title: MrBayes tgMC3++: A High Performance and Resource-Efficient GPU-Oriented Phylogenetic Analysis Method.
abstract: MrBayes is a widespread phylogenetic inference tool harnessing empirical evolutionary models and Bayesian statistics. However, the computational cost on the likelihood estimation is very expensive, resulting in undesirably long execution time. Although a number of multi-threaded optimizations have been proposed to speed up MrBayes, there are bottlenecks that severely limit the GPU thread-level parallelism of likelihood estimations. This study proposes a high performance and resource-efficient method for GPU-oriented parallelization of likelihood estimations. Instead of having to rely on empirical programming, the proposed novel decomposition storage model implements high performance data transfers implicitly. In terms of performance improvement, a speedup factor of up to 178 can be achieved on the analysis of simulated datasets by four Tesla K40 cards. In comparison to the other publicly available GPU-oriented MrBayes, the tgMC3++ method (proposed herein) outperforms the tgMC3(v1.0), nMC3(v2.1.1) and oMC3(v1.00) methods by speedup factors of up to 1.6, 1.9 and 2.9, respectively. Moreover, tgMC3++ supports more evolutionary models and gamma categories, which previous GPU-oriented methods fail to take into analysis.
authors.forename: Cheng
authors.initials: C
authors.lastname: Ling
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Hamada
authors.forename: Jingyang
authors.initials: J
authors.lastname: Gao
authors.forename: Guoguang
authors.initials: G
authors.lastname: Zhao
authors.forename: Donghong
authors.initials: D
authors.lastname: Sun
authors.forename: Weifeng
authors.initials: W
authors.lastname: Shi
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D003196:Computer Graphics / Q000295:instrumentation*; D003627:Data Interpretation, Statistical; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D016013:Likelihood Functions; D010802:Phylogeny; D012984:Software