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On 4/02/2012 5:20 AM, Christoph Klein wrote:
<blockquote
cite="mid:CAADfth3EYiQmW4-R9yFhF0rju8OkkRfK0jpepN4MU2f_j0s72Q@mail.gmail.com"
type="cite">
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<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>
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</span></div>
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</blockquote>
<br>
Are you sure you have the right performance number (and not ns/day
or something)!<br>
<br>
<blockquote
cite="mid:CAADfth3EYiQmW4-R9yFhF0rju8OkkRfK0jpepN4MU2f_j0s72Q@mail.gmail.com"
type="cite">
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<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>
</span></div>
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</blockquote>
<br>
The simplest explanation is that your network (or MPI settings for
it) is not up to the job. Very low latency is required. Gigabit
ethernet is not good enough.<br>
<br>
You could try installing OpenMPI, also.<br>
<br>
Mark<br>
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