[Bug 1205139] New: FTBFS: openSUSE:Factory/votca fails to build (killed after 90 minutes without output)
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 Bug ID: 1205139 Summary: FTBFS: openSUSE:Factory/votca fails to build (killed after 90 minutes without output) Classification: openSUSE Product: openSUSE Tumbleweed Version: Current Hardware: Other OS: Other Status: NEW Severity: Normal Priority: P5 - None Component: Other Assignee: screening-team-bugs@suse.de Reporter: dimstar@opensuse.org QA Contact: qa-bugs@suse.de Found By: --- Blocker: --- The package votca fails to build in openSUSE:Factory. Earlier notifications by email to the bugowner and Maintainer have remained without reaction / fix. If the package is not being fixed within 2 weeks, it will be scheduled for removal from Tumbleweed The build does not 'fail' in a traditional way, but actually is being killed for not having any output for > 90 minutes ��� [ 2874s] 154/247 Test #154: unit_test_triplelist ............................... Passed 0.01 sec [ 2874s] Start 155: unit_iie.py [ 2874s] 155/247 Test #155: unit_iie.py ........................................ Passed 0.32 sec [ 2874s] Start 156: template_serialHelp [ 2874s] 156/247 Test #156: template_serialHelp ................................ Passed 0.01 sec [ 2874s] Start 157: template_threadedHelp [ 2874s] 157/247 Test #157: template_threadedHelp .............................. Passed 0.01 sec [ 2874s] Start 158: regression_spce_ibi_lammps [ 8280s] qemu-kvm: terminating on signal 15 from pid 67420 (<unknown process>) [ 8280s] ### VM INTERACTION END ### [ 8280s] No buildstatus set, either the base system is broken (kernel/initrd/udev/glibc/bash/perl) [ 8280s] or the build host has a kernel or hardware problem... Job seems to be stuck here, killed. (after 5400 seconds of inactivity) Seems the timeout is simply stalling - for whatever ill reason (disk space? memory? actual a real bug somewhere?) -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 Dominique Leuenberger <dimstar@opensuse.org> changed: What |Removed |Added ---------------------------------------------------------------------------- Assignee|screening-team-bugs@suse.de |junghans@votca.org -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c1 --- Comment #1 from Christoph Junghans <junghans@votca.org> --- It is hanging a lammps test, so this must have something to with the lammps package. Looking a the lammps build failures: [ 7138s] The following tests FAILED: [ 7138s] 6 - AtomStyles (Timeout) [ 7138s] 7 - PairUnitConvert (Timeout) [ 7138s] 8 - PotentialFileReader (Timeout) [ 7138s] 9 - EIMPotentialFileReader (Timeout) [ 7138s] 10 - FileOperations (Timeout) [ 7138s] 11 - DumpAtom (Timeout) [ 7138s] 12 - DumpCustom (Timeout) [ 7138s] 13 - DumpCfg (Timeout) [ 7138s] 14 - SimpleCommands (Timeout) [ 7138s] 15 - LatticeRegion (Timeout) [ 7138s] 16 - KimCommands (Timeout) [ 7138s] 17 - ResetIDs (Timeout) [ 7138s] 18 - LibraryOpen (Timeout) [ 7138s] 19 - LibraryCommands (Timeout) [ 7138s] 20 - LibraryProperties (Timeout) [ 7138s] 21 - LibraryConfig (Timeout) [ 7138s] 22 - LammpsClass (Timeout) [ 7138s] 23 - InputClass (Timeout) [ 7138s] 24 - FortranOpen (Timeout) [ 7138s] 25 - FortranCommands (Timeout) [ 7138s] 26 - PythonPackage (Timeout) [ 7138s] 27 - PythonOpen (Timeout) [ 7138s] 28 - PythonCommands (Timeout) [ 7138s] 30 - PythonCapabilities (Timeout) [ 7138s] 31 - PythonPyLammps (Timeout) [ 7138s] 32 - LammpsShell (Failed) [ 7138s] Errors while running CTest It seems that is the problem, or it might be the problem in openmpi that gromacs has as well. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 Christoph Junghans <junghans@votca.org> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |junghans@votca.org Assignee|junghans@votca.org |badshah400@gmail.com Summary|FTBFS: |FTBFS: |openSUSE:Factory/votca |openSUSE:Factory/{gromacs,l |fails to build (killed |ammps,votca} fails to build |after 90 minutes without |(killed after 90 minutes |output) |without output) -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c2 --- Comment #2 from Atri Bhattacharya <badshah400@gmail.com> --- Why am I assigned this? I am not the maintainer of these packages. Anyway, it seems that several other (all of them mpi based) packages are similarly getting timed out with their tests recently: * python-mpi4py * python-pytest-mpi * sundials (so far only in the devel project and only for openmpi4) We had some discussion about this for the gromacs pkg: https://build.opensuse.org/request/show/1033722 -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 Atri Bhattacharya <badshah400@gmail.com> changed: What |Removed |Added ---------------------------------------------------------------------------- Assignee|badshah400@gmail.com |screening-team-bugs@suse.de -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 Atri Bhattacharya <badshah400@gmail.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |badshah400@gmail.com -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c3 Atri Bhattacharya <badshah400@gmail.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |eich@suse.com --- Comment #3 from Atri Bhattacharya <badshah400@gmail.com> --- @eeich Any ideas about these timeouts when running tests for packages building against openmpi? Thanks in advance for any inputs. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c4 Egbert Eich <eich@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |nmoreychaisemartin@suse.com Flags| |needinfo?(nmoreychaisemarti | |n@suse.com) --- Comment #4 from Egbert Eich <eich@suse.com> --- (In reply to Atri Bhattacharya from comment #3)
@eeich Any ideas about these timeouts when running tests for packages building against openmpi? Thanks in advance for any inputs.
Hrm, has anyone ever succeeded in running anything involving openmpi right out of the box? ;p It's quite ambitious to run a test job involving openmpi inside OBS - granted this is a single node test, but still... Of course it doesn't help if package test suites suppress any output data that may give a clue. Has anyone succeeded in getting these tests to work locally - using 'osc build' - in a chroot, in a VM? I'm adding Nicolas as he might have an idea... I don't have the time to have a deep dive into this, however, we could work with a maintainer of an affected package to see whether we can come up with a solution together - which may be valid for other packages as well. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c5 Daniel Garcia <daniel.garcia@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |daniel.garcia@suse.com --- Comment #5 from Daniel Garcia <daniel.garcia@suse.com> --- Looks like setting pml=ob1 make it work, I've just done that for: * python-mpi4py * python-pytest-mpi -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c6 Atri Bhattacharya <badshah400@gmail.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |stefan.bruens@rwth-aachen.d | |e --- Comment #6 from Atri Bhattacharya <badshah400@gmail.com> --- (In reply to Egbert Eich from comment #4)
Has anyone succeeded in getting these tests to work locally - using 'osc build' - in a chroot, in a VM?
Yes, oddly tests mostly seem to work locally (Stefan says gromacs builds locally for him [1], sundials works for my local build). Stefan, cc'ing you since you have seen this issue with gromacs first hand. [1] https://build.opensuse.org/request/show/1033722 -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c7 --- Comment #7 from Atri Bhattacharya <badshah400@gmail.com> --- (In reply to Daniel Garcia from comment #5)
Looks like setting pml=ob1 make it work, I've just done that for:
* python-mpi4py * python-pytest-mpi
Many thanks for hunting this down! Will this be done for the openmpi packages so that mpiexec sets this directly, or should we do this for each package in its specific specfile? -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c10 --- Comment #10 from OBSbugzilla Bot <bwiedemann+obsbugzillabot@suse.com> --- This is an autogenerated message for OBS integration: This bug (1205139) was mentioned in https://build.opensuse.org/request/show/1034513 Factory / gromacs -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c11 --- Comment #11 from Christoph Junghans <junghans@votca.org> --- I think, as part of this whole rebuild chain we should make lammps a multibuild as well. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c13 --- Comment #13 from OBSbugzilla Bot <bwiedemann+obsbugzillabot@suse.com> --- This is an autogenerated message for OBS integration: This bug (1205139) was mentioned in https://build.opensuse.org/request/show/1035014 Factory / python-mpi4py -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c15 --- Comment #15 from OBSbugzilla Bot <bwiedemann+obsbugzillabot@suse.com> --- This is an autogenerated message for OBS integration: This bug (1205139) was mentioned in https://build.opensuse.org/request/show/1035092 Factory / python-mpi4py -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1205139 http://bugzilla.opensuse.org/show_bug.cgi?id=1205139#c16 --- Comment #16 from OBSbugzilla Bot <bwiedemann+obsbugzillabot@suse.com> --- This is an autogenerated message for OBS integration: This bug (1205139) was mentioned in https://build.opensuse.org/request/show/1035099 Factory / python-pytest-mpi -- You are receiving this mail because: You are on the CC list for the bug.
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