Enhanced molecular dynamics performance with a programmable graphics processor

DOI10.1016/J.CPC.2010.12.029zbMATH Open1221.82013arXiv0911.5631OpenAlexW2144574395MaRDI QIDQ634067FDOQ634067

D. C. Rapaport

Publication date: 2 August 2011

Published in: Computer Physics Communications (Search for Journal in Brave)

Abstract: Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware necessitates a reformulation of the underlying algorithm. Performance measurements demonstrate the considerable benefit and cost-effectiveness of such an approach, which produces a factor of 2.5 speed improvement over previous work for the case of the soft-sphere potential.

Full work available at URL: https://arxiv.org/abs/0911.5631

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zbMATH Keywords

performance evaluationCUDAGPUcomputer architecturemolecular dynamics simulationoptimized algorithmgraphics processor

Mathematics Subject Classification ID

Parallel numerical computation (65Y05) Numerical algorithms for specific classes of architectures (65Y10)

Cites Work

• The Art of Molecular Dynamics Simulation
• General purpose molecular dynamics simulations fully implemented on graphics processing units
• Multibillion-atom molecular dynamics simulation: design considerations for vector-parallel processing

Cited In (10)

• Accelerating Molecular Dynamics Simulations on PlayStation 3 Platform Using Virtual-GRAPE Programming Model
• A special purpose array processor architecture for the molecular dynamics simulation of point-mutated proteins
• Massively parallel Monte Carlo for many-particle simulations on GPUs
• Pseudo-random number generation for Brownian dynamics and dissipative particle dynamics simulations on GPU devices
• General purpose molecular dynamics simulations fully implemented on graphics processing units
• GPU implementations of the Bond fluctuation model
• Title not available (Why is that?)
• GPU accelerated molecular dynamics simulation of thermal conductivities
• GPAMM-software package for molecular dynamics on graphical processing units
• A GPU-based large-scale Monte Carlo simulation method for systems with long-range interactions

Uses Software

• CUDA

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