Breakthtrough BLAST-N solution from SGI and Mitrionics speeds query performance by up to 16 times

SGI (NASDAQ: SGIC) and Mitrionics™, Inc., today unveiled the world’s first turnkey bioinformatics appliance based on Field Programmable Gate Array (FPGA) technology and open source software. This solution is designed to break through query logjams that result from next-generation sequencing instruments and multiple genome studies using NCBI BLAST-n.

The new SGI® RASC™ Appliance for Bioinformatics – Featuring Mitrion™-Accelerated BLAST-n achieves faster query times by combining SGI RASC (Reconfigurable Application-Specific Computing) technology, an accelerated version of BLAST-n software developed by Mitrionics, and the acclaimed SGI® Altix® server platform.

Leveraging powerful and energy-efficient FPGA technology and the Mitrion Virtual processor, the new appliance completes complex BLAST-n queries up to 16 times faster than a standard server based on Intel® Itanium® 2 processors, and 10 times faster than a server based on AMD Opteron™ processors . BLAST-n (Basic Local Alignment Search Tool for nucleotides) is the world’s most widely used bioinformatics application.

SGI is demonstrating capabilities of the new solution this week in Booth 405 at the Bio-IT World Conference and Expo through May 2 at the World Trade Center in Boston.

Unlike other FPGA offerings that require extensive end-user optimization, the SGI RASC Appliance for Bioinformatics is a pre-configured solution that dramatically simplifies the deployment of a platform for running nucleotide sequence queries using BLAST-n. The industrial-scale appliance addresses productivity problems in a range of bioinformatics environments – from those that serve thousands of users running BLAST queries against a single database, to others with smaller numbers of users running complex queries against databases that are hundreds of Gigabytes in size.

Using Mitrionics software and FPGA technology specifically optimized for BLAST-n, the SGI RASC Appliance for BioInformatics offloads workloads from typical Linux clusters. The SGI RASC appliance further increases throughput by executing multiple BLAST-n queries in parallel on multiple FPGAs.

“The accelerating pace of genomics research means scientists are running more and larger nucleotide sequence queries,” said Michael Brown, sciences segment manager, SGI. “As traditional servers fail to keep up, SGI and Mitrionics have developed a turnkey BLAST appliance that transforms long-running batch jobs into interactive scientific investigation. We believe that the combination of higher performance, simplified system management, and as little as one-tenth the power consumption per BLAST-n query will drive wide adoption throughout the scientific community.”

Available to customers starting at $39,950 US, the new appliance is far more cost- and energy- efficient than traditional rack server deployments, because it relies on FPGA technology for the bulk of BLAST-n query processing. In fact, the SGI RASC Appliance for BLAST consumes up to 90 percent less power than an Opteron- or Xeon-based rack system. This equates to lower cost of ownership and longer asset life.

BLAST Optimization via the Mitrion Virtual Processor
The fine-grained, massively parallel Mitrion Virtual Processor is the core of the Mitrion Platform and a vital component of the new SGI RASC Appliance for BLAST. It runs software written in the Mitrion-C parallel programming language in FPGAs and completely eliminates the need for the programmer to master hardware design. The Mitrion Virtual Processor has a unique architecture that lets it be adapted to each program it is running in order to maximize performance. This dramatically reduces the total development costs for FPGA-based software acceleration, and more importantly, enables the whole supercomputing industry to benefit from FPGA application acceleration.

“This is an exciting time for Mitrionics and SGI as we demonstrate how the Mitrion Virtual Processor and SGI RASC platform are able to accelerate computationally intensive portions of the code by up to 100x, resulting in an application speed-up of up to 16x,” said Anders Dellson, CEO of Mitrionics, Inc. “We look forward to our continued strong collaboration with SGI in delivering BLASTn and additional turnkey bioinformatics applications. As we work together, we plan to accelerate applications in other industries, such as financial, imaging, seismology, and encryption – all of which can benefit from similarly dramatic productivity gains.”

The SGI RASC Appliance for BLAST is available today from SGI in two pre-configured blade packages: a single-blade version suitable for most environments serving internal BLAST users, and a dual-blade configuration for environments that serve hundreds or thousands of BLAST users. The appliance features an SGI Altix 450 server installed in a single SGI® Altix® 450 IRU with 8GB to 72GB of memory. (Users can also upgrade the appliance to a general-purpose server powered by up to 68 processor cores and more than 400GB of memory.) The appliance features one or two SGI® RASC™ RC100 blades powered by dual Xilinx Virtex™ 4 LX200 FPGAs with Mitrion™ Virtual Processors. The solution also includes a single SAS disk, DVD drive, Novell SUSE Linux Enterprise Server 10, and SGI’s RASC library, RASClib 2.1

For users already outfitted with SGI® Altix® 450 or SGI® Alti®x 4700 systems, and who have an available blade slot in their system, SGI also is offering an SGI RASC Appliance for BLAST-n Upgrade. With customer pricing starting at $29,950 US, the upgrade package includes an SGI RASC blade, Mitrion Virtual Processor and bioinformatics software, and RASClib 2.1.