[gmx-users] Benchmarking gromacs over large number of cores
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:
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 ?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users