[gmx-developers] Possible bug in gmx

[Berk Hess]

Hi,

I assume that your old and be coordinates being identical is correct and 
not a cut-and-paste error.
This seems a bit strange or do you freeze part of the system?
The only things moving here are then the domain boundaries and I don't 
see an issue there, since they only moved a little.

Do you have any more output besides the error message? PDB dump files maybe?

Cheers,

Berk

On 09/28/2014 02:22 PM, Alexey Shvetsov wrote:
> Hi,
>
> just wanna add that this error seems to be reproducable even on single 
> node. Also i get same error for gpu runs.
> However i dont see it in large systems (800k+ atoms) running on large 
> number of cpus (512+)
>
> Alexey Shvetsov писал 28-09-2014 13:44:
>> Hi,
>>
>> DD grid is
>>
>> Domain decomposition grid 4 x 1 x 1, separate PME ranks 0
>> PME domain decomposition: 4 x 1 x 1
>>
>> for 4 node setup
>>
>> and
>>
>> Domain decomposition grid 4 x 2 x 1, separate PME ranks 0
>> PME domain decomposition: 4 x 2 x 1
>>
>> for 8 node setup
>>
>> It's reproducable with 5.0 release and latest git master. I try to
>> check if its reproducable with 1 node. Also i can provide tpr file for
>> this system
>>
>> Mark Abraham писал 28-09-2014 13:28:
>>> 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 [1]
>>>> -------------------------------------------------------
>>>>
>>>> -- 
>>>> 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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>>>>
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>>>
>>>
>>>
>>> Links:
>>> ------
>>> [1] http://www.gromacs.org/Documentation/Errors
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>>> [4] 
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>>
>> -- 
>> 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
>