Parallel and bias-free RSA algorithm for maximal Poisson-sphere sampling

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications Pub Date : 2024-08-23 DOI:10.1016/j.cpc.2024.109354

Marc Josien, Raphaël Prat

引用次数: 0

Abstract

In this paper we propose and benchmark an innovative implementation of the Random Sequential Addition (or adsorption) (Rsa) algorithm. It provides Mpi parallelization and is designed to generate a high number of spheres aiming for maximal compactness, without introducing any bias. Although parallelization of such an algorithm has been successfully undertaken with shared memory (and in particular with Gpu), this is seemingly the first available implementation with distributed memory (Mpi). Our implementation successfully generated more than 12 billions of spheres over 131,072 Mpi processes in 16 seconds in dimension $d = 3$ .

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最大泊松球采样的并行和无偏差 RSA 算法

在本文中，我们提出了随机顺序加法（或吸附）（Rsa）算法的创新实现，并对其进行了基准测试。该算法提供 Mpi 并行化，旨在生成大量球体，追求最大紧凑性，同时不引入任何偏差。虽然共享内存（特别是 Gpu）已经成功实现了这种算法的并行化，但这似乎是首个使用分布式内存（Mpi）实现的算法。在维度 d=3 的情况下，我们的实现在 16 秒内通过 131,072 个 Mpi 进程成功生成了超过 120 亿个球体。

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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来源期刊

Computer Physics Communications 物理-计算机：跨学科应用

CiteScore

12.10

自引率

3.20%

发文量

287

审稿时长

5.3 months

期刊介绍： The focus of CPC is on contemporary computational methods and techniques and their implementation, the effectiveness of which will normally be evidenced by the author(s) within the context of a substantive problem in physics. Within this setting CPC publishes two types of paper. Computer Programs in Physics (CPiP) These papers describe significant computer programs to be archived in the CPC Program Library which is held in the Mendeley Data repository. The submitted software must be covered by an approved open source licence. Papers and associated computer programs that address a problem of contemporary interest in physics that cannot be solved by current software are particularly encouraged. Computational Physics Papers (CP) These are research papers in, but are not limited to, the following themes across computational physics and related disciplines. mathematical and numerical methods and algorithms; computational models including those associated with the design, control and analysis of experiments; and algebraic computation. Each will normally include software implementation and performance details. The software implementation should, ideally, be available via GitHub, Zenodo or an institutional repository.In addition, research papers on the impact of advanced computer architecture and special purpose computers on computing in the physical sciences and software topics related to, and of importance in, the physical sciences may be considered.