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

[Mark Abraham]

Hi,

You're not compiling properly for your cluster, which might have different
hardware in different places. Read its docs and talk to your admins.

Mark

On Mon, Sep 18, 2017 at 4:07 AM Vidya R <vidyadevi2811 at gmail.com> wrote:

> 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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