Our Beowulf Clusters have been designed for high-throughput bioinformatic analyses, with an emphasis upon sequence similarity searching (e.g. BLAST, HMMER) and phylogenetics (e.g. MrBayes, PAUP). Whenever possible, custom software has been developed to utilize many processors per analysis. For example, BLAST and PAUP can use every processor on a Cluster to complete analyses quickly.

The Beowulf Clusters support a subset of the available software and local databases. We are happy to develop support for additional software upon request (contact biocomp@lists.mbl.edu). Even if we are unable to develop parallelization for the requested software, the ability to batch submit many single-processor jobs to the Clusters can be very productive for your research.

All software (e.g. PAUP, PUZZLE, BLAST, etc.) must be run using specialized programs. For example, you will be unable to simply type paup to use PAUP. Below is the current list of available programs. If you attempt to run your own executable, it will not migrate to a free processor and will instead interfere with the Master Node. Such jobs will be terminated - please seek assistance from biocomp@lists.mbl.edu before running your own executables or scripts on the Beowulf Clusters. Users with advanced parallel programming skills are welcome to develop their own direct-to-cluster tools, in consultation with the JBPC BioComp Staff.

Available Beowulf Clusters

The most up to date list of available computing facilities are maintained as the login message on evol5.mbl.edu.

Queue Management and Tools

The clusters utilize Sun Grid Engine for job scheduling and execution. If a cluster is in full use, your jobs will wait in a queue until processors become available (there is some load balancing to make usage balanced between users). We added an email notice feature to all of the programs so you can log in and start a job that will wait in the queue until processors are available and then will email you when it is done. You can view the current Cluster Status at the command line by using the qstat command. At the command line, you can additionally Kill One of Your Jobs using qdel <jobId> command (the jobId is the left most column in the output of qstat). If you need help managing your queue, please contact biocomp@lists.mbl.edu.

Cluster Software

For help using these commands, type them in without arguments to see the help screen or email biocomp@lists.mbl.edu.

Note, programs that have an interactive interface, such as PHYLIP programs or PUZZLE, are difficult to impliment on the clusters. To do so, we have opted to use command files that contain the keystrokes you would have used interactively. Here is an example for distance tree construction and bootstrapping.