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The Performance Test and Optimization of Crystal-MD Program on Tianhe-2

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 913))

Abstract

In the research field of virtual reactor, the study of materials is one of the most significant issues, and in the research of materials irradiation effect, Molecular Dynamics (MD) is the widely used method. In this paper, the existing Crystal-MD simulation program has been tested in a homogeneous way on the platform of Tianhe-2 supercomputer, and the program has also been rewritten according to the heterogeneous multi-core architecture of Tianhe-2, and finally tested on the Tianhe-2 platform. Our experimentation results show that homogeneous Crystal-MD simulation program has a good expansion on Tianhe-2 and with the same number of nodes, the heterogeneous program is more efficient than the homogeneous one.

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References

  1. TOP500 supercomputer sites. https://www.top500.org

  2. Li, D., Xu, C., Wang, Y., et al.: Parallelizing and optimizing large-scale 3D multi-phase flow simulations on the Tianhe-2 supercomputer. Concurrency Comput. Pract. Experience 28(5), 1678–1692 (2016)

    Article  Google Scholar 

  3. Sandia National Laboratories. LAMMPS user manual, p. 996 (2014)

    Google Scholar 

  4. Hu, C., Wang, X., Li, J., et al.: Kernel optimization for short-range molecular dynamics. Comput. Phys. Commun. 211, 31–40 (2016)

    Article  Google Scholar 

  5. Bai, H., Hu, C., He, X., Zhang, B., Wang, J.: Crystal MD: molecular dynamic simulation software for metal with BCC structure. In: Chen, W., et al. (eds.) BDTA 2015. CCIS, vol. 590, pp. 247–258. Springer, Singapore (2016). https://doi.org/10.1007/978-981-10-0457-5_23

    Chapter  Google Scholar 

  6. CoMD. http://www.exmatex.org/comd.html

  7. Lawson G, Sosonkina M, Shen Y.: Performance and energy evaluation of CoMD on Intel Xeon Phi co-processors. In: Proceedings of the 1st International Workshop on Hardware-Software Co-design for High Performance Computing, pp. 49–54. IEEE Press, New York (2014)

    Google Scholar 

  8. Alder, B.J., Wainwright, T.E.: Phase transition for a hard sphere system. J. Chem. Phys. 27(5), 1208 (1957)

    Article  Google Scholar 

  9. Alder, B.J., Wainwright, T.E.: Studies in molecular dynamics. I. General method. J. Chem. Phys. 31(2), 459–466 (1959)

    Article  MathSciNet  Google Scholar 

  10. Lammps manual. http://lammps.sandia.gov

  11. Stadler, J., Mikulla, R., Trebin, H.R.: IMD: a software package for molecular dynamics studies on parallel computers. Int. J. Mod. Phys. C 8(5), 1131–1140 (1997)

    Article  Google Scholar 

  12. Large systems 1: molecular dynamics. http://www.ls1-mardyn.de

  13. Niethammer, C., Becker, S., Bernreuther, M., et al.: ls1 mardyn: the massively parallel molecular dynamics code for large systems. J. Chem. Theor. Comput. 10(10), 4455–4464 (2014)

    Article  Google Scholar 

  14. Peng, S., Zhang, X., Lu, Y., et al.: High-scalable collaborated parallel framework for large-scale molecular dynamic simulation on Tianhe-2 supercomputer. IEEE/ACM Trans. Comput. Biol. Bioinform. PP, 99 (2018)

    Google Scholar 

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Acknowledgments

This work was supported by the National Key R&D Program of China (2017YFB0202003, 2017YFB0202104).

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Correspondence to Peng Wei .

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Li, J., Zhang, K., Wei, P., Wang, J., Hu, C. (2019). The Performance Test and Optimization of Crystal-MD Program on Tianhe-2. In: Hu, C., Yang, W., Jiang, C., Dai, D. (eds) High-Performance Computing Applications in Numerical Simulation and Edge Computing. HPCMS HiDEC 2018 2018. Communications in Computer and Information Science, vol 913. Springer, Singapore. https://doi.org/10.1007/978-981-32-9987-0_13

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  • DOI: https://doi.org/10.1007/978-981-32-9987-0_13

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-32-9986-3

  • Online ISBN: 978-981-32-9987-0

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