Abstract
A parallel design and implementation of FM-index is presented in this paper. In applications, the performance of the FM-index is crucial, which is a self-contained, highly compressed indexing algorithm. With the popularity of multi-core processors, parallel computing allows the FM-index to run faster by performing multiple computations simultaneously when possible. Our approach works by splitting input data into overlapping blocks with equal size, and running them through the FM-index algorithm simultaneously on multiple processors. After analyzing and refactoring the sequential version, we organize the data flows of all operations according to a unified parallel framework. The experimental results show that, in general our approach has achieved a significant and sub-linear speedup on widespread symmetrical multi-processing architectures. This will greatly reduce the running time of executing operations on large data sets.
Original language | English |
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Title of host publication | IEEE International Conference on High Performance Computing and Communications |
Place of Publication | USA |
Publisher | IEEE, Institute of Electrical and Electronics Engineers |
Pages | 169-173 |
Number of pages | 5 |
ISBN (Electronic) | 9780769533520 |
DOIs | |
Publication status | Published - 2008 |
Event | HPCC 2008: 10th International Conference - Dalian, China, China Duration: 25 Sept 2008 → 27 Sept 2008 |
Conference
Conference | HPCC 2008: 10th International Conference |
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Country/Territory | China |
Period | 25/09/08 → 27/09/08 |