Regular Paper Optimization Techniques for Parallel Biophysical Simulations Generated by insilico IDE

Recent work in biophysical science increasingly focuses on modeling and simulating human biophysical systems to better understand the human physiome. One program to generate such models is insilicoIDE. These models may consist of thousands or millions of components with complex relations. Simulations of such models can require millions of time steps and take hours or days to run on a single machine. To improve the speed of biophysical simulations generated by insilicoIDE, we propose techniques for augmenting the simulations to support parallel execution in an MPI-enabled environment. In this paper we discuss the methods involved in efficient parallelization of such simulations, including classification and identification of model component relationships and work division among multiple machines. We demonstrate the effectiveness of the augmented simulation code in a parallel computing environment by performing simulations of large scale neuron and cardiac models.

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