[gmx-users] decomposition error
Chang Woon Jang
changwoonjang at gmail.com
Sat Jul 23 04:00:35 CEST 2016
Dear Mark Abraham,
I am actually using gromacs with VOTCA Package in order to obtain
non-bonded potentials using Iterative Boltzmann inversion (IBI). In the
output file, the mdrun would be the following.
gmx mdrun -v
As I described in the previous email, the error message is related to
domain decomposition. Therefore, I would like to know how to solve this
problem. The other system was ok, but this system with more bead types has
DD problem.
How can I set the mdrun options?
I appreciate your helpful advice.
Thank you.
Best regards,
Changwoon Jang
On Fri, Jul 22, 2016 at 9:50 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> You haven't given us much information about how you're running mdrun, so I
> can't tell. Much useful material is in the documentation eg.
>
> http://manual.gromacs.org/documentation/5.1.3/user-guide/mdrun-performance.html
>
> Mark
>
> On Sat, 23 Jul 2016 03:34 Chang Woon Jang <changwoonjang at gmail.com> wrote:
>
> > Dear Mark Abraham,
> >
> > I am a little confused about the number of ranks. How can I choose
> the
> > number of ranks? Is this mdrun option or something else? Is "number of
> > ranks" different with "number of processors" in parallel machine?
> >
> > Thank you very much for your help.
> >
> > Best regards,
> > Changwoon Jang
> >
> > On Fri, Jul 22, 2016 at 9:16 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Sat, 23 Jul 2016 03:05 Chang Woon Jang <changwoonjang at gmail.com>
> > wrote:
> > >
> > > > Dear Mark Abraham,
> > > >
> > > > Thank you for the details. Do 27, 18, or 12 mean -dds option or
> > > > something else?
> > >
> > >
> > > No, the number of ranks. -dds pertains to how much margin DD requires
> to
> > > make sure the largest interactions will be computable over the lifetime
> > of
> > > the decomposition as particles move. This comes back to my question
> about
> > > the ranges of your largest interactions, and how fast things move.
> > >
> > > How can I set up proper DD option?
> > > >
> > >
> > > DD will do what it can with the number of ranks you choose, but it
> can't
> > > handle factors of bigger than three for a system like yours. One way it
> > can
> > > use 16 is in a 4x2x2 grid but it can't do that.
> > >
> > > Mark
> > >
> > >
> > > > 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!
> > > > > > >>>
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> > > > > > >>>
> > > > > > >>>
> > > > > > > --
> > > > > > > ==================================================
> > > > > > >
> > > > > > > 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
> > > > > > >
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> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
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