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<font face="Helvetica, Arial, sans-serif">Hi,<br>
</font><br>
I'm not really a Gromacs user, but I'm currently benchmarking
Gromacs 4.5.4 on a large cluster. It seems that my communication
(PME) is really high and gromacs keeps complaining for more PME
nodes :<br>
<br>
<blockquote><tt> Average load imbalance: 113.6 %</tt><br>
<tt> Part of the total run time spent waiting due to load
imbalance: 3.3 %</tt><br>
<tt> Steps where the load balancing was limited by -rdd, -rcon
and/or -dds: X 9 % Y 9 % Z 9 %</tt><br>
<tt> Average PME mesh/force load: 3.288</tt><br>
<tt> Part of the total run time spent waiting due to PP/PME
imbalance: 32.6 %</tt><br>
<br>
<tt>NOTE: 32.6 % performance was lost because the PME nodes</tt><br>
<tt> had more work to do than the PP nodes.</tt><br>
<tt> You might want to increase the number of PME nodes</tt><br>
<tt> or increase the cut-off and the grid spacing.</tt><br>
</blockquote>
<br>
I can't modify the original dataset as I only have the TPR file. I
switched from dlb yes -> dlb auto since it seems to have trouble
with more than 6000 / 8000 cores.<br>
<br>
I tried to add " -gcom " parameter. This speedup the computation.
This parameter is not really explained in the Gromacs documentation.
Could you give me some advice on how I could use it ?<br>
<br>
Best regards,<br>
Bruno Monnet<br>
<br>
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