transfer dependencies in Bundle easyblock and fix sanity check for module only by Thyre · Pull Request #4037 · easybuilders/easybuild-easyblocks

Thyre · 2026-01-06T13:02:39Z

(created using eb --new-pr)

Edit:

--sanity-check-only is still broken, see #4037 (comment)

Edit 2:

Maybe solved by 5010c6f

During test builds of ROCm-LLVM, one sanity check was failing on jsc-zen3 due to libraries not being found when trying to link a test program. Investigating further, I was able to create a reproducer EasyConfig and EasyBlock (see #4009 (comment)), which mirrored the same issue.

When building a normal EasyConfig, self.toolchain.dependencies is set to include all the dependencies of the EasyConfig. For a Bundle however, this value is empty. I'm not sure if this is because we're setting most of the values in __init__. Could be.
In Framework, the dependencies are initialized during prepare_step. To correctly transfer the dependencies to components, add a prepare_step to the Bundle EasyBlock, simply transferring the dependencies as they are.

Additionally, --module-only and --sanity-check-only builds were not executing the sanity check of Bundle components. This is due to install-step being skipped in both cases. To fix this, move the logic for determining components, for which the sanity check should run, to the same prepare_step.

Resolves #4008, Resolves #4009

…dule only

Thyre · 2026-01-06T13:37:33Z

@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 --installpath=/tmp/$USER/ebpr-4037"

boegelbot · 2026-01-06T13:53:08Z

@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=4037 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 --installpath=/tmp/$USER/ebpr-4037" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_4037 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9336

Test results coming soon (I hope)...

Details

- notification for comment with ID 3714731172 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 · 2026-01-06T17:06:39Z

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

Build succeeded for 8 out of 8 (total: 3 hours 13 mins 11 secs) (8 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/d13ff1203e6feee882cbccf42959b9f7 for a full test report.

bedroge

Lgtm, but maybe @boegel could check it as well.

Thyre · 2026-01-12T15:31:34Z

I'll try a module only and sanity check only build as well, just too see if we get any unexpected results...

Thyre · 2026-01-12T15:46:24Z

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS foss-2025b.eb
SUCCESS buildenv-default-foss-2025b.eb
SUCCESS OpenSSL-3.eb
SUCCESS gfbf-2025b.eb
SUCCESS X11-20250608-GCCcore-14.3.0.eb

Build succeeded for 5 out of 5 (total: 9 mins 22 secs) (5 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), Python 3.14.2
See https://gist.github.com/Thyre/b05928fcadd48a4f2b692e8bf8281320 for a full test report.

Thyre · 2026-01-12T15:52:04Z

--module-only

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS foss-2025b.eb
SUCCESS buildenv-default-foss-2025b.eb
SUCCESS OpenSSL-3.eb
SUCCESS gfbf-2025b.eb
SUCCESS X11-20250608-GCCcore-14.3.0.eb

Build succeeded for 5 out of 5 (total: 1 min 5 secs) (5 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), Python 3.14.2
See https://gist.github.com/Thyre/81143313c8cb4403b74f1d45faa04b3a for a full test report.

Thyre · 2026-01-12T15:52:41Z

--sanity-check-only

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS foss-2025b.eb
FAIL buildenv-default-foss-2025b.eb (unhandled exception: expected str, bytes or os.PathLike object, not NoneType)

Traceback (most recent call last):
File "/data/EasyBuild/lib/python3.14/site-packages/easybuild/main.py", line 180, in build_and_install_software
  (ec_res['success'], app_log, err_msg, err_code) = build_and_install_one(ec, init_env)
                                                    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
File "/data/EasyBuild/lib/python3.14/site-packages/easybuild/framework/easyblock.py", line 5109, in build_and_install_one
  result = app.run_all_steps(run_test_cases=run_test_cases)
File "/data/EasyBuild/lib/python3.14/site-packages/easybuild/framework/easyblock.py", line 4922, in run_all_steps
  self.run_step(step_name, step_methods)
  ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/EasyBuild/lib/python3.14/site-packages/easybuild/framework/easyblock.py", line 4763, in run_step
  current_method()
  ~~~~~~~~~~~~~~^^
File "/tmp/eb-jq353oc9/included-easyblocks-qvyk046p/easybuild/easyblocks/generic/bundle.py", line 486, in sanity_check_step
  fake_mod_data = self.load_fake_module(purge=True)
File "/data/EasyBuild/lib/python3.14/site-packages/easybuild/framework/easyblock.py", line 1902, in load_fake_module
  fake_mod_path = self.make_module_step(fake=True)
File "/data/EasyBuild/lib/python3.14/site-packages/easybuild/easyblocks/generic/buildenv.py", line 119, in make_module_step
  wrappers_dir = os.path.join(self.rpath_wrappers_dir, RPATH_WRAPPERS_SUBDIR)
File "<frozen posixpath>", line 77, in join
TypeError: expected str, bytes or os.PathLike object, not NoneType

SUCCESS OpenSSL-3.eb
SUCCESS gfbf-2025b.eb
SUCCESS X11-20250608-GCCcore-14.3.0.eb

Build succeeded for 4 out of 5 (total: 4 secs) (5 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), Python 3.14.2
See https://gist.github.com/Thyre/d3c52bb9f4d5ffcc74446981668fde3c for a full test report.

Thyre · 2026-01-12T15:53:20Z

Looks like I found two (unrelated) bugs with buildenv during testing...

  >> generating module file @ /data/EasyBuild-develop/modules/all/MPI/GCC/14.3.0/OpenMPI/5.0.8/buildenv/default.lua
== comparing module file with backup /data/EasyBuild-develop/modules/all/MPI/GCC/14.3.0/OpenMPI/5.0.8/buildenv/default.bak_20260112165059_1226463; diff is:
--- /data/EasyBuild-develop/modules/all/MPI/GCC/14.3.0/OpenMPI/5.0.8/buildenv/default.bak_20260112165059_1226463
+++ /data/EasyBuild-develop/modules/all/MPI/GCC/14.3.0/OpenMPI/5.0.8/buildenv/default.lua
@@ -31,12 +31,12 @@
 depends_on("ScaLAPACK/2.2.2-fb")

 prepend_path("CMAKE_PREFIX_PATH", root)
-prepend_path("PATH", "/data/EasyBuild-develop/software/buildenv/default-foss-2025b/bin/rpath_wrappers/gcc_wrapper")
-prepend_path("PATH", "/data/EasyBuild-develop/software/buildenv/default-foss-2025b/bin/rpath_wrappers/ld.gold_wrapper")
-prepend_path("PATH", "/data/EasyBuild-develop/software/buildenv/default-foss-2025b/bin/rpath_wrappers/gxx_wrapper")
-prepend_path("PATH", "/data/EasyBuild-develop/software/buildenv/default-foss-2025b/bin/rpath_wrappers/ld.bfd_wrapper")
-prepend_path("PATH", "/data/EasyBuild-develop/software/buildenv/default-foss-2025b/bin/rpath_wrappers/ld_wrapper")
-prepend_path("PATH", "/data/EasyBuild-develop/software/buildenv/default-foss-2025b/bin/rpath_wrappers/gfortran_wrapper")
+prepend_path("PATH", "/data/EasyBuild-develop/build/buildenv/default/foss-2025b/rpath_wrappers/gcc_wrapper")
+prepend_path("PATH", "/data/EasyBuild-develop/build/buildenv/default/foss-2025b/rpath_wrappers/ld.gold_wrapper")
+prepend_path("PATH", "/data/EasyBuild-develop/build/buildenv/default/foss-2025b/rpath_wrappers/gxx_wrapper")
+prepend_path("PATH", "/data/EasyBuild-develop/build/buildenv/default/foss-2025b/rpath_wrappers/ld.bfd_wrapper")
+prepend_path("PATH", "/data/EasyBuild-develop/build/buildenv/default/foss-2025b/rpath_wrappers/ld_wrapper")
+prepend_path("PATH", "/data/EasyBuild-develop/build/buildenv/default/foss-2025b/rpath_wrappers/gfortran_wrapper")

Thyre · 2026-01-12T16:29:41Z

--sanity-check-only still doesn't behave as expected. This PR tries to fix both issues by using prepare_step. However, it looks like this step is skipped entirely when one passes --sanity-check-only. get_steps defines prepare_step as a step that is not skippable, yet, this is ignored in skip_step. This skippable attribute comes only into play when using --skip.

I'd consider this a bug, but maybe there's a good reason for it. Unfortunately, I don't see how we can get this fixed for --sanity-check-only, as we need to be after __init__.

See also https://easybuild.slack.com/archives/C34UA1HT7/p1768235026763329

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

Thyre · 2026-01-12T17:01:24Z

Latest commit should've fixed the sanity check, tested with a manual change in the X11 EasyConfig.

Thyre · 2026-01-12T17:03:06Z

--sanity-check-only

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS foss-2025b.eb
FAIL buildenv-default-foss-2025b.eb (unhandled exception: expected str, bytes or os.PathLike object, not NoneType) (see buildenv EasyBlock incorrectly sets PATH on --module-only and crashes on --sanity-check-only #4040)
SUCCESS OpenSSL-3.eb
SUCCESS gfbf-2025b.eb
SUCCESS X11-20250608-GCCcore-14.3.0.eb

Build succeeded for 4 out of 5 (total: 4 secs) (5 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), Python 3.14.2
See https://gist.github.com/Thyre/95b694add3497ec9cbc650dbad477f6f for a full test report.

Thyre · 2026-01-12T17:04:34Z

--module-only

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS foss-2025b.eb
SUCCESS buildenv-default-foss-2025b.eb
SUCCESS OpenSSL-3.eb
SUCCESS gfbf-2025b.eb
SUCCESS X11-20250608-GCCcore-14.3.0.eb

Build succeeded for 5 out of 5 (total: 1 min 16 secs) (5 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), Python 3.14.2
See https://gist.github.com/Thyre/ee6dcd1be44b9f49f8a835b58b57d0de for a full test report.

Thyre · 2026-01-12T17:14:14Z

Test report by @Thyre

Overview of tested easyconfigs (in order)

SUCCESS foss-2025b.eb
SUCCESS buildenv-default-foss-2025b.eb
SUCCESS OpenSSL-3.eb
SUCCESS gfbf-2025b.eb
SUCCESS X11-20250608-GCCcore-14.3.0.eb

Build succeeded for 5 out of 5 (total: 9 mins 28 secs) (5 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.18.4-arch1-1(linux@archlinux)(gcc(GCC)15.2.120260103,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,09Jan202619:43:48+0000), Python 3.14.2
See https://gist.github.com/Thyre/77d2c9ef8f1570f04bf9f3085edd5cc4 for a full test report.

boegel · 2026-01-20T18:06:43Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16
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 --installpath=/tmp/$USER/ebpr-4037"

boegel

lgtm

boegelbot · 2026-01-20T18:13:09Z

@boegel: 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=4037 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 --installpath=/tmp/$USER/ebpr-4037" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_4037 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9448

Test results coming soon (I hope)...

Details

- notification for comment with ID 3774254980 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 · 2026-01-20T21:20:33Z

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

Build succeeded for 8 out of 8 (total: 3 hours 6 mins 25 secs) (8 easyconfigs in total)
jsczen3c3.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/abf27000289030c773e1618fac645780 for a full test report.

boegel · 2026-01-20T21:39:51Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS zlib-ng-2.2.1-GCCcore-13.3.0.eb
SUCCESS tokenizers-0.21.4-GCCcore-13.3.0.eb
SUCCESS X11-20250608-GCCcore-14.3.0.eb
SUCCESS Xvfb-21.1.9-GCCcore-13.2.0.eb
SUCCESS BioPerl-1.7.8-GCCcore-13.3.0.eb
SUCCESS SentencePiece-0.2.0-GCC-13.2.0.eb
SUCCESS FlexiBLAS-3.4.5-GCC-14.3.0.eb
SUCCESS intel-compilers-2025.2.0-CUDA-12.9.0.eb

Build succeeded for 8 out of 8 (total: 1 hour 42 mins 19 secs) (8 easyconfigs in total)
node4247.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/9a11af2ef40cce744bcfb50d4206bdc0 for a full test report.

Flamefire · 2026-02-04T09:21:01Z

@Thyre For super() calls you must NOT pass self explicitly as in super().prepare_step(self, *args, **kwargs) or you'll have self twice overwriting other args!

Noticed (and fixed) while resolving conflict in #3778

Flamefire · 2026-02-04T09:28:10Z

Fix only in #4057

Thyre added 2 commits January 6, 2026 14:02

transfer dependencies in Bundle easyblock and fix sanity check for mo…

a46a4a8

…dule only

fix style in Bundle easyblock

3742f0f

Thyre added the bug fix label Jan 6, 2026

fix missing kwargs for patch_step in Bundle easyblock

b0b62fc

boegelbot mentioned this pull request Jan 7, 2026

{tools}[GCCcore/14.2.0] ROCm-LLVM v19.0.0 w/ ROCm 6.4.1 easybuilders/easybuild-easyconfigs#23304

Merged

4 tasks

bedroge previously approved these changes Jan 12, 2026

View reviewed changes

Thyre mentioned this pull request Jan 12, 2026

buildenv EasyBlock incorrectly sets PATH on --module-only and crashes on --sanity-check-only #4040

Open

set builddirs and sanity check even earlier in bundle easyblock

5010c6f

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

Thyre dismissed bedroge’s stale review via 5010c6f January 12, 2026 17:00

boegel added this to the next release (5.2.1?) milestone Jan 12, 2026

boegel approved these changes Jan 20, 2026

View reviewed changes

boegel merged commit f8ee0db into easybuilders:develop Jan 21, 2026
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