[gmx-users] Software inconsistency error: One or more interactions were multiple assigned in the domain decomposition

[Bogdan Costescu]

On Fri, Apr 20, 2012 at 14:49, Olivia Waring <owaring at princeton.edu> wrote:

> My invocation of mdrun, using 8 processors and the following mdp file:
> ...
> There are: 1184 Atoms
> ...
> DD  step 4 load imb.: force 181.0%
>
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells

Hi Olivia!

The translation to English would be: "you have too few atoms for a
domain decomposition on 8 processors to succeed, given the parameters
in your setup." :)

With so few atoms, you won't get much speedup, if at all, when running
on more than 1 processor. The rule of thumb posted on this very list
quite often is 1000 atoms/processor for a reasonably good scaling. To
convince GROMACS 4.5.x to use only one processor on a multi-core
machine, run with the '-nt 1' command line option.

Cheers,
Bogdan