🚀 go-pugleaf

In article <11758@cgl.ucsf.EDU> seibel@cgl.ucsf.edu (George Seibel) writes:
>  Molecular Dynamics people are rather keen on 1/sqrt(r).   It's used
>in evaluating the coulomb interaction between two charged particles.
>It wouldn't be unusual to do it 10^10 to 10^11 times in a run.  On some
>machines it may amount to half the cycles.

Good MD code will NOT use square root this way.  By working with potentials
that are transformed to use the square of the distance, one can avoid doing
these costly operations for every pair potential, resulting in substantial
preformance improvements.  The fastest MD codes I know of use table look up
and interpolation to evaluate potential functions. Another advantage of this
technique is that it works for complex potentials, as well as simple ones.

At least from my experience (and I've done both many CPU day and week long
scientific calculations, and worked with top researchers in computer
architecture), the best thing computer designers can do is make the machine
as fast as possible on 64 bit floating point multiply and adds (and maybe
add hardware assist for divide), and let the software do the rest.  Cray has
the right idea, but we knew that already.

Scott Nettles
Scott.Nettles@cs.cmu.edu