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However, it introduces a significant penalty in performance, power, electricity, and running time. Consequently, once the simulation size scales up and computing demands keep growing, it comes at substantial costs in performance and energy usage. In this paper, an optimized MD implementation on the Sunway TaihuLight supercomputer with heterogeneous many\u2010core processors is developed to address the abovementioned issues. The Sunway TaihuLight is a totally independently designed and developed Chinese supercomputer with a profusely customized integration approach and a brand new many\u2010core processor, the SW26010. The computing power mainly supported by the homegrown many\u2010core SW26010 processors differs from other existing heterogeneous supercomputers. The Sunway TaihuLight is a heterogeneous supercomputer that ranks first in the world with its peak performance over 100 PFLOPS. Firstly, we propose a new algorithm based on cluster particles to fit the special architecture of SW26010. Then, three optimization methods of the MD simulation are implemented step by step: parallelized extensions to SW26010, memory\u2010access optimizations, and vectorization. After these optimization processes, a 14x speedup is achieved on a single computing node and yields significant performance and energy improvements. Superiorly, almost 24,000 computing nodes (6,000,000 cores) are applied in our experiments, which gain an almost linear speedup. Besides, the proposed methods also can be adapted and fit to other molecular dynamics codes, even other similar scientific applications.<\/jats:p>","DOI":"10.1002\/cpe.4468","type":"journal-article","created":{"date-parts":[[2018,4,10]],"date-time":"2018-04-10T23:40:42Z","timestamp":1523403642000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Implementing molecular dynamics simulation on the Sunway TaihuLight system with heterogeneous many\u2010core processors"],"prefix":"10.1002","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8823-4757","authenticated-orcid":false,"given":"Wenqian","family":"Dong","sequence":"first","affiliation":[{"name":"College of Computer Science and Electronic Engineering Hunan University  Changsha 410082 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenli","family":"Li","sequence":"additional","affiliation":[{"name":"College of Computer Science and Electronic Engineering Hunan University  Changsha 410082 China"},{"name":"National Supercomputing Center in Changsha  Changsha 410082 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Letian","family":"Kang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Electronic Engineering Hunan University  Changsha 410082 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhe","family":"Quan","sequence":"additional","affiliation":[{"name":"College of Computer Science and Electronic Engineering Hunan University  Changsha 410082 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keqin","family":"Li","sequence":"additional","affiliation":[{"name":"College of Computer Science and Electronic Engineering Hunan University  Changsha 410082 China"},{"name":"National Supercomputing Center in Changsha  Changsha 410082 China"},{"name":"Department of Computer Science State University of New York  New Paltz NY 12561 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2018,4,10]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1006\/jcph.1995.1039"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1006\/jcph.1996.0046"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRev.159.98"},{"key":"e_1_2_9_5_1","volume-title":"Computer Simulation Using Particles","author":"Eastwood JW","year":"1981"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.4822471"},{"key":"e_1_2_9_7_1","unstructured":"Top500.Top500 supercomputer site.https:\/\/www.top500.org\/lists\/"},{"key":"e_1_2_9_8_1","doi-asserted-by":"crossref","unstructured":"YangC XueW FuH et al.10m\u2010core scalable fully\u2010implicit solver for nonhydrostatic atmospheric dynamics. 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