[gmx-users] GROMACS 5.1.0 crashes on pbs queue system

[Mark Abraham]

Hi,

That error message is from mpirun, which does not clearly inform us. Look
at the log files and terminal output from mdrun. And don't install 5.1 when
you have the option of installing the latest in the series of bug-fix
releases from that time.

Mark

On Thu, 16 Feb 2017 08:50 Neha Gandhi <n.gandhiau at gmail.com> wrote:

> Dear List,
>
> I have compiled gromacs 5.1.0 using MPI. The job runs interactively as well
> as through pbs submission using two nodes. However, the job crashes
> immediately when I submit more than two jobs. Below is the error:
> --------------------------------------------------------------------------
> mpirun noticed that process rank 18 with PID 153374 on node
> cl2n045.ib0.hpc.qut.edu.au exited on signal 4 (Illegal instruction).
> --------------------------------------------------------------------------
> 24 total processes killed (some possibly by mpirun during cleanup)
>
> -----
> PBS Job 1662894.pbs
> CPU time  : 00:00:34
> Wall time : 00:00:05
> Mem usage : 256kb
>
> Any input is much appreciated.
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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