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High-performance computing for computational biology of the heart

McFarlane, Ross (2010) High-performance computing for computational biology of the heart. Doctoral thesis, University of Liverpool.

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Abstract

This thesis describes the development of Beatbox — a simulation environment for computational biology of the heart. Beatbox aims to provide an adaptable, approachable simulation tool and an extensible framework with which High Performance Computing may be harnessed by researchers. Beatbox is built upon the QUI software package, which is studied in Chapter 2. The chapter discusses QUI’s functionality and common patterns of use, and describes its underlying software architecture, in particular its extensibility through the addition of new software modules called ‘devices’. The chapter summarises good practice for device developers in the Laws of Devices. Chapter 3 discusses the parallel architecture of Beatbox and its implementation for distributed memory clusters. The chapter discusses strategies for domain decomposition, halo swapping and introduces an efficient method for exchange of data with diagonal neighbours called Magic Corners. The development of Beatbox’s parallel Input/Output facilities is detailed, and its impact on scaling performance discussed. The chapter discusses the way in which parallelism can be hidden from the user, even while permitting the runtime execution user-defined functions. The chapter goes on to show how QUI’s extensibility can be continued in a parallel environment by providing implicit parallelism for devices and defining Laws of Parallel Devices to guide third-party developers. Beatbox’s parallel performance is evaluated and discussed. Chapter 4 describes the extension of Beatbox to simulate anatomically realistic tissue geometry. Representation of irregular geometries is described, along with associated user controls. A technique to compute no-flux boundary conditions on irregular boundaries is introduced. The Laws of Devices are further developed to include irregular geometries. Finally, parallel performance of anatomically realistic meshes is evaluated.

Item Type:Thesis (Doctoral)
Subjects:Q Science > QA Mathematics > QA76 Computer software
Q Science > QP Physiology
Departments, Research Centres and Related Units:Academic Faculties, Institutes and Research Centres > Faculty of Science > Department of Computer Science
Status:Unpublished
ID Code:3173
Deposited On:24 Aug 2011 10:37
Last Modified:24 Aug 2011 10:37

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