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IPPS
2007
IEEE

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

13 years 10 months ago
RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine
Computational phylogeny is a challenging application even for the most powerful supercomputers. It is also an ideal candidate for benchmarking emerging multiprocessor architectures, because it exhibits fine- and coarse-grain parallelism at multiple levels. 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 Cell Broadband Engine, a heterogeneous multi-core processor with SIMD accelerators which was initially marketed for set-top boxes, is currently being deployed on supercomputers and high-end server architectures. We present both conventional and unconventional, Cell-specific optimizations for RAxML’s search algorithm on a real Cell multiprocessor. While exploring these optimizations, we present solutions to problems related to floating point code execution, complex control flow, communi...
Filip Blagojevic, Alexandros Stamatakis, Christos
Added 03 Jun 2010
Updated 03 Jun 2010
Type Conference
Year 2007
Where IPPS
Authors Filip Blagojevic, Alexandros Stamatakis, Christos D. Antonopoulos, Dimitrios S. Nikolopoulos
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