[OT] Maximum performance on single processor ?

John Bushnell bushnell at chem.ucsb.edu
Fri Jun 20 20:19:44 EDT 2003


On Fri, 20 Jun 2003, Marc Baaden wrote:
> landman at scalableinformatics.com said:
> >>  As it does not appear that you have profiled the code (just a guess),
> 
> Half-right half-wrong guess. I have very rapidly profiled the code, just
> confirming what I already guessed, that the bottleneck (> 80% of the time)
> is the energy calculation subroutine, which calculates pairwise interactions
> between atoms in the system.
> There are indeed potential speedup factors in this code, like
> - introduction of a neighbour list
> - parallelization
> .. or maybe the use of a specialized board (MD-GRAPE) for just these 
> calculations.

  Looking at some of the info on the Riken site who evidently makes
these GRAPE cards, this sound like a good bet if pairwise energy
calculations are really where most of the speedup is needed.  They
give a peak performance for the 4-cpu GRAPE-2 as 64GFLOPS (ouch).
Very interesting.  I've never heard of these cards.  I wonder what
the approx. cost is?  They look very easy to implement, and even
have a really simple piece of Fortran code showing how to use one
on their web site.  One of their benchmarks shows an almost 100x
speedup using three cards on a Sun...

        - John

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