[Bioclusters] Benchmarks on a dual core Xeon

[Christopher Dwan]

Please feel free to download the test suite.  The URL to download the  
code and data that I used is in the paper at the bottom of page 7:

http://bioteam.net/intel_benchmarks

-Chris Dwan
  The BioTeam

On Jan 20, 2006, at 1:43 PM, Kathleen wrote:

> Chris:
>
> We find that we can mitigate the binding size problems with our  
> distributed
> approach, which allows end-to-end scaling to be such that we can  
> assure
> enough processors to guarantee that we don't have indices exceeding  
> RAM.
> We'd like to download your test suite and run a benchmark on our  
> system to
> demonstrate our scaling efficiencies.
>
> Cheers,
>
> Kathleen Erickson
> Massively Parallel Technologies, Inc.
>
> -----Original Message-----
> From: Christopher Dwan [mailto:cdwan at bioteam.net]
> Sent: Friday, January 20, 2006 10:58 AM
> To: Clustering, compute farming & distributed computing in life  
> science
> informatics
> Subject: Re: [Bioclusters] Benchmarks on a dual core Xeon
>
>
> 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
>>>  The BioTeam _______________________________________________
>>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>> --
>> Joseph Landman, Ph.D
>> Founder and CEO
>> Scalable Informatics LLC,
>> email: landman at scalableinformatics.com web  :
>> http://www.scalableinformatics.com
>> phone: +1 734 786 8423
>> fax  : +1 734 786 8452
>> cell : +1 734 612 4615
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
>
>
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters