This thesis studies how the multi-core hardware architecture can be efficiently used for real-world scientific applications that arise from computational cardiology and computational geoscience. The investigation has been carried out from different angles: numerical algorithms, parallel programming and performance modeling and prediction. It is shown that high-performance implementations and optimizations must match both the underlying computations and the target parallel platform. Several good practices are summarized for parallel programming and performance analysis on the multi-core architecture, which can be of help to many other scientists.
List of papers. The papers are removed from the thesis due to copyright restrictions.
Paper I Evolution of Intracellular Ca2+ Waves from about 10,000 RyR Clusters: Towards Solving a Computationally Daunting Task P. Li, W. Wei, X. Cai, C. Soeller, M. Cannell, A. V. Holden Published in Proceedings of the Fifth International Conference on Functional Imaging and Modeling of the Heart, Lecture Notes in Computer Science Volume 5528, 2009, pp 11-20 doi:10.1007/978-3-642-01932-6_2
Paper II Computational Modeling of the Initiation and Development of Spontaneous Intracellular Ca2+ Waves in Ventricular Myocytes P. Li, W. Wei, X. Cai, C. Soeller, M. Cannell, A. V. Holden Published in Philosophical Transactions of the Royal Society A, Volume 368, 2010, Pages 3953-3965. doi:10.1098/rsta.2010.0146
Paper III An OpenMP-enabled Parallel Simulator for Particle Transport in Fluid Flows W. Wei, O. Al-Khayat, X. Cai Published in Procedia Computer Science, Volume 4, 2011, Pages 1475-1484. doi:10.1016/j.procs.2011.04.160
Paper IV Numerical Analysis of a Dual-sediment Transport Model Applied to Lake Okeechobee, Florida S. R. Clark, W. Wei, X. Cai Published in Proceedings of the Ninth International Symposium on Parallel and Distributed Computing, 2010, Pages 189-194. doi:10.1109/ISPDC.2010.29
Paper V Balancing Efficiency and Accuracy for Sediment Transport Simulations W. Wei, S. R. Clark, H. Su, M. Wen, X. Cai Submitted to journal for publication.