[gmx-users] Software inconsistency error with version 2016.1

[Mark Abraham]

Hi,

This is generally one of many final stages of a simulation blowing up. That
one degree of parallelism does or does not show the symptoms is merely
related to the fact that the simulation proceeds equivalently, but
differently, at different numbers of ranks.

Mark

On Fri, 27 Jan 2017 11:55 Qasim Pars <qasimpars at gmail.com> wrote:

> Dear gmx users,
>
> When I type gmx mdrun -v -deffnm npt, I get the below error in the NPT step
> for a few protein-ligand complexes that have the different atom numbers.
> But with -nt 16 I don't get it. For instance, the number of atoms in a
> system is ~40000. That works with -nt 16 flag (gmx mdrun -v -deffnm npt -nt
> 16).
> I would ask you how can I fix that error and use all cores (32 cores with
> hyperthreading) on my machine?
> By the way, gmx mdrun -v  npt -ntmpi 4 -ntomp 8 gives the same error.
>
> Error:
>
> Program:     gmx mdrun, version 2016.1
> Source file: src/gromacs/domdec/domdec_topology.cpp (line 238)
> MPI rank:    23 (out of 32)
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
>
> Any help will be appreciated.
>
> --
> Qasim Pars
> --
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