A thread-level parallelization of pairwise additive potential and force calculations suitable for current many-core architectures

Andoh, Yoshimichi; Suzuki, Soichiro; Ohshima, Satoshi; Sakashita, Tatsuya; Ogino, Masao; Katagiri, Takahiro; Yoshii, Noriyuki; Okazaki, Susumu

doi:10.1007/s11227-018-2272-2

Cited by 4 publications

(2 citation statements)

References 22 publications

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“…Calculation procedures in the P2P are just the same as in the original code, regardless of the branch type. So, our recently proposed thread‐level parallelization techniques of P2P suited for current many‐core architectures could be utilized for the present extended FMM algorithm. Calculation procedures in the M2L are the same as in the original code, whereas

N_{normalM 2 normalL}^{(L)}

are not uniform at each L with the anisotropic partition tree as described in Section 2.1.4.…”

Section: Methodsmentioning

confidence: 99%

Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure

2020

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The fast multipole method (FMM) is an order N method for the numerically rigorous calculation of the electrostatic interactions among point charges in a system of interest. The FMM is utilized for massively parallelized software for molecular dynamics (MD) calculations. However, an inconvenient limitation is imposed on the implementation of the FMM: In three-dimensional case, a cubic MD unit cell is hierarchically divided by the octree partitioning under isotropic periodic boundary conditions along three axes. Here, we extended the FMM algorithm adaptive to a rectangular MD unit cell with different periodicity along the axes by applying an anisotropic hierarchical partitioning. The algorithm was implemented into the parallelized general-purpose MD calculation software designed for a system with uniform distribution of point charges in the unit cell. The partition tree can be a mixture of binary and ternary branches, the branches being chosen arbitrarily with respect to the coordinate axes at any levels. Errors in the calculated electrostatic interactions are discussed in detail for a selected partition tree structure. The extension enables us to execute MD calculations under more general conditions for the shape of the unit cell, partition tree, and boundary conditions, keeping the accuracy of the calculated electrostatic interactions as high as that with the conventional FMM. An extension of the present FMM algorithm to other prime number branches, such as 5 and 7, is straightforward.anisotropic partition tree, fast multipole method, high-performance computing, large-scale systems, molecular dynamics calculations, rectangular unit cell

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N_{normalM 2 normalL}^{(L)}

are not uniform at each L with the anisotropic partition tree as described in Section 2.1.4.…”

Section: Methodsmentioning

confidence: 99%

Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure

2020

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“…In contrast, in FMM, communications are mainly between adjacent computation nodes, and there are no all‐to‐all communications. Thus, a high efficiency can be achieved, even in a highly parallel environment …”

Section: Introductionmentioning

confidence: 99%

Fast multipole method for three‐dimensional systems with periodic boundary condition in two directions

2020

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We derived a new expression for the electrostatic interaction of three‐dimensional charge‐neutral systems with two‐dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells are expressed as a sum of real and reciprocal space terms, and a self‐interaction term. The reciprocal space contribution consists of two parts: zero and nonzero terms of the absolute value of the reciprocal lattice vector. To test the new expressions, electrostatic interactions were calculated for a randomly placed charge distribution in a cubic box and liquid water produced by molecular dynamics calculation. The accuracy could be controlled by the degree of expansion of the FMM. In the present expression, the computational complexity of the electrostatic interaction of N‐particle systems is order N, which is superior to that of the conventional two‐dimensional periodic Ewald method for a slab geometry and the particle mesh Ewald method with a large empty space at an interface of the unit cell. © 2020 Wiley Periodicals, Inc.

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Acceleration of Classical Molecular Dynamics Simulations

Andoh

Yoshii

Jung

et al. 2019

The Art of High Performance Computing for Computational Science, Vol. 2

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A thread-level parallelization of pairwise additive potential and force calculations suitable for current many-core architectures

Cited by 4 publications

References 22 publications

Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure

Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure

Fast multipole method for three‐dimensional systems with periodic boundary condition in two directions

Acceleration of Classical Molecular Dynamics Simulations

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