Carla Jamous wrote:
Yes, but I forgot to say that I got this note that followed:
5.4 % performance was lost because the PME nodes
had less work to do than the PP nodes.
You might want to decrease the number of PME nodes
or decrease the cut-off and the grid spacing.
5% loss still isn't that bad. I've achieved good results with worse loss :) It
all depends (again) on your setup. When you built the .tpr file, grompp should
have reported what it predicted for the % of the load that PME should be
calculating. For most cases, it will be best if it is 25-33%, such that the
PP/PME ratio can be 3:1 or 2:1. If you don't achieve absolute perfection (which
is rare), you're going to experience some small performance loss. You can (as
the message is indicating to you) tweak some of the input parameters, such as
the Fourier grid spacing, to try to re-balance things.
Again, much of this is in the manual and the Gromacs 4 paper.
-Justin
Carla
On Fri, Jan 22, 2010 at 1:34 PM, Erik Marklund <er...@xray.bmc.uu.se
<mailto:er...@xray.bmc.uu.se>> wrote:
Carla Jamous skrev:
Hi everyone,
Lately I've been using gromacs version 3.3.3. Yesterday, I
started simulations in a cluster where gromacs version is 4.0.3.
After a run, I got this error message:
Average load imbalance: 0.5 %
Part of the total run time spent waiting due to load imbalance:
0.3 %
Steps where the load balancing was limited by -rdd, -rcon
and/or -dds: X 0 % Y 0 %
Average PME mesh/force load: 0.898
Part of the total run time spent waiting due to PP/PME
imbalance: 2.7 %
I don't have a clue what this means & how can I fix it?
Please can anyone help?
Thank you
Carla
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.
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se <mailto:er...@xray.bmc.uu.se>
http://xray.bmc.uu.se/molbiophys
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Justin A. Lemkul
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Virginia Tech
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