<div><div><span style="white-space:pre-wrap"><div><div><font face="Verdana">Hi all,</font></div><div><font face="Verdana"><br></font></div><div><font face="Verdana">I am running a water/surfactant system with just under 100000 atoms using MPI on a local cluster and not getting the scaling I was hoping for. The cluster consists of 8 core xeon nodes and I'm running gromacs 4.5 with mpich2-gnu. I've tried running a few benchmarks using 100ps runs and get the following results:</font></div>
<div><font face="Verdana"><br></font></div><div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline">Threads: 8 16 24 32 40 48 56 64</span></b>
</div><div><b style="font-family:Verdana"><span style="font-weight:normal;text-decoration:none;vertical-align:baseline">hr/n</span><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline">s: 15 18 53 54 76 117 98 50 </span></b></div>
</div><div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline"><br></span></b></div><div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline">Each set of 8 threads is being sent to one node and the 8 threaded run was performed without MPI. I have tried changing the -npme settings for all permissible values on runs with 16 threads. In every instance the results were worse than if I didn't specify anything.</span></b></div>
<div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline"><br></span></b></div><div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline">The fact that I am getting negative scaling leads me to believe that something is wrong with my set up. Any tips on what I could try?</span></b></div>
<div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline"><br></span></b></div><div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline">Many thanks,</span></b></div>
<div><b style="font-family:Verdana"><span style="font-size:13px;font-weight:normal;text-decoration:none;vertical-align:baseline">--</span></b></div></span></div></div>Christoph Klein<div>University of Virginia</div><div>
B.S. Chemical Engineering</div>
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