[gmx-developers] Possible bug in gmx

[Alexey Shvetsov]

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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>> 
>> 
>> 
>> Links:
>> ------
>> [1] http://www.gromacs.org/Documentation/Errors
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>> [4] 
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> 
> --
> 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