RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

dc.contributor.authorBlagojevic, Filipen
dc.contributor.authorStamatakis, Alexandrosen
dc.contributor.authorAntonopoulos, Christos D.en
dc.contributor.authorNikolopoulos, Dimitrios S.en
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2013-06-19T14:35:59Zen
dc.date.available2013-06-19T14:35:59Zen
dc.date.issued2006en
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
dc.format.mimetypeapplication/pdfen
dc.identifierhttp://eprints.cs.vt.edu/archive/00000929/en
dc.identifier.sourceurlhttp://eprints.cs.vt.edu/archive/00000929/01/paper.pdfen
dc.identifier.trnumberTR-06-23en
dc.identifier.urihttp://hdl.handle.net/10919/19567en
dc.language.isoenen
dc.publisherDepartment of Computer Science, Virginia Polytechnic Institute & State Universityen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectParallel computationen
dc.subjectBioinformaticsen
dc.titleRAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engineen
dc.typeTechnical reporten
dc.type.dcmitypeTexten

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