[gmx-developers] GB Dom Decomp problem

[hess at sbc.su.se]

Hi,

This should not happen.
Did you get some information on the grid size/shift somewhere?

Berk

> Hi,
>
> I'm running a long GV simulation on 8 cores, and after tens of
> nanoseconds it crashes with this error:
>
> Program mdrun, VERSION 4.5-beta1-20100730-f9ac35b
> Source code file: /scratch/spoel/GG/gromacs/src/mdlib/domdec.c, line: 2629
>
> Fatal error:
> Step 83099555: The domain decomposition grid has shifted too much in the
> Y-direction around cell 1 0 0
>
> Original output is:
>
> Making 3D domain decomposition 2 x 2 x 2
> starting mdrun 'Generated by trjconv : MPRA t= 2000.00000'
> 100000000 steps, 200000.0 ps (continuing from step 82508605, 165017.2 ps).
> step 82508605, will finish Tue Aug 10 16:01:41 2010
>
> Simulations run with angular comm removed, so the protein should not
> move away from the center of the box.
>
> Can this be prevented?
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>