<scp>GPU</scp> Accelerated Hybrid Particle‐Field Molecular Dynamics: Multi‐Node/Multi‐<scp>GPU</scp> Implementation and Large‐Scale Benchmarks of the <scp>OCCAM</scp> Code

A parallelization strategy for hybrid particle-field molecular dynamics (hPF-MD) simulations on multi-node multi-GPU architectures is proposed. Two design principles have been followed to achieve a massively parallel version of the OCCAM code for distributed GPU computing: performing all the computations only on GPUs, minimizing data exchange between CPU and GPUs, and among GPUs. The hPF-MD scheme is particularly suitable to develop a GPU-resident and low data exchange code. Comparison of performances obtained using the previous multi-CPU code with the proposed multi-node multi-GPU version are reported. Several non-trivial issues to enable applications for systems of considerable sizes, including large input files handling and memory occupation, have been addressed. Large-scale benchmarks of hPF-MD simulations for system sizes up to 10 billion particles are presented. Performances obtained using a moderate quantity of computational resources highlight the feasibility of hPF-MD simulations in systematic studies of large-scale multibillion particle systems. This opens the possibility to perform systematic/routine studies and to reveal new molecular insights for problems on scales previously inaccessible to molecular simulations.

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Publication Details

Journal
Journal of Computational Chemistry
Published
2025-05-14
DOI
https://doi.org/10.1002/jcc.70126
Citations
2
Primary Topic
Block Copolymer Self-Assembly
Type
article
Field-Weighted Citation Impact
1.04

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article

GPU Accelerated Hybrid Particle‐Field Molecular Dynamics: Multi‐Node/Multi‐GPU Implementation and Large‐Scale Benchmarks of the OCCAM Code

Ying Zhao, Yan Zhou, Toshihiro Kawakatsu, Giuseppe Mensitieri et al.
2 citations
Journal of Computational Chemistry
Block Copolymer Self-Assembly
1.04
article

GPU Accelerated Hybrid Particle‐Field Molecular Dynamics: Multi‐Node/Multi‐GPU Implementation and Large‐Scale Benchmarks of the OCCAM Code

Ying Zhao, Yan Zhou, Toshihiro Kawakatsu, Giuseppe Mensitieri, Zhong‐Yuan Lu, Giuseppe Milano, Rosario Esposito
article en
2 citations

Abstract

A parallelization strategy for hybrid particle-field molecular dynamics (hPF-MD) simulations on multi-node multi-GPU architectures is proposed. Two design principles have been followed to achieve a massively parallel version of the OCCAM code for distributed GPU computing: performing all the computations only on GPUs, minimizing data exchange between CPU and GPUs, and among GPUs. The hPF-MD scheme is particularly suitable to develop a GPU-resident and low data exchange code. Comparison of performances obtained using the previous multi-CPU code with the proposed multi-node multi-GPU version are reported. Several non-trivial issues to enable applications for systems of considerable sizes, including large input files handling and memory occupation, have been addressed. Large-scale benchmarks of hPF-MD simulations for system sizes up to 10 billion particles are presented. Performances obtained using a moderate quantity of computational resources highlight the feasibility of hPF-MD simulations in systematic studies of large-scale multibillion particle systems. This opens the possibility to perform systematic/routine studies and to reveal new molecular insights for problems on scales previously inaccessible to molecular simulations.

Journal of Computational ChemistryVol. 46(13)
Jilin University (CN), Tohoku University (JP), State Key Laboratory of Supramolecular Structure and Materials, Dalian Minzu University (CN), University of Naples Federico II (IT)
National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities
Openalex Percentile: Top 25%
Block Copolymer Self-Assembly
1.04
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