FM-Index on GPU: A Cooperative Scheme to Reduce Memory Footprint

Alejandro Chacon, Santiago Marco Sola, Antonio Espinosa, Paolo Ribeca, Juan Carlos Moure
2014 2014 IEEE International Symposium on Parallel and Distributed Processing with Applications  
The FM-index is a data structure which is seeing more and more pervasive use, in particular in the field of highthroughput bioinformatics. Algorithms based on it show a pseudo-random memory access pattern. As a consequence, they are usually bound by memory bandwidth rather than CPU usage. Naive GPU implementations are no exception. Here we show that the combination of a compact design of the FM-index and a thread-cooperative approach can be used to restore a proper balance. The resulting
more » ... n is less memory-bandwidth intensive, and allows full exploitation of the computational resources of the GPU across several GPU architectures.
doi:10.1109/ispa.2014.10 dblp:conf/ispa/ChaconMERM14 fatcat:o3qar2lhxvfn3da2g544k2mdmi