[gmx-users] Multi-node Replica Exchange Segfault
mark.j.abraham at gmail.com
Fri Oct 30 09:15:01 CET 2015
I've never heard of such. You could try a multisim without -replex, to help
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
> simulations right at the first successful exchange on a multi-node run.
> 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
> (-nb cpu). Each node has 20 CPU's so I'm using 20 MPI ranks on each
> 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
> 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
> to see if anyone has had a similar issue or any further steps to
> 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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users