Optimized CUDA-Based PDE Solver for Reaction Diffusion Systems on Arbitrary Surfaces

Dhillon, Daljit Singh Joginder Singh; Descombes, Samira Michèle; Zwicker, Matthias (2 April 2016). Optimized CUDA-Based PDE Solver for Reaction Diffusion Systems on Arbitrary Surfaces. In: Parallel Processing and Applied Mathematics. 10.1007/978-3-319-32149-3_49

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Partial differential equation (PDE) solvers are commonly employed to study and characterize the parameter space for reaction-diffusion (RD) systems while investigating biological pattern formation. Increasingly, biologists wish to perform such studies with arbitrary surfaces representing ‘real’ 3D geometries for better insights. In this paper, we present a highly optimized CUDA-based solver for RD equations on triangulated meshes in 3D. We demonstrate our solver using a chemotactic model that can be used to study snakeskin pigmentation, for example. We employ a finite element based approach to perform explicit Euler time integrations. We compare our approach to a naive GPU implementation and provide an in-depth performance analysis, demonstrating the significant speedup afforded by our optimizations. The optimization strategies that we exploit could be generalized to other mesh based processing applications with PDE simulations.

Item Type: Conference or Workshop Item (Paper)
Division/Institute: 08 Faculty of Science > Institute of Computer Science (INF) > Computer Graphics Group (CGG)
08 Faculty of Science > Institute of Computer Science (INF)
UniBE Contributor: Dhillon, Daljit Singh Joginder Singh; Descombes, Samira Michèle and Zwicker, Matthias
Subjects: 000 Computer science, knowledge & systems
500 Science > 510 Mathematics
ISBN: 978-3-319-32148-6
Series: Lecture Notes in Computer Science
Funders: [4] Swiss National Science Foundation
Language: English
Submitter: Matthias Zwicker
Date Deposited: 08 Jul 2016 09:20
Last Modified: 08 Jul 2016 09:20
Publisher DOI: 10.1007/978-3-319-32149-3_49
BORIS DOI: 10.7892/boris.83429
URI: http://boris.unibe.ch/id/eprint/83429

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