[gmx-developers] distance restraints and domain decomposition

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 7 07:02:58 CEST 2018

Den 2018-06-06 kl. 15:07, skrev Kutzner, Carsten:
> Dear developers,
> we have a ~ 40,000 atom MD system with distance restraints (bond type 6)
> that does not want to run in parallel, although I assume it should.
> It runs fine without DD, e.g. -ntmpi 1 -ntomp 20, however with DD the
> following happens:
> mdrun -ntmpi 2
> Fatal error:
> There is no domain decomposition for 2 ranks that is compatible with the given
> box and a minimum cell size of 11.4939 nm
> The maximum distance restraint distance is however at 4.0 nm, so 11.49 nm as
> reported cannot be true, unless the PBC distance is not taken properly
> into account. Is this the expected behaviour or worth generating a redmine
> issue?
> Thanks,
>   Carsten
Which version?

It should work with OpenMP anyway.

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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