[gmx-users] Segmentation fault on HPC

[Mark Abraham]

Hi,

What do the ends of  the .log files say?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up is a heavy
favourite.

Mark

On Sat, Jan 3, 2015 at 1:56 PM, Tomek Wlodarski <tomek.wlodarski at gmail.com>
wrote:

> Hi,
>
> I am trying to set up simulation on HPC.
> Energy minimization in vacuum and in water works great (using 4 nodes with
> 96 cores altogether)
> But when I am trying to run standard md with:
>
> aprun -n 96 mdrun_mpi -v -deffnm md >& out
>
> I always end up with this error (I tried it also on different gromacs
> versions: 4.6.5, 5.0, 5.0.4):
>
>
> starting mdrun 'Protein in water'
> 500000 steps,   1000.0 ps.
> step 0
>
> NOTE: Turning on dynamic load balancing
>
> _pmiu_daemon(SIGCHLD): [NID 00383] [c1-0c2s15n3] [Sat Jan  3 12:26:44 2015]
> PE RANK 72 exit signal Segmentation fault
> _pmiu_daemon(SIGCHLD): [NID 00380] [c1-0c2s15n0] [Sat Jan  3 12:26:44 2015]
> PE RANK 1 exit signal Segmentation fault
> _pmiu_daemon(SIGCHLD): [NID 00382] [c1-0c2s15n2] [Sat Jan  3 12:26:44 2015]
> PE RANK 48 exit signal Segmentation fault
> [NID 00380] 2015-01-03 12:26:44 Apid 12376091: initiated application
> termination
> Application 12376091 exit codes: 139
> Application 12376091 exit signals: Killed
> Application 12376091 resources: utime ~16s, stime ~8s, Rss ~63064, inblocks
> ~363834, outblocks ~1173496
>
>
> Do you have any suggestion what is wrong (why I can run EM not MD?)? I
> checked different system and gromacs run ok.
> Thanks.
> Best,
>
> tomek
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