Convey HC-1 x86 + FPGA

There are 14 FPGAs on the Convey coprocessor. Four FPGAs serve as the application engines that execute the personality’s instruction set; two FPGAs comprise the application engine hub that handles communication to and from the host x86 processor; and eight FPGA-based memory controllers provide the very fast memory.

“Convey systems are 2U rack-mountable systems and run industry-standard Linux. They cluster like other off the shelf servers, are managed like other servers, and connect into your HPC fabric like other servers. The point is, to the outside world, there’s nothing exotic about the HC-1. It’s just blindingly faster on bioinformatics algorithms than any off-the-shelf server”.
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"Convey’s hybrid-core computers have achieved impressive performance on a variety of bioinformatics applications, allowing researchers to tackle problems previously deemed impractical. For example:

• Sequencing. The Convey implementation of the Smith-Waterman algorithm (used for aligning DNA and protein sequences) is 172x faster than the best software implementation on conventional servers and represents the fastest Smith-Waterman implementation on a single system to date.

• Proteomics. University of California, San Diego (UCSD) researchers achieved a roughly 100-fold faster performance of their sophisticated MS/MS database search tool program — InsPecT — that is able to accurately identify post-translational modifications (PTM).

• Computational Phylogeny Inference. The University of South Carolina developed and accelerated MrBayes, a phylogenetics application able to accurately infer “evolutionary trees,” a problem that was previously considered impractical on most computer systems. Performance is significantly faster even than other FPGA implementations.

• Genomics. The Virginia Bioinformatics Institute (VBI) is using Convey hybrid-core systems for its microsatellite analysis work for the 1000 Genomes Project, an international effort to sequence the genomes of approximately 2,500 people from about 20 populations around the world."