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

[Mohsen Ramezanpour]

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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-- 
*Rewards work better than punishment ...*