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We describe our approach in augmenting the BEAGLE library for high-performance statistical phylogenetic inference to support concurrent computation of independent partial likelihoods arrays. Our solution involves identifying independent likelihood estimates in analyses of partitioned datasets and in proposed tree topologies, and configuring concurrent computation of these likelihoods via CUDA and OpenCLl frameworks. We evaluate the effect of each increase in concurrency on throughput performance for our partial likelihoods kernel for a four-state nucleotide substitution model on a variety of parallel computing hardware, such as NVIDIA and AMD GPUs, and Intel multicore CPUs, observing up to 16-fold speedups over our previous implementation. Finally, we evaluate the effect of these gains on an domain application program, mrbayes. For a partitioned nucleotide-model analysis we observe an average speedup for the overall run time of 2.1-fold over our previous parallel implementation, and 10-fold over the native mrbayes with sse.
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Rerooting Trees Increases Opportunities for Concurrent Computation and Results in Markedly Improved Performance for Phylogenetic Inference
Parallel computing algorithms benefit from in- creases in concurrency when the hardware capacity is being under utilized. For likelihood-based molecular evolution in- ferences this can be due to small problem sizes, or because hardware capacity has increased beyond dataset sizes. A central concept in this domain is a bifurcating tree, which represents evolutionary relationships. The topology of the tree being evaluated directly affects the degree of parallelism that can be exploited by likelihood-based algorithms. For time-reversible evolutionary models we can reroot an unbalanced tree in order to make it more symmetric, without affecting the likelihood. Based on the reduction in number of concurrent operation sets, we define a best-case theoretical expectations, based on tree size and topology, for speedup due to rerooting which approaches 2-fold as the number of tip nodes increases for pectinate trees, and much higher values for some random topologies as the number of tip nodes increases. Empirical results using the NVIDIA CUDA implementation of the BEAGLE library confirm the merit of this approach. For pectinate trees we observe speedups of up to 1.93-fold due to rerooting and even larger speedups for random trees for the core likelihood-evaluation function in BEAGLE.
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- Award ID(s):
- 1661443
- PAR ID:
- 10061764
- Date Published:
- Journal Name:
- IEEE International Parallel and Distributed Processing Symposium Workshops
- Page Range / eLocation ID:
- 247-256
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/IPDPSW.2018.00049
