[gmx-users] domain decomposition

[Dhrubajyoti Maji]

Thank you sir. The problem is sorted out. Decreasing number of processors
did the trick. Thanks again

On Wed, 21 Aug 2019 at 22:02, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/21/19 12:30 PM, Dhrubajyoti Maji wrote:
> > Many tanks Dr. Lemkul for your kind reply. I have checked the link. I
> have
> > done the equlibration step successfully but the error appears at
> production
> > run. The change is only that now I am writing the output trajectory. So,
> if
> > I had any problem in topology or mdp file then I think my equilibration
> > should have been failed. I am a newbie and I can't understand what
> exactly
> > is going wrong. Any kind of suggestion will be highly appreciated.
>
> Use fewer processors. You can't arbitrarily split any system over a
> given number of processors. Prior runs may have worked if, for instance,
> box dimensions were different, but now you have to adjust.
>
> -Justin
>
> > Thanks and regards.
> > Dhrubajyoti Maji
> >
> >
> > On Wed, 21 Aug 2019 at 16:21, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 8/21/19 1:00 AM, Dhrubajyoti Maji wrote:
> >>> Dear all,
> >>>       I am simulating a system consisting urea molecules. After
> >> successfully
> >>> generating tpr file while I am trying to run mdrun, the following error
> >> is
> >>> appearing.
> >>> Fatal error:
> >>> There is no domain decomposition for 72 ranks that is compatible with
> the
> >>> given box and a minimum cell size of 0.5924 nm
> >>> Change the number of ranks or mdrun option -rcon or -dds or your LINCS
> >>> settings.
> >>> All bonds are constrained are by LINCS algorithm in my system and
> >> dimension
> >>> of my box is 3.40146 nm. I have checked gromacs site as well as mailing
> >>> list but couldn't understand what to do. Please help me with the issue.
> >>
> >>
> http://manual.gromacs.org/current/user-guide/run-time-errors.html#there-is-no-domain-decomposition-for-n-ranks-that-is-compatible-with-the-given-box-and-a-minimum-cell-size-of-x-nm
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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