enhance generic `Bundle` easyblock to transfer module requirements of components, but do not create logfile in components by Thyre · Pull Request #3509 · easybuilders/easybuild-easyblocks

Thyre · 2024-11-15T07:37:12Z

This fixes the increased disk usage when running the EasyConfig test suite as log files would stay open.
See easybuilders/easybuild-easyconfigs#21841 for more information.

Requires:

enhance EasyBlock class to allow passing in logfile easybuild-framework#4707

test: Test suite doesn't remove log files for QuantumESPRESSO (nested EasyBlocks?) easybuild-easyconfigs#21841

See #3472 for the initial review and #3504 for the occurring issue, causing a revert of the PR.

Thyre · 2024-11-15T08:15:22Z

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS GCC-13.3.0.eb
SUCCESS Autotools-20231222-GCCcore-13.3.0.eb

Build succeeded for 2 out of 2 (2 easyconfigs in total)
Linux - Linux EndeavourOS UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x NVIDIA NVIDIA GeForce RTX 3070, 565.57.01, Python 3.12.7
See https://gist.github.com/Thyre/91835076bbb9bad8921c1b8608402863 for a full test report.

Thyre · 2024-11-15T09:08:08Z

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS buildenv-default-foss-2023b.eb
SUCCESS OpenSSL-3.eb
SUCCESS Circuitscape-5.12.3-Julia-1.9.2.eb
SUCCESS Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
SUCCESS gfbf-2024a.eb
SUCCESS crypt4gh-1.7-GCC-12.3.0.eb
SUCCESS GCC-system.eb
SUCCESS jiter-0.4.1-GCCcore-12.3.0.eb
SUCCESS X11-20240607-GCCcore-13.3.0.eb
FAIL (build issue) GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/6f3d91d68baa3c97cfa6d9ed2683e5ad)
FAIL (build issue) zlib-1.2.11-GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/e541a256d17e7d3715aecff84ddcd3f9)
FAIL (build issue) help2man-1.47.4-GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/7c36d43e230398aeb56e3302b60cb00e)
FAIL (build issue) M4-1.4.18-GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/9cb1e0636cdccc6c62f4f001875cb45d)
FAIL (build issue) Bison-3.0.4-GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/fe629550dd9f592436576ea79ec71176)
FAIL (build issue) Bison-3.0.5-GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/4b424dad19836326ce8fb3c2e5aa8ca3)
FAIL (build issue) flex-2.6.4-GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/43223f50e4d0c4f8dad64299831388fa)
FAIL (build issue) binutils-2.29-GCCcore-system.eb (partial log available at https://gist.github.com/Thyre/7e2d5975ec8ca2b202a330e0b1d6881e)
FAIL (build issue) GCC-system-2.29.eb (partial log available at https://gist.github.com/Thyre/6e226ad1fb92a1026d9c1dfdee56bd89)
FAIL (build issue) OpenMPI-system-GCC-system-2.29.eb (partial log available at https://gist.github.com/Thyre/7eccf5edc389270d4acef962053f247c)

Build succeeded for 9 out of 19 (10 easyconfigs in total)
datenlager - Linux Ubuntu 24.04, x86_64, AMD Ryzen 7 3700X 8-Core Processor, Python 3.12.3
See https://gist.github.com/Thyre/1f2efb9ca0b89f91030fc316828e19d2 for a full test report.

Thyre · 2024-11-15T09:10:04Z

Test report by @Thyre

Overview of tested easyconfigs (in order)

[...]

Build succeeded for 9 out of 19 (10 easyconfigs in total) datenlager - Linux Ubuntu 24.04, x86_64, AMD Ryzen 7 3700X 8-Core Processor, Python 3.12.3 See https://gist.github.com/Thyre/1f2efb9ca0b89f91030fc316828e19d2 for a full test report.

Failures due to #3402 missing.

== 2024-11-15 09:07:43,949 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/tools/build_log.py:111 in caller_info): No viable license specifications found; specify 'license_file', or define $INTEL_LICENSE_FILE or $LM_LICENSE_FILE (at easybuild/easyblocks/generic/intelbase.py:308 in prepare_step)

easybuild/easyblocks/generic/bundle.py

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

This fixes the increased memory usage when running the EasyConfig test suite as log files would stay open. Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

boegel · 2024-12-04T18:43:51Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS matplotlib-3.8.2-gfbf-2023b.eb
**FAIL (unhandled exception: expected str, bytes or os.PathLike object, not list)Traceback (most recent call last):
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/main.py", line 137, in build_and_install_software
(ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 4282, in build_and_install_one
result = app.run_all_steps(run_test_cases=run_test_cases)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 4161, in run_all_steps
self.run_step(step_name, step_methods)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3996, in run_step
step_method(self)()
File "/tmp/eb-6kii0jqq/included-easyblocks-yrkr96bg/easybuild/easyblocks/generic/bundle.py", line 378, in sanity_check_step
fake_mod_data = self.load_fake_module(purge=True)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 1721, in load_fake_module
fake_mod_path = self.make_module_step(fake=True)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3763, in make_module_step
txt += self.make_module_req()
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 1603, in make_module_req
paths = sum((glob.glob(path) if path else [path] for path in reqs), []) # sum flattens to list
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 1603, in
paths = sum((glob.glob(path) if path else [path] for path in reqs), []) # sum flattens to list
File "/usr/lib64/python3.9/glob.py", line 22, in glob
return list(iglob(pathname, recursive=recursive))
File "/usr/lib64/python3.9/glob.py", line 43, in _iglob
dirname, basename = os.path.split(pathname)
File "/usr/lib64/python3.9/posixpath.py", line 103, in split
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not list
** FlexiBLAS-3.3.1-GCC-12.3.0.eb
**FAIL (unhandled exception: expected str, bytes or os.PathLike object, not list)Traceback (most recent call last):
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/main.py", line 137, in build_and_install_software
(ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 4282, in build_and_install_one
result = app.run_all_steps(run_test_cases=run_test_cases)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 4161, in run_all_steps
self.run_step(step_name, step_methods)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3996, in run_step
step_method(self)()
File "/tmp/eb-6kii0jqq/included-easyblocks-yrkr96bg/easybuild/easyblocks/generic/bundle.py", line 375, in sanity_check_step
super(Bundle, self).sanity_check_step(*args, **kwargs)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3089, in sanity_check_step
self._sanity_check_step(*args, **kwargs)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3622, in _sanity_check_step
self.fake_mod_data = self.sanity_check_load_module(extension=extension, extra_modules=extra_modules)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3549, in sanity_check_load_module
self.fake_mod_data = self.load_fake_module(purge=True, extra_modules=extra_modules, verbose=True)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 1721, in load_fake_module
fake_mod_path = self.make_module_step(fake=True)
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3763, in make_module_step
txt += self.make_module_req()
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 1603, in make_module_req
paths = sum((glob.glob(path) if path else [path] for path in reqs), []) # sum flattens to list
File "/arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 1603, in
paths = sum((glob.glob(path) if path else [path] for path in reqs), []) # sum flattens to list
File "/usr/lib64/python3.9/glob.py", line 22, in glob
return list(iglob(pathname, recursive=recursive))
File "/usr/lib64/python3.9/glob.py", line 43, in _iglob
dirname, basename = os.path.split(pathname)
File "/usr/lib64/python3.9/posixpath.py", line 103, in split
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not list
** X11-20231019-GCCcore-13.2.0.eb

Build succeeded for 1 out of 3 (3 easyconfigs in total)
node3141.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/a09672728e55530c7cda76daab6ee7bc for a full test report.

easybuild/easyblocks/generic/bundle.py

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Thyre · 2024-12-04T19:47:10Z

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS FlexiBLAS-3.3.1-GCC-12.3.0.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
datenlager - Linux Ubuntu 24.04, x86_64, AMD Ryzen 7 3700X 8-Core Processor, Python 3.12.3
See https://gist.github.com/Thyre/d3a7d60b320f3bcb317d4c55d0b79166 for a full test report.

Thyre · 2024-12-04T20:33:43Z

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS buildenv-default-foss-2023b.eb
SUCCESS OpenSSL-3.eb
SUCCESS Circuitscape-5.12.3-Julia-1.9.2.eb
SUCCESS Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
SUCCESS gfbf-2024a.eb
SUCCESS crypt4gh-1.7-GCC-12.3.0.eb
SUCCESS jiter-0.4.1-GCCcore-12.3.0.eb
SUCCESS X11-20240607-GCCcore-13.3.0.eb

Build succeeded for 8 out of 8 (8 easyconfigs in total)
datenlager - Linux Ubuntu 24.04, x86_64, AMD Ryzen 7 3700X 8-Core Processor, Python 3.12.3
See https://gist.github.com/Thyre/3e6e109c6a568293be8b285416d628af for a full test report.

Thyre · 2024-12-04T21:33:12Z

@boegelbot please test @ jsc-zen3
EB_ARGS="buildenv-default-foss-2023b.eb OpenSSL-3.eb Circuitscape-5.12.3-Julia-1.9.2.eb Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb gfbf-2024a.eb crypt4gh-1.7-GCC-12.3.0.eb jiter-0.4.1-GCCcore-12.3.0.eb X11-20240607-GCCcore-13.3.0.eb Clang-AOMP-4.5.0-GCCcore-11.2.0.eb"

boegelbot · 2024-12-04T21:53:08Z

@Thyre: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=3509 EB_ARGS="buildenv-default-foss-2023b.eb OpenSSL-3.eb Circuitscape-5.12.3-Julia-1.9.2.eb Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb gfbf-2024a.eb crypt4gh-1.7-GCC-12.3.0.eb jiter-0.4.1-GCCcore-12.3.0.eb X11-20240607-GCCcore-13.3.0.eb Clang-AOMP-4.5.0-GCCcore-11.2.0.eb" EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3509 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5384

Test results coming soon (I hope)...

Details

- notification for comment with ID 2518605340 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 · 2024-12-04T23:04:17Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

SUCCESS buildenv-default-foss-2023b.eb
SUCCESS OpenSSL-3.eb
SUCCESS Circuitscape-5.12.3-Julia-1.9.2.eb
SUCCESS Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
SUCCESS gfbf-2024a.eb
SUCCESS crypt4gh-1.7-GCC-12.3.0.eb
SUCCESS jiter-0.4.1-GCCcore-12.3.0.eb
SUCCESS X11-20240607-GCCcore-13.3.0.eb
SUCCESS ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb
FAIL (build issue) Clang-AOMP-4.5.0-GCCcore-11.2.0.eb (partial log available at https://gist.github.com/boegelbot/d82fb4858e7f8509d04629748780597a)

Build succeeded for 9 out of 10 (9 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/6f439391fecc47536c2a2c3e0be99993 for a full test report.

Thyre · 2024-12-05T08:55:06Z

FAIL (build issue) Clang-AOMP-4.5.0-GCCcore-11.2.0.eb (partial log available at https://gist.github.com/boegelbot/d82fb4858e7f8509d04629748780597a)

Build succeeded for 9 out of 10 (9 easyconfigs in total) jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19 See https://gist.github.com/boegelbot/6f439391fecc47536c2a2c3e0be99993 for a full test report.

The gist unfortunately did not include the error. Checking on jsc-zen3 directly, I see the following error message:

/dev/shm/reuter1/ClangAOMP/4.5.0/GCCcore-11.2.0/llvm-project-rocm-4.5.0/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cpp:146:10: fatal error: linux/cyclades.h: No such file or directory
  146 | #include <linux/cyclades.h>
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [projects/compiler-rt/lib/sanitizer_common/CMakeFiles/RTSanitizerCommon.x86_64.dir/build.make:345: projects/compiler-rt/lib/sanitizer_common/CMakeFiles/RTSanitizerCommon.x86_64.dir/sanitizer_platform_limits_posix.cpp.o] Error 1
make[2]: Leaving directory '/dev/shm/reuter1/ClangAOMP/4.5.0/GCCcore-11.2.0/easybuild_obj'
make[1]: *** [CMakeFiles/Makefile2:21910: projects/compiler-rt/lib/sanitizer_common/CMakeFiles/RTSanitizerCommon.x86_64.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

This looks unrelated to the changes in this PR.

Well, looking into it further, this is a header being removed in newer Linux kernels. Not much we can do about that aside from porting patches, if they exist.

boegel · 2024-12-18T16:42:33Z

@boegelbot please test @ generoso
EB_ARGS="Clang-AOMP-4.5.0-GCCcore-11.2.0.eb "

boegelbot · 2024-12-18T16:50:06Z

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

PR test command 'EB_PR=3509 EB_ARGS="Clang-AOMP-4.5.0-GCCcore-11.2.0.eb " EB_CONTAINER= EB_REPO=easybuild-easyblocks /opt/software/slurm/bin/sbatch --job-name test_PR_3509 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14883

Test results coming soon (I hope)...

Details

- notification for comment with ID 2551801188 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 · 2024-12-18T18:46:07Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

SUCCESS Clang-AOMP-4.5.0-GCCcore-11.2.0.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/bcce16a46456242fbcbb9efbd856830d for a full test report.

boegel

lgtm

boegel · 2024-12-26T18:28:28Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS Clang-AOMP-4.5.0-GCCcore-11.2.0.eb
SUCCESS matplotlib-3.8.2-gfbf-2023b.eb
SUCCESS FlexiBLAS-3.3.1-GCC-12.3.0.eb
SUCCESS X11-20231019-GCCcore-13.2.0.eb

Build succeeded for 4 out of 4 (4 easyconfigs in total)
node4001.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/boegel/eaa3dac9f747beb8e6056f01203da28b for a full test report.

Thyre changed the title ~~Reintroduce #3472 (transfer Bundle requirements to module), but do not transfer logfile~~ Reintroduce #3472 (transfer Bundle requirements to module) but do not create logfile in components Nov 15, 2024

Thyre marked this pull request as ready for review November 15, 2024 08:45

Thyre commented Nov 15, 2024

View reviewed changes

easybuild/easyblocks/generic/bundle.py Show resolved Hide resolved

Thyre mentioned this pull request Nov 18, 2024

{compiler}[system/system] Add CodePlay CUDA SYCL plug-in variants for oneAPI 2023.0.0 to 2025.0.0 easybuilders/easybuild-easyconfigs#21582

Merged

6 tasks

bartoldeman added the enhancement label Nov 20, 2024

boegel changed the title ~~Reintroduce #3472 (transfer Bundle requirements to module) but do not create logfile in components~~ enhance generic Bundle easyblock to transfer module requirements of components, but do not create logfile in components Dec 4, 2024

boegel added this to the release after 4.9.4 milestone Dec 4, 2024

boegel requested changes Dec 4, 2024

View reviewed changes

boegel mentioned this pull request Dec 4, 2024

adopt module_load_environment in Bundle easyblock #3513

Merged

Thyre added 4 commits December 4, 2024 15:33

Reintroduce easybuilders#3472 after framework changes

14c889f

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Update clang_aomp for bundle changes

fd3cd65

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Transfer logfile from bundle to components

43ec355

This fixes the increased memory usage when running the EasyConfig test suite as log files would stay open. Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Bundle: Address review comments

bce45f5

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Thyre force-pushed the generic-bundle-include-module-requirements branch from 995cf1b to 16c5dd6 Compare December 4, 2024 14:33

Bundle: Add comment to try-except block in make_module_req_guess()

4ebf4a3

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Thyre force-pushed the generic-bundle-include-module-requirements branch from 16c5dd6 to 4ebf4a3 Compare December 4, 2024 15:35

boegel changed the title ~~enhance generic Bundle easyblock to transfer module requirements of components, but do not create logfile in components~~ enhance generic Bundle easyblock to transfer module requirements of components, but do not create logfile in components Dec 4, 2024

Thyre commented Dec 4, 2024

View reviewed changes

easybuild/easyblocks/generic/bundle.py Outdated Show resolved Hide resolved

Bundle: Replace append with extend when copying reqs

4b0522a

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

boegel approved these changes Dec 26, 2024

View reviewed changes

boegel merged commit 69530e9 into easybuilders:develop Dec 26, 2024

boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025

Thyre mentioned this pull request Jun 26, 2025

Bundle EasyBlock once again doesn't set PATH correctly for Bundle components #3800

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4 participants

Thyre commented Nov 15, 2024 •

edited by boegel

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Thyre commented Nov 15, 2024 •

edited

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Thyre commented Dec 5, 2024 •

edited

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