AMBER Archive (2005)

Subject: Re: AMBER: RE: system comparison for amber

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Apr 07 2005 - 12:00:18 CDT

>>I wish to know about the comparison of two systems.A two Xeon
>>processor system fromIBM(IBM Xseries) and a single processor SGI ALTIX
>>with 2gb memory. Which one will be better for molecular dynamics
>>calculations with AMBER(sander)
>>
>>
>
>There are a series of benchmarks on these types of systems posted on
>http://amber.scripps.edu/amber8.bench1.html you can check these for timings.
>
>In "my opinion" you will be better off with the Dual Xeon machine. The
>reason I say this is that the Intel P4 xeon chips are generally as fast, if
>not faster in some cases, than the Itanium chips in the Altix.
>

this isn't true in our experience- even for small systems Amber on the
Itanium can be twice as fast
as the Xeon. Of course, all of this depends on clock speeds and cache
sizes, which vary a lot
with both chip types. Also, PME works well on Itanium and GB works
better on Xeons,
but I think Amber 9 will have better GB performance on Itanium.

Of course none of that concerns cost/performance ratio, which I think
Ross summed up pretty well.
Carlos
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