Hardware acceleration of reaction-diffusion systems

a guide to optimisation of pattern formation algorithms using OpenACC

Ruth E. Falconer, Alasdair N. Houston, Xavier Portell, Wilfred Otten

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Abstract

Reaction Diffusion Systems (RDS) have widespread applications in computational ecology, biology, computer graphics and the visual arts. For the former applications a major barrier to the development of effective simulation models is their computational complexity - it takes a great deal of processing power to simulate enough replicates such that reliable conclusions can be drawn. Optimizing the computation is thus highly desirable in order to obtain more results with less resources. Existing optimizations of RDS tend to be low-level and GPGPU based. Here we apply the higher-level OpenACC framework to two case studies: a simple RDS to learn the ‘workings’ of OpenACC and a more realistic and complex example. Our results show that simple parallelization directives and minimal data transfer can produce a useful performance improvement. The relative simplicity of porting OpenACC code between heterogeneous hardware is a key benefit to the scientific computing community in terms of speed-up and portability.
Original languageEnglish
Title of host publicationSpring Simulation Conference (SpringSim), 2019
PublisherIEEE
Pages472-483
Number of pages12
ISBN (Electronic)9781510883888
ISBN (Print)9781728135472
DOIs
Publication statusPublished - 10 Jun 2019
Event2019 Spring Simulation Conference - University of Arizona, Tucson, United States
Duration: 29 Apr 20192 May 2019
http://scs.org/springsim/

Conference

Conference2019 Spring Simulation Conference
Abbreviated titleSpringSim'19
CountryUnited States
CityTucson
Period29/04/192/05/19
Internet address

Fingerprint

Hardware
Natural sciences computing
Ecology
Computer graphics
Data transfer
Computer hardware
Computational complexity
Processing

Cite this

Falconer, R. E., Houston, A. N., Portell, X., & Otten, W. (2019). Hardware acceleration of reaction-diffusion systems: a guide to optimisation of pattern formation algorithms using OpenACC. In Spring Simulation Conference (SpringSim), 2019 (pp. 472-483). IEEE . https://doi.org/10.23919/SpringSim.2019.8732883
Falconer, Ruth E. ; Houston, Alasdair N. ; Portell, Xavier ; Otten, Wilfred. / Hardware acceleration of reaction-diffusion systems : a guide to optimisation of pattern formation algorithms using OpenACC. Spring Simulation Conference (SpringSim), 2019. IEEE , 2019. pp. 472-483
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abstract = "Reaction Diffusion Systems (RDS) have widespread applications in computational ecology, biology, computer graphics and the visual arts. For the former applications a major barrier to the development of effective simulation models is their computational complexity - it takes a great deal of processing power to simulate enough replicates such that reliable conclusions can be drawn. Optimizing the computation is thus highly desirable in order to obtain more results with less resources. Existing optimizations of RDS tend to be low-level and GPGPU based. Here we apply the higher-level OpenACC framework to two case studies: a simple RDS to learn the ‘workings’ of OpenACC and a more realistic and complex example. Our results show that simple parallelization directives and minimal data transfer can produce a useful performance improvement. The relative simplicity of porting OpenACC code between heterogeneous hardware is a key benefit to the scientific computing community in terms of speed-up and portability.",
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Falconer, RE, Houston, AN, Portell, X & Otten, W 2019, Hardware acceleration of reaction-diffusion systems: a guide to optimisation of pattern formation algorithms using OpenACC. in Spring Simulation Conference (SpringSim), 2019. IEEE , pp. 472-483, 2019 Spring Simulation Conference, Tucson, United States, 29/04/19. https://doi.org/10.23919/SpringSim.2019.8732883

Hardware acceleration of reaction-diffusion systems : a guide to optimisation of pattern formation algorithms using OpenACC. / Falconer, Ruth E.; Houston, Alasdair N.; Portell, Xavier; Otten, Wilfred.

Spring Simulation Conference (SpringSim), 2019. IEEE , 2019. p. 472-483.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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