Thanks, Mark. I didn't see this bug noted in the bug list so I thought I was just going crazy
=================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Thursday, March 31, 2016 2:57 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error: Lost Particles while sorting Hi, Starting a new series of calculations on the earliest of a series of patch releases means you have chosen to accept all the bugs that have been fixed since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed. Mark On Thu, 31 Mar 2016 19:40 Smith, Micholas D. <smit...@ornl.gov> wrote: > Dear other users (and developers) > > > I moved some simulations that were working pretty well on one > supercomputer to another (the previous one did not have gpu nodes) to take > advantage of some gpus, but I am now getting a sporadic error: > > > ---- > > Program gmx_mpi, VERSION 5.0 > Source code file: > /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom > acs/mdlib/nbnxn_search.c, line: 728 > > Software inconsistency error: > Lost particles while sorting > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > ----- > > > in one of my simulations (but not the others), when I start to use more 16 > MPI processes per simulation. I should note that I am using mdrun -multidir > in order to launch these simulations at the same time, and it doesn't seem > to be a specific simulation that it causing the issue. Additionally, it is > rather sporadic, sometimes the simulations will run with no problems, other > times it run for 2 minutes and then fails (and I get stuck back in the > queue). Any ideas? > > > > =================== > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > -- > 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. > -- 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. -- 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.