SPRINT

SPRINT Beta 2

The main change in SPRINT beta 0.2.0 is the addition of a permutation test function to the SPRINT library of parallelised statistical R functions. It parallelizes the mt.maxT function found in the multtest R package.

multtest

Also changes to the implementation of the SPRINT pcor() function allows for the distance matrix to be returned as the output of pcor() instead of the correlation coefficient matrix.

Finaly, SPRINT Beta 0.2.0 has simplified installation process and a reduced set of requirements.

Download it now!

Functionality

The SPRINT function library contains three functions:

  • pmaxT(): a permutation test function
  • pcor(): a Pearson correlation function
  • ptest(): a simple 'Hello World!' function

Performance

The graph below was obtained on the UK National Supercomputing Service, HECToR, using up to 512 cores for calculating 150,000 permutations on a 6,102 x 76 input matrix.

pmaxT scaling

References

Optimization of a parallel permutation testing function for the SPRINT R package, S. Petrou et all, Concurrency and Computation: Practice and Experience, Jun 2011.

This work was presented at the International ACM Symposium on High Performance Parallel and Distributed Computing, HPDC 2010, Chicago, Illinois, USA.

Optimization of a parallel permutation testing function for the SPRINT R Package, S. Petrou et all, HPDC 2010 Proceedings, Jun 2010.