Simplifying Index File Structure to Improve I/O Performance of Parallel Indexing

Complex indexing techniques are needed to reduce the time of analyzing massive scientific datasets, but generating these indexing data structures can be very time consuming. In this work, we propose a set of strategies to simplify the index file structure and to improve the I/O performance during index construction using FastQuery, which is a parallel indexing and querying system for scientific data. FastQuery has been used to analyze data from various scientific applications, including a trillion plasma particles simulation. To accelerate query process, FastQuery uses FastBit to build indexes, and then stores the indexes into file system through parallel scientific data format libraries, such as HDF5. Although these data format libraries are designed to support more complex multi-dimensional arrays, we observed that it still takes considerable work to map the indexing data structures into arrays, especially on parallel machines. To address this problem, in this paper, we attempt to minimize the I/O time by storing indexes into our self-defined binary data format. By fully controlling the data structure, we can minimize the I/O synchronization overhead and explore more efficient I/O strategy for storing indexes. Our experiments of indexing a trillion particle dataset using 20,000 cores of a supercomputer show that the proposed binary I/O driver can reach 85% of the peak I/O bandwidth on the system, and achieves a speedup of up to 4X in terms of the total execution time comparing to the previous FastQuery implementation with HDF5 I/O driver.