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