[gmx-users] Load imbalance

[Erik Marklund]

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.

/Erik

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.
>
> Carla
>
> 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
>         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
>     erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>  
>      http://xray.bmc.uu.se/molbiophys
>
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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