[gmx-users] fatal error with mpi

[Mark Abraham]

Hi,

Recompiling won't fix anything relevant. Molecular frustration isn't just
about long bonds. Rearrangment of side chain groupings can do similar
things despite looking happy. The sudden injection of KE means collisions
can be more violent than normal, and the timestep is now too large. But you
need to look at the trajectory to understand if this might be the case.

Mark

On Fri, Jun 22, 2018 at 3:19 PM Stefano Guglielmo <
stefano.guglielmo at unito.it> wrote:

> Dear Mark,
>
> thanks for your answer. The version is 2016.5, but I apparently solved the
> problem recompiling gromacs: now the simulation is running quite stable. I
> had minimized and gradually equilibrated the system and I could not see any
> weird bonds or contacts. So in the end, as extrema ratio, I decided to
> recompile.
>
> Thanks again
> Stefano
>
> 2018-06-22 15:07 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > This could easily be that your system is actually not yet well
> equilibrated
> > (e.g. something was trapped in a high energy state that eventually
> relaxed
> > sharply). Or it could be a code bug. What version were you using?
> >
> > Mark
> >
> > On Thu, Jun 21, 2018 at 2:36 PM Stefano Guglielmo <
> > stefano.guglielmo at unito.it> wrote:
> >
> > > Dear users,
> > >
> > > I have installed gromacs with MPI instead of its native tMPI and I am
> > > encountering the following error:
> > > "Fatal error:
> > > 4 particles communicated to PME rank 5 are more than 2/3 times the
> > cut-off
> > > out
> > > of the domain decomposition cell of their charge group in dimension y.
> > > This usually means that your system is not well equilibrated."
> > >
> > > I am using 8 MPI ranks with 4 omp threads per rank (it was the
> > > configuration used on the same machine by tMPI), but I also tried 4
> ranks
> > > with 8 threads, but it did not solve the problem.
> > >
> > > I don't think this is an issue related to my system because the same
> > system
> > > run with the native tMPI works properly (it has already been termalized
> > and
> > > gradually equilibrated); neverthless I tried to reduce dt and
> temperature
> > > but without any benefit. Does anybody have any suggestions?
> > >
> > > Thanks in advance
> > > Stefano
> > >
> > > --
> > > Stefano GUGLIELMO PhD
> > > Assistant Professor of Medicinal Chemistry
> > > Department of Drug Science and Technology
> > > Via P. Giuria 9
> > > 10125 Turin, ITALY
> > > ph. +39 (0)11 6707178 <011-670%2071%2078> <011-670%2071%2078>
> > > --
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> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178 <011-670%2071%2078>
> --
> Gromacs Users mailing list
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