[gmx-users] decomposition error

Chang Woon Jang changwoonjang at gmail.com
Sat Jul 23 01:42:26 CEST 2016


Dear Justin Lemkul,

   I have looked at the log file as below.

Initializing Domain Decomposition on 16 ranks

Dynamic load balancing: auto

Will sort the charge groups at every domain (re)decomposition

Initial maximum inter charge-group distances:

    two-body bonded interactions: 0.668 nm, Tab. Bonds, atoms 1277 1278

  multi-body bonded interactions: 1.460 nm, Tab. Dih., atoms 1226 1229

Minimum cell size due to bonded interactions: 1.500 nm

Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25

Optimizing the DD grid for 16 cells with a minimum initial size of 1.875 nm

The maximum allowed number of cells is: X 3 Y 3 Z 3


Does this mean that I need to use "-dds 1.25" mdrun option?

Thank you.

Best regards,
Changwoon Jang

On Fri, Jul 22, 2016 at 7:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/22/16 7:03 PM, Chang Woon Jang wrote:
>
>> Dear Justin A. Lumkul,
>>
>>    Thank you for your answer. I am sorry for asking what is DD. My
>> topology
>> topol.top file is below. Would you please tell me about what is DD? How
>> can
>> I set up in topology file?
>>
>>
> DD = domain decomposition.  Please look in the .log file for how it is
> being set up and provide that information if you need help troubleshooting
> it.  Also use Google; this error comes up (and gets solved) every couple of
> days.
>
> -Justin
>
>
> Thank you.
>>
>> Best regards,
>> Changwoon Jang
>>
>>
>>
>> [ defaults ]
>>
>> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>>
>>   1             1               no              0.0     0.0
>>
>>
>> [ atomtypes ]
>>
>> ;type    mass    charge       ptype          sigma      epsilon
>>
>>  A     75.087799  0.000       A        1.000000000  1.000000000
>>
>>  B     76.097998  0.000       A        1.000000000  1.000000000
>>
>>  C     42.080999  0.000       A        1.000000000  1.000000000
>>
>>  D     74.103099  0.000       A        1.000000000  1.000000000
>>
>>  E     99.153398 0.000       A        1.000000000  1.000000000
>>
>>  F     116.160799  0.000       A        1.000000000  1.000000000
>>
>>  G     58.080399 0.000       A        1.000000000  1.000000000
>>
>>
>> [ moleculetype ]
>>
>> DGA 3
>>
>>
>> [atoms]
>>
>> ; nr type resnr residue atom cgnr charge mass
>>
>> 1 A 1 DGA A1 1 0.000000 75.087799
>>
>> 2 B 1 DGA B1 2 0.000000 76.097998
>>
>> 3 C 1 DGA C 3 0.000000 42.080999
>>
>> 4 B 1 DGA B2 4 0.000000 76.097998
>>
>> 5 A 1 DGA A2 5 0.000000 75.087799
>>
>>
>>
>> [ bonds ]
>>
>> 1 2  8 1  1.0 ; 1:bond:1
>>
>> 2 3  8 1  1.0 ; 1:bond:2
>>
>> 3 4  8 1  1.0 ; 1:bond:3
>>
>> 4 5  8 1  1.0 ; 1:bond:4
>>
>>
>> [ angles ]
>>
>> 1 2 3  8 1 1.0 ; 1:angle:1
>>
>> 2 3 4  8 1 1.0 ; 1:angle:2
>>
>> 3 4 5  8 1 1.0 ; 1:angle:3
>>
>>
>> [ dihedrals ]
>>
>> 1 2 3 4  8 1 1.0 ; 1:ABCBdihedral:1
>>
>> 2 3 4 5  8 1 1.0 ; 1:ABCBdihedral:2
>>
>>
>> [ moleculetype ]
>>
>> J400 3
>>
>>
>> [atoms]
>>
>> ; nr type resnr residue atom cgnr charge mass
>>
>> 1 D 1 J400 D1 1 0.000000 74.103099
>>
>> 2 E 1 J400 E1 2 0.000000 99.153398
>>
>> 3 F 1 J400 F1 3 0.000000 116.160799
>>
>> 4 G 1 J400 G1 4 0.000000 58.080399
>>
>> 5 D 1 J400 D2 5 0.000000 74.103099
>>
>>
>> [ bonds ]
>>
>> 1 2  8 1 1.0 ; 1:bond:1
>>
>> 2 3  8 1 1.0 ; 1:bond:2
>>
>> 3 4  8 1 1.0 ; 1:bond:3
>>
>> 4 5  8 1 1.0 ; 1:bond:4
>>
>>
>> [ angles ]
>>
>> 1 2 3  8 1 1.0 ; 1:angle:1
>>
>> 2 3 4  8 1 1.0 ; 1:angle:2
>>
>> 3 4 5  8 1 1.0 ; 1:angle:3
>>
>>
>> [ dihedrals ]
>>
>> 1 2 3 4   8 1 1.0 ; 1:dihedral:1
>>
>> 2 3 4 5   8 1 1.0 ; 1:dihedral:2
>>
>>
>> [ system ]
>>
>> ; Name
>>
>> Built with Packmol
>>
>>
>> [ molecules ]
>>
>> ; Compound        #mols
>>
>> DGA       200
>>
>> J400       100
>>
>>
>> On Fri, Jul 22, 2016 at 6:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/22/16 6:50 PM, Chang Woon Jang wrote:
>>>
>>> Dear Grimaces Users,
>>>>
>>>> I have the decomposition error. I have tried to reduce the number of
>>>> cores
>>>> but still have the same problem. In my conf.gro, the cell size is about
>>>> 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm.
>>>>
>>>>  Would you please give me some comments or relevant topics addressed?
>>>>
>>>>
>>>> The .log file tells you how DD is being set up and what the the limiting
>>> interactions are.  Verify that your topology is sound from what the .log
>>> tells you.
>>>
>>> -------------------------------------------------------
>>>
>>>>
>>>> Program gmx, VERSION 5.0.7-dev-20151003-1909f2f
>>>>
>>>> Source code file:
>>>>
>>>> /home1/02271/huddack/votca_install/src/gromacs/src/gromacs/mdlib/domdec.c,
>>>> line: 6902
>>>>
>>>>
>>>> Also make sure your run isn't failing because of something due to hacked
>>> code. Development versions generally shouldn't be used for
>>> production-level
>>> science.
>>>
>>> -Justin
>>>
>>>
>>> Fatal error:
>>>>
>>>> There is no domain decomposition for 16 ranks that is compatible with
>>>> the
>>>> given box and a minimum cell size of 1.875 nm
>>>>
>>>> Change the number of ranks or mdrun option -rdd or -dds
>>>>
>>>> Look in the log file for details on the domain decomposition
>>>>
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>>
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>> -------------------------------------------------------
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj395 at drexel.edu


More information about the gromacs.org_gmx-users mailing list