Long-time Simulation of Calcium Induced Calcium Release in a Heart Cell using the Finite Element Method on a Hybrid CPU/GPU Node
Links to Fileshttps://dl.acm.org/citation.cfm?id=2872618
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Type of Work8 pages
conference proceeding pre-print
Citation of Original PublicationXuan Huang, Matthias K. Gobbert, Long-time simulation of calcium induced calcium release in a heart cell using the finite element method on a hybrid CPU/GPU node, HPC '15 Proceedings of the Symposium on High Performance Computing Pages 150-157, 2015, https://dl.acm.org/citation.cfm?id=2872618
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SubjectsCalcium Induced Calcium Release
High Performance Computing Facility (HPCF)
finite element method
A mathematical model of Calcium Induced Calcium Release in a heart cell has been developed that consists of three coupled non-linear advection-di usion-reaction equations. A program in C with MPI based on matrixfree Newton-Krylov method gives very good scalability, but still requires large run times for ne meshes. A programming model with CUDA and MPI that utilizes GPUs on a hybrid node can signi cantly reduce the wall clock time. This paper reports initial results that demonstrate speedup using a hybrid node with two GPUs over the best results on a CPU node.