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

机译:生物学中基于个体的模型的并行实现:公告板和非公告板方法

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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. [References: 22]
机译:基于粒子的模型是模拟,其中物理现象的离散表示涉及相互作用的粒子。本文研究了在UNIX工作站网络上实现这些模型的两种不同方法的效率。测试了两种对粒子建模的数据并行方法:公告板和非公告板。在前一种方法中,程序通过逻辑共享的关联存储(称为公告板)进行通信。随着处理器上处理负载的变化,模拟的粒子会动态地分布在工作站之间。在后一种方法中,粒子在负载边缘静态地在网络工作站之间分配。该模拟系统是在二维空间中移动和觅食的蚂蚁的集合。本文以速度,元组粒度和通信成本为衡量标准,分析和比较了两种实现方式对不同组合的粒子和工作站数量的执行时间。分析表明,选择正确的粒度后,公告板方法更适合基于粒子的模拟。 (C)1998 Elsevier Science Ireland Ltd.保留所有权利。 [参考:22]

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