[gmx-users] Bug?! Lost particles while sorting

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 19 10:47:03 CEST 2017


Hi,

Such changes are merely cosmetic, and are at best hiding the real issue by
allowing the simulation to run slightly differently. It may recur later.
There are other users reporting issues leading to this error, and we would
like a bug report from at least one of them, so we can have a chance to
understand and maybe fix the problem :-)

Mark

On Thu, 19 Oct 2017 03:36 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
wrote:

> 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.abraham at 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.mohsen at 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.abraham at 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.mohsen at 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 ...*
> > > > > --
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