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UID:submissions.supercomputing.org_SC20_sess159_pap267@linklings.com
SUMMARY:Cell-List based Molecular Dynamics on Many-Core Processors: A Case
  Study on Sunway TaihuLight Supercomputer
DESCRIPTION:Paper\n\nCell-List based Molecular Dynamics on Many-Core Proce
 ssors: A Case Study on Sunway TaihuLight Supercomputer\n\nDuan, Gao, Zhang
 , Zhang, Meng...\n\nMolecular dynamics (MD) simulations are playing an inc
 reasingly important role in several research areas. The most frequently us
 ed potentials in MD simulations are pair-wise potentials. Due to the memor
 y wall, computing pair-wise potentials on many-core processors is usually 
 memory bounded.\n\nIn this paper, we take the SW26010 processor as an exam
 ple platform to explore the possibility of breaking the memory bottleneck 
 by improving data reuse via neighbor-list-free methods. We use cell-lists 
 instead of neighbor-lists in the potential computation, and apply several 
 novel optimization methods. These methods include; an adaptive replica arr
 angement strategy, a parameter-profile data structure and a particle-cell 
 cutoff checking filter. Also, an incremental cell-list building method is 
 realized to accelerate the construction of cell-lists.\n\nExperiments show
  our implementation is up to 170% faster than previous ports on the same p
 latform. And our ESMD framework can scale to 1,024 nodes with a weak scala
 bility of 95%.\n\nTag: Algorithms, Applications, Sparse Computation\n\nReg
 istration Category: Tech Program Reg Pass\n\nAward Finalist: Best Paper Fi
 nalist, Best Student Paper Finalists
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