Cluster of re-configurable nodes for scanning large genomic banks

Acceleration of a content-based image-retrieval application on the RDISK cluster

“…Our model architecture is that of a so-called smart disk, whose prototype is RDISK [9], implemented and available at IRISA. In short, a smart disk is a collection of disk drives, each one controlled by a reconfigurable, FPGA-based processor, called a filter.…”

“…The RDISK system [9] was designed to provide high performance with low-cost hardware components. Our initial goal was to build a system whose nodes would cost no more than one tenth of a PC cluster (i.e.…”

“…The chip is a Spartan-II FPGA from Xilinx, and it offers an equivalent density of 200,000 logic gates. It is used to implement a generic System on a Chip design, the fixed part of which includes a hard disk-drive controller, a 16-bit RISC embedded CPU, and an Ethernet chip-set interface (for more details, see Guyetant et al [9]). The reconfigurable (i.e.…”

“…Our RDISK cluster prototype is fully functional and has already proved to be a very promising platform: two applications of computing biology have been successfully implemented and speed-ups of two orders of magnitude have been reported [9].…”

Hardware Acceleration of HMMER on FPGAs

“…Among others, FPGA implementations of Smith and Waterman [16], BLAST [1,11], ClustalW [17] or even Weighted Finite Automaton [8] algorithms have exhibited impressive speed-up S. Derrien (B) · P. Quinton IRISA, Rennes, France e-mail: sderrien@irisa.fr factors, making them a very viable alternative to expensive supercomputing infrastructures such as vector computers or PC clusters.…”