HDF5-FastQuery: Accelerating Complex Queries on HDF Datasets usingFast Bitmap Indices

Conference · Thu Mar 30 04:00:00 EST 2006

OSTI ID:881620

Gosink, Luke; Shalf, John; Stockinger, Kurt; Wu, Kesheng; Bethel, Wes

Large scale scientific data is often stored in scientific data formats such as FITS, netCDF and HDF. These storage formats are of particular interest to the scientific user community since they provide multi-dimensional storage and retrieval. However, one of the drawbacks of these storage formats is that they do not support semantic indexing which is important for interactive data analysis where scientists look for features of interests such as ''Find all supernova explosions where energy > 10{sup 5} and temperature > 10{sup 6}''. In this paper we present a novel approach called HDF5-FastQuery to accelerate the data access of large HDF5 files by introducing multi-dimensional semantic indexing. Our implementation leverages an efficient indexing technology called bitmap indexing that has been widely used in the database community. Bitmap indices are especially well suited for interactive exploration of large-scale read only data. Storing the bitmap indices into the HDF5 file has the following advantages: (a) Significant performance speedup of accessing subsets of multi-dimensional data and (b) portability of the indices across multiple computer platforms. We will present an API that simplifies the execution of queries on HDF5 files for general scientific applications and data analysis. The design is flexible enough to accommodate the use of arbitrary indexing technology for semantic range queries. We will also provide a detailed performance analysis of HDF5-FastQuery for both synthetic and scientific data. The results demonstrate that our proposed approach for multi-dimensional queries is up to a factor of 2 faster than HDF5.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director. Office of Science. Office of AdvancedScientific Computing Research
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 881620
• Report Number(s): LBNL--59602; BnR: KJ0101030
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS
Bitmap index data access scientific file formats hdf
COMPUTERS
DATA ANALYSIS
DESIGN
EXPLORATION
EXPLOSIONS
IMPLEMENTATION
MANAGEMENT
PERFORMANCE
STORAGE