A hybrid architecture for bioinformatics

Authors:
Bertil Schmidt;Heiko Schröder;Manfred Schimmler
Affiliations:
School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Singapore;School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Singapore;Institut für Datentechnik und Kommunikationsnetze, Technische Universität Braunschweig, Hans-Sommer-Str. 66, 38106 Braunschweig, Germany
Venue:
Future Generation Computer Systems - Parallel computing technologies (PaCT-2001)
Year:
2002

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Abstract

We present a hybrid parallel system based on commodity components to gain supercomputer power at low cost. The architecture is built around a coarse-grained PC-cluster linked by a high-speed network and fine-grained parallel processor arrays connected to each node. Identifying applications that profit from this kind of processing power is critical to justify the use of such a system. In this paper, we present a new approach to high performance protein database scanning with hybrid computing. To derive an efficient mapping onto this architecture, we designed an instruction systolic sequence comparison algorithm. This results in a database scanning implementation with significant runtime savings.