[gmx-developers] mdrun hanging in pdb2gmx tests

[Szilárd Páll]

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