[gmx-developers] Possible bug in gmx

[Alexey Shvetsov]

Hi Berk!

Its not a cut and paste error, also there are no pdb dumps.
Also I see this error before with other systems.

I can provide tpr file for that system


https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr


Berk Hess писал 28-09-2014 16:37:
> 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
>>>>> -- Gromacs Developers mailing list
>>>>> 
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>>>>> [2]
>>>>> before posting!
>>>>> 
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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
>> 

-- 
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