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Abstract
Bioinformatics applications are one of the most relevant and compute-demanding applications today. While normally these applications are executed on clusters or dedicated parallel systems, in this work we explore the use of an alternative architecture. We focus on exploiting the compute-intensive characteristics offered by the graphics processors (GPU) in order to accelerate a bioinformatics application. The GPU is a good match for these applications as it is an inexpensive, high-performance SIMD architecture.
In our initial experiments we evaluate the use of a regular graphics card to improve the performance of RAxML, a bioinformatics program for phylogenetic tree inference. In this paper we focus on porting to the GPU the most time-consuming loop, which accounts for nearly 50% of the total execution time. The preliminary results show that the loop code achieves a speedup of 3x while the whole application with a single loop optimization, achieves a speedup of 1.2x.
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Authors and Affiliations
Department of Computer Science, University of Cyprus, 75 Kallipoleos Ave., P.O.Box 20537, 1678, Nicosia, Cyprus
Maria Charalambous & Pedro Trancoso
Institute of Computer Science, Foundation for Research and Technology-Hellas, P.O. Box 1385, Heraklion, Crete, GR-771 10, Greece
Alexandros Stamatakis
- Maria Charalambous
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- Pedro Trancoso
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- Alexandros Stamatakis
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Editors and Affiliations
Department of Computer and Communication Engineering, University of Thessaly, Glavani 37, 382 21, Volos, Greece
Panayiotis Bozanis
Department of Computer and Communication Engineering, University of Thessaly, 382 21, Volos, Greece
Elias N. Houstis
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Charalambous, M., Trancoso, P., Stamatakis, A. (2005). Initial Experiences Porting a Bioinformatics Application to a Graphics Processor. In: Bozanis, P., Houstis, E.N. (eds) Advances in Informatics. PCI 2005. Lecture Notes in Computer Science, vol 3746. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11573036_39
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