Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German conference on bioinformatics 2009 P-157, 67-80 (2009).

Gesellschaft für Informatik, Bonn

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CUDA-based multi-core implementation of MDS-based bioinformatics algorithms

T. Fester , F. Schreiber and M. Strickert


Solving problems in bioinformatics often needs extensive computational power. Current trends in processor architecture, especially massive multi-core processors for graphic cards, combine a large number of cores into a single chip to improve the overall performance. The Compute Unified Device Architecture (CUDA) provides programming interfaces to make full use of the computing power of graphics processing units. We present a way to use CUDA for substantial performance improvement of methods based on multi-dimensional scaling (MDS). The suitability of the CUDA architecture as a high-performance computing platform is studied by adapting a MDS algorithm on specific hardware properties. We show how typical bioinformatics problems related to dimension reduction and network layout benefit from the multi-core implementation of the MDS algorithm. CUDA-based methods are introduced and compared to standard solutions, demonstrating 50-fold acceleration and above.

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Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-251-2

Last changed 04.10.2013 18:29:27