Enabling Real World Scale Structural Superlubricity All-Atom Simulation on the Next-Generation Sunway Supercomputer
Molecular dynamics (MD) simulation can provide an affordable way for inspecting microscopic phenomena, which is a powerful complement to real-world experiments. But the spatial scale of MD simulations is usually magnitudes smaller than experiment systems. In this paper, we present our work, redesign...
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| Vydáno v: | International Conference for High Performance Computing, Networking, Storage and Analysis (Online) s. 1 - 14 |
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| Jazyk: | angličtina |
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ACM
11.11.2023
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| ISSN: | 2167-4337 |
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| Abstract | Molecular dynamics (MD) simulation can provide an affordable way for inspecting microscopic phenomena, which is a powerful complement to real-world experiments. But the spatial scale of MD simulations is usually magnitudes smaller than experiment systems. In this paper, we present our work, redesigning the widely used inter-layer potential in structural superlubricity. By carrying out a specialized neighbor list for inter-layer potential computation, the total memory access amount is reduced significantly. Besides, a simple but efficient vectorization strategy is implemented based on the new neighbor list. In the extreme case, our work can scale to 38 million cores to achieve a sustainable performance of 61 PFLOPS, enabling a simulation of a superlubricity system of 32\ \mu m^{2} with 7.2 billion atoms at 4.75\ ns/day , which is 11,834 times of reported largest scale simulation in superlubricity systems in contact area and almost ten times faster in time-to-solution. Furthermore, we have done a simulation at 9\ \mu m^{2} which results in consistency with real-world experiments and verified some theoretical predictions in the mesoscopic scale. |
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| AbstractList | Molecular dynamics (MD) simulation can provide an affordable way for inspecting microscopic phenomena, which is a powerful complement to real-world experiments. But the spatial scale of MD simulations is usually magnitudes smaller than experiment systems. In this paper, we present our work, redesigning the widely used inter-layer potential in structural superlubricity. By carrying out a specialized neighbor list for inter-layer potential computation, the total memory access amount is reduced significantly. Besides, a simple but efficient vectorization strategy is implemented based on the new neighbor list. In the extreme case, our work can scale to 38 million cores to achieve a sustainable performance of 61 PFLOPS, enabling a simulation of a superlubricity system of 32\ \mu m^{2} with 7.2 billion atoms at 4.75\ ns/day , which is 11,834 times of reported largest scale simulation in superlubricity systems in contact area and almost ten times faster in time-to-solution. Furthermore, we have done a simulation at 9\ \mu m^{2} which results in consistency with real-world experiments and verified some theoretical predictions in the mesoscopic scale. |
| Author | Yang, Guangwen Duan, Xiaohui Chen, Dexun Gao, Ping Wang, Jin Gan, Lin Xue, Wei Liu, Xin Fu, Haohuan Ma, Ming Liu, Weiguo |
| Author_xml | – sequence: 1 givenname: Xiaohui surname: Duan fullname: Duan, Xiaohui email: sunrise_duan@126.com organization: School of Software, Shandong University,China – sequence: 2 givenname: Jin surname: Wang fullname: Wang, Jin email: wangjin16@tsinghua.org.cn organization: International School for Advanced Studies,Italy – sequence: 3 givenname: Ping surname: Gao fullname: Gao, Ping email: qdgaoping@gmail.com organization: Tsinghua University,Department of Computer Science and Technology,China – sequence: 4 givenname: Ming surname: Ma fullname: Ma, Ming email: maming16@tsinghua.edu.cn organization: Tsinghua University,Center for Nano and Micro Mechanics,Department of Engineering Mechanics,China – sequence: 5 givenname: Lin surname: Gan fullname: Gan, Lin email: lingan@tsinghua.edu.cn organization: Tsinghua University,Department of Computer Science and Technology,China – sequence: 6 givenname: Xin surname: Liu fullname: Liu, Xin email: yyylx@263.net organization: National Supercomputing Center in Wuxi,China – sequence: 7 givenname: Haohuan surname: Fu fullname: Fu, Haohuan email: haohuan@tsinghua.edu.cn organization: Tsinghua University,Ministry of Education Key Lab for Earth System Modeling,Department of Earth System Science,China – sequence: 8 givenname: Wei surname: Xue fullname: Xue, Wei email: xuewei717@gmail.com organization: Tsinghua University,Department of Computer Science and Technology,China – sequence: 9 givenname: Dexun surname: Chen fullname: Chen, Dexun email: adch@263.net organization: National Supercomputing Center in Wuxi,China – sequence: 10 givenname: Guangwen surname: Yang fullname: Yang, Guangwen email: ygw@tsinghua.edu.cn organization: Tsinghua University,Department of Computer Science and Technology,China – sequence: 11 givenname: Weiguo surname: Liu fullname: Liu, Weiguo email: weiguo.liu@sdu.edu.cn organization: School of Software, Shandong University,China |
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| Snippet | Molecular dynamics (MD) simulation can provide an affordable way for inspecting microscopic phenomena, which is a powerful complement to real-world... |
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| SubjectTerms | Atoms Force High performance computing Layered Materials Force Field Memory management Microscopy Molecular Dynamics Next generation networking Structural Superlubricity Sunway Supercomputer Supercomputers |
| Title | Enabling Real World Scale Structural Superlubricity All-Atom Simulation on the Next-Generation Sunway Supercomputer |
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