Paper Info
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.
Year
DOI
Venue
2010
10.1002/cpe.1787
Concurrency and Computation: Practice and Experience
Keywords
DocType
Volume
parallel permutation testing function,bioconductor package,permutation,hpc,high performance computing system,sprint implementation,high performance computing,statistical language r,microarray data,parallelized function,common bioinformatics,hpc system,microarray,common desktop machine,r permutation testing function,parallelized permutation testing function,parallel r interface,sprint r package,mpi,easy access,permutation test
Conference
23
Issue
ISSN
Citations 
17
1532-0626
2
PageRank 
References 
Authors
0.45
2
9
Name
Order
Citations
PageRank
Savvas Petrou120.45
Terence M. Sloan2555.43
Muriel Mewissen3583.67
Thorsten Forster4432.23
Michal Piotrowski561.71
Bartosz Dobrzelecki6102.05
Peter Ghazal7241.55
Arthur Trew820.45
J. Hill9575.27