A Refinement Method of Biological Morphology Data Division for Parallel Computing of Distributed Parameter Systems

In this research, we propose a method to improve the simulation speed of MPI parallel program by automatically repartitioning the target simulation space. By using the MPI parallel program, the total simulation time is reduced compared to the sequential program, however, the performance strongly depends on the simulation space partition. In this method, we used the measured computation time of each processing element (PE) to refine the assigned area of each PE which leads to the balanced computational time of all PE.

[1]  Yoshitoshi Kunieda,et al.  A general CellML simulation code generator using ODE solving scheme description , 2011, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[2]  Sergey Missan,et al.  CESE: Cell Electrophysiology Simulation Environment. , 2005, Applied bioinformatics.

[3]  Denis Noble,et al.  Cellular Open Resource (COR): current status and future directions , 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[4]  Yoshiyuki Asai,et al.  A platform for in silico modeling of physiological systems III , 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[5]  Yoram Rudy,et al.  Rate Dependence and Regulation of Action Potential and Calcium Transient in a Canine Cardiac Ventricular Cell Model , 2004, Circulation.

[6]  Denis Noble,et al.  The IUPS human physiome project , 2002, Pflügers Archiv.

[7]  Peter J. Hunter,et al.  An Overview of CellML 1.1, a Biological Model Description Language , 2003, Simul..

[8]  David P. Nickerson,et al.  Reference descriptions of cellular electrophysiology models , 2008, Bioinform..

[9]  Rodrigo Weber dos Santos,et al.  CellML and associated tools and techniques , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.