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Optimization of a parallel permutation testing function for the SPRINT R package
Author(s) -
Petrou Savvas,
Sloan Terence M.,
Mewissen Muriel,
Forster Thorsten,
Piotrowski Michal,
Dobrzelecki Bartosz,
Ghazal Peter,
Trew Arthur,
Hill Jon
Publication year - 2011
Publication title -
concurrency and computation: practice and experience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.309
H-Index - 67
eISSN - 1532-0634
pISSN - 1532-0626
DOI - 10.1002/cpe.1787
Subject(s) - sprint , permutation (music) , r package , computer science , function (biology) , parallel computing , mathematics , programming language , physics , biology , software engineering , genetics , acoustics
SUMMARY 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.