Enabling computer models of the heart for high-performance computers and the grid

Author:

Pitt-Francis Joe1,Garny Alan2,Gavaghan David1

Affiliation:

1. Oxford University Computing LaboratoryWolfson Building, Parks Road, Oxford OX1 3QD, UK

2. Department of Physiology, Anatomy and Genetics, University of OxfordParks Road, Oxford OX1 3PT, UK

Abstract

Although it is now feasible to compute multi-cellular models of the heart on a personal desktop or laptop computer, it is not feasible to undertake the detailed sweeps of high-dimensional parameter spaces required if we are to undertake in silico experimentation of the complex processes that constitute heart disease. For this research, modelling requirements move rapidly beyond the limit of commodity computers' resource both in terms of their memory footprint and the speed of calculation, so that multi-processor architectures must be considered. In addition, as such models have become more mature and have been validated against experimental data, there is increasing pressure for experimentalists to be able to make use of these models themselves as a key tool for hypothesis formulation and in planning future experimental studies to test those hypotheses. This paper discusses our initial experiences in a large-scale project (the Integrative Biology (IB) e-Science project) aimed at meeting these dual aims. We begin by putting the research in context by describing in outline the overall aims of the IB project, in particular focusing on the challenge of enabling novice users to make full use of high-performance resources without the need to gain detailed technical expertise in computing. We then discuss our experience of adapting one particular heart modelling package, Cellular Open Resource, and show how the solving engine of this code was dissected from the rest of the package, ported to C++ and parallelized using the Message-Passing Interface. We show that good parallel efficiency and realistic memory reduction can be achieved on simple geometries. We conclude by discussing lessons learnt in this process.

Publisher

The Royal Society

Subject

General Physics and Astronomy,General Engineering,General Mathematics

Reference19 articles.

Cited by 19 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. An Approach to Accelerate Three-dimensional Cardiac Simulation on GPU;2023 IEEE 13th International Workshop on Computational Intelligence and Applications (IWCIA);2023-11-11

2. A Heart for Diversity: Simulating Variability in Cardiac Arrhythmia Research;Frontiers in Physiology;2018-07-20

3. Images as drivers of progress in cardiac computational modelling;Progress in Biophysics and Molecular Biology;2014-08

4. Computational approaches to understand cardiac electrophysiology and arrhythmias;American Journal of Physiology-Heart and Circulatory Physiology;2012-10-01

5. PRACTICAL STEADY-STATE SCHEDULING FOR TREE-SHAPED TASK GRAPHS;Parallel Processing Letters;2011-12

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