Towards Decoupling the Selection of Compression Algorithms from Quality Constraints – An Investigation of Lossy Compression Efficiency

Julian Martin Kunkel, Anastasiia Novikova, Eugen Betke

Abstract


Data intense scientific domains use data compression to reduce the storage space needed. Lossless data compression preserves information accurately but lossy data compression can achieve much higher compression rates depending on the tolerable error margins. There are many ways of defining precision and to exploit this knowledge, therefore, the field of lossy compression is subject to active research. From the perspective of a scientist, the qualitative definition about the implied loss of data precision should only matter.

With the Scientific Compression Library (SCIL), we are developing a meta-compressor that allows users to define various quantities for acceptable error and expected performance behavior. The library then picks a suitable chain of algorithms yielding the user’s requirements, the ongoing work is a preliminary stage for the design of an adaptive selector. This approach is a crucial step towards a scientifically safe use of much-needed lossy data compression, because it disentangles the tasks of determining scientific characteristics of tolerable noise, from the task of determining an optimal compression strategy. Future algorithms can be used without changing application code.

In this paper, we evaluate various lossy compression algorithms for compressing different scientific datasets (Isabel, ECHAM6), and focus on the analysis of synthetically created data that serves as blueprint for many observed datasets. We also briefly describe the available quantitiesof SCIL to define data precision and introduce two efficient compression algorithms for individualdata points. This shows that the best algorithm depends on user settings and data properties.


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References


Baker, A.H., Hammerling, D.M., Mickelson, S.A., Xu, H., Stolpe, M.B., Naveau, P., Sanderson, B., Ebert-Uphoff, I., Samarasinghe, S., De Simone, F., Gencarelli, C.N., Dennis, J.M., Kay, J.E., Lindstrom, P.: Evaluating lossy data compression on climate simulation data within a large ensemble. Geoscientific Model Development, 9 pp. 4381–4403 (2016), DOI: 10.5194/gmd-9-4381-2016

Bicer, T., Agrawal, G.: A Compression Framework for Multidimensional Scientific Datasets. Parallel and Distributed Processing Symposium Workshops and PhD Forum (IPDPSW), 2013 IEEE 27th International pp. 2250–2253 (2013), DOI: 10.1109/IPDPSW.2013.186

Di, S., Cappello, F.: Fast Error-bounded Lossy HPC Data Compression with SZ. In: Parallel and Distributed Processing Symposium, 2016 IEEE International. pp. 730–739. IEEE (2016), DOI: 10.1109/IPDPS.2016.11

Huffman, D.A.: A method for the construction of minimum-redundancy codes. Proceedings of the IRE 40(9), 1098–1101 (1952), DOI: 10.1109/JRPROC.1952.273898

Hubbe, N., Wegener, A., Kunkel, J., Ling, Y., Ludwig, T.: Evaluating Lossy Compression on Climate Data. In: Kunkel, J.M., Ludwig, T., Meuer, H.W. (eds.) Supercomputing. pp. 343–356. No. 7905 in Lecture Notes in Computer Science, Springer, Berlin, Heidelberg (2013), DOI: 10.1007/978-3-642-38750-0 26

Hubbe, N., Kunkel, J.: Reducing the HPC-Datastorage Footprint with MAFISC – Multidimensional Adaptive Filtering Improved Scientific data Compression. Computer Science - Research and Development pp. 231–239 (2013), DOI: 10.1007/s00450-012-0222-4

Iverson, J., Kamath, C., Karypis, G.: Fast and effective lossy compression algorithms for scientific datasets, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7484, pp. 843–856. Springer (2012), DOI: 10.1007/978-3-642-32820-6 83

Kunkel, J.: Analyzing Data Properties using Statistical Sampling Techniques – Illustrated on Scientific File Formats and Compression Features. In: Taufer, M., Mohr, B., Kunkel, J. (eds.) High Performance Computing: ISC High Performance 2016 International Workshops, ExaComm, E-MuCoCoS, HPC-IODC, IXPUG, IWOPH, P3MA, VHPC, WOPSSS. pp. 130–141. No. 9945 2016 in Lecture Notes in Computer Science, Springer (2016), DOI: 10.1007/978-3-319-46079-6 10

Kunkel, J., Novikova, A., Betke, E., Schaare, A.: Toward Decoupling the Selection of Compression Algorithms from Quality Constraints. In: High Performance Computing. No. 10524 in Lecture Notes in Computer Science, Springer (2017), DOI: 10.1007/978-3-319-67630-2 1

Lagae, A., Lefebvre, S., Cook, R., DeRose, T., Drettakis, G., Ebert, D.S., Lewis, J.P., Perlin, K., Zwicker, M.: A survey of procedural noise functions. In: Computer Graphics Forum. vol. 29, pp. 2579–2600. Wiley Online Library (2010), DOI: 10.1111/j.1467-8659.2010.01827.x

Lakshminarasimhan, S., Shah, N., Ethier, S., Klasky, S., Latham, R., Ross, R., Samatova, N.: Compressing the Incompressible with ISABELA: In-situ Reduction of Spatio-Temporal Data. European Conference on Parallel and Distributed Computing (Euro-Par), Bordeaux, France (2011), DOI: 10.1007/978-3-642-23400-2 34

Laney, D., Langer, S., Weber, C., Lindstrom, P., Wegener, A.: Assessing the Effects of Data Compression in Simulations Using Physically Motivated Metrics. Super Computing (2013), DOI: 10.3233/SPR-140386

Lindstrom, P.: Fixed-Rate Compressed Floating-Point Arrays. IEEE Transactions on Visualization and Computer Graphics 2012 (2014), DOI: 10.1109/BigData.2013.6691591

Lindstrom, P., Isenburg, M.: Fast and efficient compression of floating-point data. IEEE transactions on visualization and computer graphics 12(5), 1245–1250 (2006), DOI: 10.1109/TVCG.2006.143

Roeckner, E., B¨auml, G., Bonaventura, L., Brokopf, R., Esch, M., Giorgetta, M., Hagemann, S., Kirchner, I., Kornblueh, L., Manzini, E., et al.: The atmospheric general circulation model ECHAM 5. PART I: Model description (2003)

Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Transactions on information theory 23(3), 337–343 (1977), DOI: 10.1109/TIT.1977.1055714




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