CBL maintains a 304-core compute cluster for computational biology under a National Science Foundation Computing Research Infrastructure grant and a National Institutes of Health R01 grant. The cluster is used for large-scale computations such as protein modeling and quantitative genetics. The majority of the hosts run two, dual core 2.4Ghz Xeon processors with 8G of shared RAM. The configuration provides excellent support for multi-processor shared memory programs such as BLAST. It also supports MPI for larger parallel-processing programs. Job management is handled by Sun's Grid Engine using the "share tree" mechanism to balance fractional usage over time.

The system runs the "Bio" software suite that includes Clustalw, Fasta, HMMer, Mr Bayes, Phylip, EMBOSS, glimmer, MPI Blast, T-Coffee, and the NCBI toolkit (including MegaBlast and PsiBlast). A customized MPI version of the Rosetta protein folding software is a mainstay.

Fractional use of the facility is available to western Massachusetts academic or industry researchers working on computational biology. Individuals interested in obtaining an account should contact Oliver Brock for further information.

Cluster Details

• 64 Compute Nodes with a total of 304 cores:
  • 8 nodes each with two single-core Xeon CPUs @ 3.2 GHz with 4GB RAM and 40GB Hard Disk Space(total of 16 cores)
  • 40 nodes each with two dual-core Xeon CPUs @ 2.4 GHz with 8GB RAM and 73GB Hard Disk Space(total of 160 cores)
  • 16 nodes each with two quad-core Xeon CPUs @ 2.6 GHz with 16GB RAM and 250GB Hard Disk Space(total of 128 cores)
• 1 head node
  • two dual-core Xeon CPUs @ 2.4 GHz with 8GB RAM and 250G raid storage
• 1 storage node
  • two dual-core Xeon CPUs @ 2.4 GHz with 8GB RAM 11TB storage

(Photo shows first rack of nodes.)