Subject: Re: Origin300, Linux Cluster

From: "C. Klein" <[email-masked]>
Date: Thu, 04 Jul 2002 19:41:31 +0200

Hi, 

take a look at this:
.............
~/bin> uptime
  7:32pm  up 50 days,  4:10,  7 users,  load average: 0.01, 0.09, 0.06
.............

That is the front end of our linux cluster, a bunch of athlons with a
dual PIII front end machine. This all came for maybe 15000 USD and the
performance is extremely good. The uptimes of the compute nodes are
equally high. So do not worry about stability. 

The price/performance ratio is much much better for linux clusters than
for SGI systems. 

I do not have a lot of time to write, but there is one very important
issue: Once you get your cluster hardware, check it thoroughly. Check if
all the hardware meets the specification (amounts of RAM, NIC types
etc.). I had some surprises with that. And even more important: Do test
runs of your software, if possible in parallel, for maybe a week. I had
to send back 10 dual PIIIs because they would give unexplainable
crashes!!!!! Do not pay the bill before everything is up and running...
Take care not to buy cheap NICs. 

Best regards, 

Chris

-- 
Dr. C. Klein; cklein(at)pharma.anbi.ethz.ch
Dept. of Applied Biosciences, Pharmaceutical Chemistry
Swiss Federal Institute of Technology / ETH Zuerich
Winterthurerstr. 190
CH-8057 Zuerich
Phone: +41 1 6356062
FAX  : +41 1 6356884

---

From: Christoph Steinbeck <[email-masked]>
Date: Fri, 05 Jul 2002 10:36:41 +0200

>   7:32pm  up 50 days,  4:10,  7 users,  load average: 0.01, 0.09, 0.06

That's nothing. Check this out:

[stein@cn01 stein]$ uptime
  10:47am  up 161 days, 20:19,  11 users,  load average: 0.87, 0.94, 0.96

This is the front machine of our 16-nodes linux cluster.

:-)

> The price/performance ratio is much much better for linux clusters than

I can only support this.
And I would also suggest using no no-name, garage-built hardware.
There are lots of good x86-based systems available which are specially 
made for 19'' racks (see for example 
http://www.fujitsu-siemens.com/rl/products/primergy/rackservers.html).
We are running Siemens hardware and we are very satisfied, but I think 
there are tons of comparable systems from other major producers.

Cheers,

Chris

-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

---

From: Stéphane Teletchéa <[email-masked]>
Date: Fri, 5 Jul 2002 10:48:03 +0200

> take a look at this:

I agree with Chris about stability and performance (you can even get athlons 
instead of PII/PIV, you will get a much more efficiency on your calculation: 
for example amber is 30% rapidlyer on an athlon 1.0Ghz than a 1.0Ghz pentium).
The only problem you will need to solve is the definition of your needs :
- first; will you use your cluster as a superparallel computer ?
in that case for example, you will not get a good speedup with explicit water 
in sander, but a good one in GB. For PME on, you will better dedicate one 
node per person.
- second: do your programs run under linux ? you talked about some virtual 
screening, and if you think of Accelrys'product, they do not run under linux 
for the moment.

Stef