Yes, but I forgot to say that I got this note that followed:<br>5.4 % performance was lost because the PME nodes<br> had less work to do than the PP nodes.<br> You might want to decrease the number of PME nodes<br>
or decrease the cut-off and the grid spacing.<br><br>Carla<br><br><div class="gmail_quote">On Fri, Jan 22, 2010 at 1:34 PM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</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;">Carla Jamous skrev:<div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi everyone,<br>
<br>
Lately I've been using gromacs version 3.3.3. Yesterday, I started simulations in a cluster where gromacs version is 4.0.3.<br>
After a run, I got this error message:<br>
Average load imbalance: 0.5 %<br>
Part of the total run time spent waiting due to load imbalance: 0.3 %<br>
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 %<br>
Average PME mesh/force load: 0.898<br>
Part of the total run time spent waiting due to PP/PME imbalance: 2.7 %<br>
<br>
I don't have a clue what this means & how can I fix it?<br>
<br>
Please can anyone help?<br>
<br>
Thank you<br>
Carla<br>
</blockquote></div></div>
This is no error message. 0.5 % load imbalance just means that the workload was distributed in a good way over procesors throughout your simulation.<br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Laboratory of Molecular Biophysics,<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://xray.bmc.uu.se/molbiophys" target="_blank">http://xray.bmc.uu.se/molbiophys</a><br><font color="#888888">
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