[gmx-users] another question about performance

Dallas Warren Dallas.Warren at monash.edu
Fri Jan 6 05:33:49 CET 2012

Recheck the units for that last number ….

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Albert
Sent: Friday, 6 January 2012 3:24 PM
To: gromacs maillist
Subject: [gmx-users] another question about performance

  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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