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Benchmarking SciDB data import on HPC systems
- Source :
- HPEC
- Publication Year :
- 2016
- Publisher :
- IEEE, 2016.
-
Abstract
- 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.<br />5 pages, 4 figures, IEEE High Performance Extreme Computing (HPEC) 2016, best paper finalist
- Subjects :
- FOS: Computer and information sciences
0301 basic medicine
Computer Science - Performance
Computer science
business.industry
Databases (cs.DB)
Supercomputer
Quantitative Biology - Quantitative Methods
Data modeling
Computational science
Performance (cs.PF)
03 medical and health sciences
030104 developmental biology
Software
Computer Science - Databases
Computer Science - Distributed, Parallel, and Cluster Computing
Data model
FOS: Biological sciences
Computer data storage
Scalability
Benchmark (computing)
Distributed, Parallel, and Cluster Computing (cs.DC)
business
Massively parallel
Quantitative Methods (q-bio.QM)
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- 2016 IEEE High Performance Extreme Computing Conference (HPEC)
- Accession number :
- edsair.doi.dedup.....3e034526d9018ca85f79e03676dd60d0