FastQuery: A Parallel Indexing System for Scientific Data

Jerry Chou, Kesheng Wu, Prabhat,


Modern scientific datasets present numerous data management and analysis challenges. State-of-the-art index and query technologies such as FastBit can significantly improve accesses to these datasets by augmenting the user data with indexes and other secondary information. However, a challenge is that the indexes assume the relational data model but the scientific data generally follows the array data model. To match the two data models, we design a generic mapping mechanism and implement an efficient input and output interface for reading and writing the data and their corresponding indexes. To take advantage of the emerging many-core architectures, we also develop a parallel strategy for indexing using threading technology. This approach complements our on-going MPI-based parallelization efforts.
We demonstrate the flexibility of our software by applying it to two of the most commonly used scientific data formats, HDF5 and NetCDF. We present two case studies using data from a particle accelerator model and a global climate model. We also conducted a detailed performance study using these scientific datasets. The results show that FastQuery speeds up the query time by a factor of 2.5x to 50x, and it reduces the indexing time by a factor of 16 on 24 cores.

full text of LBNL-5315E (PDF)

FastQuery multi-thread version at Cluster 2011
FastQuery MPI version at SSDBM 2011

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