AMBER Archive (2002)

Subject: Re: Origin300, Linux Cluster

From: Dow Hurst (dhurst_at_kennesaw.edu)
Date: Mon Jul 08 2002 - 09:40:34 CDT

Linux is great as a cluster but SGI hardware can be just as good. We
tend to purchase used equipment such as Origin 200's with R12K CPUs at
270MHz. We purchased a quad R12K at 270MHz w/2 Gb RAM for $8K a couple
of months ago. Considering we can have hardware support for a year for
about $750 on the machine, I think it is well worth it. All of our in
house software runs on IRIX. You can't beat the dependability and
uptime either.

If you want an expanding cluster then Linux or IRIX is great. I think
it would be great if we could get some run time comparisons though.
 Clusters have to be built right or the throughput drops dramatically.
 Cluster require more admin and support time too, since you have more
parts to break down.

Why don't you use a Linux based PC for your data analysis and get a nice
SGI Origin for your backend compute engine? We use www.xsnet.com for
our hardware support and used hardware purchases. Below are some
uptimes from Origin 200 and Octane machines we have. These times are as
short due to administrative UPS battery replacements not OS crashes or
glitches:

Hughes1 1% uptime
 11:15am up 109 days, 20:07, 1 user, load average: 2.00, 2.00, 2.00
Walker 1% uptime
 11:16am up 109 days, 19:39, 1 user, load average: 1.06, 1.01, 1.00
Raven 1% uptime
 11:22am up 109 days, 20:06, 2 users, load average: 2.06, 2.01, 2.00
Per 1% uptime
 11:18am up 109 days, 19:49, 1 user, load average: 2.03, 2.00, 2.00

Your time is more valuable than fiddling with hardware so evaluate
reputable vendor Linux clusters or SGI solutions than trying to hack
together your own Linux cluster. If you decide on a SGI make sure you
get a working licensed compiler installed. Sorry I can't supply
comparison numbers on Linux cluster performance versus SGI performance
for the problems you will be looking at. Don't forget to include UPSes
and a Linux firewall in your lab setup.
Dow

Jianhui Wu wrote:

>Dear Colleagues,
>
>I have a budget around $40k CN to shop for a new computer system, which
>will be used for MD simulation, virtual screening and some bioinformative
>stuff. Currently, I am looking at two options: Origin 300 (2 cpu) or PC
>Linux Cluster. I would like to hear your experience with these systems and
>spend the limited budget right.
>
>(1) An Origin 300 2cpu 500MHZ cost around $35k. Are you using this kind of
>system? Do you have benchmark of MD simulation (such as Amber) for this
>system? Do you regret your purchase?
>
>(2) What is the best configuration for a PC Linux cluster now? Is your
>cluster stable enough? For example, it only break down once a month
>instead of once a week or two weeks. How do you take care of the maintance
>issue? Do you keep a spare node to serve as spare parts for other nodes?
>How much it cost to mantain a PC cluster (service, parts, etc)?
>
>If you make the choice, what kind of system would you go for it? Any
>suggestion will be greatly appreciated.
>
>Best wishes,
>
>Jian Hui Wu
>
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