[Beowulf] Bioinformatics Benchmark System version 3 released

Joe Landman landman at scalableinformatics.com
Thu Aug 12 21:08:59 PDT 2004

Version 3 of the Bioinformatics Benchmark System (BBS v3) has been 
released. Many new features, bug fixes, and suggested changes have been 
made. New benchmarks have been added and updated for mpiBLAST, HMMer, 
NCBI BLAST, and others in the baseline tests.  The version 1 tests are 
still there if you wish to run them.

The Bioinformatics Benchmark System is an attempt to build a flexible 
and power testing framework, and meaningful tests,  to enable end users 
and vendors to probe the performance of their systems.  As the most 
important benchmark is your benchmark, and not a pre-packaged benchmark, 
the system is specifically designed to allow you to easily modify or add 
new tests.

 Moreover, the source to these tests are available under GPL, and are 
hosted on Bioinformatics.org (http://bioinformatics.org/bbs) and 
Scalable Informatics (http://www.scalableinformatics.com/BBS).

For those who wish to run their own tests by hand without any testing 
framework, the --dryrun switch will emit the final command line that 
would be run. 

Additional documentation on the XML input format is forthcoming.  A 
submission system for results, and baseline curation and data set 
tagging will commence in short order.  Better handling of errors is in 
place, as are better IPC methods.

You can pull the binary tarball from 
http://downloads.scalableinformatics.com/downloads/bbs/bbsv3.tar.gz .  
Please note that this includes data for a rather large mpiBLAST job.  If 
someone has a sizeable cluster they are willing to play with, mpiBLAST 
installed and some time, we would like to see the speedup curve for 16 - 
256 nodes (or higher).  We would be happy to help out with this.


Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 612 4615

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