Parallel detection of regulatory elements with gMP

Schmidt, Bertil; Lin, Feng; Laud, Amey; Santoso, Yusdi

doi:10.1109/ipdps.2003.1213294

Cited by 3 publications

(1 citation statement)

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“…Our future work in parallel program design patterns will include identifying more applications that benefit from this technique. The results of this study will influence our design of a new API, which will extend the functionality of gMP (the gRNA message passing interface -introduced in [5]) to these patterns and thus allow easy parallelization of many compute-intensive genomics applications.…”

Section: Discussionmentioning

confidence: 99%

Parallel design pattern for computational biology and scientific computing applications

Liu

Schmidt

2003

Proceedings IEEE International Conference on Cluster Computing CLUSTR-03

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Dynamic programming is an important algorithm design technique in computational biology and scientific computing. Typical applications using this technique are very compute-intensive and suffer from long runtimes on sequential architectures. Parallel program design patterns provide a new tool to semi-automatically generate parallel programs. In this paper we present a new parallel pattern called the " block-cyclic based wavefront" to parallelize typical dynamic programming algorithms in computational biology and scientific computing. We show how this technique leads to significant run-time savings on PC clusters.

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Section: Discussionmentioning

confidence: 99%