[gmx-developers] Possible bug in gmx

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Sun Sep 28 22:08:59 CEST 2014 

Mark Abraham писал 28-09-2014 18:17:
> How about a redmine issue - this thread's not about GROMACS
> development, per se ;-)

Sorry about that =D

Redmine issue http://redmine.gromacs.org/issues/1607
With relevant tpr file attached
> 
> Mark
> 
> On Sun, Sep 28, 2014 at 3:18 PM, Alexey Shvetsov
> <alexxy at omrb.pnpi.spb.ru> wrote:
> 
>> 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 [1]
>> 
>> 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 [2] [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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> 
>  -- 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
>  --
>  Gromacs Developers mailing list
> 
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> before posting!
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> 
> Links:
> ------
> [1] https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr
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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

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