[gmx-users] fatal error with mpi

[Stefano Guglielmo]

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>
> > --
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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