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SGI Positions Origin 300 Server as Flexible Option for Dedicated Bioinformatics


Later this week, SGI of Mountain View, Calif., will announce the release of its Origin 300 server for technical mid-range applications.

The launch comes within a week of Sun’s introduction of the Sun Fire 15K server and IBM’s release of the E-server p690. But SGI said its product is better geared toward bioinformatics applications than either of these offerings.

The Origin 300 borrows the NUMAflex modular approach to configurability that SGI developed for its high-end Origin 3000 series. Separate modules are available that can be added to the base server for enhanced I/O bandwidth, storage capacity, or scalability, providing the “flexibility to create a system based on your organization’s definition of performance,” said SGI’s Addison Snell.

Bioinformatics teams who may not need the same capabilities of the Origin 3000 can use the various modules to create a cost-effective “dedicated appliance,” said Dan Stevens of SGI. He added that SGI’s application engineers have written wrappers around a number of bioinformatics applications, including Blast, FastA, ClustalW, and Hmmer, to ensure they operate effectively on the system. These applications are freely available to SGI customers.

SGI said that in a benchmark against its own Origin 3000, the Compaq Alpha, the HP 9000, the IBM pSeries and SP high node, and Sun Fire, the Origin 300 had the best performance at any price point up to $750,000 in both floating point performance and integer performance.

But according to Stevens, high-performance computing vendors are not the primary competition for SGI in the bioinformatics sector — Linux clusters are. While many HPC users are turning to Linux clusters as a low-cost option to meet their number-crunching needs, Stevens said many don’t consider the total cost of ownership involved in maintaining such a cluster. System administration costs, the amount of electricity required, the amount of floor space required, as well as other considerations, make shopping for a computer system “not just the price of the box,” Stevens said.

Recognizing the threat posed by Linux clusters, SGI also ran a benchmark of a 12-CPU Origin 300 against a 32-CPU Dell PowerEdge 2250 (1 GHz Pentium III) cluster. Each system ran 100,000 BlastX searches per day for 1,140 EST sequence queries against a database of more than 600,000 sequences. SGI calculated that the three-year total cost of ownership of the Origin 300 was $140,100 vs. $225,600 for the Linux cluster.

Stevens noted that the Origin 300 is better suited to dedicated tasks such as running Blast rather than providing general purpose computing. But while this feature may set the company in direct competition with bioinformatics accelerator providers, Stevens said he’s confident that “hardware accelerators are not a viable long-term solution for bioinformatics customers.”

SGI is also launching its TP900 storage system this week, an entry-level disk array that can stand alone or serve as an expansion module for the Origin 300.

— BT


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