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<font size="-1"><font face="Helvetica, Arial, sans-serif">I am a
computational scientist working with a physical chemist to try to
parallelize her use of gromacs -- today is my first day using the
application and I am not succeeding in getting multiple threads.<br>
<br>
I have an MPI-compiled version of gromacs v4.0 and am attempting to get
parallel execution on a 2x2 core AMD Opteron system via:<br>
<br>
$ lamboot<br>
$ mdrun -np 4 -s ../1WOM.tpr -v -N 4<br>
<br>
however there is then only a single thread executing. Do I need to
preprocess the topology file?<br>
<br>
In the first instance, getting mdrun going in parallel on an SMP
machine is the higher priority. Next I will look at running it on a
cluster.<br>
<br>
TIA.<br>
<br>
Ian<br>
</font></font>
<pre class="moz-signature" cols="72">--
Ian Stokes-Rees, Research Associate
SBGrid, Harvard Medical School
<a class="moz-txt-link-freetext" href="http://sbgrid.org">http://sbgrid.org</a>
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