[Bioclusters] Benchmarks on a dual core Xeon

[Christopher Dwan]

Joe,

Good catch. Sorry to be confusing.

It's pretty clear that on NT, the results are cached in memory.  I  
think that I mention that a little further down in the same  
section.   For WGS, a much larger dataset, it was certainly bound by  
I/O.  A clearer way to say it would be "BLAST can be bound by I/O  
unless available RAM exceeds the space needed for the indices."

After the test period was complete, we had the chance to crank the  
memory on the machine all the way up to 32GB.  At that level, even  
WGS scaled like NT, so it's certainly a memory thing.

-Chris

On Jan 20, 2006, at 12:48 PM, Joe Landman wrote:

> Hi Chris:
>
>   Interesting results.  In the report you wrote that your blastn nt  
> results were limited by IO.  Could you clarify this?  That is, on a  
> 16 GB ram machine, one should expect that the indices are  
> completely cached upon the first scan through the sequences, as the  
> indices fit into much less than 16 GB ram.  We see this happen on 8  
> GB ram machines and below.
>
>   Thanks.
>
> Joe
>
> Christopher Dwan wrote:
>> I recently had the opportunity to perform some benchmarks (BLAST,   
>> Clustalw, Clustalw-mpi, and MrBayes) on one of the new quad chip,   
>> dual core Xeon (Paxville) servers from Intel.  This isn't a   
>> comparative study between chips, but rather a look at how batch,   
>> multi-thread, and MPI jobs scale on this machine.
>> The report is linked from our main page:  http://bioteam.net
>> Disclaimer:  I did this work in my corporate guise at Bioteam.     
>> Intel provided the hardware, access to their compilers, and they  
>> paid  for the preparation of the report.  They did not, however,  
>> exercise  editorial control over the content.
>> -Chris Dwan
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> -- 
> Joseph Landman, Ph.D
> Founder and CEO
> Scalable Informatics LLC,
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