AMBER Archive (2007)

Subject: Re: AMBER: Any experience on Dell two quad core system?

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Mon Aug 13 2007 - 15:59:58 CDT

For a 37,054 atom MD simulation of Streptavidin tetramer, octahedral box,
cut=9.0, 1fs timestep, and other standard parameters, PMEMD obtains:

System # Proc. Wall Time / ps Processor Wall Time / ps
Quad Xeon, 2.66GHz 2 262 seconds 524 seconds
Quad Xeon, 2.66GHz 4 146 seconds 584 seconds
Quad Xeon, 2.66GHz 8 94 seconds 752 seconds
Quad Xeon, 3.00GHz 4 136 seconds 544 seconds

So, with eight-way parallelization on a dual-quad box there is a ~30% loss of
efficiency versus 2-way parallelization.

Dave
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