[gmx-users] Load imbalance
erikm at xray.bmc.uu.se
Fri Jan 22 13:44:32 CET 2010
Well, there you go. That message tells you how to improve performance.
Changing the number of PME-nodes to improve performance may or may not
be doable, depending on the number of processors availvable. On the
other hand, 5.4 % performance loss is not that bad in my oppinion.
There is a tool fopr tuning the number of PME-nodes that you could try:
g_tune_pme. I've never used it myself though, so I don't know what to
expect form it.
Carla Jamous skrev:
> 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.
> On Fri, Jan 22, 2010 at 1:34 PM, Erik Marklund <erikm at xray.bmc.uu.se
> <mailto:erikm at 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
> 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
> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
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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
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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