On Thu, Mar 31, 2016 at 9:25 PM, Smith, Micholas D. <smit...@ornl.gov> wrote:
> Hi, > > Good to know. I'll ask the supercomputing folks to update gromacs from > 5.0.4 to 5.0.7 at the next scheduled downtime. > I don't think the machine needs to be offline just to install a version of GROMACS. ;) > -Micholas > > ________________________________________ > 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 3:22 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Error: Lost Particles while sorting > > Hi, > > I was thinking of http://redmine.gromacs.org/issues/1153 but on general > principles that should not have showed up in 5.0. Nonetheless the early 5.0 > versions had enough GPU-related issues that you still want to follow my > suggestion and see how you go. > > Mark > > On Thu, 31 Mar 2016 20:11 Smith, Micholas D. <smit...@ornl.gov> wrote: > > > 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? 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