Meet Darwin

The Southwest Biotechnology and Informatics Center would like to introduce you to its bioinformatics computer system, darwin. “darwin” is the name of SWBIC’s Beowulf cluster for high-throughput bioinformatics computing. A Beowulf cluster is a collection of small computers (nodes) connected by a high speed network. A host computer controls parallel processing applications. Programs may be run in a truly parallel mode (i.e., one program divides its processing among multiple nodes), or many programs may be run concurrently, each on a different node.

SWBIC’s cluster consists of 32 nodes, each with an 800 MHz Pentium III processor and 256 megabytes of RAM. There are two 100 megabit network switches that divide the load of communicating with the host computer. The host computer is a dual-processor 800 MHz Pentium III machine with 150 gigabytes of SCSI hard drive storage. The host and all the nodes are using RedHat© Linux as their operating system.

SWBIC is using darwin for bioinformatics research at New Mexico State University and for the bioinformatics services provided by the SWBIC web site. As a benchmark, darwin can BLAST (blastp) a 400 amino acid protein sequence against the NCBI non-redundant protein database (600,000+ sequences) in 24 seconds (elapsed time) on a single node. This equates to the capability of completing 4,800 such BLASTs in one hour, using all 32 nodes.

The dual-processor host computer
100 megabit network switch (seen on top of two nodes)