Multibillion-atom molecular dynamics simulation: design considerations for vector-parallel processing

DOI10.1016/J.CPC.2005.11.008MaRDI QIDQ709880zbMATH OpenOpenAlexFDO

Authors D. C. Rapaport

Publication date 18 October 2010

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

Full work available at URL https://doi.org/10.1016/j.cpc.2005.11.008

zbMATH Keywords

supercomputeralgorithmperformance evaluationparallel processingmolecular dynamics simulationvector processing

Mathematics Subject Classification ID

Parallel numerical computation (65Y05) Molecular physics (81V55)

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Cites work

• A high-performance, portable implementation of the MPI message passing interface standard
• The Art of Molecular Dynamics Simulation

Cited in

(10)

• Molecular-dynamics simulations using spatial decomposition and task-based parallelism
• Computer simulation of complex, strongly coupled nanometer-scale systems: Breaking the billion atom barrier
• The linked neighbour list (LNL) method for fast off-lattice Monte Carlo simulations of fluids
• Design and analysis of a parallel molecular dynamics application
• Large scale atomistic polymer simulations using Monte Carlo methods for parallel vector processors
• AMR-based molecular dynamics for non-uniform, highly dynamic particle simulations
• Substructured molecular dynamics using multibody dynamics algorithms
• Enhanced molecular dynamics performance with a programmable graphics processor
• Domain-decomposition parallelization for molecular dynamics algorithm with short-ranged potentials on Epiphany architecture
• Scalable I/O of large-scale molecular dynamics simulations: A data-compression algorithm

Describes a project that uses

Uses Software

• MPI/MPICH

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