[gmx-users] Benchmarking gromacs over large number of cores

Bruno Monnet bruno.monnet at hp.com
Thu Apr 28 16:05:34 CEST 2011


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 :

        Average load imbalance: 113.6 %
      Part of the total run time spent waiting due to load imbalance: 3.3 %
      Steps where the load balancing was limited by -rdd, -rcon and/or
    -dds: X 9 % Y 9 % Z 9 %
      Average PME mesh/force load: 3.288
      Part of the total run time spent waiting due to PP/PME imbalance:
    32.6 %

    NOTE: 32.6 % performance was lost because the PME nodes
           had more work to do than the PP nodes.
           You might want to increase the number of PME nodes
           or increase the cut-off and the grid spacing.

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.

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 ?

Best regards,
Bruno Monnet

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