make Z3 & zstd explicit dependency for numba to fix non-rpath build by Thyre · Pull Request #24406 · easybuilders/easybuild-easyconfigs

Thyre · 2025-10-30T08:25:35Z

(created using eb --new-pr)

Fixes the following sanity check failure with numba, when the rpath build option is disabled:

  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/ffi.py", line 141, in __getattr__
    return self._fntab[name]
           ~~~~~~~~~~~^^^^^^
KeyError: 'LLVMPY_AddSymbol'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/ffi.py", line 122, in _load_lib
    self._lib_handle = ctypes.CDLL(str(lib_path))
                       ~~~~~~~~~~~^^^^^^^^^^^^^^^
  File "/data/EasyBuild-develop/software/Python/3.13.5-GCCcore-14.3.0/lib/python3.13/ctypes/__init__.py", line 390, in __init__
    self._handle = _dlopen(self._name, mode)
                   ~~~~~~~^^^^^^^^^^^^^^^^^^
OSError: libz3.so.4.15: cannot open shared object file: No such file or directory

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/bin/numba", line 5, in <module>
    from numba.misc.numba_entry import main
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/numba/__init__.py", line 73, in <module>
    from numba.core import config
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/numba/core/config.py", line 17, in <module>
    import llvmlite.binding as ll
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/__init__.py", line 4, in <module>
    from .dylib import *
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/dylib.py", line 36, in <module>
    ffi.lib.LLVMPY_AddSymbol.argtypes = [
    ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/ffi.py", line 144, in __getattr__
    cfn = getattr(self._lib, name)
                  ^^^^^^^^^
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/ffi.py", line 136, in _lib
    self._load_lib()
    ~~~~~~~~~~~~~~^^
  File "/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/ffi.py", line 130, in _load_lib
    raise OSError("Could not find/load shared object file") from e
OSError: Could not find/load shared object file
)

Thyre · 2025-10-30T08:34:16Z

Looking at the libtree output, it should be actually sufficient to only provide Z3 as a dependency. LLVM can stay a build-dep. Will update the PR.

Edit: Also added zstd, as this was still using the "default path":

$ libtree /data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/libllvmlite.so
libllvmlite.so
├── libz.so.1 [LD_LIBRARY_PATH]
├── libzstd.so.1 [default path]
└── libz3.so.4.15 not found
    ┊ Paths considered in this order:
    ┊ 1. rpath:
    ┊ 2. LD_LIBRARY_PATH:
[...]
    ┊ 3. runpath was not set
    ┊ 4. ld config files:
    ┊    /usr/lib32
    ┊    /opt/rocm/lib
    ┊    /usr/lib/libfakeroot
    ┊ 5. Standard paths:
    ┊    /lib
    ┊    /lib64
    ┊    /usr/lib
    ┊    /usr/lib64
Error [/data/EasyBuild-develop/software/numba/0.62.0-foss-2025b/lib/python3.13/site-packages/llvmlite/binding/libllvmlite.so]: Not all dependencies were found

Thyre · 2025-10-30T08:41:11Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/$USER/ecpr-24406 --disable-rpath"

boegelbot · 2025-10-30T08:50:10Z

@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=24406 EB_ARGS="--installpath=/tmp/$USER/ecpr-24406 --disable-rpath" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24406 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8588

Test results coming soon (I hope)...

Details

- notification for comment with ID 3466679581 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).

Thyre · 2025-10-30T09:24:53Z

With --disable-rpath

Test report by @Thyre
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor (zen4), 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.17.5-arch1-1(linux@archlinux)(gcc(GCC)15.2.120250813,GNUld(GNUBinutils)2.45.0)#1SMPPREEMPT_DYNAMICThu,23Oct202518:49:03+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.17.5-arch1-1(linux@archlinux)(gcc(GCC)15.2.120250813,GNUld(GNUBinutils)2.45.0)#1SMPPREEMPT_DYNAMICThu,23Oct202518:49:03+0000), Python 3.13.7
See https://gist.github.com/Thyre/929ce7cff87bed21dd0b1e5a2f402370 for a full test report.

boegelbot · 2025-10-30T10:12:47Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/b8947bbe25e9d4f9e3d9b72c42a56ff5 for a full test report.

Thyre · 2025-10-30T11:35:51Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/$USER/ecpr-24406"

boegelbot · 2025-10-30T11:40:09Z

@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=24406 EB_ARGS="--installpath=/tmp/$USER/ecpr-24406" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24406 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8594

Test results coming soon (I hope)...

Details

- notification for comment with ID 3467558901 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 · 2025-10-30T13:03:23Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/70e2aeed7c2a8101d0a763db16f99a1d for a full test report.

Micket

lgtm

make LLVM explicit dependency for numba to fix non-rpath build

fd6b029

Thyre modified the milestones: 5.x, next release (5.2.0?) Oct 30, 2025

Thyre added bug fix 2025a issues & PRs related to 2025a common toolchains 2025b issues & PRs related to 2025b common toolchains labels Oct 30, 2025

github-actions Bot added the change label Oct 30, 2025

Make Z3 explicit dependency instead of LLVM

591a1f4

Thyre changed the title ~~make LLVM explicit dependency for numba to fix non-rpath build~~ make Z3 explicit dependency for numba to fix non-rpath build Oct 30, 2025

Thyre changed the title ~~make Z3 explicit dependency for numba to fix non-rpath build~~ make Z3 & zstd explicit dependency for numba to fix non-rpath build Oct 30, 2025

Make zstd explicit dependency of numba

8433cbd

Thyre added ready-to-review and removed change labels Oct 30, 2025

Micket approved these changes Nov 4, 2025

View reviewed changes

Micket merged commit da3ccfd into easybuilders:develop Nov 4, 2025
8 checks passed

Thyre mentioned this pull request Feb 12, 2026

RPATH-linking can hide runtime dependencies easybuilders/easybuild-framework#5117

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

make Z3 & zstd explicit dependency for numba to fix non-rpath build#24406

make Z3 & zstd explicit dependency for numba to fix non-rpath build#24406
Micket merged 3 commits intoeasybuilders:developfrom
Thyre:20251030092530_new_pr_numba0620

Thyre commented Oct 30, 2025 •

edited

Loading

Uh oh!

Thyre commented Oct 30, 2025 •

edited

Loading

Uh oh!

Thyre commented Oct 30, 2025

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

Thyre commented Oct 30, 2025 •

edited

Loading

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

Thyre commented Oct 30, 2025

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

Micket left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Conversation

Thyre commented Oct 30, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Thyre commented Oct 30, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Thyre commented Oct 30, 2025

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

Thyre commented Oct 30, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

Thyre commented Oct 30, 2025

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

boegelbot commented Oct 30, 2025

Uh oh!

Micket left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Thyre commented Oct 30, 2025 •

edited

Loading

Thyre commented Oct 30, 2025 •

edited

Loading

Thyre commented Oct 30, 2025 •

edited

Loading