Cluster of re-configurable nodes for scanning large genomic banks

Authors:
Stéphane Guyetant;Mathieu Giraud;Ludovic L'Hours;Steven Derrien;Stéphane Rubini;Dominique Lavenier;Frédéric Raimbault
Affiliations:
IRISA/CNRS/Université de Rennes 1, 35042 Rennes Cedex, France;IRISA/CNRS/Université de Rennes 1, 35042 Rennes Cedex, France;IRISA/CNRS/Université de Rennes 1, 35042 Rennes Cedex, France;IRISA/CNRS/Université de Rennes 1, 35042 Rennes Cedex, France;Université de Bretagne Occidentale, BP 809, 29285 Brest Cedex, France;IRISA/CNRS/Université de Rennes 1, 35042 Rennes Cedex, France;Université de Bretagne Sud, BP 573, 56017 Vannes Cedex, France
Venue:
Parallel Computing
Year:
2005

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Abstract

Genomic data are growing exponentially and are daily scanned by thousands of biologists. To reduce the scan time, efficient parallelism can be exploited by dispatching data among a cluster of processing units able to scan locally and independently their own data. If PC clusters are well suited to support this type of parallelism, we propose to substitute PCs by re-configurable hardware closely connected to a hard disk. We show that low cost FPGA nodes interconnected through a standard Ethernet network may advantageously compete against high performance clusters. A prototype of 48 re-configurable processing nodes has been experimented on two genomic applications: a content-based similarity search and a pattern search.