Bug 1347788
| Summary: | [abrt] nwchem-openmpi: dassertp_fail(): nwchem_openmpi killed by SIGSEGV | ||||||||||||||||||||||||||||
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| Product: | [Fedora] Fedora | Reporter: | Dmitry <amidius.1992> | ||||||||||||||||||||||||||
| Component: | nwchem | Assignee: | marcindulak <Marcin.Dulak> | ||||||||||||||||||||||||||
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||||||||||||||||||||||||
| Severity: | unspecified | Docs Contact: | |||||||||||||||||||||||||||
| Priority: | unspecified | ||||||||||||||||||||||||||||
| Version: | 24 | CC: | Marcin.Dulak | ||||||||||||||||||||||||||
| Target Milestone: | --- | ||||||||||||||||||||||||||||
| Target Release: | --- | ||||||||||||||||||||||||||||
| Hardware: | x86_64 | ||||||||||||||||||||||||||||
| OS: | Unspecified | ||||||||||||||||||||||||||||
| URL: | https://retrace.fedoraproject.org/faf/reports/bthash/43225c3fa08f692a610ab27d4e459b51f407c6d3 | ||||||||||||||||||||||||||||
| Whiteboard: | abrt_hash:d3405b23c02f213fcd06531965c66b81bdfa1d8c;VARIANT_ID=workstation; | ||||||||||||||||||||||||||||
| Fixed In Version: | nwchem-6.6.27746-27.fc24 | Doc Type: | If docs needed, set a value | ||||||||||||||||||||||||||
| Doc Text: | Story Points: | --- | |||||||||||||||||||||||||||
| Clone Of: | Environment: | ||||||||||||||||||||||||||||
| Last Closed: | 2016-08-08 20:29:50 UTC | Type: | --- | ||||||||||||||||||||||||||
| Regression: | --- | Mount Type: | --- | ||||||||||||||||||||||||||
| Documentation: | --- | CRM: | |||||||||||||||||||||||||||
| Verified Versions: | Category: | --- | |||||||||||||||||||||||||||
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |||||||||||||||||||||||||||
| Cloudforms Team: | --- | Target Upstream Version: | |||||||||||||||||||||||||||
| Embargoed: | |||||||||||||||||||||||||||||
| Attachments: |
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Description
Dmitry
2016-06-17 15:56:30 UTC
Created attachment 1169159 [details]
File: backtrace
Created attachment 1169160 [details]
File: cgroup
Created attachment 1169161 [details]
File: core_backtrace
Created attachment 1169162 [details]
File: dso_list
Created attachment 1169163 [details]
File: environ
Created attachment 1169164 [details]
File: limits
Created attachment 1169165 [details]
File: maps
Created attachment 1169166 [details]
File: mountinfo
Created attachment 1169167 [details]
File: namespaces
Created attachment 1169168 [details]
File: open_fds
Created attachment 1169169 [details]
File: proc_pid_status
Created attachment 1169170 [details]
File: var_log_messages
maybe related to bug #1356735 nwchem-6.6.27746-26.fc24 has been submitted as an update to Fedora 24. https://bodhi.fedoraproject.org/updates/FEDORA-2016-f10b67dbd7 Looks we experienced the same problem as Debian maintainers of Nwchem: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=767481 Native optimization compiler flags were on and the build produced by koji were not portable. nwchem-6.6.27746-26.fc24 has been pushed to the Fedora 24 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2016-f10b67dbd7 (In reply to Fedora Update System from comment #16) > nwchem-6.6.27746-26.fc24 has been pushed to the Fedora 24 testing > repository. If problems still persist, please make note of it in this bug > report. > See https://fedoraproject.org/wiki/QA:Updates_Testing for > instructions on how to install test updates. > You can provide feedback for this update here: > https://bodhi.fedoraproject.org/updates/FEDORA-2016-f10b67dbd7 Doesn't work for me. I recieved the same message: Attempting to read a basis set from a non-existing file: /builddir/build/BUILD/nwchem-6.6/src/basis/libraries/6-311gs Are you sure the env variables are set: 0. source /etc/profile.d/nwchem.sh&& echo $NWCHEM_BASIS_LIBRARY Yes: [madchem@desktop ~]$ source /etc/profile.d/nwchem.sh && $NWCHEM_BASIS_LIBRARY bash: /usr/share/nwchem/libraries/:/usr/nwchem/libraries/: No such file or directory And then: [madchem@desktop ~]$ mpiexec -np 4 `which nwchem_openmpi` test.nw ... warning:::::::::::::: from_environment NWCHEM_BASIS_LIBRARY set to: </usr/share/nwchem/libraries/:/usr/nwchem/libraries/> but file does not exist ! using .nwchemrc or compiled library warning:::::::::::::: from_compile NWCHEM_BASIS_LIBRARY is: </builddir/build/BUILD/nwchem-6.6/src/basis/libraries/> but file does not exist or you do not have access to it ! Attempting to read a basis set from a non-existing file: /builddir/build/BUILD/nwchem-6.6/src/basis/libraries/6-31g And: [madchem@desktop ~]$ locate 6-31g /usr/share/nwchem/libraries/6-31g /usr/share/nwchem/libraries/6-31g-blaudeau /usr/share/nwchem/libraries/6-31g3df_3pd /usr/share/nwchem/libraries/6-31gs /usr/share/nwchem/libraries/6-31gs-blaudeau /usr/share/nwchem/libraries/6-31gs_polarization /usr/share/nwchem/libraries/6-31gss /usr/share/nwchem/libraries/6-31gss_polarization /usr/share/nwchem/libraries/m6-31g /usr/share/nwchem/libraries/m6-31gs /usr/share/nwchem/libraries/qmmm_zhang_6-31gs_ecp /usr/share/nwchem/libraries/s6-31g /usr/share/nwchem/libraries/s6-31gs I tried to compile nwchem on my machine. But as I get executable file, it returns SEGFAULT. I'm frustrated with it... This is the problem: bash: /usr/share/nwchem/libraries/:/usr/nwchem/libraries/: No such file or directory you need: unset NWCHEM_BASIS_LIBRARY unset NWCHEM_NWPW_LIBRARY source /etc/profile.d/nwchem.sh I see the NWCHEM variables must not be prepended, just set to a single path. I fix that at the coming nwchem-6.6.27746-27 build. Look at bug #1356735 - currently the nwchem-6.6.27746-26 executables are broken due to some gfortran 6 flags used during the build. Oh! Thank you very much!!! It works! nwchem-6.6.27746-27.fc24 has been submitted as an update to Fedora 24. https://bodhi.fedoraproject.org/updates/FEDORA-2016-96b3062018 nwchem-6.6.27746-27.fc24 has been pushed to the Fedora 24 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2016-96b3062018 nwchem-6.6.27746-27.fc24 has been pushed to the Fedora 24 stable repository. If problems still persist, please make note of it in this bug report. |