Show simple item record

dc.contributor.authorBlagojevic, Filipen_US
dc.contributor.authorStamatakis, Alexandrosen_US
dc.contributor.authorAntonopoulos, Christosen_US
dc.contributor.authorNikolopoulos, Dimitriosen_US
dc.date.accessioned2013-06-19T14:35:59Z
dc.date.available2013-06-19T14:35:59Z
dc.date.issued2006
dc.identifierhttp://eprints.cs.vt.edu/archive/00000929/en_US
dc.identifier.urihttp://hdl.handle.net/10919/19567
dc.description.abstractPhylogenetic tree reconstruction is one of the grand challenge problems in Bioinformatics. The search for a best-scoring tree with 50 organisms, under a reasonable optimality criterion, creates a topological search space which is as large as the number of atoms in the universe. Computational phylogeny is challenging even for the most powerful supercomputers. It is also an ideal candidate for benchmarking emerging multiprocessor architectures, because it exhibits various levels of fine and coarse-grain parallelism. In this paper, we present the porting, optimization, and evaluation of RAxML on the Cell Broadband Engine. RAxML is a provably efficient, hill climbing algorithm for computing phylogenetic trees based on the Maximum Likelihood (ML) method. The algorithm uses an embarrassingly parallel search method, which also exhibits data-level parallelism and control parallelism in the computation of the likelihood functions. We present the optimization of one of the currently fastest tree search algorithms, on a real Cell blade prototype. We also investigate problems and present solutions pertaining to the optimization of floating point code, control flow, communication, scheduling, and multi-level parallelization on the Cell.en_US
dc.format.mimetypeapplication/pdfen_US
dc.publisherDepartment of Computer Science, Virginia Polytechnic Institute & State Universityen_US
dc.subjectParallel computationen_US
dc.subjectBioinformaticsen_US
dc.titleRAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engineen_US
dc.typeTechnical reporten_US
dc.identifier.trnumberTR-06-23en_US
dc.type.dcmitypeTexten_US
dc.identifier.sourceurlhttp://eprints.cs.vt.edu/archive/00000929/01/paper.pdf


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record