nagel
-
Alexandre
-
Alan
-
Alex Domingo (Vrije Universiteit Brussel, Belgium)
-
Fotis Georgatos (SDSC, Switzerland)
-
Adam Huffman (Big Data Institute, Oxford, UK)
-
Terje Kvernes (University of Oslo, Norway)
-
Mikael Öhman (Chalmers University of Technology, Sweden)
-
Bart Oldeman (ComputeCanada)
-
Victor Rusu (CSCS, Switzerland)
-
Jörg Saßmannshausen (NIHR Biomedical Research Centre, UK)
-
Åke Sandgren (Umeå University, Sweden)
-
Shahzeb Siddiqui (DassaultSystemes)
-
Alexandre Strube (JSC, Germany)
-
Lars Viklund (Umeå University, Sweden)
- overview of recent changes to be included with upcoming EasyBuild v4.2.1
- update on progress on 2020a generation of easyconfigs
- Q&A
-
project in GitHub with overview of things to be done for EasyBuild v4.2.1
- maintainers: if any issues/PRs pop up that really must be included in next release, assign them to the
4.2.1
project!
- maintainers: if any issues/PRs pop up that really must be included in next release, assign them to the
framework: merged PRs in 4.2.1 milestone
-
recently merged PRs:
- automatic changing of directory by
extract_file
is deprecated (PR #3292)- also fixed in easyblocks (PR #2051)
- proper fix for PyPI download problem, parse page served by PyPI's
/simple
API as HTML (not XML) (PR #3329)- it looks like the cause of the problems in EasyBuild will be fixed on the PyPI side too (see here)
- cleaning up locks on signals (PR #3291)
- this is not enough to auto-cleanup locks for EasyBuild sessions run in Slurm jobs that get killed though... (issue #3280)
- requires looking into
fcntl
style looks; looks doable, maybe even should be the default locking mechanism?
- stop using
distutils.dir_util
incopy_dir
(PR #3310) - make ModulesTool.exist more robust w.r.t. module wrappers & co (PR #3216)
- this introduced a regression (issue #3335)
- fix problems with parsing easyconfigs using a Cray toolchain when there are no actual external modules (PR #3319)
- this fixed
--list-installed-software
crash when using HMNS
- this fixed
- add constants for common OS dependencies (PR #3309, PR #3334)
-
OS_PKG_IBVERBS_DEV
,OS_PKG_OPENSSL_DEV
,OS_PKG_PAM_DEV
, ...
-
- bug fixes for
--try-update-deps
experimental feature (PR #3325), (PR #3326), (PR #3330), - cleaned up output for
--list-toolchains --output-format=rst
(PR #3246) - add
--disable-job
in 'eb
' command used in jobs, to prevent infinite job cycle (PR #3328) - avoid empty entries in $LD_LIBRARY_PATH and other path-like environment variables (PR #)
- automatic changing of directory by
- open PRs/issues that should be merged/fixed for EasyBuild 4.2.1 release:
- bugs to fix:
-
Java/11
module wrapper is not seen as installed when using HierarchicalMNS (issue #3335, introduced by PR #3216)
-
- bugfix PRs to review/merge:
- expand glob paths when checking for multiple inclusion of easyblocks (bugfix for
--include-easyblocks*
) (PR #3311)
- expand glob paths when checking for multiple inclusion of easyblocks (bugfix for
- new features:
- allow copying of tweaked easyconfigs when using
--try-*
(PR #3332)
- allow copying of tweaked easyconfigs when using
- bugs to fix:
easyblocks: merged PRs in 4.2.1 milestone
- recently merged PRs:
- open PRs/issues that should be merged/fixed for EasyBuild 4.2.1 release:
- correct download url for test data in WPS easyblock (PR #2055)
- use updated
config.guess
for installing R packages (PR #1949) - fix for CMakeMake easyblock w.r.t. switch to building outside source tree (PR#2032)
- rewrite GROMACS easyblock to build all four variations in the same build (PR #1991)
- generically find the arch folder and add top-level bin/lib symlinks in PDT & TAU easyblocks (PR #2029)
- new easyblock to install XALT (PR #1942)
- fix problem with forced reinstallation of ROOT (issue #2023)
easyconfigs merged PRs in 4.2.1 milestone
- recently merged PRs:
- patch for h5py to avoid workaround for MPI_Init at
import h5py
(PR #10626, original workaround in PR #10246)- will need more work, current approach of disabling auto-init by
mpi4py
isn't working out well - see also https://github.com/h5py/h5py/pull/1544
- will need more work, current approach of disabling auto-init by
- fix for R 3.6.2 + R 3.6.3 on POWER (PR #9830, PR #10531)
- patch for h5py to avoid workaround for MPI_Init at
- open issues/PRs:
- gradually collapsing easyconfigs prepared in
2020a
branch intodevelop
- TODO:
- CUDA compatible with GCC 9.3.0 (for
fosscuda/2020a
) is coming soon?
- Henrik:
Java/11
wrapper doesn't seem to work for us in HMNS context- could be an issue with old Lmod version not picking up
.modulerc.lua
?- Lmod 7.8
- fix could be to install
Java/11
wrapper with Tcl module syntax (because older Lmod versions don't pick up on.modulerc.lua
, only.modulerc
)
- could be an issue with old Lmod version not picking up
- Alexandre: issues with updating PyTorch to 1.5.0 with
fosscuda
toolchain, CMake build dep is not being found?- easier to discuss in Slack, CMake using GCCcore easyconfig should be picked up when using
fosscuda
- easier to discuss in Slack, CMake using GCCcore easyconfig should be picked up when using
- Alexandre: starting point for implementing
--new-draft-pr
?- see
easybuild/tools/github.py
- add option to
new_pr_from_branch
function, act in it after figuring out magic incantation via GitHub PR, expose it via new--new-draft-pr
CLI option
- see