[gmx-users] fatal error with mpi

Stefano Guglielmo stefano.guglielmo at unito.it
Thu Jun 21 14:36:03 CEST 2018

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
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

Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178

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