[gmx-users] Re: MPI tips

[Dallas B. Warren]

As already noted, it is due to the fact you have very short jobs here.
And most of the time you are seeing there is the setting up the jobs.
Doing a scaling check of something that only takes 60 seconds on one CPU
makes very little sense.

You will see better scaling the longer the job is run by.  Also, the
larger the system that is being simulated also improves the scaling,
i.e. larger chunks of the simulation to be distributed.  Check the
archives for this emailing list, the various scaling effects have been
discussed in depth and I wouldn't be surprised if it wasn't discussed in
the manual as well.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
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When the only tool you own is a hammer, every problem begins to resemble
a nail.