Tempest: a fast spatially explicit model of ecological dynamics on parallel machines

Abstract

The spatial and temporal aspects of population dynamics are pivotal to computational biology. This paper focuses on a spatially explicit model of four species in an environment that behaves like a large probabilistic cellular automaton. The cells of the automaton represent discrete sites into which the environment is partitioned. Probabilistic local state transitions are executed synchronously at all sites making the simulation suitable for parallel implementation on SIMD architectures. Measuring the simulation results requires computing global parameters of the ecological environment. Such computations are challenging to implement efficiently on SIMD machines. The simulation produces a large volume of data, requiring the use of visualization for model verification and result interpretation. In this paper, the parallel implementation of a spatially explicit two-species competition is discussed. First, the model performance is analyzed. The results indicate that the use of a massively parallel machine was necessary and efficient. There is also a discussion of implementation and use of visualization tools. Finally, the biological results are presented. Some of these results could arise only in spatially explicit ecological models.