Re: the relationship between system size and cpu numbers

From: Cesar Luis Avila (
Date: Tue Mar 27 2007 - 11:19:18 CDT

I read somewhere that an estimate for good scaling you might use 1 cpu
every 1000 atoms. But you should also take into account the
communication latency between cpus as it will also affect scaling.

Dong Luo escribió:
> Parallel simulation in NAMD is based on space
> division, which won't be a problem for large systems.
> However, when dealing with small system like a short
> peptide in water box, running the simulation with more
> than 32 cpus may not get a good space distribution.
> Based on my experience of heat annealing simulation of
> a 22 residue peptide in water box, the system exploded
> easily on 32 cpus, but stay quite stable with only one
> cpu.
> My question is that is there a rough relationship
> between system size and cpu numbers that we can
> follow?
> Dong Luo
> Department of physiology and biophysics
> Boston University
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