Hey Mark, On Fri, 2015-10-30 at 08:14 +0000, Mark Abraham wrote: > Hi, > > I've never heard of such. You could try a multisim without -replex, to help > diagnose.
A multidir simulation runs without issue when -replex is omitted. > > On Fri, 30 Oct 2015 03:33 Barnett, James W <jbarn...@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 jbarn...@tulane.edu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * 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-requ...@gromacs.org.