[gmx-users] em mdrun

[Nick]

Hello Justin,

I forgot to say that with 16 nodes I am getting message below. I search the
list and used -pd option but it takes much much loner than one processor!

-------------------------------------------------------
Program mdrun, VERSION 4.5.3
Source code file: domdec.c, line: 6428

Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 4.56121 nm
Change the number of nodes or mdrun option -rdd
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
-------------------------------------------------------


On 24 February 2011 16:21, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Nick wrote:
>
>> Hello all,
>>
>> When I issue mdrun  program for EM altough this is not a parallel
>> simulation, 6 nodes are getting involved.
>>
>> I am using 4.5.3 and get the error:
>>
>> Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision)
>> Starting 16 threads
>>
>> Does anyone have idea why is this happening?
>>
>>
> mdrun now uses thread-based parallelization by default, using all available
> nodes.  To suppress this effect, use mdrun -nt 1.  Otherwise, yes, it is a
> parallel calculation :)
>
> -Justin
>
>  Thanks
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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