Hi, Currently I'm running this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html) to simulate restart with fewer nodes. at restart, I changed the amount of nodes from 3 to 2 nodes. I also changed the amount of processes from 24 to 16 processes.
While the application is running, I tried to see the output file. This is the content of the output file : #########################output file######################## Reading checkpoint file md_0_1.cpt generated: Sat May 14 13:10:25 2016 #ranks mismatch, current program: 16 checkpoint file: 24 #PME-ranks mismatch, current program: -1 checkpoint file: 6 GROMACS patchlevel, binary or parallel settings differ from previous run. Continuation is exact, but not guaranteed to be binary identical. Using 16 MPI processes Using 1 OpenMP thread per MPI process starting mdrun 'LYSOZYME in water' 500000 steps, 1000.0 ps (continuing from step 54500, 109.0 ps). ############################################################################ I got a mismatch note as described in the output file above. it is not a problem, isn't it ? I just want to make sure. is it not allowed to use a different user when we restart simulation from checkpoint file ? Previously, I failed to restart simulation based on checkpoint file. I guess, it is failed because I used a different user (Only a guess). Thank you in advance. regards, Husen On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/13/16 8:53 PM, Husen R wrote: > >> Dear all >> >> Does simulation able to be restarted from checkpoint file with fewer >> nodes ? >> let's say, at the first time, I run simulation with 3 nodes. At running >> time, one of those nodes is crashed and the simulation is terminated. >> >> I want to restart that simulation immadiately based on checkpoint file >> with >> the remaining 2 nodes. does gromacs support such case ? >> I need help. >> > > Have you tried it? It should work. You will probably get a note about > the continuation not being exact due to a change in the number of cores, > but the run should proceed fine. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.