To Compress or Not To Compress: Energy Trade-Offs and Benefits of Lossy Compressed I/O (2410.23497v1)
Abstract: Modern scientific simulations generate massive volumes of data, creating significant challenges for I/O and storage systems. Error-bounded lossy compression (EBLC) offers a solution by reducing dataset sizes while preserving data quality within user-specified limits. This study provides the first comprehensive energy characterization of state-of-the-art EBLC algorithms across various scientific datasets, CPU architectures, and operational modes. We analyze the energy consumption patterns of compression and decompression operations, as well as the energy trade-offs in data I/O scenarios. Our findings demonstrate that EBLC can significantly reduce I/O energy consumption, with savings of up to two orders of magnitude compared to uncompressed I/O for large datasets. In multi-node HPC environments, we observe energy reductions of approximately 25% when using EBLC. We also show that EBLC can achieve compression ratios of 10-100x, potentially reducing storage device requirements by nearly two orders of magnitude. Our work demonstrates the relationships between compression ratios, energy efficiency, and data quality, highlighting the importance of considering compressors and error bounds for specific use cases. Based on our results, we estimate that large-scale HPC facilities could save nearly two orders of magnitude the energy on data writing and significantly reduce storage requirements by integrating EBLC into their I/O subsystems. This work provides a framework for system operators and computational scientists to make informed decisions about implementing EBLC for energy-efficient data management in HPC environments.
- J. W. Hurrell, M. M. Holland, P. R. Gent, S. Ghan, J. E. Kay, P. J. Kushner, J.-F. Lamarque, W. G. Large, D. Lawrence, K. Lindsay, W. H. Lipscomb, M. C. Long, N. Mahowald, D. R. Marsh, R. B. Neale, P. Rasch, S. Vavrus, M. Vertenstein, D. Bader, W. D. Collins, J. J. Hack, J. Kiehl, and S. Marshall, “The community earth system model: A framework for collaborative research,” Bulletin of the American Meteorological Society, vol. 94, no. 9, pp. 1339 – 1360, 2013.
- J. E. Kay, C. Deser, A. Phillips, A. Mai, C. Hannay, G. Strand, J. M. Arblaster, S. C. Bates, G. Danabasoglu, J. Edwards, M. Holland, P. Kushner, J.-F. Lamarque, D. Lawrence, K. Lindsay, A. Middleton, E. Munoz, R. Neale, K. Oleson, L. Polvani, and M. Vertenstein, “The community earth system model (cesm) large ensemble project: A community resource for studying climate change in the presence of internal climate variability,” Bulletin of the American Meteorological Society, vol. 96, no. 8, pp. 1333 – 1349, 2015.
- P. E. Dewdney, P. J. Hall, R. T. Schilizzi, and T. J. L. W. Lazio, “The square kilometre array,” Proceedings of the IEEE, vol. 97, no. 8, pp. 1482–1496, 2009.
- P. Lindstrom, “Fixed-rate compressed floating-point arrays,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12, pp. 2674–2683, 2014.
- D. Tao, S. Di, Z. Chen, and F. Cappello, “Significantly improving lossy compression for scientific data sets based on multidimensional prediction and error-controlled quantization,” in 2017 IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp. 1129–1139, 2017.
- X. Yu, S. Di, K. Zhao, J. Tian, D. Tao, X. Liang, and F. Cappello, “Ultrafast error-bounded lossy compression for scientific datasets,” in Proceedings of the 31st International Symposium on High-Performance Parallel and Distributed Computing, HPDC ’22, (New York, NY, USA), p. 159–171, Association for Computing Machinery, 2022.
- X. Liang, S. Di, D. Tao, S. Li, S. Li, H. Guo, Z. Chen, and F. Cappello, “Error-controlled lossy compression optimized for high compression ratios of scientific datasets,” in 2018 IEEE International Conference on Big Data (Big Data), pp. 438–447, 2018.
- X. Liang, K. Zhao, S. Di, S. Li, R. Underwood, A. M. Gok, J. Tian, J. Deng, J. C. Calhoun, D. Tao, Z. Chen, and F. Cappello, “Sz3: A modular framework for composing prediction-based error-bounded lossy compressors,” IEEE Transactions on Big Data, vol. 9, no. 2, pp. 485–498, 2023.
- K. Zhao, S. Di, M. Dmitriev, T.-L. D. Tonellot, Z. Chen, and F. Cappello, “Optimizing error-bounded lossy compression for scientific data by dynamic spline interpolation,” in 2021 IEEE 37th International Conference on Data Engineering (ICDE), pp. 1643–1654, 2021.
- M. Ainsworth, O. Tugluk, B. Whitney, and S. Klasky, “Multilevel techniques for compression and reduction of scientific data—the univariate case,” Computing and Visualization in Science, vol. 19, no. 5, pp. 65–76, 2018.
- M. Ainsworth, O. Tugluk, B. Whitney, and S. Klasky, “Multilevel techniques for compression and reduction of scientific data—the multivariate case,” SIAM Journal on Scientific Computing, vol. 41, no. 2, pp. A1278–A1303, 2019.
- M. Ainsworth, O. Tugluk, B. Whitney, and S. Klasky, “Multilevel techniques for compression and reduction of scientific data—the unstructured case,” SIAM Journal on Scientific Computing, vol. 42, no. 2, pp. A1402–A1427, 2020.
- X. Liang, B. Whitney, J. Chen, L. Wan, Q. Liu, D. Tao, J. Kress, D. Pugmire, M. Wolf, N. Podhorszki, and S. Klasky, “Mgard+: Optimizing multilevel methods for error-bounded scientific data reduction,” IEEE Transactions on Computers, vol. 71, no. 7, pp. 1522–1536, 2022.
- Q. Gong, J. Chen, B. Whitney, X. Liang, V. Reshniak, T. Banerjee, J. Lee, A. Rangarajan, L. Wan, N. Vidal, Q. Liu, A. Gainaru, N. Podhorszki, R. Archibald, S. Ranka, and S. Klasky, “Mgard: A multigrid framework for high-performance, error-controlled data compression and refactoring,” SoftwareX, vol. 24, p. 101590, Dec. 2023.
- J. Liu, S. Di, K. Zhao, X. Liang, Z. Chen, and F. Cappello, “Dynamic quality metric oriented error bounded lossy compression for scientific datasets,” in SC22: International Conference for High Performance Computing, Networking, Storage and Analysis, pp. 1–15, 2022.
- G. Wilkins and J. C. Calhoun, “Modeling power consumption of lossy compressed i/o for exascale hpc systems,” in 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp. 1118–1126, 2022.
- M. Govett, B. Bah, P. Bauer, D. Berod, V. Bouchet, S. Corti, C. Davis, Y. Duan, T. Graham, Y. Honda, A. Hines, M. Jean, J. Ishida, B. Lawrence, J. Li, J. Luterbacher, C. Muroi, K. Rowe, M. Schultz, M. Visbeck, and K. Williams, “Exascale computing and data handling: Challenges and opportunities for weather and climate prediction,” Bulletin of the American Meteorological Society, 2024.
- “Lustre,” 2024. http://lustre.org/.
- “BeeGFS.” https://www.beegfs.io/content.
- The HDF Group, “Hierarchical Data Format, version 5.”
- NSF Unidata, G. Davis, R. Rew, D. Heimbigner, E. Hartnett, W. Fisher, and M. Others, “NetCDF-C .”
- W. F. Godoy, N. Podhorszki, R. Wang, C. Atkins, G. Eisenhauer, J. Gu, P. Davis, J. Choi, K. Germaschewski, K. Huck, A. Huebl, M. Kim, J. Kress, T. Kurc, Q. Liu, J. Logan, K. Mehta, G. Ostrouchov, M. Parashar, F. Poeschel, D. Pugmire, E. Suchyta, K. Takahashi, N. Thompson, S. Tsutsumi, L. Wan, M. Wolf, K. Wu, and S. Klasky, “Adios 2: The adaptable input output system. a framework for high-performance data management,” SoftwareX, vol. 12, p. 100561, 2020.
- S. Huss-Lederman, B. Gropp, A. Skjellum, A. Lumsdaine, B. Saphir, J. Squyres, et al., “Mpi-2: Extensions to the message passing interface,” University of Tennessee, available online at http://www. mpiforum. org/docs/docs. html, 1997.
- U. Ayachit, B. Whitlock, M. Wolf, B. Loring, B. Geveci, D. Lonie, and E. W. Bethel, “The sensei generic in situ interface,” in 2016 Second Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization (ISAV), pp. 40–44, 2016.
- M. Oh, S. Lee, S. Just, Y. J. Yu, D.-H. Bae, S. Weil, S. Cho, and H. Y. Yeom, “TiDedup: A new distributed deduplication architecture for ceph,” in 2023 USENIX Annual Technical Conference (USENIX ATC 23), (Boston, MA), pp. 117–131, USENIX Association, July 2023.
- S. Park, M. Bhowmik, and A. Uta, “Daos: Data access-aware operating system,” in Proceedings of the 31st International Symposium on High-Performance Parallel and Distributed Computing, HPDC ’22, (New York, NY, USA), p. 4–15, Association for Computing Machinery, 2022.
- J. Yu, G. Liu, W. Dong, X. Li, J. Zhang, and F. Sun, “On the load imbalance problem of i/o forwarding layer in hpc systems,” in 2017 3rd IEEE International Conference on Computer and Communications (ICCC), pp. 2424–2428, 2017.
- X. Liang, S. Di, D. Tao, S. Li, B. Nicolae, Z. Chen, and F. Cappello, “Improving performance of data dumping with lossy compression for scientific simulation,” in 2019 IEEE International Conference on Cluster Computing (CLUSTER), pp. 1–11, 2019.
- K. Zhao, S. Di, D. Perez, X. Liang, Z. Chen, and F. Cappello, “Mdz: An efficient error-bounded lossy compressor for molecular dynamics,” in 2022 IEEE 38th International Conference on Data Engineering (ICDE), pp. 27–40, 2022.
- Blosc Development Team, “A fast, compressed and persistent data store library,” 2009-2023. https://blosc.org.
- Meta, “Zstandard.” https://pypi.org/project/zstd/, 2023.
- Gailly, Jean-loup and Adler, Mark, “A Massively Spiffy Yet Delicately Unobtrusive Compression Library,” 1995-2023. https://zlib.net/.
- L. Ibarria, P. Lindstrom, J. Rossignac, and A. Szymczak, “Out-of-core compression and decompression of large n-dimensional scalar fields.,” Comput. Graph. Forum, vol. 22, pp. 343–348, 09 2003.
- J. Tian, S. Di, K. Zhao, C. Rivera, M. H. Fulp, R. Underwood, S. Jin, X. Liang, J. Calhoun, D. Tao, and F. Cappello, “cusz: An efficient gpu-based error-bounded lossy compression framework for scientific data,” in Proceedings of the ACM International Conference on Parallel Architectures and Compilation Techniques, PACT ’20, (New York, NY, USA), p. 3–15, Association for Computing Machinery, 2020.
- J. Wang, T. Liu, Q. Liu, X. He, H. Luo, and W. He, “Compression ratio modeling and estimation across error bounds for lossy compression,” IEEE Transactions on Parallel and Distributed Systems, vol. 31, no. 7, pp. 1621–1635, 2019.
- W. Lin, F. Shi, W. Wu, K. Li, G. Wu, and A.-A. Mohammed, “A taxonomy and survey of power models and power modeling for cloud servers,” ACM Comput. Surv., vol. 53, Sept. 2020.
- K. O’brien, I. Pietri, R. Reddy, A. Lastovetsky, and R. Sakellariou, “A survey of power and energy predictive models in hpc systems and applications,” ACM Comput. Surv., vol. 50, June 2017.
- M. Dayarathna, Y. Wen, and R. Fan, “Data center energy consumption modeling: A survey,” IEEE Communications surveys & tutorials, vol. 18, no. 1, pp. 732–794, 2015.
- J. Baliga, R. W. Ayre, K. Hinton, and R. S. Tucker, “Green cloud computing: Balancing energy in processing, storage, and transport,” Proceedings of the IEEE, vol. 99, no. 1, pp. 149–167, 2010.
- M. Gamell, I. Rodero, M. Parashar, and S. Poole, “Exploring energy and performance behaviors of data-intensive scientific workflows on systems with deep memory hierarchies,” in 20th Annual International Conference on High Performance Computing, pp. 226–235, IEEE, 2013.
- S. L. Song, K. Barker, and D. Kerbyson, “Unified performance and power modeling of scientific workloads,” in Proceedings of the 1st International Workshop on Energy Efficient Supercomputing, pp. 1–8, 2013.
- 2013.
- K. Chasapis, M. Dolz, M. Kuhn, and T. Ludwig, “Evaluating power-performace benefits of data compression in hpc storage servers,” in IARIA Conference, pp. 29–34, 2014.
- K. C. Barr and K. Asanović, “Energy-aware lossless data compression,” ACM Trans. Comput. Syst., vol. 24, p. 250–291, aug 2006.
- J. Wang, Q. Chen, T. Liu, Q. Liu, and X. He, “zperf: A statistical gray-box approach to performance modeling and extrapolation for scientific lossy compression,” IEEE Transactions on Computers, vol. 72, no. 9, pp. 2641–2655, 2023.
- A. Tarraf, M. Schreiber, A. Cascajo, J.-B. Besnard, M.-A. Vef, D. Huber, S. Happ, A. Brinkmann, D. E. Singh, H.-C. Hoppe, et al., “Malleability in modern hpc systems: Current experiences, challenges, and future opportunities,” IEEE Transactions on Parallel and Distributed Systems, 2024.
- K. Sen, S. Vadhiyar, and P. Vinayachandran, “Strategies for fast i/o throughput in large-scale climate modeling applications,” in 2023 IEEE 30th International Conference on High Performance Computing, Data, and Analytics (HiPC), pp. 203–212, IEEE, 2023.
- B. Xie, J. Chase, D. Dillow, O. Drokin, S. Klasky, S. Oral, and N. Podhorszki, “Characterizing output bottlenecks in a supercomputer,” in SC ’12: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, pp. 1–11, 2012.
- J. Liu, S. Di, K. Zhao, X. Liang, Z. Chen, and F. Cappello, “Faz: A flexible auto-tuned modular error-bounded compression framework for scientific data,” in Proceedings of the 37th ACM International Conference on Supercomputing, ICS ’23, (New York, NY, USA), p. 1–13, Association for Computing Machinery, 2023.
- D. Tao, S. Di, H. Guo, Z. Chen, and F. Cappello, “Z-checker: A framework for assessing lossy compression of scientific data,” The International Journal of High Performance Computing Applications, vol. 33, no. 2, pp. 285–303, 2019.
- S. T. Brown, P. Buitrago, E. Hanna, S. Sanielevici, R. Scibek, and N. A. Nystrom, “Bridges-2: A platform for rapidly-evolving and data intensive research,” in Practice and Experience in Advanced Research Computing 2021: Evolution Across All Dimensions, PEARC ’21, (New York, NY, USA), Association for Computing Machinery, 2021.
- R. Underwood, V. Malvoso, J. C. Calhoun, S. Di, and F. Cappello, “Productive and performant generic lossy data compression with libpressio,” in 2021 7th International Workshop on Data Analysis and Reduction for Big Scientific Data (DRBSD-7), pp. 1–10, IEEE, 2021.
- J. Veiga, J. Enes, R. R. Expósito, and J. Touriño, “Bdev 3.0: Energy efficiency and microarchitectural characterization of big data processing frameworks,” Future Generation Computer Systems, vol. 86, pp. 565–581, 2018.
- D. Terpstra, H. Jagode, H. You, and J. Dongarra, “Collecting performance data with papi-c,” in Tools for High Performance Computing 2009 (M. S. Müller, M. M. Resch, A. Schulz, and W. E. Nagel, eds.), (Berlin, Heidelberg), pp. 157–173, Springer Berlin Heidelberg, 2010.
- K. Zhao, S. Di, X. Lian, S. Li, D. Tao, J. Bessac, Z. Chen, and F. Cappello, “Sdrbench: Scientific data reduction benchmark for lossy compressors,” in 2020 IEEE International Conference on Big Data (Big Data), pp. 2716–2724, 2020.
- K. Heitmann, T. D. Uram, H. Finkel, N. Frontiere, S. Habib, A. Pope, E. Rangel, J. Hollowed, D. Korytov, P. Larsen, et al., “Hacc cosmological simulations: First data release,” The Astrophysical Journal Supplement Series, vol. 244, no. 1, p. 17, 2019.
- A. S. Almgren, J. B. Bell, M. J. Lijewski, Z. Lukić, and E. Van Andel, “Nyx: A massively parallel amr code for computational cosmology,” The Astrophysical Journal, vol. 765, no. 1, p. 39, 2013.
- J. H. Chen, A. Choudhary, B. de Supinski, M. DeVries, E. R. Hawkes, S. Klasky, W. K. Liao, K. L. Ma, J. Mellor-Crummey, N. Podhorszki, R. Sankaran, S. Shende, and C. S. Yoo, “Terascale direct numerical simulations of turbulent combustion using s3d,” Computational Science and Discovery, vol. 2, p. 015001, jan 2009.