[gmx-developers] mdrun hanging in pdb2gmx tests

[Mark Abraham]

No, but I can grep for tMPI_Thread_cond_wait and work backwards to see that
this happens in communicator splitting. I would step through
gmx_setup_nodecomm and perhaps gmx_setup.

Mark


On Tue, Nov 19, 2013 at 2:25 AM, Szilárd Páll <pall.szilard at gmail.com>wrote:

> Hi,
>
> The nightly builds on the Mac build slave have been suffering from an
> issue which manifests in mdrun hanging during "make check" in one of
> the pdb2gmx tests, see:
> http://jenkins.gromacs.org/job/Coverage_Gerrit_4_6/297/
> http://jenkins.gromacs.org/job/Coverage_Gerrit_4_6/299/
>
> Looking at the working directory I could not decipher in which tests
> did it get stuck with and I've no idea why and attaching a debugger to
> mdrun did not help much either:
> Attaching to process 43196.
> Reading symbols for shared libraries . done
> Reading symbols for shared libraries
> ......................................... done
> Reading symbols for shared libraries + done
> 0x00007fff903e2bca in __psynch_cvwait ()
> (gdb) bt
> #0  0x00007fff903e2bca in __psynch_cvwait ()
> #1  0x00007fff92e7c274 in _pthread_cond_wait ()
> #2  0x000000010341d195 in tMPI_Thread_cond_wait ()
> Previous frame inner to this frame (gdb could not unwind past this frame)
>
> Does anybody have an idea what's going on?
>
> Cheers,
> --
> Szilárd
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