Carlos -
Actually, there are some sander8 benchmarks, along with the pmemd ones on
the two pages of additonal benchmarks (off the main page) from me. These
are for the dual xeon on one page, and for ibm sp4's,
alphaserver/quadrics,
and the itanium cluster at ncsa (thanks to Tom C. for cluster access). I
presume you are interested in the sander numbers for extrapolating to LES.
Regards - 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
