Re: The link is out

From: David Case <>
Date: Wed 20 Feb 2002 09:20:00 -0800

On Wed, Feb 20, 2002, St?phane Teletch?a wrote:

> Nevertheless, i was searching for any benchmark of the cluster with
> water-explicit simulations (PME on). Here, it seems that having two nodes
> working instead of one doesn't prove to be very usefull.

You should be able to get good speedup (factor > 1.8) on two nodes with
any reasonable interconnect (even 100 Mbyte ethernet) with PME. If you
are not getting that, it's worth trying to figure out why...the detailed
timings that come with Amber 7 often help, but it still can be a difficult

> Le Mardi 19 Février 2002 21:45, Jung-Hsing Lin a écrit :
> >
> > sander 7 is about twice as fast as sander 6, also the scalabilty is
> > better. sander 7 can also use more nodes than sander 6.

This is over-optimistic for most problems, in my experience. The final
sander code is now frozen, and we will post benchmarks soon, probably next


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Feb 20 2002 - 09:20:00 PST
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