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

Thilo Fester, Falk Schreiber, Marc Strickert

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

5 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationGCB 2009 - German Conference on Bioinformatics 2009
PublisherSchloss Dagstuhl
Pages67-79
Number of pages13
ISBN (Print)9783885792512
Publication statusPublished - 2009
Externally publishedYes
EventGerman Conference on Bioinformatics 2009, GCB 2009 - Halle-Wittenberg, Germany
Duration: 28 Sep 200930 Sep 2009

Conference

ConferenceGerman Conference on Bioinformatics 2009, GCB 2009
CountryGermany
CityHalle-Wittenberg
Period28/09/0930/09/09

Cite this

Fester, T., Schreiber, F., & Strickert, M. (2009). CUDA-based multi-core implementation of MDS-based bioinformatics algorithms. In GCB 2009 - German Conference on Bioinformatics 2009 (pp. 67-79). Schloss Dagstuhl.