[Bioclusters] NCBI 2.2.9 compile error on x86-64 Fedora Core 2

Joe Landman bioclusters@bioinformatics.org
Mon, 28 Jun 2004 14:38:51 -0400


On Mon, 2004-06-28 at 14:32, Doug Shubert wrote:
> Hello Joe,
> 
> Your numbers look very linear to ours.
> I would expect a 45%-50% performance
> increase based on CPU speed (240 vs 246).
> 
> Other factors could be in memory speeds and OS tuning.
> Our Opteron is running DDR Reg ECC 266 memory.
> 
> If you have a chance to run memtest86+, I would be interested
> in the memory speed of a 246 system.

Ok.  Are you using a particular memtest?  I found 3.1 was needed for
Opteron.  I am using DDR 333 memory.  Lets also check the layout of your
ram. Is it all piled on one processing node?  If so, you want to set it
up as interleaved.  I get streams of about 2GB/s per CPU with streams
triad.

I am in the middle of some other stuff now, so I'll try to get the
memtest86 data later tonight (unless you meant a different memtest...)

> 
> Thanks for the link, I will test your NCBI patch too.
> Doug
> 
> >Our most
> >recent BBS v1 run for a 246 gave:
> >
> >1,1,1083
> >2,2,1086
> >2,1,1093
> >3,2,2168
> >3,3,2168
> >3,1,2174
> >3,4,2174
> >4,1,559
> >5,1,1099
> >5,2,1107
> >6,1,556
> >
> >  
> >
> >>
> >>BBS times run in 2GB ram disk for a 240
> >>
> >>1,1,1641
> >>2,1,1647
> >>2,2,1685
> >>3,4,3289
> >>3,1,3296
> >>3,3,3332
> >>3,2,3335
> >>4,1,863
> >>5,1,1683
> >>5,2,1690
> >>6,1,848
> >>
> >>
> >>    
> >>
> 
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-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615