[gmx-users] mdrun_mpi crashes for no apparent reason

Mehmet Suezen suzen at theochem.tu-muenchen.de
Tue Jul 2 10:46:05 CEST 2002

Hi Vishal,
May be analyizing debug files md.out would give you an idea. If you are
4 cpu then networking also will play a role or due to NFS. *I had such a
behavior with
MPICH. I would suggest you to update LAM-MPI lam-6.5.6.

Good luck,


Vishal Vaidyanathan wrote:
> Hi,
>   I am using mdrun_mpi from release 3.1.4 and I am facing the following
> problem: the program stops executing and crashes without warning or error
> to stderr or log. This does not seem to be a simulation issue since
> resuming the run from the last frame works fine.  There are no LINCS
> warnings or errors. I get several hours to 1-2 days of runtime before a
> crash.
>   Any ideas why this could be happening? Seems to be some technical issue
> rather than a simulation problem.
>   System:
>           SMP dual athlons, Suse linux 8.0, kernel 2.4.18-64GB-SMP
>           LAM MPI, lam-6.5.4-usysv.1, from gmx webpage
>           fftw packages from gmx webpage
>           Everything was installed from the rpm's provided
>   I'm using MPI only for processors on the same board - ie. nothing should
> really be depending on the network, so I don't think it's a networking
> issue either. And there's ample disk space.
>   Sometimes while using tpbconv to resume, I get a SIGSEGV when it reads
> the last frame of the trajectory (no incomplete frame warning, just
> SIGSEG). Have to use the -time option to resume in that case. But
> mosttimes I get the "incomplete frame" warning and tpbconv exits normally.
>   Has anybody else noticed such behaviour? It's hard to guess what's wrong
> because there's absolutely no error message...
>   Any suggestions are welcome.
>   Thanks,
>                                                                 Vishal
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