[gmx-users] another question about performance

Albert mailmd2011 at gmail.com
Fri Jan 6 05:24:02 CET 2012

   here is my log file for mdrun:
Writing final coordinates.
step 100000, remaining runtime:     0 s

  Average load imbalance: 10.8 %
  Part of the total run time spent waiting due to load imbalance: 4.3 %
  Steps where the load balancing was limited by -rdd, -rcon and/or -dds: 
X 0 % Y 19 % Z 0 %
  Average PME mesh/force load: 0.665
  Part of the total run time spent waiting due to PP/PME imbalance: 5.7 %

NOTE: 5.7 % 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.

NOTE: 9 % of the run time was spent communicating energies,
       you might want to use the -gcom option of mdrun

         Parallel run - timing based on wallclock.

                NODE (s)   Real (s)      (%)
        Time:   2435.554   2435.554    100.0
                (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    409.701     22.103      7.095      3.383

gcq#149: "It's Against the Rules" (Pulp Fiction)

As we can see from the end of this log file, the performance is 
7.1ns/day, 3.4ns/hour. I am very confused about this output. How could 
this happen? Is there only two hours something each day?

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