<div dir="ltr">Hi Gavin,<br><br>I had exactly the same problem a few days ago. <br>you have 2 options for parallel runs: domain decomposition (default) and particle decomposition<br>you can either try to manipulate the parameters of your system such that they fit domain decomposition or choose the easier way..that is using particle decomposition (mdrun -pd)<br>
i use it and it works fine, though I'm not sure it the most efficient algorithm for parallel runs.<br><br>Cheers,<br>Amir<br><br><div class="gmail_quote">On Tue, Jun 22, 2010 at 6:58 PM, Gavin Melaugh <span dir="ltr"><<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi all<br>
<br>
I have a ran a simulation of 64 molecules in a cubic box with side 6 nm,<br>
using nose-hoover thermostat, parinello-rahman pressure coupling, and<br>
pme. Runnin the simulation in parallel is no problem (using 16 CPUs).<br>
However when I want to run an almost identical molecule using the exact<br>
same conditions as the previous case I get the following error (below),<br>
until eventual I reduce the number of CPUs to 4 and then everything is<br>
fine. I would however like to run the simulation using more processors<br>
if anyone can give me some advise. Note the following error is from the<br>
log file.<br>
<br>
*Program mdrun, VERSION 4.0.7<br>
Source code file: domdec.c, line: 5888<br>
<br>
Fatal error:<br>
There is no domain decomposition for 13 nodes that is compatible with<br>
the given box and a minimum cell size of 1.25784 nm<br>
Change the number of nodes or mdrun option -rdd or -dds<br>
Look in the log file for details on the domain decomposition*<br>
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