Scalable Molecular Dynamics with NAMD on the Summit System

IBM Journal of Research and Development
B AcunJ E Stone

Abstract

NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and dynamics of large biomolecular complexes, such as viruses like HIV and various types of influenza. State-of-the-art biomolecular simulations often require integration of billions of timesteps, computing all interatomic forces for each femtosecond timestep. Molecular dynamics simulation of large biomolecular systems and long-timescale biological phenomena requires tremendous computing power. NAMD harnesses the power of thousands of heterogeneous processors to meet this demand. In this paper, we present algorithm improvements and performance optimizations that enable NAMD to achieve high performance on the IBM Newell platform (with POWER9 processors and NVIDIA Volta V100 GPUs) which underpins the Oak Ridge National Laboratory's Summit and Lawrence Livermore National Laboratory's Sierra supercomputers. The Top-500 supercomputers June 2018 list shows Summit at the number one spot with 187 Petaflop/s peak performance and Sierra third with 119 Petaflop/s. Optimizations for NAMD on Summit include: data layout changes for GPU acceleration and CPU vectorization, improving GPU offloa...Continue Reading

References

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Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Sep 27, 2007·Journal of Computational Chemistry·John E StoneKlaus Schulten
Mar 1, 2012·The European Physical Journal. Special Topics·Ron ElberBerk Hess
Jun 20, 2014·Computer Physics Communications·Wei JiangBenoît Roux
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Jun 1, 2016·High Performance Computing : 31st International Conference, ISC High Performance 2016, Frankfurt, Germany, June 19-23, 2016, Proceedings·John E StoneKlaus Schulten

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Citations

Mar 27, 2019·Journal of Biomolecular Structure & Dynamics·Varun DewakerYenamandra S Prabhakar
Aug 6, 2020·The Journal of Chemical Physics·James C PhillipsEmad Tajkhorshid
Aug 6, 2020·The Journal of Chemical Physics·Xiaohua ZhangJames N Glosli
Aug 10, 2020·Scientific Reports·Nicholas LubbersHari S Viswanathan
Oct 10, 2020·The Journal of Chemical Physics·Szilárd PállErik Lindahl
Jan 14, 2021·The Journal of Physical Chemistry. B·Shanlin RaoMark S P Sansom
Apr 17, 2021·Nature Communications·Simon Bo JensenNikos S Hatzakis
May 7, 2021·Journal of Chemical Information and Modeling·Ai ShinobuYuji Sugita
Aug 24, 2021·Nature Computational Science·Tamar Schlick, Stephanie Portillo-Ledesma

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