A Parallel Implementation of the Stau-DPP Stochastic Simulator for the Modelling of Biological Systems

E. Mosca, I. Merelli, L. Milanesi, A. Clematis, D. D'Agostino
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引用次数: 3

Abstract

In the last decade, different computing paradigms and modelling frameworks for the description and simulation of biochemical systems based on stochastic modelling have been proposed. From a computational point of view, many simulations of the model are necessary to identify the behaviour of the system. The execution of thousands of simulation can require huge amount of time, therefore the parallelization of these algorithms is highly desirable. In this work we discuss the different strategies that can be implemented for the parallelization of a space aware τ-DPP variant, that is proving a C-MPI implementation of the system and discussing its performances according to the simulation of a particle diffusion in a crowded environment.
生物系统建模中Stau-DPP随机模拟器的并行实现
在过去的十年中,基于随机建模的生物化学系统的描述和模拟已经提出了不同的计算范式和建模框架。从计算的角度来看,许多模型的模拟是必要的,以确定系统的行为。数千次模拟的执行可能需要大量的时间,因此这些算法的并行化是非常可取的。在这项工作中,我们讨论了可以实现空间感知τ-DPP变体并行化的不同策略,即证明了系统的C-MPI实现,并根据拥挤环境中粒子扩散的模拟讨论了其性能。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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