Benchmarking SciDB data import on HPC systems

Siddharth Samsi, Laura Brattain, William Arcand, David Bestor, Bill Bergeron, Chansup Byun, Vijay Gadepally, Matthew Hubbell, Michael Jones, Anna Klein, Peter Michaleas, Lauren Milechin, Julie Mullen, Andrew Prout, Antonio Rosa, Charles Yee, Jeremy Kepner, Albert Reuther

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

9 Scopus citations


SciDB is a scalable, computational database management system that uses an array model for data storage. The array data model of SciDB makes it ideally suited for storing and managing large amounts of imaging data. SciDB is designed to support advanced analytics in database, thus reducing the need for extracting data for analysis. It is designed to be massively parallel and can run on commodity hardware in a high performance computing (HPC) environment. In this paper, we present the performance of SciDB using simulated image data. The Dynamic Distributed Dimensional Data Model (D4M) software is used to implement the benchmark on a cluster running the MIT SuperCloud software stack. A peak performance of 2.2M database inserts per second was achieved on a single node of this system. We also show that SciDB and the D4M toolbox provide more efficient ways to access random sub-volumes of massive datasets compared to the traditional approaches of reading volumetric data from individual files. This work describes the D4M and SciDB tools we developed and presents the initial performance results. This performance was achieved by using parallel inserts, a in-database merging of arrays as well as supercomputing techniques, such as distributed arrays and single-program-multiple-data programming.

Original languageEnglish
Title of host publication2016 IEEE High Performance Extreme Computing Conference, HPEC 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781509035250
StatePublished - Nov 28 2016
Externally publishedYes
Event2016 IEEE High Performance Extreme Computing Conference, HPEC 2016 - Waltham, United States
Duration: Sep 13 2016Sep 15 2016

Publication series

Name2016 IEEE High Performance Extreme Computing Conference, HPEC 2016


Conference2016 IEEE High Performance Extreme Computing Conference, HPEC 2016
Country/TerritoryUnited States


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