[gmx-users] Multi-node Replica Exchange Segfault

[Mark Abraham]

Hi,

I've never heard of such. You could try a multisim without -replex, to help
diagnose.

Mark

On Fri, 30 Oct 2015 03:33 Barnett, James W <jbarnet4 at tulane.edu> wrote:

> Good evening here,
>
> I get a segmentation fault with my GROMACS 5.1 install only for replica
> exchange
> simulations right at the first successful exchange on a multi-node run.
> Normal
> simulations across multiple nodes work fine, and replica exchange
> simulations on
> one node work fine.
>
> I've reproduced the problem with just 2 replicas on 2 nodes with GPU's
> disabled
> (-nb cpu). Each node has 20 CPU's so I'm using 20 MPI ranks on each
> (OpenMPI).
>
> I get a segfault right when the first exchange is successful.
>
> The only other error I get sometimes is that the Infiniband connection
> timed out
> retrying the communication between nodes at the exact same moment as the
> segfault, but I don't get that every time, and it's usually with all
> replicas
> going (my goal is to do 30 replicas on 120 cpus). No other error logs, and
> mdrun's log does not indicate an error.
>
> PBS log: http://bit.ly/1P8Vs49
> mdrun log: http://bit.ly/1RD0ViQ
>
> I'm currently troubleshooting this some with the sysadmin, but I wanted to
> check
> to see if anyone has had a similar issue or any further steps to
> troubleshoot.
> I've also searched the mailing list and used my Google-fu, but it has
> failed me
> so far.
>
> Thanks for your help.
>
> --
> James "Wes" Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
>
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarnet4 at tulane.edu
> --
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