Simulations of complex and microscopic models of cardiac electrophysiology powered by multi-GPU platforms
type: Item
instance of: scholarly article
title: Simulations of complex and microscopic models of cardiac electrophysiology powered by multi-GPU platforms
zbMATH Open document ID: 1261.92009
DOI: 10.1155/2012/824569
author: Bruno Gouvêa De Barros
author: Rafael Sachetto Oliveira
author: Wagner jun. Meira
author: Marcelo Lobosco
author: Rodrigo Weber Dos Santos
published in: Computational \& Mathematical Methods in Medicine
publication date: 2013-01-09T00:00:00Z
review text: Summary: Key aspects of cardiac electrophysiology, such as slow conduction, conduction block, and saltatory effects have been the research topic of many studies since they are strongly related to cardiac arrhythmia, reentry, fibrillation, or defibrillation. However, to reproduce these phenomena the numerical models need to use subcellular discretization for the solution of the PDEs and nonuniform, heterogeneous tissue electric conductivity. Due to the high computational costs of simulations that reproduce the fine microstructure of cardiac tissue, previous studies have considered tissue experiments of small or moderate sizes and used simple cardiac cell models. We develop a cardiac electrophysiology model that captures the microstructure of cardiac tissue by using a very fine spatial discretization (\(8 \mu \)m) and uses a very modern and complex cell model based on Markov chains for the characterization of ion channel's structure and dynamics. To cope with the computational challenges, the model was parallelized using a hybrid approach: cluster computing and GPGPUs (general-purpose computing on graphics processing units). Our parallel implementation of this model using a multi-GPU platform was able to reduce the execution times of the simulations from more than 6 days (on a single processor) to 21 minutes (on a small 8-node cluster equipped with 16 GPUs, i.e., 2 GPUs per node).
Mathematics Subject Classification ID: 92C30
Mathematics Subject Classification ID: 92C05
Mathematics Subject Classification ID: 65Y05
Mathematics Subject Classification ID: 35Q92
Mathematics Subject Classification ID: 68U99
zbMATH DE Number: 6123568
describes a project that uses: CUDA
describes a project that uses: OpenCL
describes a project that uses: MPI/MPICH
describes a project that uses: PETSc
MaRDI profile type: Publication
full work available at URL: https://doi.org/10.1155/2012/824569
OpenAlex ID: W1971533812
Wikidata QID: Q42380128
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description: scientific article; zbMATH DE number 6123568