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...

• Type: Conference
• Year: 2007
• Where: IPPS
• Authors: Filip Blagojevic, Alexandros Stamatakis, Christos D. Antonopoulos, Dimitrios S. Nikolopoulos
• Keywords: Cell Broadband Engine, Distributed And Parallel Computing, Heterogeneous Multi-core Processor, IPPS 2007, Real Cell Multiprocessor