Optimizing Lossy Compression with Adjacent Snapshots for N-body Simulation Data

Sihuan Li, Sheng Di, Xin Liang, Zizhong Chen, Franck Cappello

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

13 Scopus citations

Abstract

Today's N-body simulations are producing extremely large amounts of data. The Hardware/Hybrid Accelerated Cosmology Code (HACC), for example, may simulate trillions of particles, producing tens of petabytes of data to store in a parallel file system, according to the HACC users. In this paper, we design and implement an efficient, in situ error-bounded lossy compressor to significantly reduce the data size for N-body simulations. Not only can our compressor save significant storage space for N-body simulation researchers, but it can also improve the I/O performance considerably with limited memory and computation overhead. Our contribution is threefold. (1) We propose an efficient data compression model by leveraging the consecutiveness of the cosmological data in both space and time dimensions as well as the physical correlation across different fields. (2) We propose a lightweight, efficient alignment mechanism to align the disordered particles across adjacent snapshots in the simulation, which is a fundamental step in the whole compression procedure. We also optimize the compression quality by exploring best-fit data prediction strategies and optimizing the frequencies of the space-based compression vs. time-based compression. (3) We evaluate our compressor using both a cosmological simulation package and molecular dynamics simulation data - two major categories in the N-body simulation domain. Experiments show that under the same distortion of data, our solution produces up to 43% higher compression ratios on the velocity field and up to 300% higher on the position field than do other state-of-the-art compressors (including SZ, ZFP, NUMARCK, and decimation). With our compressor, the overall I/O time on HACC data is reduced by up to 20% compared with the second-best compressor.

Original languageEnglish
Title of host publicationProceedings - 2018 IEEE International Conference on Big Data, Big Data 2018
EditorsNaoki Abe, Huan Liu, Calton Pu, Xiaohua Hu, Nesreen Ahmed, Mu Qiao, Yang Song, Donald Kossmann, Bing Liu, Kisung Lee, Jiliang Tang, Jingrui He, Jeffrey Saltz
Pages428-437
Number of pages10
ISBN (Electronic)9781538650356
DOIs
StatePublished - Jul 2 2018
Event2018 IEEE International Conference on Big Data, Big Data 2018 - Seattle, United States
Duration: Dec 10 2018Dec 13 2018

Publication series

NameProceedings - 2018 IEEE International Conference on Big Data, Big Data 2018

Conference

Conference2018 IEEE International Conference on Big Data, Big Data 2018
Country/TerritoryUnited States
CitySeattle
Period12/10/1812/13/18

Bibliographical note

Publisher Copyright:
© 2018 IEEE.

Keywords

  • Error-bounded lossy compression
  • I/O performance
  • N-body simulation
  • large science data

ASJC Scopus subject areas

  • Computer Science Applications
  • Information Systems

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