Subject: help about the computing ability of my cluster

From: "weiz" <[email-masked]>
Date: Mon, 23 Sep 2002 11:11:33 -0400

Hi, all:

I have a 16 nodes AMD cluster. each node has 2GH CPU. if one
project need to be run for 1 hour by 4 processors of a
silicon graphic origin 2000. how long it will take if using
my cluster. just give me a very rough estimation will be
ok!!! thank you very much.

wei zhuang
[email-masked]

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From: Rick Venable <[email-masked]>
Date: Mon, 23 Sep 2002 15:44:26 -0400

> ok!!! thank you very much.

My best guess is under 2 hours for 2 procs on the same node; predictions
for more processors aren't so easy.

Parallel scaling is application and architecture dependent; while the
AMD machines may compare favorably for 1 or 2 proc calculations, that
may not be the case for 4, 8, or 16 proc calcs.  A key issue is the
amount of inter-process communication needed by the application; data
intensive MD codes like AMBER and CHARMM don't scale very well on Linux
clusters without taking some additional steps.  Some examples are:

+ Use Linux 2.2.x kernel and apply the 'tcpfix' patch
+ Use Myrinet switch and host PCI boards; expensive

I've heard (but haven't tested) that newer machines with the 2.4.x
Linux kernel and Gigabit NICs now show a significant improvement in
parallel scaling over the use of 100baseT for the ethernet TCP/IP
connectivity.

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Rick Venable           29/500
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From: David <[email-masked]>
Date: 23 Sep 2002 22:28:44 +0200

> for more processors aren't so easy.
Assuming perfect scaling on the SGI that would mean 4 hours on a single
CPU. The 2 GHz AMD will be 4 to 10 times faster than the SGI, depending
on  your code, compiler etc., so let us say, between 0.5 and 1 hour on a
single AMD chip. Scaling on duals is quite good usually, so: between
0.25 and 0.5 hour on a dual box. 

Beyond that I agree with Rick, it depends on your network and your
problem. Try it out and report back to the list, just for fun.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
[email-masked]	[email-masked]   http://zorn.bmc.uu.se/~spoel
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