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2016 | OriginalPaper | Buchkapitel

GPU-Accelerated Molecular Dynamics: Energy Consumption and Performance

verfasst von : Vyacheslav Vecher, Vsevolod Nikolskii, Vladimir Stegailov

Erschienen in: Supercomputing

Verlag: Springer International Publishing

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Abstract

Energy consumption of hybrid systems is an actual problem of modern high-performance computing. The trade-off between power consumption and performance becomes more and more prominent. In this paper, we discuss the energy and power efficiency of two modern hybrid minicomputers Jetson TK1 and TX1. We use the Empirical Roofline Tool to obtain peak performance data and the molecular dynamics package LAMMPS as an example of a real-world benchmark. Using the precise wattmeter, we measure Jetsons power consumption profiles. The effectiveness of DVFS is examined as well. We determine the optimal GPU and DRAM frequencies that give the minimum energy-to-solution value.

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Literatur
1.
Zurück zum Zitat Morozov, I., Kazennov, A., Bystryi, R., Norman, G., Pisarev, V., Stegailov, V.: Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs. Comput. Phys. Commun. 182(9), 1974–1978 (2011). doi:10.1016/j.cpc.2010.12.026 CrossRef Morozov, I., Kazennov, A., Bystryi, R., Norman, G., Pisarev, V., Stegailov, V.: Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs. Comput. Phys. Commun. 182(9), 1974–1978 (2011). doi:10.​1016/​j.​cpc.​2010.​12.​026 CrossRef
2.
Zurück zum Zitat Budea, A., Derzsi, A., Hartmann, P., Donko, Z.: Shear viscosity of liquid-phase yukawa plasmas from molecular dynamics simulations on graphics processing units. Contrib. Plasma Phys. 52(3), 194–198 (2012). doi:10.1002/ctpp.201100083 CrossRef Budea, A., Derzsi, A., Hartmann, P., Donko, Z.: Shear viscosity of liquid-phase yukawa plasmas from molecular dynamics simulations on graphics processing units. Contrib. Plasma Phys. 52(3), 194–198 (2012). doi:10.​1002/​ctpp.​201100083 CrossRef
3.
Zurück zum Zitat French, W.R., Pervaje, A.K., Santos, A.P., Iacovella, C.R., Cummings, P.T.: Probing the statistical validity of the ductile-to-brittle transition in metallic nanowires using GPU computing. J. Chem. Theory Comput. 9(12), 5558–5566 (2013). doi:10.1021/ct400885z CrossRef French, W.R., Pervaje, A.K., Santos, A.P., Iacovella, C.R., Cummings, P.T.: Probing the statistical validity of the ductile-to-brittle transition in metallic nanowires using GPU computing. J. Chem. Theory Comput. 9(12), 5558–5566 (2013). doi:10.​1021/​ct400885z CrossRef
5.
Zurück zum Zitat Wu, Q., Yang, C., Tang, T., Xiao, L.: MIC acceleration of short-range molecular dynamics simulations. In: Proceedings of the First International Workshop on Code OptimiSation for MultI and Many Cores, COSMIC 2013, pp. 2:1–2:8. ACM, New York (2013). doi:10.1145/2446920.2446922 Wu, Q., Yang, C., Tang, T., Xiao, L.: MIC acceleration of short-range molecular dynamics simulations. In: Proceedings of the First International Workshop on Code OptimiSation for MultI and Many Cores, COSMIC 2013, pp. 2:1–2:8. ACM, New York (2013). doi:10.​1145/​2446920.​2446922
10.
Zurück zum Zitat Hoefler, T., Belli, R.: Scientific benchmarking of parallel computing systems: twelve ways to tell the masses when reporting performance results. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2015, pp. 73:1–73:12. ACM, New York (2015). doi:10.1145/2807591.2807644 Hoefler, T., Belli, R.: Scientific benchmarking of parallel computing systems: twelve ways to tell the masses when reporting performance results. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2015, pp. 73:1–73:12. ACM, New York (2015). doi:10.​1145/​2807591.​2807644
11.
Zurück zum Zitat Pruitt, D.D., Freudenthal, E.A.: Preliminary investigation of mobile system features potentially relevant to HPC. In: Proceedings of the 4th International Workshop on Energy Efficient Supercomputing, E2SC 2016, pp. 54–60. IEEE Press, Piscataway (2016). doi:10.1109/E2SC.2016.13 Pruitt, D.D., Freudenthal, E.A.: Preliminary investigation of mobile system features potentially relevant to HPC. In: Proceedings of the 4th International Workshop on Energy Efficient Supercomputing, E2SC 2016, pp. 54–60. IEEE Press, Piscataway (2016). doi:10.​1109/​E2SC.​2016.​13
12.
Zurück zum Zitat Scogland, T., Azose, J., Rohr, D., Rivoire, S., Bates, N., Hackenberg, D.: Node variability in large-scale power measurements: perspectives from the Green500, Top500 and EEHPCWG. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2015, pp. 74:1–74:11. ACM, New York (2015). doi:10.1145/2807591.2807653 Scogland, T., Azose, J., Rohr, D., Rivoire, S., Bates, N., Hackenberg, D.: Node variability in large-scale power measurements: perspectives from the Green500, Top500 and EEHPCWG. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2015, pp. 74:1–74:11. ACM, New York (2015). doi:10.​1145/​2807591.​2807653
13.
Zurück zum Zitat Su, C.L., Tsui, C.Y., Despain, A.M.: Low power architecture design and compilation techniques for high-performance processors. In: Compcon Spring 1994, Digest of Papers, pp. 489–498 (1994). doi:10.1109/CMPCON.1994.282878 Su, C.L., Tsui, C.Y., Despain, A.M.: Low power architecture design and compilation techniques for high-performance processors. In: Compcon Spring 1994, Digest of Papers, pp. 489–498 (1994). doi:10.​1109/​CMPCON.​1994.​282878
14.
Zurück zum Zitat Joseph, R., Martonosi, M.: Run-time power estimation in high performance microprocessors. In: Proceedings of the 2001 International Symposium on Low Power Electronics and Design, ISLPED 2001, pp. 135–140. ACM, New York (2001). doi:10.1145/383082.383119 Joseph, R., Martonosi, M.: Run-time power estimation in high performance microprocessors. In: Proceedings of the 2001 International Symposium on Low Power Electronics and Design, ISLPED 2001, pp. 135–140. ACM, New York (2001). doi:10.​1145/​383082.​383119
15.
Zurück zum Zitat Russell, J.T., Jacome, M.F.: Software power estimation and optimization for high performance, 32-bit embedded processors. In: Proceedings International Conference on Computer Design. VLSI in Computers and Processors (Cat. No. 98CB36273), pp. 328–333 (1998). doi:10.1109/ICCD.1998.727070 Russell, J.T., Jacome, M.F.: Software power estimation and optimization for high performance, 32-bit embedded processors. In: Proceedings International Conference on Computer Design. VLSI in Computers and Processors (Cat. No. 98CB36273), pp. 328–333 (1998). doi:10.​1109/​ICCD.​1998.​727070
17.
Zurück zum Zitat Zhang, L., Tiwana, B., Qian, Z., Wang, Z., Dick, R.P., Mao, Z.M., Yang, L.: Accurate online power estimation and automatic battery behavior based power model generation for smartphones. In: Proceedings of the Eighth IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis, CODES/ISSS 2010, pp. 105–114. ACM, New York (2010). doi:10.1145/1878961.1878982 Zhang, L., Tiwana, B., Qian, Z., Wang, Z., Dick, R.P., Mao, Z.M., Yang, L.: Accurate online power estimation and automatic battery behavior based power model generation for smartphones. In: Proceedings of the Eighth IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis, CODES/ISSS 2010, pp. 105–114. ACM, New York (2010). doi:10.​1145/​1878961.​1878982
18.
Zurück zum Zitat Lopez-Novoa, U., Mendiburu, A., Miguel-Alonso, J.: A survey of performance modeling and simulation techniques for accelerator-based computing. IEEE Trans. Parallel Distrib. Syst. 26(1), 272–281 (2015). doi:10.1109/TPDS.2014.2308216 CrossRef Lopez-Novoa, U., Mendiburu, A., Miguel-Alonso, J.: A survey of performance modeling and simulation techniques for accelerator-based computing. IEEE Trans. Parallel Distrib. Syst. 26(1), 272–281 (2015). doi:10.​1109/​TPDS.​2014.​2308216 CrossRef
19.
Zurück zum Zitat Li, S., Ahn, J.H., Strong, R.D., Brockman, J.B., Tullsen, D.M., Jouppi, N.P.: McPat: an integrated power, area, and timing modeling framework for multicore and manycore architectures. In: Proceedings of the 42nd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 42, pp. 469–480. ACM, New York (2009). doi:10.1145/1669112.1669172 Li, S., Ahn, J.H., Strong, R.D., Brockman, J.B., Tullsen, D.M., Jouppi, N.P.: McPat: an integrated power, area, and timing modeling framework for multicore and manycore architectures. In: Proceedings of the 42nd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 42, pp. 469–480. ACM, New York (2009). doi:10.​1145/​1669112.​1669172
20.
Zurück zum Zitat Leng, J., Hetherington, T., ElTantawy, A., Gilani, S., Kim, N.S., Aamodt, T.M., Reddi, V.J.: GPUWattch: enabling energy optimizations in GPGPUs. SIGARCH Comput. Archit. News 41(3), 487–498 (2013). doi:10.1145/2508148.2485964 CrossRef Leng, J., Hetherington, T., ElTantawy, A., Gilani, S., Kim, N.S., Aamodt, T.M., Reddi, V.J.: GPUWattch: enabling energy optimizations in GPGPUs. SIGARCH Comput. Archit. News 41(3), 487–498 (2013). doi:10.​1145/​2508148.​2485964 CrossRef
21.
Zurück zum Zitat Calore, E., Schifano, S.F., Tripiccione, R.: Energy-performance tradeoffs for HPC applications on low power processors. In: Hunold, S., et al. (eds.) Euro-Par 2015. LNCS, vol. 9523, pp. 737–748. Springer, Heidelberg (2015). doi:10.1007/978-3-319-27308-2_59 CrossRef Calore, E., Schifano, S.F., Tripiccione, R.: Energy-performance tradeoffs for HPC applications on low power processors. In: Hunold, S., et al. (eds.) Euro-Par 2015. LNCS, vol. 9523, pp. 737–748. Springer, Heidelberg (2015). doi:10.​1007/​978-3-319-27308-2_​59 CrossRef
23.
Zurück zum Zitat Nikolskiy, V.P., Stegailov, V.V., Vecher, V.S.: Efficiency of the Tegra K1 and X1 systems-on-chip for classical molecular dynamics. In: 2016 International Conference on High Performance Computing Simulation (HPCS), pp. 682–689 (2016). doi:10.1109/HPCSim.2016.7568401 Nikolskiy, V.P., Stegailov, V.V., Vecher, V.S.: Efficiency of the Tegra K1 and X1 systems-on-chip for classical molecular dynamics. In: 2016 International Conference on High Performance Computing Simulation (HPCS), pp. 682–689 (2016). doi:10.​1109/​HPCSim.​2016.​7568401
24.
Zurück zum Zitat Gallardo, E., Teller, P.J., Argueta, A., Jaloma, J.: Cross-accelerator performance profiling. In: Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, XSEDE16, pp. 19:1–19:8. ACM, New York (2016). doi:10.1145/2949550.2949567 Gallardo, E., Teller, P.J., Argueta, A., Jaloma, J.: Cross-accelerator performance profiling. In: Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, XSEDE16, pp. 19:1–19:8. ACM, New York (2016). doi:10.​1145/​2949550.​2949567
25.
Zurück zum Zitat Rojek, K., Ilic, A., Wyrzykowski, R., Sousa, L.: Energy-aware mechanism for stencil-based MPDATA algorithm with constraints. Concurr. Comput.: Pract. Exp. (2016). doi:10.1002/cpe.4016 Rojek, K., Ilic, A., Wyrzykowski, R., Sousa, L.: Energy-aware mechanism for stencil-based MPDATA algorithm with constraints. Concurr. Comput.: Pract. Exp. (2016). doi:10.​1002/​cpe.​4016
26.
Zurück zum Zitat Rajovic, N., Rico, A., Mantovani, F., Ruiz, D., Vilarrubi, J.O., Gomez, C., Backes, L., Nieto, D., Servat, H., Martorell, X., Labarta, J., Ayguade, E., Adeniyi-Jones, C., Derradji, S., Gloaguen, H., Lanucara, P., Sanna, N., Mehaut, J.F., Pouget, K., Videau, B., Boyer, E., Allalen, M., Auweter, A., Brayford, D., Tafani, D., Weinberg, V., Brömmel, D., Halver, R., Meinke, J.H., Beivide, R., Benito, M., Vallejo, E., Valero, M., Ramirez, A.: The Mont-Blanc prototype: an alternative approach for HPC systems. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2016, pp. 38:1–38:12. IEEE Press, Piscataway (2016). http://dl.acm.org/citation.cfm?id=3014904.3014955 Rajovic, N., Rico, A., Mantovani, F., Ruiz, D., Vilarrubi, J.O., Gomez, C., Backes, L., Nieto, D., Servat, H., Martorell, X., Labarta, J., Ayguade, E., Adeniyi-Jones, C., Derradji, S., Gloaguen, H., Lanucara, P., Sanna, N., Mehaut, J.F., Pouget, K., Videau, B., Boyer, E., Allalen, M., Auweter, A., Brayford, D., Tafani, D., Weinberg, V., Brömmel, D., Halver, R., Meinke, J.H., Beivide, R., Benito, M., Vallejo, E., Valero, M., Ramirez, A.: The Mont-Blanc prototype: an alternative approach for HPC systems. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2016, pp. 38:1–38:12. IEEE Press, Piscataway (2016). http://​dl.​acm.​org/​citation.​cfm?​id=​3014904.​3014955
27.
Zurück zum Zitat Stegailov, V.V., Orekhov, N.D., Smirnov, G.S.: HPC hardware efficiency for quantum and classical molecular dynamics. In: Malyshkin, V. (ed.) PaCT 2015. LNCS, vol. 9251, pp. 469–473. Springer, Heidelberg (2015). doi:10.1007/978-3-319-21909-7_45 CrossRef Stegailov, V.V., Orekhov, N.D., Smirnov, G.S.: HPC hardware efficiency for quantum and classical molecular dynamics. In: Malyshkin, V. (ed.) PaCT 2015. LNCS, vol. 9251, pp. 469–473. Springer, Heidelberg (2015). doi:10.​1007/​978-3-319-21909-7_​45 CrossRef
30.
Zurück zum Zitat Lo, Y.J., Williams, S., Straalen, B., Ligocki, T.J., Cordery, M.J., Wright, N.J., Hall, M.W., Oliker, L.: Roofline model toolkit: a practical tool for architectural and program analysis. In: Jarvis, S.A., Wright, S.A., Hammond, S.D. (eds.) PMBS 2014. LNCS, vol. 8966, pp. 129–148. Springer, Heidelberg (2015). doi:10.1007/978-3-319-17248-4_7 Lo, Y.J., Williams, S., Straalen, B., Ligocki, T.J., Cordery, M.J., Wright, N.J., Hall, M.W., Oliker, L.: Roofline model toolkit: a practical tool for architectural and program analysis. In: Jarvis, S.A., Wright, S.A., Hammond, S.D. (eds.) PMBS 2014. LNCS, vol. 8966, pp. 129–148. Springer, Heidelberg (2015). doi:10.​1007/​978-3-319-17248-4_​7
32.
Zurück zum Zitat Glaser, J., Nguyen, T.D., Anderson, J.A., Lui, P., Spiga, F., Millan, J.A., Morse, D.C., Glotzer, S.C.: Strong scaling of general-purpose molecular dynamics simulations on GPUs. Comput. Phys. Commun. 192, 97–107 (2015). doi:10.1016/j.cpc.2015.02.028 CrossRef Glaser, J., Nguyen, T.D., Anderson, J.A., Lui, P., Spiga, F., Millan, J.A., Morse, D.C., Glotzer, S.C.: Strong scaling of general-purpose molecular dynamics simulations on GPUs. Comput. Phys. Commun. 192, 97–107 (2015). doi:10.​1016/​j.​cpc.​2015.​02.​028 CrossRef
35.
Zurück zum Zitat Brown, W.M., Kohlmeyer, A., Plimpton, S.J., Tharrington, A.N.: Implementing molecular dynamics on hybrid high performance computers – particle-particle particle-mesh. Comput. Phys. Commun. 183(3), 449–459 (2012). doi:10.1016/j.cpc.2011.10.012 CrossRef Brown, W.M., Kohlmeyer, A., Plimpton, S.J., Tharrington, A.N.: Implementing molecular dynamics on hybrid high performance computers – particle-particle particle-mesh. Comput. Phys. Commun. 183(3), 449–459 (2012). doi:10.​1016/​j.​cpc.​2011.​10.​012 CrossRef
Metadaten
Titel
GPU-Accelerated Molecular Dynamics: Energy Consumption and Performance
verfasst von
Vyacheslav Vecher
Vsevolod Nikolskii
Vladimir Stegailov
Copyright-Jahr
2016
DOI
https://doi.org/10.1007/978-3-319-55669-7_7

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