Abstract:International audienceThis article describes the design of an individual-based simulation engine that can harness the full potential of modern general-purpose multicore and multiprocessor computers. This design aims to enable interactive simulations of highly dynamic multiagent systems in which entities can move, change, appear, disappear, and interact with one another and the user at any time
“…As detailed in [22], we previously designed a simulation engine that can harness the full potential of all the Central Processing Units (CPUs) (would they be processors, physical cores, or logical cores) in a parallel computer.…”
“…This cache-aware simulation engine shows a very good scalability related to the number of CPUs used [22]. However, it was formerly dedicated to synchronous simulations and, as stated in section 2.1, our particle-based biochemical model relies on an asynchronous scheduling scheme.…”
Abstract. This work takes place in the context of biochemical kinetics simulation for the understanding of complex biological systems such as haemostasis. The classical approach, based on the numerical solving of differential systems, cannot satisfactorily handle local geometrical constraints, such as membrane binding events. To address this problem, we propose a particle-based system in which each molecular species is represented by a three-dimensional entity which diffuses and may undergo reactions. Such a system can be computationaly intensive, since a small time step and a very large number of entities are required to get significant results. Therefore, we propose a model that is suitable for parallel computing and that can especially take advantage of recent multicore and multiprocessor architectures. We present our particle-based system, detail the behaviour of our entities, and describe our parallel computing algorithms. Comparisons between simulations and theoretical results are exposed, as well as a performance evaluation of our algorithms.
“…As detailed in [22], we previously designed a simulation engine that can harness the full potential of all the Central Processing Units (CPUs) (would they be processors, physical cores, or logical cores) in a parallel computer.…”
“…This cache-aware simulation engine shows a very good scalability related to the number of CPUs used [22]. However, it was formerly dedicated to synchronous simulations and, as stated in section 2.1, our particle-based biochemical model relies on an asynchronous scheduling scheme.…”
Abstract. This work takes place in the context of biochemical kinetics simulation for the understanding of complex biological systems such as haemostasis. The classical approach, based on the numerical solving of differential systems, cannot satisfactorily handle local geometrical constraints, such as membrane binding events. To address this problem, we propose a particle-based system in which each molecular species is represented by a three-dimensional entity which diffuses and may undergo reactions. Such a system can be computationaly intensive, since a small time step and a very large number of entities are required to get significant results. Therefore, we propose a model that is suitable for parallel computing and that can especially take advantage of recent multicore and multiprocessor architectures. We present our particle-based system, detail the behaviour of our entities, and describe our parallel computing algorithms. Comparisons between simulations and theoretical results are exposed, as well as a performance evaluation of our algorithms.
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