Hello Justin,<br><br>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! <br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.3<br>Source code file: domdec.c, line: 6428<br><br>Fatal error:<br>There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 4.56121 nm<br>Change the number of nodes or mdrun option -rdd<br>
Look in the log file for details on the domain decomposition<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br><br><br><div class="gmail_quote">On 24 February 2011 16:21, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<br>
Nick wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello all,<br>
<br>
When I issue mdrun program for EM altough this is not a parallel simulation, 6 nodes are getting involved.<br>
<br>
I am using 4.5.3 and get the error:<br>
<br>
Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision)<br>
Starting 16 threads<br>
<br>
Does anyone have idea why is this happening?<br>
<br>
</blockquote>
<br></div></div>
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 :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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