Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
skip to main content
10.1145/3149393.3149400acmconferencesArticle/Chapter ViewAbstractPublication PagesscConference Proceedingsconference-collections
research-article
Public Access

Performance analysis of emerging data analytics and HPC workloads

Published: 12 November 2017 Publication History

Abstract

Supercomputers are increasingly being used to run a data analytics workload in addition to a traditional simulation science workload. This mixed workload must be rigorously characterized to ensure that appropriately balanced machines are deployed. In this paper we analyze a suite of applications representing the simulation science and data workload at the NERSC supercomputing center. We show how time is spent in application compute, library compute, communication and I/O, and present application performance on both the Intel Xeon and Intel Xeon-Phi partitions of the Cori supercomputer. We find commonality in the libraries used, I/O motifs and methods of parallelism, and obtain similar node-to-node performance for the base application configurations. We demonstrate that features of the Intel Xeon-Phi node architecture and a Burst Buffer can improve application performance, providing evidence that an exascale-era energy-efficient platform can support a mixed workload.

References

[1]
2016. MiniDFT. http://www.nersc.gov/research-and-development/apex/apex-benchmarks/minidft/; accessed 7 September 2017. (March 2016).
[2]
2016. MPI implementations of PCA and RPCA. https://github.com/alexgittens/mpi_pcavariants; accessed 7 September 2017. (2016).
[3]
2017. IPM. https://github.com/nerscadmin/IPM; accessed 7 September 2017. (2017).
[4]
2017. The DECam Legacy Survey. http://legacysurvey.org/; accessed 7 September 2017. (2017).
[5]
2017. XC Series DataWarp User Guide. Technical Report CLE 6.0.UP04 S-2558. Cray. http://docs.cray.com/PDF/XC_Series_DataWarp_User_Guide_CLE60UP04_S-2558.pdf; accessed 7 September 2017.
[6]
Ann S. Almgren, John B. Bell, Mike J. Lijewski, Zarija Lukić, and Ethan Van Andel. 2013. Nyx: A Massively Parallel AMR Code for Computational Cosmology. The Astrophysical Journal 765, 1 (2013), 39. http://stacks.iop.org/0004-637X/765/i=1/a=39
[7]
T. Barnes, B. Cook, J. Deslippe, D. Doerfler, B. Friesen, Y. He, T. Kurth, T. Koskela, M. Lobet, T. Malas, L. Oliker, A. Ovsyannikov, A. Sarje, J. L. Vay, H. Vincenti, S. Williams, P. Carrier, N. Wichmann, M. Wagner, P. Kent, C. Kerr, and J. Dennis. 2016. Evaluating and Optimizing the NERSC Workload on Knights Landing. In 2016 7th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS). 43--53.
[8]
E. Bertin. 2011. Automated Morphometry with SExtractor and PSFEx. In Astronomical Data Analysis Software and Systems XX (ADASSXX) (Astronomical Society of the Pacific Conference Series), I.N. Evans, A. Accomazzi, D.J. Mink, and A.H. Rots (Eds.), Vol. 442. 435.
[9]
E. Bertin and S. Arnouts. 1996. SExtractor: Software for source extraction. Astronomy & Astrophysics, Supplement 117 (June 1996), 393--404.
[10]
W. Bhimji et al. 2016. Accelerating Science with the NERSC Burst Buffer Early User Program. In Cray User Group CUG. https://cug.org/proceedings/cug2016_proceedings/includes/files/papl62.pdf
[11]
C. Byun, J. Kepner, W. Arcand, D. Bestor, B. Bergeron, V. Gadepally, M. Houle, M. Hubbell, M. Jones, A. Klein, P. Michaleas, L. Milechin, J. Mullen, A. Prout, A. Rosa, S. Samsi, C. Yee, and A. Reuther. 2017. Benchmarking Data Analysis and Machine Learning Applications on the Intel KNL Many-Core Processor. ArXiv e-prints (July 2017). arXiv:cs.PF/1707.03515
[12]
Paolo Giannozzi, Stefano Baroni, Nicola Bonini, Matteo Calandra, Roberto Car, Carlo Cavazzoni, Davide Ceresoli, Guido L Chiarotti, Matteo Cococcioni, Ismaila Dabo, Andrea Dal Corso, Stefano de Gironcoli, Stefano Fabris, Guido Fratesi, Ralph Gebauer, Uwe Gerstmann, Christos Gougoussis, Anton Kokalj, Michele Lazzeri, Layla Martin-Samos, Nicola Marzari, Francesco Mauri, Riccardo Mazzarello, Stefano Paolini, Alfredo Pasquarello, Lorenzo Paulatto, Carlo Sbraccia, Sandro Scandolo, Gabriele Sclauzero, Ari P Seitsonen, Alexander Smogunov, Paolo Umari, and Renata M Wentzcovitch. 2009. QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. Journal of Physics: Condensed Matter 21, 39 (2009), 395502 (19pp). http://www.quantum-espresso.org
[13]
Alex Gittens, Aditya Devarakonda, Evan Racah, Michael F. Ringenburg, Lisa Gerhardt, Jey Kottalam, Jialin Liu, Kristyn J. Maschhoff, Shane Canon, Jatin Chhugani, Pramod Sharma, Jiyan Yang, James Demmel, Jim Harrell, Venkat Krishnamurthy, Michael W. Mahoney, and Prabhat. 2016. Matrix Factorization at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies. CoRR abs/1607.01335 (2016). http://arxiv.org/abs/1607.01335
[14]
D. Henseler, B. Landsteiner, D. Petesch, C. Wright, and N.J. Wright. 2016. Architecture and Design of Cray DataWarp. In Cray User Group CUG. https://cug.org/proceedings/cug2016_proceedings/includes/files/papl05.pdf
[15]
N. Liu, J. Cope, P. Carns, C. Carothers, R. Ross, G. Grider, A. Crume, and C. Maltzahn. 2012. On the role of burst buffers in leadership-class storage systems. In IEEE 28th Symposium on Mass Storage Systems and Technologies (MSST). 1--11.
[16]
Office of Advanced Scientific Computing Research. DOE Office of Science. 2015. Management, Visualization, and Analysis of Experimental and Observational Data (EOD). The Convergence of Data and Computing Workshop Final Report. Technical Report LBNL-1005155. https://science.energy.gov/~/media/ascr/pdf/programdocuments/docs/ascr-eod-workshop-2015-report_160524.pdf; accessed 7 September 2017.
[17]
A. Ovsyannikov, M. Romanus, B. V. Straalen, G. H. Weber, and D. Trebotich. 2016. Scientific Workflows at DataWarp-Speed: Accelerated Data-Intensive Science Using NERSC's Burst Buffer. In 2016 1st Joint International Workshop on Parallel Data Storage and data Intensive Scalable Computing Systems (PDSW-DISCS). 1--6.
[18]
Md. Mostofa Ali Patwary, Pradeep Dubey, Suren Byna, Nadathur Rajagopalan Satish, Narayanan Sundaram, Zarija Lukić, Vadim Roytershteyn, Michael J. Anderson, Yushu Yao, and Prabhat. 2015. BD-CATS: big data clustering at trillion particle scale. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '15. ACM Press, New York, New York, USA, 1--12.
[19]
K. Sato, K. Mohror, A. Moody, T. Gamblin, B. R. d. Supinski, N. Maruyama, and S. Matsuoka. 2014. A User-Level InfiniBand-Based File System and Checkpoint Strategy for Burst Buffers. In Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on. 21--30.
[20]
J.S. Vetter, S. Lee, D. Li, G. Marin, C. McCurdy, J. Meredith, P.C. Roth, and K. Spafford. 2014. Quantifying Architectural Requirements of Contemporary Extreme-Scale Scientific Applications. In High Performance Computing Systems. Performance Modeling, Benchmarking and Simulation, S.A. Jarvis, S.A. Wright, and S.D. Hammond (Eds.). Lecture Notes in Computer Science, Vol. 8551. Springer International Publishing, 3--24.

Recommendations

Comments

Information & Contributors

Information

Published In

cover image ACM Conferences
PDSW-DISCS '17: Proceedings of the 2nd Joint International Workshop on Parallel Data Storage & Data Intensive Scalable Computing Systems
November 2017
74 pages
ISBN:9781450351348
DOI:10.1145/3149393
© 2017 Association for Computing Machinery. ACM acknowledges that this contribution was authored or co-authored by an employee, contractor or affiliate of the United States government. As such, the United States Government retains a nonexclusive, royalty-free right to publish or reproduce this article, or to allow others to do so, for Government purposes only.

Sponsors

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 12 November 2017

Permissions

Request permissions for this article.

Check for updates

Author Tags

  1. big data
  2. data analytics
  3. high performance computing
  4. workload characteristics

Qualifiers

  • Research-article

Funding Sources

Conference

SC '17
Sponsor:

Acceptance Rates

Overall Acceptance Rate 17 of 41 submissions, 41%

Upcoming Conference

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • 0
    Total Citations
  • 372
    Total Downloads
  • Downloads (Last 12 months)70
  • Downloads (Last 6 weeks)18
Reflects downloads up to 09 Nov 2024

Other Metrics

Citations

View Options

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Get Access

Login options

Media

Figures

Other

Tables

Share

Share

Share this Publication link

Share on social media