| Item type |
学術雑誌論文 / Journal Article(1) |
| 公開日 |
2023-07-14 |
| タイトル |
|
|
タイトル |
An exa-scale high-performance molecular dynamics simulation program : MODYLAS |
|
言語 |
en |
| 言語 |
|
|
言語 |
eng |
| 資源タイプ |
|
|
資源タイプ識別子 |
http://purl.org/coar/resource_type/c_6501 |
|
資源タイプ |
journal article |
| アクセス権 |
|
|
アクセス権 |
open access |
|
アクセス権URI |
http://purl.org/coar/access_right/c_abf2 |
| 著者 |
安藤, 嘉倫
Ichikawa, Shin-ichi
坂下, 達哉
藤本, 和士
吉井, 範行
永井, 哲郎
Zhiye, Tang
岡崎, 進
|
| 概要 |
|
|
内容記述タイプ |
Other |
|
内容記述 |
A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, SIMD processing, and on-cache arithmetic operations. The system’s performance deteriorated only slightly, even under high parallelization. In particular, a newly developed minimum transferred data (MTD) method, requiring a significantly lower amount of data transfer compared to conventional communications, showed a significantly high performance. The coordinates and forces of 101,810,176 atoms and the multipole coefficients of the subcells could be distributed to the 32,768 nodes (1,572,864 cores) in 2.3 ms during one MD step calculation. The SIMD effective instruction rates for floating-point arithmetic operations in direct force and FMM calculations measured on Fugaku were 78.7% and 31.5%, respectively. The development of a data reuse algorithm enhanced the on-cache processing; the cache miss rate for direct force and FMM calculations were only 2.74% and 1.43%, respectively, on the L1 cache and 0.08% and 0.60%, respectively, on the L2 cache. The modified MODYLAS could complete one MD single time-step calculation within 8.5 ms for the aforementioned large system. Additionally, the program contains numerous functions for material research that enable free energy calculations, along with the generation of various ensembles and molecular constraints. |
|
言語 |
en |
| 書誌情報 |
en : The journal of chemical physics
巻 158,
号 19,
p. 1-35,
発行日 2023-05-15
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| ISSN |
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収録物識別子タイプ |
PISSN |
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収録物識別子 |
00219606 |
| 書誌レコードID |
|
|
収録物識別子タイプ |
NCID |
|
収録物識別子 |
AA00694991 |
| DOI |
|
|
関連タイプ |
isVersionOf |
|
|
識別子タイプ |
DOI |
|
|
関連識別子 |
https://doi.org/10.1063/5.0144361 |
| 権利 |
|
|
言語 |
en |
|
権利情報 |
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 158, 194803 (2023) and may be found at https://doi.org/10.1063/5.0144361. |
| 著者版フラグ |
|
|
出版タイプ |
AM |
|
出版タイプResource |
http://purl.org/coar/version/c_ab4af688f83e57aa |
| 出版者 |
|
|
出版者 |
AIP Publishing |
|
言語 |
en |
| キーワード |
|
|
言語 |
ja |
|
主題Scheme |
Other |
|
主題 |
関西大学 |
| キーワード |
|
|
言語 |
en |
|
主題Scheme |
Other |
|
主題 |
Kansai University |
KU-1100-20230515-01.pdf (1.2 MB)
