wall clock vs secs/step metrics

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Sep 05 2006 - 12:02:29 CDT


I have been comparing timing differences between NAMD 2.5 and 2.6 on the
apoa1 benchmark.
I noticed something strange. The secs/step for 32 cpus decrease
0.077 to 0.070 which I thought was great, however, the final wall clock
actually increase from 51.43s (namd2.5) to 55.11s (namd2.6) for the same
32 cpus.

Then I looked at the last timing output statement at step 500 and saw that
namd2.5 was 45.03s while namd2.6 was 41.72s. So the ouputs during runtime
seem to be congruent, but the final wall clocks don't follow in the same

My questions are then, which metric should be trusted and secondly why are
the final wall clock values backwards?

Thank you for your help.


   Brian Bennion, Ph.D.
   Biosciences Directorate
   Lawrence Livermore National Laboratory
   P.O. Box 808, L-446 bennion1_at_llnl.gov
   7000 East Avenue phone: (925) 422-5722
   Livermore, CA 94550 fax: (925) 424-5513

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