Literature DB >> 22003276

On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods.

Anthony Lee1, Christopher Yau, Michael B Giles, Arnaud Doucet, Christopher C Holmes.   

Abstract

We present a case-study on the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. Graphics cards, containing multiple Graphics Processing Units (GPUs), are self-contained parallel computational devices that can be housed in conventional desktop and laptop computers and can be thought of as prototypes of the next generation of many-core processors. For certain classes of population-based Monte Carlo algorithms they offer massively parallel simulation, with the added advantage over conventional distributed multi-core processors that they are cheap, easily accessible, easy to maintain, easy to code, dedicated local devices with low power consumption. On a canonical set of stochastic simulation examples including population-based Markov chain Monte Carlo methods and Sequential Monte Carlo methods, we nd speedups from 35 to 500 fold over conventional single-threaded computer code. Our findings suggest that GPUs have the potential to facilitate the growth of statistical modelling into complex data rich domains through the availability of cheap and accessible many-core computation. We believe the speedup we observe should motivate wider use of parallelizable simulation methods and greater methodological attention to their design.

Entities:  

Year:  2010        PMID: 22003276      PMCID: PMC3191530          DOI: 10.1198/jcgs.2010.10039

Source DB:  PubMed          Journal:  J Comput Graph Stat        ISSN: 1061-8600            Impact factor:   2.302


  5 in total

1.  The incomplete beta function law for parallel tempering sampling of classical canonical systems.

Authors:  Cristian Predescu; Mihaela Predescu; Cristian V Ciobanu
Journal:  J Chem Phys       Date:  2004-03-01       Impact factor: 3.488

2.  Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures.

Authors:  Marc A Suchard; Quanli Wang; Cliburn Chan; Jacob Frelinger; Andrew Cron; Mike West
Journal:  J Comput Graph Stat       Date:  2010-06-01       Impact factor: 2.302

3.  Accelerating molecular modeling applications with graphics processors.

Authors:  John E Stone; James C Phillips; Peter L Freddolino; David J Hardy; Leonardo G Trabuco; Klaus Schulten
Journal:  J Comput Chem       Date:  2007-12       Impact factor: 3.376

4.  Accelerating molecular dynamic simulation on graphics processing units.

Authors:  Mark S Friedrichs; Peter Eastman; Vishal Vaidyanathan; Mike Houston; Scott Legrand; Adam L Beberg; Daniel L Ensign; Christopher M Bruns; Vijay S Pande
Journal:  J Comput Chem       Date:  2009-04-30       Impact factor: 3.376

5.  Many-core algorithms for statistical phylogenetics.

Authors:  Marc A Suchard; Andrew Rambaut
Journal:  Bioinformatics       Date:  2009-04-15       Impact factor: 6.937

  5 in total
  14 in total

1.  Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures.

Authors:  Marc A Suchard; Quanli Wang; Cliburn Chan; Jacob Frelinger; Andrew Cron; Mike West
Journal:  J Comput Graph Stat       Date:  2010-06-01       Impact factor: 2.302

2.  A general construction for parallelizing Metropolis-Hastings algorithms.

Authors:  Ben Calderhead
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-24       Impact factor: 11.205

3.  Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.

Authors:  Kevin Dialdestoro; Jonas Andreas Sibbesen; Lasse Maretty; Jayna Raghwani; Astrid Gall; Paul Kellam; Oliver G Pybus; Jotun Hein; Paul A Jenkins
Journal:  Genetics       Date:  2016-02-08       Impact factor: 4.562

4.  Graphics Processing Units and High-Dimensional Optimization.

Authors:  Hua Zhou; Kenneth Lange; Marc A Suchard
Journal:  Stat Sci       Date:  2010-08-01       Impact factor: 2.901

5.  Massive parallelization of serial inference algorithms for a complex generalized linear model.

Authors:  Marc A Suchard; Shawn E Simpson; Ivan Zorych; Patrick Ryan; David Madigan
Journal:  ACM Trans Model Comput Simul       Date:  2013-01       Impact factor: 1.075

6.  A self-organizing state-space-model approach for parameter estimation in hodgkin-huxley-type models of single neurons.

Authors:  Dimitrios V Vavoulis; Volko A Straub; John A D Aston; Jianfeng Feng
Journal:  PLoS Comput Biol       Date:  2012-03-01       Impact factor: 4.475

7.  Harnessing graphics processing units for improved neuroimaging statistics.

Authors:  Anders Eklund; Mattias Villani; Stephen M Laconte
Journal:  Cogn Affect Behav Neurosci       Date:  2013-09       Impact factor: 3.526

8.  Massive parallelization boosts big Bayesian multidimensional scaling.

Authors:  Andrew J Holbrook; Philippe Lemey; Guy Baele; Simon Dellicour; Dirk Brockmann; Andrew Rambaut; Marc A Suchard
Journal:  J Comput Graph Stat       Date:  2020-06-08       Impact factor: 2.302

9.  Scalable Bayesian inference for self-excitatory stochastic processes applied to big American gunfire data.

Authors:  Andrew J Holbrook; Charles E Loeffler; Seth R Flaxman; Marc A Suchard
Journal:  Stat Comput       Date:  2021-01-12       Impact factor: 2.559

10.  Accelerating compartmental modeling on a graphical processing unit.

Authors:  Roy Ben-Shalom; Gilad Liberman; Alon Korngreen
Journal:  Front Neuroinform       Date:  2013-03-18       Impact factor: 4.081

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