Re: AMBER: amber on sgi

From: Karol Miaskiewicz <>
Date: Wed, 9 Mar 2005 08:37:31 -0500 (EST)

> Our university is planning to purchase an sgi
> machine.What is your openion about a machine with
> R16000 processor? Is it suitable for the calculations?
> What about the altix350 system with itanium processor?
> Which one is better?

Itanium (IA-64) processors on Altix are substantially faster than R16k
MIPS processors. For floating point calculations, such as Sander in
AMBER, Altix is a superior choice (at least, from performance point of
view). Keep in mind, however, than Altix does not have any graphics
capabilities (unless you buy something like SGI Prism), and, so, you
cannot run any graphical applications there (such as Leap from AMBER).

While Altix is a very fast system, there are a few drawbacks. The number
of applications available for Linux on IA-64 is substantially smaller
than for Irix. Also, compilation and porting of applications to IA-64 is
quite difficult when compared to most other platforms.

Note, that while GNU compilers are available for IA-64 you would need
Intel's compilers for IA-64 to get good performance from AMBER (and
other applications that you compiler on Altix).

You may also want to look at AMD Opteron based systems for your AMBER
simulations. 4-processor, and even 8-processor SMP systems with AMD
Opteron are available on the market. Such systems should be a good
choice for floating point heavy simulations, such as Sander simulations.

 Karol Miaskiewicz [Contractor]
 Advanced Biomedical Computing Center
 NCI-Frederick, PO Box B, Frederick, MD 21702, phone 301-8465664, fax 301-8465762

> ===========================================================================
> /\/\athew
> Mathew K Varghese
> Research Scholar
> School of Pure and Applied Physics
> M.G.University
> Kottayam, Kerala
> India
> email
> ===========================================================================
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Received on Wed Mar 09 2005 - 13:53:01 PST
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