Some timings for 64 bit Opteron (ATLAS, GOTO, std) - R-devel

Tue, Mar 2, 2004 12:25 PM #

My understanding is far below `imperfect'!  However, our box has all 8 slots
filled with 2GB PC2100s...  Not a whole lot of room for change.

Best,
Andy

From: rossini@blindglobe.net [mailto:rossini@blindglobe.net] 

And my understanding is completely imperfect, but note that
organization (and selection) of memory modules on the motherboard can
be critical for speed with the opterons; well known issue on the
beowulf lists.

best,
-tony

Peter Dalgaard <p.dalgaard@biostat.ku.dk> writes:

"Liaw, Andy" <andy_liaw@merck.com> writes:

Hi Martin,

When I attended the LinuxWorld Expo in NYC back in

January, I chatted with

some folks at the AMD booth, as well as guys from Penguin

Computing (where

we bought our Opteron box).  I was told that the Operton

has this somewhat

strange setup that the memory is controlled by one CPU.

The net effect of

this being that when both CPUs are running, one might only

be running at

around 90% instead of 99%.  The `NUMA' kernel is supposed

to fix this

problem.  I wonder if this is related to the performance

of the threaded

GOTO lib that you saw.  Has anyone tried the NUMA kernel?

Best,
Andy

My understanding is slightly different (I could be wrong though, I'm
hardly a hardware engineer): Each CPU controls one block of memory,
and only some motherboard have memory slots for both CPUs. If CPU2
wants to talk to CPU1's memory it has to ask CPU1 for it, with the
obvious potential for a performance hit.

I'll see if I can get around to redoing my Opteron builds and trying
Martin's benchmarks in the next couple of days.

        -p

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
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 (*) \(*) -- University of Copenhagen   Denmark      Ph:

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~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX:

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-- 
rossini@u.washington.edu            
http://www.analytics.washington.edu/ 
Biomedical and Health 
Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer 
Research Center
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Peter Dalgaard

Tue, Mar 2, 2004 12:56 PM #

"Liaw, Andy" <andy_liaw@merck.com> writes:

Right. Mine, however, has only 1G split as 4 x 256K over the 4+2 slots
with 2 in each bank, and there was a reason why this was the right way
for that amount of memory. (The intention is to buy more when the
memory prices drop, but just now one 2GB module is about 1500USD
around here, and I seem to need 4, so I think I might wait a little
longer...on the other hand 1GB modules are available at 200USD. Hmmm.)

O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907

A.J. Rossini

Tue, Mar 2, 2004 1:19 PM #

Peter Dalgaard <p.dalgaard@biostat.ku.dk> writes:

This is the point I was imperfectly alluding to, though -- there is a
right way from a financial perspective, and a right way from the
expansion perspective, and a right way from a performance perspective,
and at least 2 differ...

rossini@u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

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