[BiO BB] Bioinformatics Benchmark System version 3 released
landman at scalableinformatics.com
Fri Aug 13 00:08:59 EDT 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
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
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
More information about the BBB