[gmx-users] decomposition error
Chang Woon Jang
changwoonjang at gmail.com
Sat Jul 23 03:04:59 CEST 2016
Dear Mark Abraham,
Thank you for the details. Do 27, 18, or 12 mean -dds option or
something else? How can I set up proper DD option?
Thank you for your advice.
Best regards,
Changwoon Jang
On Fri, Jul 22, 2016 at 8:58 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Well, is it reasonable that your system has a dihedral where the furthest
> particles are 1.4nm apart? If so, then your system is quite small with
> respect to the range of interactions within it, and as that output notes
> mdrun is limited to three ranks in each direction. So 27, 18 or 12 can give
> you more joy
>
> Mark
>
> On Sat, 23 Jul 2016 01:42 Chang Woon Jang <changwoonjang at gmail.com> wrote:
>
> > 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
> > --
> > 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.
> >
> --
> 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.
>
More information about the gromacs.org_gmx-users
mailing list