Carlos -
ALL the numbers are pmemd, except for the G5 and GB data. - Bob
----- Original Message -----
From: "Carlos Simmerling" <carlos.ilion.bio.sunysb.edu>
To: <amber-developers.scripps.edu>
Sent: Tuesday, April 27, 2004 6:54 PM
Subject: Re: amber-developers: UNC JAC benchmark?
> except that the numbers for UNC/duke are pmemd, right?
>
> ----- Original Message -----
> From: "Robert Duke" <rduke.email.unc.edu>
> To: <amber-developers.scripps.edu>
> Sent: Tuesday, April 27, 2004 6:41 PM
> Subject: Re: amber-developers: UNC JAC benchmark?
>
>
> > Dave -
> > I think your analysis is basically correct in all respects. - Bob
> >
> > ----- Original Message -----
> > From: "David A. Case" <case.scripps.edu>
> > To: <amber-developers.scripps.edu>
> > Sent: Tuesday, April 27, 2004 6:34 PM
> > Subject: Re: amber-developers: UNC JAC benchmark?
> >
> >
> > > On Tue, Apr 27, 2004, Carlos Simmerling wrote:
> > >
> > > > is that JAC timing of 202ps/day for single 3.2ghz Xeon at UNC/duke
> > > > correct? (on the benchmarks page)
> > > >
> > > > if yes, then why is the "fix" number for UNC/duke much closer to
the
> > bohr
> > > > data?
> > > >
> > >
> > >
> > > Just to make sure you are looking at the correct ratios:
> > >
> > > For clock speeds, unc/bohr = 3.2/2.4 = 1.33
> > >
> > > for JAC (2 cpu) unc/bohr = 330/165 = 2.0
> > >
> > > for fix (2 cpu) unc/bohr = 120/78 = 1.54
> > >
> > > My guess (assuming no typos....) is that the new 3.2 GHz PIV have a
much
> > > bigger L2 cache, which is why both ratios are better than the ratio
of
> > > clock speeds per se. For the smaller JAC problem, the "extra" cache
on
> > the
> > > newer machine is a real win, but for the bigger system, both
processors
> > > blow cache more often, and the "win" for the unc system is not so
great.
> > >
> > > Note also that the relative speeds of altix vs. unc are reasonably
> similar
> > > for both the jac and fix benchmarks.
> > >
> > > And, according to Bob, going to ifc8 will make the new 3.2 Xeon
chips
> look
> > > even better than the ifc7 numbers shown on the benchmark page.
> > >
> > > [Now, you can wait for the correct answers from others on this
list....]
> > >
> > > ...dac
> > >
> > > --
> > >
> > > ==================================================================
> > > David A. Case | e-mail: case.scripps.edu
> > > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > > The Scripps Research Institute | phone: +1-858-784-9768
> > > 10550 N. Torrey Pines Rd. | home page:
> > > La Jolla CA 92037 USA | http://www.scripps.edu/case
> > > ==================================================================
> > >
> >
> >
> >
>
>
Received on Wed Apr 05 2006 - 23:50:03 PDT
