MrBayes on a graphics processing unit

Jianfu Zhou, Xiaoguang Liu, Douglas Stones, Qiang Xie, Gang Wang

Research output: Contribution to journalArticleResearchpeer-review

47 Citations (Scopus)

Abstract

tree of life for a collection of species whose DNA sequences are known. While there are many packages available that implement Bayesian phylogenetic inference, such as the popular MrBayes, running these programs poses significant computational challenges. Parallelized versions of the Metropolis coupled Markov chain Monte Carlo (MC(3)) algorithm in MrBayes have been presented that can run on various platforms, such as a graphics processing unit (GPU). The GPU has been used as a cost-effective means for computational research in many fields. However, until now, some limitations have prevented the GPU from being used to run MrBayes MC(3) effectively. Results: We give an appraisal of the possibility of realistically implementing MrBayes MC(3) in parallel on an ordinary four-core desktop computer with a GPU. An earlier proposed algorithm for running MrBayes MC(3) in parallel on a GPU has some significant drawbacks (e. g. too much CPU-GPU communication) which we resolve. We implement these improvements on the NVIDIA GeForce GTX 480 as most other GPUs are unsuitable for running MrBayes MC(3) due to a range of reasons, such as having insufficient support for double precision floating-point arithmetic. Experiments indicate that run-time can be decreased by a factor of up to 5.4 by adding a single GPU (versus state-of-the-art multicore parallel algorithms). We can also achieve a speedup (versus serial MrBayes MC(3)) of more than 40 on a sufficiently large dataset using two GPUs.
Original languageEnglish
Pages (from-to)1255 - 1261
Number of pages7
JournalBioinformatics
Volume27
Issue number9
DOIs
Publication statusPublished - 2011

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