If m=17 we're fine, I'm told newer force fields have m > 50 well on their
way to m > 100 so this isn't sustainable...
sig and eps are stored in single-precision, 1280 atoms at a time, in the
cache...
On Wed, May 30, 2012 at 8:37 PM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, May 30, 2012, Scott Le Grand wrote:
> >
> > However, pmemd.cuda attains its performance boost by running entirely out
> > of cache. With the old approach, 8 * O(m^2) + 4 bytes per atom in the
> > cache is consumed as opposed to 8 bytes per atom for storing per atom.
>
> I'm still lost. Don't you need both cn1 and cn2 (or r*, eps)
> for each atom (giving 16 bytes per atom), vs. 4 bytes per atom for the
> table lookup scheme (plus 8 * O(m^2) for the table itself.) ?
>
> For dhfr, m=17, n=23000, the table only takes 2300 bytes. Factor ix is
> four
> times bigger, but still has only 19 atom types. Cellulose has 400,000
> atoms
> but only 8 atom types. Generally, the number of types grows only slowly
> with
> system size, and few systems have 50 atom types. So maybe we could check
> the
> number of atom types, and support the full O(m^2) table as long as m is
> small
> enough?
>
> Just a thought on the train...maybe I am missing something here....dac
>
>
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Received on Wed May 30 2012 - 22:00:03 PDT
