title: Optimization of a parallel permutation testing function for the SPRINT R package.
abstract: 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. Copyright © 2011 John Wiley & Sons, Ltd.
authors: Edinburgh Parallel Computing Centre, University of Edinburgh Edinburgh, EH9 3JZ, UK.
authors: Savvas
authors: S
authors: Petrou
authors: Terence M
authors: TM
authors: Sloan
authors: Muriel
authors: M
authors: Mewissen
authors: Thorsten
authors: T
authors: Forster
authors: Michal
authors: M
authors: Piotrowski
authors: Bartosz
authors: B
authors: Dobrzelecki
authors: Peter
authors: P
authors: Ghazal
authors: Arthur
authors: A
authors: Trew
authors: Jon
authors: J
authors: Hill