CUDA-based multi-core implementation of MDS-based bioinformatics algorithms
| dc.contributor.author | Fester, Thilo | |
| dc.contributor.author | Schreiber, Falk | |
| dc.contributor.author | Strickert, Marc | |
| dc.contributor.editor | Grosse, Ivo | |
| dc.contributor.editor | Neumann, Steffen | |
| dc.contributor.editor | Posch, Stefan | |
| dc.contributor.editor | Schreiber, Falk | |
| dc.contributor.editor | Stadler, Peter | |
| dc.date.accessioned | 2019-02-20T09:48:31Z | |
| dc.date.available | 2019-02-20T09:48:31Z | |
| dc.date.issued | 2009 | |
| dc.description.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. | en |
| dc.identifier.isbn | 978-3-88579-251-2 | |
| dc.identifier.pissn | 1617-5468 | |
| dc.identifier.uri | https://dl.gi.de/handle/20.500.12116/20311 | |
| dc.language.iso | en | |
| dc.publisher | Gesellschaft für Informatik e.V. | |
| dc.relation.ispartof | German conference on bioinformatics 2009 | |
| dc.relation.ispartofseries | Lecture Notes in Informatics (LNI) - Proceedings, Volume P-157 | |
| dc.title | CUDA-based multi-core implementation of MDS-based bioinformatics algorithms | en |
| dc.type | Text/Conference Paper | |
| gi.citation.endPage | 79 | |
| gi.citation.publisherPlace | Bonn | |
| gi.citation.startPage | 67 | |
| gi.conference.date | 28th to 30th September 2009 | |
| gi.conference.location | Halle-Wittenberg | |
| gi.conference.sessiontitle | Regular Research Papers |
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