Parallel implementations of individual-based models in biology: bulletin- and non-bulletin-board approaches

Authored by JW Haefner, V Nugala, SJ Allan

Date Published: 1998

DOI: 10.1016/s0303-2647(97)00069-5

Sponsors: No sponsors listed

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Model Documentation: Other Narrative

Model Code URLs: Model code not found

Abstract

Particle-based models are simulations in which the discrete representation of physical phenomenon involves interacting particles. This paper studies the efficiency of two different methods of implementing these models on a network of UNIX workstations. Two data parallel methods of modeling particles are tested: bulletin-board and non-bulletin-board. In the former method, the programs communicate through a logically shared, associative memory called a bulletin-board. The simulated particles are distributed among the workstations dynamically as the processing load on the processors changes. In the latter method, the particles are divided amongst the networked workstations statically at load rime. The simulated system is a collection of ants moving and foraging in a two-dimensional space. This paper analyzes and compares the execution times of both implementations for different combinations of particles and number of workstation, using speed-up, tuple granularity and communication cost as measures. Analysis shows that the bulletin-board method is better for particle-based simulations when the correct granularity is chosen. (C) 1998 Elsevier Science Ireland Ltd. All rights reserved.

Tags

algorithms Memory