Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

DOI10.1016/J.CPC.2015.10.024MaRDI QIDQ2374010zbMATH OpenOpenAlexWikidataFDO

Authors Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, Yuji Sugita

Publication date 14 December 2016

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

Full work available at URL https://doi.org/10.1016/j.cpc.2015.10.024

zbMATH Keywords

molecular dynamics (MD) simulationfast Fourier transform (FFT)hybrid (MPI+OpenMP) parallelizationmidpoint cell methodparticle mesh Ewald (PME) calculationvolumetric decomposition

Mathematics Subject Classification ID

Parallel numerical computation (65Y05) Numerical methods for discrete and fast Fourier transforms (65T50)

Recommendations

• P3DFFT: A framework for parallel computations of Fourier transforms in three dimensions
• DL_POLY_3: the CCP5 national UK code for molecular–dynamics simulations
• Parallel fast Fourier transforms for electronic structure calculations
• Parallel three-dimensional nonequispaced fast Fourier transforms and their application to particle simulation
• An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations

Cites work

• A parallel FFT on an MIMD machine
• An Algorithm for the Machine Calculation of Complex Fourier Series
• An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations
• P3DFFT: A framework for parallel computations of Fourier transforms in three dimensions
• PFFT: An extension of FFTW to massively parallel architectures
• Performance of the 3D FFT on the 6D network torus QCDOC parallel supercomputer
• Scalable parallel FFT for spectral simulations on a Beowulf cluster

Cited in

(5)

• Minimizing Communication in the Multidimensional FFT
• Parallel three-dimensional nonequispaced fast Fourier transforms and their application to particle simulation
• Fast multipole preconditioners for sparse matrices arising from elliptic equations
• Multi-axis decomposition of density functional program for strong scaling up to 82,944 nodes on the K computer: compactly folded 3D-FFT communicators in the 6D torus network
• A flexible framework for multidimensional DFTs

Describes a project that uses

Uses Software

• 2DECOMP
• PFFT

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