AMBER Archive (2006)

Subject: RE: AMBER: Execution time discrepancies

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 17 2006 - 22:00:29 CDT

Hi Kevin,
 
Were the runs single processor or multiprocessor? Were the executables used
identical? Built with the same compilers, compilation options etc? Also are
you certain the system was dedicated for the run? If you are sharing a
system with other users (i.e. not using a properly configured queuing
system) then you will see massive variation in the wallclock time.
 
Also, was the test case large enough such that the benchmarks are
statistically relevant? Typically you want a total runtime of at least 10
seconds or so before you can get reproducible numbers. E.g. comparing runs
that complete in milliseconds will give you huge error bars on the wallclock
time.
 
All the best
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Glass, Kevin A
Sent: Thursday, August 17, 2006 17:18
To: amber_at_scripps.edu
Subject: AMBER: Execution time discrepancies

A user on our system made some test runs with Amber 8 and found significant
(50%) discrepancies in the execution times of her code. The two runs used
identical decks. Is there a programmatic reason why this happened?

Thanks,
Kevin

Kevin A. Glass, Ph.D.
MSCF - Visualization and User Services
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
P.O. Box 999 MS:K8-91
3335 Q Ave. Phone: 1-509-376-1543
Richland, WA 99352 Fax: 1-509-376-0420
Email: kevin.glass_at_pnl.gov
Web: <http://mscf.emsl.pnl.gov> http://mscf.emsl.pnl.gov

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