Title: Applications of heterogeneous computing in computational and simulation science

Authors: Luke Domanski; Tomasz Bednarz; Timur Gureyev; Lawrence Murray; Bevan Emma Huang; Yakov Nesterets; Darren Thompson; Emlyn Jones; Colin Cavanagh; Dadong Wang; Pascal Vallotton; Changming Sun; Alex Khassapov; Andrew Stevenson; Sheridan Mayo; Matthew Morell; Andrew W. George; John A. Taylor

Addresses: CSIRO Mathematics, Informatics and Statistics, Locked Bag 17, North Ryde, NSW 1670, Australia ' CSIRO Mathematics, Informatics and Statistics, Locked Bag 17, North Ryde, NSW 1670, Australia ' CSIRO Materials Science and Engineering, Private Bag 33, Clayton South, VIC 3169, Australia ' CSIRO Mathematics, Informatics and Statistics, Private Bag 5, Wembley, WA 6913, Australia ' CSIRO Mathematics, Informatics and Statistics, Queensland Ecosciences Precinct, P.O. Box 2583, Brisbane, QLD 4001, Australia ' CSIRO Materials Science and Engineering, Private Bag 33, Clayton South, VIC 3169, Australia ' CSIRO Materials Science and Engineering, Private Bag 33, Clayton South, VIC 3169, Australia ' CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, TAS 7001, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia ' CSIRO Enquiries, Locked Bag 10, Clayton South VIC 3169, Australia

Abstract: This paper presents a summary and overview of heterogeneous algorithms and applications developed by the Commonwealth Scientific and Industrial Research Organisation (CSIRO) for solving practical and challenging science problems such as: 1) high-content analysis of brain cell images for medical research and drug discovery; 2) genetic analysis of complex experimental designs for crop breeding; 3) solving computational fluid dynamics problems; 4) deconvolving 3D images from microscopy and medical imaging; 5) reconstructing large 3D computed tomography (CT) images from medical and materials science; 6) quantifying uncertainty in complex environmental models. Applications discussed utilise GPUs and multicore CPUs on a scale ranging from single desktop workstations through to large GPU clusters. Results demonstrate that both types of system can successfully accelerate a variety of practical science applications. We have seen significant gains in productivity and opportunity as a result of leveraging GPUs, tackling computational problems in which execution time was previously infeasible.

Keywords: heterogeneous computing; GPU computing; computational science; high performance computing; HPC; scientific computing; parallel programming; graphics processing units; GPUs; GPU clusters; simulation; brain cell images; medical research; drug discovery; genetic analysis; experimental design; crop breeding; computational fluid dynamics; CFD; deconvolving 3D images; medical imaging; 3D CT images; computed tomography; image reconstruction; quantifying uncertainty; environmental modelling.

DOI: 10.1504/IJCSE.2013.055356

International Journal of Computational Science and Engineering, 2013 Vol.8 No.3, pp.240 - 252

Received: 02 Mar 2012
Accepted: 29 Apr 2012

Published online: 27 Dec 2013 *

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