Parallel Computing for Long-Time Simulations of Calcium Waves in a Heart Cell
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Wang, Yu, Marc Olano, Matthias Gobbert, and Wesley Griffin. “Parallel Computing for Long-Time Simulations of Calcium Waves in a Heart Cell.” PAMM 12, no. 1 (2012): 637–38. https://doi.org/10.1002/pamm.201210307.
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This is the pre-peer reviewed version of the following article: Wang, Yu, Marc Olano, Matthias Gobbert, and Wesley Griffin. “Parallel Computing for Long-Time Simulations of Calcium Waves in a Heart Cell.” PAMM 12, no. 1 (2012): 637–38. https://doi.org/10.1002/pamm.201210307., which has been published in final form at https://doi.org/10.1002/pamm.201210307. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.
Abstract
Calcium waves are modeled by parabolic partial differential equations, whose simulation codes contain Krylov subspace methods as computational kernels. This paper presents GPU-based parallel computations for the conjugate gradient method applied to the finite difference discretization of a Poisson equation as prototype problem for the computational kernel. The CUDA algorithm tests the three memory systems of global memory, texture memory, and shared memory of a CUDA-enabled GPU. Due to the caching mechanism and coalesced read/write operations, the CUDA algorithm using global memory and single precision floating point numbers outperforms algorithms accessing texture memory and the shared memory. (© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)