ERmod-OpenACC : GPU Acceleration of Solvation Free Energy Calculation with Energy-Representation Theory

Maruyama, Yutaka; Kojima, Hidekazu; Matubayasi, Nobuyuki

Journal of Computational Chemistry, 2025, 46(16), e70152

アクセス数:123件（2026-02-15 22:21 集計）

固定URL: https://hdl.handle.net/11094/101952

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論文情報

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タイトル
ERmod-OpenACC : GPU Acceleration of Solvation Free Energy Calculation with Energy-Representation Theory
著者
NRID
1000080390665 1000080390665
ORCID
0000-0003-4035-4885 0000-0003-4035-4885
researchmap permalink
drmaruyama drmaruyama
Scopus Author ID
54968540200 54968540200
著者名
Maruyama, Yutaka
NRID
1000020895833 1000020895833
researchmap permalink
e1kojima e1kojima
著者名
Kojima, Hidekazu
NRID
1000020281107 1000020281107
著者名
Matubayasi, Nobuyuki
内容
This is the peer reviewed version of the following article: Yutaka Maruyama, Hidekazu Kojima, Nobuyuki Matubayasi, ERmod-OpenACC: GPU Acceleration of Solvation Free Energy Calculation With Energy-Representation Theory. Journal of Computational Chemistry, Volume 46, Issue 16, e70152(2025), which has been published in final form at https://doi.org/10.1002/jcc.70152. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.
抄録
ERmod-OpenACC is a GPU-accelerated implementation of a calculation package for the solvation free energy. In the implementation, the most computationally intensive processes—the calculation of the pair energies and the construction of the correlation function—have been optimized for GPUs. ERmod-OpenACC also supports single precision to maximize performance on RTX series GPUs, which are commonly used in molecular dynamics simulations. A common problem with OpenACC is data transfer between the CPU and GPU. By minimizing data transfer, the package's performance has been significantly improved. Compared to a single Xeon core (3.1 GHz), ERmod-OpenACC achieves a speedup of up to approximately when running on RTX 4080 SUPER. The package also supports multiple GPUs via MPI, achieving a speedup of with 2 GPUs and approximately with 16 GPUs. The only external library required to compile ERmod-ACC is NVIDIA HPC SDK. The package is available at https://github.com/drmaruyama/ermod-openacc.
出版者
Wiley
収録物名
Journal of Computational Chemistry
巻(号)
46(16)
ページ
e70152
刊行年月
2025-06-08
言語
英語
ハンドルURL
https://hdl.handle.net/11094/101952
PISSN
01928651
eISSN
1096987X
関連情報 (isVersionOf)
DOI (出版社版)
https://doi.org/10.1002/jcc.70152
アクセス権
embargoed access
権利情報
© 2025 Wiley Periodicals LLC.
The full-text file will be made open to the public on 8 June 2026 in accordance with the publisher's policy.
出版タイプ
Accepted Manuscript
カテゴリ
学術雑誌論文 Journal Article