Bug 1883501
| Summary: | Relink `/lib64/libxc.so.9' with `/lib64/libm.so.6' for IFUNC symbol `sin' when running cp2k | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Dominik 'Rathann' Mierzejewski <dominik> |
| Component: | libxc | Assignee: | Dominik 'Rathann' Mierzejewski <dominik> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | 33 | CC: | dominik, fweimer, susi.lehtola |
| Target Milestone: | --- | Keywords: | Reopened |
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| Whiteboard: | |||
| Fixed In Version: | libxc-5.0.0-6.fc33 | Doc Type: | If docs needed, set a value |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2020-10-03 00:56:46 UTC | Type: | Bug |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
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Description
Dominik 'Rathann' Mierzejewski
2020-09-29 12:16:37 UTC
libxc-5.0.0-5.fc34 built in rawhide, retrying cp2k build... The rebuild seems to have fixed it. Closing. Unfortunately, I was wrong. Simple rebuild did not fix it. Additionally, F33 is also affected: $ cp2k.sopt cp2k.sopt: Relink `/lib64/libxc.so.9' with `/lib64/libm.so.6' for IFUNC symbol `sin' Segmentation fault (core dumped) $ rpm -q cp2k libxc cp2k-7.1-1.20200925gitdbf7a77.fc34.x86_64 libxc-5.0.0-4.fc33.x86_64 Perhaps this is related to bug 1452813 and bug 1312462? Hmm, actually libxc doesn't seem to be linked with libm: $ ldd -r /usr/lib64/libxc.so.9 linux-vdso.so.1 (0x00007fffc59c3000) libc.so.6 => /lib64/libc.so.6 (0x00007f6369590000) /lib64/ld-linux-x86-64.so.2 (0x00007f636b976000) undefined symbol: sincos (/usr/lib64/libxc.so.9) undefined symbol: atan2 (/usr/lib64/libxc.so.9) undefined symbol: tanh (/usr/lib64/libxc.so.9) undefined symbol: cosh (/usr/lib64/libxc.so.9) undefined symbol: sin (/usr/lib64/libxc.so.9) undefined symbol: atan (/usr/lib64/libxc.so.9) undefined symbol: exp (/usr/lib64/libxc.so.9) undefined symbol: cbrt (/usr/lib64/libxc.so.9) undefined symbol: cos (/usr/lib64/libxc.so.9) undefined symbol: log (/usr/lib64/libxc.so.9) undefined symbol: pow (/usr/lib64/libxc.so.9) undefined symbol: round (/usr/lib64/libxc.so.9) undefined symbol: sqrt (/usr/lib64/libxc.so.9) undefined symbol: erf (/usr/lib64/libxc.so.9) $ objdump -p /usr/lib64/libxc.so.9 |grep NEEDED NEEDED libc.so.6 Trying to force linking libxc with libm to see if that helps. And... yes it does. cp2k is no longer crashing. I'll push the fix to F33+ tonight. Thanks for the debug, I've fixed the issue in libxc upstream. FEDORA-2020-66e4aa529b has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-66e4aa529b FEDORA-2020-66e4aa529b has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-66e4aa529b FEDORA-2020-66e4aa529b has been pushed to the Fedora 33 stable repository. If problem still persists, please make note of it in this bug report. |