Description of problem: All cp2k tests are failing with: Relink `/lib64/libxc.so.9' with `/lib64/libm.so.6' for IFUNC symbol `sin' Version-Release number of selected component (if applicable): libxc-5.0.0-4.fc33.x86_64 How reproducible: Always Steps to Reproduce: 1. Patch cp2k HEAD with https://github.com/cp2k/cp2k/pull/914 2. Build and run test suite Actual results: All tests fail with: Relink `/lib64/libxc.so.9' with `/lib64/libm.so.6' for IFUNC symbol `sin' Expected results: Tests pass. Additional info: It looks like libxc wasn't build in rawhide (f34), so I'll try rebuilding in rawhide to see if that fixes the issue.
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 pushed to the Fedora 33 stable repository. If problem still persists, please make note of it in this bug report.