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
|Series:||Lecture Notes in Computer Science|
|Funders:|| Swiss National Science Foundation|
|Date Deposited:||08 Jul 2016 09:20|
|Last Modified:||08 Jul 2016 09:20|