[gmx-users] fatal error with mpi

[Mark Abraham]

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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