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

  • Samira Michèle Descombes
  • Daljit Singh Dhillon
  • Matthias Zwicker
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9573)

Abstract

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.

Keywords

CUDA GPU programming Reaction-diffusion systems Nonlinear PDEs FEM Explicit time-stepping 

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Samira Michèle Descombes
    • 1
  • Daljit Singh Dhillon
    • 1
  • Matthias Zwicker
    • 1
  1. 1.Institute of Computer ScienceUniversity of BernBernSwitzerland

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