Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code

Abstract--A hybrid MPI/Pthreads parallelization was implemented in the RAxML phylogenetics code. New MPI code was added to the existing Pthreads production code to exploit parallelism at two algorithmic levels simultaneously: coarsegrained with MPI and fine-grained with Pthreads. This hybrid, multi-grained approach is well suited for current highperformance computers, which typically are clusters of multicore, shared-memory nodes. The hybrid version of RAxML is especially useful for a comprehensive phylogenetic analysis, i.e., execution of many rapid bootstraps followed by a full maximum likelihood search. Multiple multi-core nodes can be used in a single run to speed up the computation and, hence, reduce the turnaround time. The hybrid code also allows more efficient utilization of a given number of processor cores. Moreover, it often returns a better solution than the stand-alone Pthreads code, because additional maximum likelihood searches are conducted in parallel using MPI. The co...

• Type: Journal
• Year: 2010
• Where: IPPS
• Authors: Wayne Pfeiffer, Alexandros Stamatakis
• Keywords: Code, Distributed And Parallel Computing, Hybrid Code, IPPS 2010, Pthreads