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Optimization of a parallel permutation testing function for the SPRINT R package

Petrou, Savvas, Sloan, Terence M., Mewissen, Muriel, Forster, Thorsten, Piotrowski, Michal, Dobrzelecki, Bartosz, Ghazal, Peter ORCID:, Trew, Arthur and Hill, Jon 2011. Optimization of a parallel permutation testing function for the SPRINT R package. Concurrency and Computation: Practice and Experience 23 (17) , pp. 2258-2268. 10.1002/cpe.1787

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The statistical language R and its Bioconductor package are favoured by many biostatisticians for processing microarray data. The amount of data produced by some analyses has reached the limits of many common bioinformatics computing infrastructures. High Performance Computing systems offer a solution to this issue. The Simple Parallel R Interface (SPRINT) is a package that provides biostatisticians with easy access to High Performance Computing systems and allows the addition of parallelized functions to R. Previous work has established that the SPRINT implementation of an R permutation testing function has close to optimal scaling on up to 512 processors on a supercomputer. Access to supercomputers, however, is not always possible, and so the work presented here compares the performance of the SPRINT implementation on a supercomputer with benchmarks on a range of platforms including cloud resources and a common desktop machine with multiprocessing capabilities.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Publisher: Wiley
ISSN: 1532-0626
Last Modified: 23 Oct 2022 14:02

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