Hi Mark, Thanks for replying on this email. I forgot to reply again and mention that it was not a bug. I could fix it simply by following some instructions in:
https://docs.computecanada.ca/wiki/GROMACS It is working perfectly fine now (GPU with version 2016.3) Here are two things I changed in my script when submitted the jobs on the cluster: 1) replacing "srun" with "mpiexec" 2) including the following line and removing the -ntomp 1 in mdrun command export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}" Cheers, Mohsen On Fri, Oct 13, 2017 at 4:02 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Unfortunately that will just get lost in my inbox, and anyway I will have > to go and make the redmine issue. We need that (rather than email) because > multiple people might find the issue and need to be able to search for the > answer. Also, somebody else fixing the issue won't be able to contact you > easily if we need to follow up to get further information, or check that > the issue is resolved. > > To file a request, please follow the link on https://redmine.gromacs.org/ > after > you register an account. All quite easy, I hope! Do let us know if some > aspect is hard. > > Mark > > On Thu, Aug 31, 2017 at 3:04 PM Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > > Hi Mark, > > > > Thanks for your reply. > > I tried but I was not sure how to do so. > > May I send the corresponding files to your personal email, instead? > > > > Cheers, > > Mohsen > > > > > > On Wed, Aug 30, 2017 at 6:25 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > That particular output indicates that the code is not working as > > intended. > > > Please open an issue on the GROMACS redmine and attach the tpr, the log > > > file from your run, and and instructions on how to reproduce. > > > > > > Thanks, > > > > > > Mark > > > > > > On Wed, 30 Aug 2017 19:34 Mohsen Ramezanpour < > > ramezanpour.moh...@gmail.com > > > > > > > wrote: > > > > > > > Dear Gromacs users, > > > > > > > > I am running simulations using Gromacs version 2016.3 while using > GPU. > > > > > > > > I get an error in my simulations as follows: > > > > > > > > Program: gmx mdrun, version 2016.3 > > > > Source file: src/gromacs/mdlib/nbnxn_grid.cpp (line 404) > > > > MPI rank: 15 (out of 16) > > > > > > > > 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 > > > > > > > > > > > > Googling the error I found that there were relevant bugs before > > > (discussed > > > > by Dr. Berk Hess): > > > > > > > > https://redmine.gromacs.org/issues/1379 > > > > > > > > https://redmine.gromacs.org/issues/1153 > > > > > > > > However, they should have been fixed in the newer versions as > mentioned > > > in > > > > the above links. > > > > > > > > Can someone please let me know what the problem could be in this > case? > > > > > > > > Many thanks in advance, > > > > > > > > Cheers, > > > > Mohsen > > > > -- > > > > *Rewards work better than punishment ...* > > > > -- > > > > 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. > > > > > > > > > > > -- > > *Rewards work better than punishment ...* > > -- > > 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. > -- *Rewards work better than punishment ...* -- 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.