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Parallel Computing for Long‐Time Simulations of Calcium Waves in a Heart Cell
Author(s) -
Wang Yu,
Olano Marc,
Gobbert Matthias,
Griffin Wesley
Publication year - 2012
Publication title -
pamm
Language(s) - English
Resource type - Journals
ISSN - 1617-7061
DOI - 10.1002/pamm.201210307
Subject(s) - cuda , computer science , parallel computing , shared memory , texture memory , krylov subspace , discretization , conjugate gradient method , distributed memory , computational science , kernel (algebra) , algorithm , graphics , mathematics , iterative method , computer graphics (images) , discrete mathematics , mathematical analysis , software rendering , 3d computer graphics
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)