Abstract
The paper describes the first experience of practical deployment of the hybrid supercomputer Desmos at the Joint Institute for High Temperatures of the Russian Academy of Sciences (JIHT RAS). We consider job scheduling statistics, energy efficiency, case studies of GPU acceleration efficiency and benchmarks of the distributed storage with a parallel file system.
The JIHT team was supported by the Russian Science Foundation (grant No. 14-50-00124). The Desmos supercomputer is a part of the Supercomputer Centre of JIHT RAS. The authors acknowledge the Shared Resource Center “Far Eastern Computing Resource” IACP FEB RAS (http://cc.dvo.ru) for granting access to the IRUS17 supercomputer.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Stegailov, V., et al.: Early performance evaluation of the hybrid cluster with torus interconnect aimed at molecular-dynamics simulations. In: Wyrzykowski, R., Dongarra, J., Deelman, E., Karczewski, K. (eds.) PPAM 2017 Part I. LNCS, vol. 10777, pp. 327–336. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-78024-5_29
Vecher, V.S., Kondratyuk, N.D., Smirnov, G.S., Stegailov, V.V.: Angara-based hybrid supercomputer for efficient acceleration of computational materials science studies. In: Proceeding of International Conference Russian Supercomputing Days 2017, pp. 557–571 (2017)
Neuwirth, S., Frey, D., Nuessle, M., Bruening, U.: Scalable communication architecture for network-attached accelerators. In: 2015 IEEE 21st International Symposium on High Performance Computer Architecture (HPCA), pp. 627–638 (2015). https://doi.org/10.1109/HPCA.2015.7056068
Puente, V., Beivide, R., Gregorio, J.A., Prellezo, J.M., Duato, J., Izu, C.: Adaptive bubble router: a design to improve performance in torus networks. In: Proceedings of the 1999 International Conference on Parallel Processing, pp. 58–67 (1999). https://doi.org/10.1109/ICPP.1999.797388
Scott, S.L., Thorson, G.M.: The Cray T3E network: adaptive routing in a high performance 3D torus. In: HOT Interconnects IV. Stanford University, 15–16 August 1996 (1996)
Adiga, N.R., et al.: Blue Gene/L torus interconnection network. IBM J. Res. Dev. 49(2), 265–276 (2005). https://doi.org/10.1147/rd.492.0265
Gómez-Martín, C., Vega-Rodríguez, M.A., González-Sánchez, J.L.: Fattened backfilling: an improved strategy for job scheduling in parallel systems. J. Parallel Distrib. Comput. 97(Suppl. C), 69–77 (2016). https://doi.org/10.1016/j.jpdc.2016.06.013
Kraemer, A., Maziero, C., Richard, O., Trystram, D.: Reducing the number of response time SLO violations by a Cloud-HPC convergence scheduler. In: 2016 2nd International Conference on Cloud Computing Technologies and Applications (CloudTech), pp. 293–300 (2016). https://doi.org/10.1109/CloudTech.2016.7847712
Mamaeva, A.A., Voevodin, V.V.: Methods for statistical analysis of large supercomputer job flow. In: Proceeding of International Conference Russian Supercomputing Days 2017, pp. 788–799 (2017)
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). https://doi.org/10.1145/2807591.2807644
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). https://doi.org/10.1145/2807591.2807653
Höhnerbach, M., Ismail, A.E., Bientinesi, P.: The vectorization of the Tersoff multi-body potential: an exercise in performance portability. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2016, pp. 7:1–7:13. IEEE Press, Piscataway (2016). https://doi.org/10.1109/SC.2016.6
Kutzner, C., Pall, S., Fechner, M., Esztermann, A., de Groot, B.L., Grubmuller, H.: Best bang for your buck: GPU nodes for gromacs biomolecular simulations. J. Comput. Chemis. 36(26), 1990–2008 (2015). https://doi.org/10.1002/jcc.24030
Luehr, N., Ufimtsev, I.S., Martínez, T.J.: Dynamic precision for electron repulsion integral evaluation on graphical processing units (GPUs). J. Chem. Theory Comput. 7(4), 949–954 (2011). https://doi.org/10.1021/ct100701w
Mills, N., Alex Feltus, F., Ligon III, W.B.: Maximizing the performance of scientific data transfer by optimizing the interface between parallel file systems and advanced research networks. Futur. Gener. Comput. Syst. 79(Part 1), 190–198 (2018). https://doi.org/10.1016/j.future.2017.04.030
Yoo, A.B., Jette, M.A., Grondona, M.: SLURM: simple linux utility for resource management. In: Feitelson, D., Rudolph, L., Schwiegelshohn, U. (eds.) JSSPP 2003. LNCS, vol. 2862, pp. 44–60. Springer, Heidelberg (2003). https://doi.org/10.1007/10968987_3
Vecher, V., Nikolskii, V., Stegailov, V.: GPU-accelerated molecular dynamics: energy consumption and performance. In: Voevodin, V., Sobolev, S. (eds.) RuSCDays 2016. CCIS, vol. 687, pp. 78–90. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-55669-7_7
Stegailov, V., Vecher, V.: Efficiency analysis of intel and AMD x86\(\_\)64 architectures for Ab initio calculations: a case study of VASP. In: Voevodin, V., Sobolev, S. (eds.) RuSCDays 2017. CCIS, vol. 793, pp. 430–441. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-71255-0_35
Stegailov, V., Vecher, V.: Efficiency analysis of Intel, AMD and Nvidia 64-Bit hardware for memory-bound problems: a case study of Ab Initio calculations with VASP. In: Wyrzykowski, R., Dongarra, J., Deelman, E., Karczewski, K. (eds.) PPAM 2017 Part II. LNCS, vol. 10778, pp. 81–90. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-78054-2_8
Smirnov, G.S., Stegailov, V.V.: Anomalous diffusion of guest molecules in hydrogen gas hydrates. High Temp. 53(6), 829–836 (2015). https://doi.org/10.1134/S0018151X15060188
Orekhov, N.D., Stegailov, V.V.: Simulation of the adhesion properties of the Polyethylene/Carbon nanotube interface. Polym. Sci. Ser. A 58(3), 476–486 (2016). https://doi.org/10.1134/S0965545X16030135
Pavlov, S.V., Kislenko, S.A.: Effects of carbon surface topography on the electrode/electrolyte interface structure and relevance to li-air batteries. Phys. Chem. Chem. Phys. 18, 30830–30836 (2016). https://doi.org/10.1039/C6CP05552D
Antropov, A.S., Fidanyan, K.S., Stegailov, V.V.: Phonon density of states for solid uranium: accuracy of the embedded atom model classical interatomic potential. J. Phys.: Conf. Ser. 946(012094), 94 (2018). https://doi.org/10.1088/1742-6596/946/1/012094
Logunov, M.A., Orekhov, N.D.: Molecular dynamics study of cavitation in carbon nanotube reinforced polyethylene nanocomposite. J. Phys.: Conf. Ser. 946(1), 2044 (2018). https://doi.org/10.1088/1742-6596/946/1/012044
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, Cham (2015). https://doi.org/10.1007/978-3-319-21909-7_45
Aristova, N.M., Belov, G.V.: Refining the thermodynamic functions of scandium triflouride SCF3 in the condensed state. Russ. J. Phys. Chemis. A 90(3), 700–703 (2016). https://doi.org/10.1134/S0036024416030031
Kochikov, I.V., Kovtun, D.M., Tarasov, Y.I.: Electron diffraction analysis for the molecules with degenerate large amplitude motions: intramolecular dynamics in arsenic pentafluoride. J. Mol. Struct. 1132, 139–148 (2017). https://doi.org/10.1016/j.molstruc.2016.09.064
Stegailov, V.V., Zhilyaev, P.A.: Warm dense gold: effective ionioninteraction and ionisation. Mol. Phys. 114(3–4), 509–518 (2016). https://doi.org/10.1080/00268976.2015.1105390
Minakov, D.V., Levashov, P.R.: Melting curves of metals with excited electrons in the quasiharmonic approximation. Phys. Rev. B 92, 224102 (2015). https://doi.org/10.1103/PhysRevB.92.224102
Minakov, D., Levashov, P.: Thermodynamic properties of LiD under compression with different pseudopotentials for lithium. Comput Mat. Sci. 114, 128–134 (2016). https://doi.org/10.1016/j.commatsci.2015.12.008
Eckhardt, W., et al.: 591 TFLOPS multi-trillion particles simulation on SuperMUC. In: Kunkel, J.M., Ludwig, T., Meuer, H.W. (eds.) ISC 2013. LNCS, vol. 7905, pp. 1–12. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-38750-0_1
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Switzerland AG
About this paper
Cite this paper
Kondratyuk, N., Smirnov, G., Dlinnova, E., Biryukov, S., Stegailov, V. (2018). Hybrid Supercomputer Desmos with Torus Angara Interconnect: Efficiency Analysis and Optimization. In: Sokolinsky, L., Zymbler, M. (eds) Parallel Computational Technologies. PCT 2018. Communications in Computer and Information Science, vol 910. Springer, Cham. https://doi.org/10.1007/978-3-319-99673-8_6
Download citation
DOI: https://doi.org/10.1007/978-3-319-99673-8_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-99672-1
Online ISBN: 978-3-319-99673-8
eBook Packages: Computer ScienceComputer Science (R0)