[gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

Vidya R vidyadevi2811 at gmail.com
Mon Sep 18 04:06:52 CEST 2017


Thank you for your reply.

When I try to run my job in a single processor through qsub command, (by
feeding the gromacs mdrun command in script file), it says SEGMENTATION
FAULT, CORE DUMPED...


But, when I run my job in login node (which we are not supposed to do), it
works very well...


Can you comment on this?


Thanks,
Vidya.R

On Mon, Sep 18, 2017 at 2:50 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You're running a thread-MPI version of GROMACS, which is probably not what
> you want to do if you're running mpirun. It should work even so, but
> whatever quirks exist with SGE are unfortunately between you, its docs and
> your cluster's docs and admins :-(
>
> Mark
>
> On Sun, Sep 17, 2017 at 7:23 AM Vidya R <vidyadevi2811 at gmail.com> wrote:
>
> > My log file is provided in the link below
> >
> > Can you please look into it and let me know why the error arises?
> >
> > I am feeding my commands in SGE cluster.   When I run it in my login
> node,
> > gmx mdrun -v -deffnm eql runs well
> >
> >
> > But, through qsub command, (with 8 processors) It says,
> >
> > mpirun noticed that process rank 7 with PID 19160 on node
> > compute-0-28.local exited on signal 11 (Segmentation fault).
> >
> > Please help me.
> >
> > I am unable to figure out, as to whether the problem is with the version
> of
> > gromacs or the method of compiling.
> >
> >
> >
> > https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/
> view?usp=sharing
> > --
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