Reconfigurable Hardware Acceleration of Canonical Graph Labelling

  • David B. Thomas
  • Wayne Luk
  • Michael Stumpf
Conference paper

DOI: 10.1007/978-3-540-71431-6_28

Volume 4419 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Thomas D.B., Luk W., Stumpf M. (2007) Reconfigurable Hardware Acceleration of Canonical Graph Labelling. In: Diniz P.C., Marques E., Bertels K., Fernandes M.M., Cardoso J.M.P. (eds) Reconfigurable Computing: Architectures, Tools and Applications. ARC 2007. Lecture Notes in Computer Science, vol 4419. Springer, Berlin, Heidelberg

Abstract

Many important algorithms in computational biology and related subjects rely on the ability to extract and to identify sub-graphs of larger graphs; an example is to find common functional structures within Protein Interaction Networks. However, the increasing size of both the graphs to be searched and the target sub-graphs requires the use of large numbers of parallel conventional CPUs. This paper proposes an architecture to allow acceleration of sub-graph identification through reconfigurable hardware, using a canonical graph labelling algorithm. A practical implementation of the canonical labelling algorithm in the Virtex-4 reconfigurable architecture is presented, examining the scaling of resource usage and speed with changing algorithm parameters and input data-sets. The hardware labelling unit is over 100 times faster than a quad Opteron 2.2GHz for graphs with few vertex invariants, and at least 10 times faster for graphs that are easier to label.

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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • David B. Thomas
    • 1
  • Wayne Luk
    • 1
  • Michael Stumpf
    • 2
  1. 1.Department of Computing, Imperial College London 
  2. 2.Centre for Bioinformatics, Imperial College London