Re: the relationship between system size and cpu numbers

From: Marcos Sotomayor (
Date: Tue Mar 27 2007 - 11:34:20 CDT

Hi Dong,

There are two different issues that you should carefully analise. First,
the system should not "explode" in 1 or 32 cpus. In fact, it should be
stable in any reasonable number of cpus. Otherwise, there is something
wrong with your binary/hardware and/or system.

Second, in order to know whether the number of processors you are using is
adequate to the system size, you may want to run a set of benchmark
simulations using different number of cpus and compare the ns/day you get
with what you would get using only one processor. Usually 1000 atoms per
processors works fine, but you need to run the mentioned benchmarks to be


On Tue, 27 Mar 2007, Dong Luo wrote:

> 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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