[gmx-users] em mdrun

[Justin A. Lemkul]

Nick wrote:
> 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!
> 

Some systems just don't scale particularly well.

> -------------------------------------------------------
> 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
> -------------------------------------------------------
> 

Seems like you've got something weird going on.  Most normal systems shouldn't 
require such a large cell size.

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

The .log file may provide more useful diagnostic information.

-Justin

> 
> On 24 February 2011 16:21, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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-- 
========================================

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

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