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
Affiliations:
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
Venue:
International Journal of Computational Science and Engineering
Year:
2013

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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.