Ompss: a proposal for programming heterogeneous multi-core architectures
In this paper, we present OmpSs, a programming model based on OpenMP and StarSs, that
can also incorporate the use of OpenCL or CUDA kernels. We evaluate the proposal on …
can also incorporate the use of OpenCL or CUDA kernels. We evaluate the proposal on …
IM a2p–parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model
A Sethuraman, J Hey - Molecular ecology resources, 2016 - Wiley Online Library
IM a2 and related programs are used to study the divergence of closely related species and
of populations within species. These methods are based on the sampling of genealogies …
of populations within species. These methods are based on the sampling of genealogies …
MrBayes on a graphics processing unit
Motivation: Bayesian phylogenetic inference can be used to propose a 'tree of life'for a
collection of species whose DNA sequences are known. While there are many packages …
collection of species whose DNA sequences are known. While there are many packages …
A Bayesian supertree model for genome-wide species tree reconstruction
Current phylogenomic data sets highlight the need for species tree methods able to deal
with several sources of gene tree/species tree incongruence. At the same time, we need to …
with several sources of gene tree/species tree incongruence. At the same time, we need to …
Fine-grain parallelism using multi-core, cell/BE, and GPU systems: accelerating the phylogenetic likelihood function
We are currently faced with the situation where applications have increasing computational
demands and there is a wide selection of parallel processor systems. In this paper we focus …
demands and there is a wide selection of parallel processor systems. In this paper we focus …
Novel parallelization schemes for large-scale likelihood-based phylogenetic inference
A Stamatakis, AJ Aberer - 2013 IEEE 27th International …, 2013 - ieeexplore.ieee.org
The molecular data avalanche generated by novel wet-lab sequencing technologies allows
for reconstructing phylogenies (evolutionary trees) using hundreds of complete genomes as …
for reconstructing phylogenies (evolutionary trees) using hundreds of complete genomes as …
Efficient implementation of MrBayes on multi-GPU
J Bao, H Xia, J Zhou, X Liu… - Molecular biology and …, 2013 - academic.oup.com
Abstract MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)
3), is a popular program for Bayesian inference. As a leading method of using DNA data to …
3), is a popular program for Bayesian inference. As a leading method of using DNA data to …
Fine-grain parallelism using multi-core, Cell/BE, and GPU systems
Currently, we are facing a situation where applications exhibit increasing computational
demands and where a large variety of parallel processor systems are available. In this paper …
demands and where a large variety of parallel processor systems are available. In this paper …
Resource-efficient utilization of CPU/GPU-based heterogeneous supercomputers for Bayesian phylogenetic inference
J Chai, H Su, M Wen, X Cai, N Wu, C Zhang - The Journal of …, 2013 - Springer
Bayesian inference is one of the most important methods for estimating phylogenetic trees in
bioinformatics. Due to the potentially huge computational requirements, several parallel …
bioinformatics. Due to the potentially huge computational requirements, several parallel …
Runtime scheduling of dynamic parallelism on accelerator-based multi-core systems
We explore runtime mechanisms and policies for scheduling dynamic multi-grain parallelism
on heterogeneous multi-core processors. Heterogeneous multi-core processors integrate …
on heterogeneous multi-core processors. Heterogeneous multi-core processors integrate …