Re: Bang for the Buck

From: Margaret Cheung <>
Date: Sat 10 Feb 2001 23:20:46 -0800 (PST)

> My research group will be purchasing a system or systems to be used for MD
> calculations and trajectory analysis. We primarily look at small
> peptide/waterbox systems using sander in Amber6. Our primary system
> currently is a 1 year old dual P3 650 running RedHat 6.2 that cost ~$2000
> built from off-the-shelf parts.
> In looking at new hardware, our one of our interests is, as the subject
> suggests, "bang for the buck". For the $2000 spent last year, we could
> currently purchase a dual 1 GHz P3 machine using PC133 SDRAM (Via
> chipset).
> Is there anything likely to be gained (given our uses) from RDRAM, Xeon P3
> processors, P4 processors, or even Alpha-based systems? My impression is
> that for the cost of each of these improvements, the "better" answer is
> simply purchase an additional dual 1GHz system and run the 1 calculation
> on X machines (or alternatively, run X calculations on X machines).


In my humble opinion, you probably also want to upgrade your peripherals,
especially a very nice video card (if it displayed to a monitor)
while upgrading MB or CPU. Else, you'll have a big problem compiling
linux redhat 6.2 (7.0) if your [AGP(PCI) clock]/[CPU FSB clock] ratio is
too low. This case may be even worse if you have a overclocked MB.
Moreover, if you have heavy I/O in your calculations,
you probably want to get a fast read/write HDD on
 100UltraATA IDE (if your old MB doesn't support scsi interface).
Also, frequent flashing new version of BIOS
of your old motherboard sometimes can give you surprising improvements
on I/Os. In general, if you have only $2000 dollars, I'd
rather bet these money on upgrading peripherals, rather than going
after ultimate combination of CPU and MB, for better overall performance.

Happy computing!

Sincerely yours,
Margaret Cheung

Physics department
Biophysics graduate program
University of California, San Diego.
La Jolla, CA 92093.
Received on Sat Feb 10 2001 - 23:20:46 PST
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