A Hybrid Parallel Framework for the Cellular Potts Model Simulations

The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most of current implementations are either sequential or approximate, which cannot be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming partial differential equation (PDE) solving, cell division, and cell reaction operation are distributed to clusters by using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system by using OpenMP. Since the Monte Carlo lattice update is much faster than the PDE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we have studied the avascular tumor growth by using a multiscale model. The application and performance analyses demonstrate that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation (∼10^8 sites) of complex collective behavior of numerous cells (∼10^6).

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