Implementing Molecular Dynamics Simulation on Sunway TaihuLight System

Molecular dynamics (MD) simulation is a common tool to study the physical movements of atoms and molecules in many research fields. However, it is an extremely time-consuming application which takes researchers weeks or months to run a single simulation when simulation size scales up and computing demands keep growing. In this paper, an improved MD implementation on Sunway TaihuLight supercomputer is developed to solve the above mentioned issues. The new implementation is extended from an existing implementation (i.e., LAMMPS) which widely uses the MD application. Sunway TaihuLight is a heterogeneous supercomputer with a fully customized integration approach and a brand new many-core processor SW26010. The Sunway TaihuLight takes the world's first place with peak performance over 100PFlops. We propose an optimization method of the MD simulation in three steps: paralleled extensions to SW26010, memory-access optimizations, and vectorization. After the optimization process, an 8x speedup is achieved on a single computing node. Superiorly, we also scale up to 95 thousands computing nodes (6 millions cores) with an almost leaner speedup. Besides, the proposed methods can also be applied to many other molecular dynamics codes, or similar applications.

[1]  Pak Lui,et al.  Strong scaling of general-purpose molecular dynamics simulations on GPUs , 2014, Comput. Phys. Commun..

[2]  Laxmikant V. Kalé,et al.  NAMD: Biomolecular Simulation on Thousands of Processors , 2002, ACM/IEEE SC 2002 Conference (SC'02).

[3]  Christian Trott,et al.  LAMMPScuda - a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses , 2012 .

[4]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[5]  Gui-Rong Liu,et al.  Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method , 2004, Comput. Phys. Commun..

[6]  T. Koishi,et al.  An 8.61 Tflop/s Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM , 2000, ACM/IEEE SC 2001 Conference (SC'01).

[7]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[8]  Peter S. Lomdahl,et al.  25 Tflop/s Multibillion-atom Molecular Dynamics Simulations and Visualization/analysis on Bluegene/l , 2005 .

[9]  Jinlong Hou,et al.  Optimizing Non-contiguous Memory Access on Intel Xeon Phi Coprocessors , 2015, 2015 IEEE 17th International Conference on High Performance Computing and Communications, 2015 IEEE 7th International Symposium on Cyberspace Safety and Security, and 2015 IEEE 12th International Conference on Embedded Software and Systems.

[10]  Yuji Sugita,et al.  Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations , 2014, J. Comput. Chem..

[11]  Klaus Schulten,et al.  Adapting a message-driven parallel application to GPU-accelerated clusters , 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

[12]  Stephen A. Jarvis,et al.  Exploring SIMD for Molecular Dynamics, Using Intel® Xeon® Processors and Intel® Xeon Phi Coprocessors , 2013, 2013 IEEE 27th International Symposium on Parallel and Distributed Processing.

[13]  Piero Procacci,et al.  Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations , 2016, J. Chem. Inf. Model..

[14]  Nitin Rai,et al.  Optimization of Molecular Dynamics application for Intel Xeon Phi coprocessor , 2014, 2014 International Conference on High Performance Computing and Applications (ICHPCA).

[15]  Toshikazu Ebisuzaki,et al.  1.34 Tflops Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM , 2000, ACM/IEEE SC 2000 Conference (SC'00).

[16]  David M. Beazley,et al.  50 GFlops molecular dynamics on the Connection Machine-5 , 1993, Supercomputing '93. Proceedings.

[17]  L. Verlet.  Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[18]  John A. Gunnels,et al.  Extending stability beyond CPU millennium: a micron-scale atomistic simulation of Kelvin-Helmholtz instability , 2007, Proceedings of the 2007 ACM/IEEE Conference on Supercomputing (SC '07).

[19]  Tao Tang,et al.  MIC acceleration of short-range molecular dynamics simulations , 2013, COSMIC '13.

[20]  Baidurya Bhattacharya,et al.  Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions , 2014, J. Parallel Distributed Comput..

[21]  Rajiv K. Kalia,et al.  Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics , 2012, The Journal of Supercomputing.