Thank you for your suggestion. It was helpful for me.
On Wed, Aug 28, 2019 at 2:26 PM Horn, Anselm <anselm.horn.fau.de> wrote:
> Dear Leena,
>
> in the past, I observed a crash of MD-executables on our HPC systems
> unless I unlimited the stacksize in the shell.
> I put the following in my bash-jobscript just before the invocation of
> pmemd:
> ulimit -s unlimited
> Maybe this is helpful for you as well.
>
> Regards,
>
> Anselm
>
> ________________________________________
> Von: Leena Aggarwal <leena.hrc.gmail.com>
> Gesendet: Mittwoch, 28. August 2019 09:31:31
> An: AMBER Mailing List
> Betreff: Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation
> fault" while running MD simulation production run
>
> I am running calculation on HPC resource. I am able to run simulation for
> other systems in AMBER 18. I have tried both with sander.MPI as well as
> with pmemd.MPI for this system but it is giving the error as I have
> mentioned in the previous mail. Till NVT equilibration, it is running
> absolutely fine, however it is giving the error for the NPT production run.
>
> On Tue, Aug 27, 2019 at 8:43 PM Andrew Sugarman <axs1724.case.edu> wrote:
>
> > Leena,
> >
> > Are you running calculations locally or on an HPC resource? I have
> > encountered segmentation faults in the past when the instruction logs for
> > CPUs have been updated or changed. From the output file, it looks like
> the
> > executable 'sander.MPI' is not being recognized. Are you able to run any
> > other AMBER18 executables in your current environment?
> >
> > Best,
> > Andrew Sugarman
> >
> > On Tue, Aug 27, 2019 at 10:03 AM Leena Aggarwal <leena.hrc.gmail.com>
> > wrote:
> >
> > > Dear Amber Users
> > >
> > > I am getting an error *forrtl: severe (174) : SIGSEGV, segmentation
> > fault*
> > > error while running the MD simulation production run in AMBER18.
> > > The simulation is smoothly running without any error in AMBER 12 but
> > > giving the above mentioned error in AMBER 18.
> > >
> > > For the reference, I have attached the logfile or error file.
> > >
> > > From
> > > Leena Aggarwal
> > > University of Delhi
> > > India
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Aug 28 2019 - 05:00:02 PDT
