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Re: [lammps-users] mprun error
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Re: [lammps-users] mprun error


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 21 May 2018 09:48:45 -0400



On Mon, May 21, 2018 at 6:39 AM, bahman daneshian <bahmanpbamp@...24...> wrote:
Dear LAMMPS and HPC experts, 

I am trying to run lammps on HPC. We installed LAMMPS (16 Mar 2018). So, lammps correctly works for small models. However, it seems that when the model becomes large(in order of 100 nm), computation cannot start and we face with this error:

mpirun noticed that process rank 56 with PID 0 on node node03 exited on signal 9 (Killed).

 please let me know whether you have any idea to solve this issue or not.

​please note, that this is not a well formulated question: when i would answer it accurately, i would have to tell you "yes" and nothing else.

​going beyond that, this doesn't look like a LAMMPS specific problem at all, but rather something related to the machine you are running on. the fact, that this is triggered by a large system size hints at you running out of available RAM on the nodes, you are running on. this is something that you have to work out with your local system managers. so my suggestion is that you work with them to determine what is causing this (i.e. whether your jobs trigger the OOM killer feature).

axe.

​[...]​

-
mpirun noticed that process rank 56 with PID 0 on node node03 exited on signal 9 (Killed).


Yours Sincerey,
Bahman Daneshian

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.