[gmx-developers] Possible bug in gmx

[Mark Abraham]

Hi,

It's hard to say on that information. There were some issues fixed in the
lead-up to GROMACS 5 with DD not always working with 2 domains in a
direction, but that's a pure guess. I'd assume you can reproduce this with
release-5-0 branch. Do you observe it with a single domain? If not, then
it's surely a bug (and should be submitted to redmine).

Mark

On Sun, Sep 28, 2014 at 11:18 AM, Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>
wrote:

> Hi all!
>
> I'm doing some tests with small peptide and constantly getting this error.
> I get it with few systems.
>
> Systems sizes are around 10k or 20k
> I run it on 4 or 8 old nodes each with two xeon 54xx series
>
> starting mdrun '2ZCH_3 in water'
> 50000000 steps, 100000.0 ps (continuing from step 1881000,   3762.0 ps).
>
> Step 13514000:
> The charge group starting at atom 6608 moved more than the distance
> allowed by the domain decomposition (1.112924) in direction X
> distance out of cell -1.193103
> Old coordinates:    5.467    0.298    3.636
> New coordinates:    5.467    0.298    3.636
> Old cell boundaries in direction X:    4.037    5.382
> New cell boundaries in direction X:    4.089    5.452
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.1-dev-20140922-20c00a9-dirty-unknown
> Source code file: /var/tmp/alexxy/portage/sci-chemistry/gromacs-9999/work/
> gromacs-9999/src/gromacs/mdlib/domdec.cpp, line: 4388
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov, PhD
> Department of Molecular and Radiation Biophysics
> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
> Leningrad region, Gatchina, Russia
> mailto:alexxyum at gmail.com
> mailto:alexxy at omrb.pnpi.spb.ru
> --
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