[gmx-users] domain decomposition

[Justin Lemkul]

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

==================================================