NDLI: Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access

Content Provider	IEEE Xplore Digital Library
Author	Chacon, A. Marco-Sola, S. Espinosa, A. Ribeca, P. Moure, J.C.
Copyright Year	2004
Abstract	The recent advent of high-throughput sequencing machines producing big amounts of short reads has boosted the interest in efficient string searching techniques. As of today, many mainstream sequence alignment software tools rely on a special data structure, called the FM-index, which allows for fast exact searches in large genomic references. However, such searches translate into a pseudo-random memory access pattern, thus making memory access the limiting factor of all computation-efficient implementations, both on CPUs and GPUs. Here, we show that several strategies can be put in place to remove the memory bottleneck on the GPU: more compact indexes can be implemented by having more threads work cooperatively on larger memory blocks, and a k-step FM-index can be used to further reduce the number of memory accesses. The combination of those and other optimisations yields an implementation that is able to process about two Gbases of queries per second on our test platform, being about 8× faster than a comparable multi-core CPU version, and about 3× to 5× faster than the FM-index implementation on the GPU provided by the recently announced Nvidia NVBIO bioinformatics library.
Sponsorship	IEEE Computer Society
Starting Page	1048
Ending Page	1059
Page Count	12
File Size	1880024
File Format	PDF
ISSN	15455963
Volume Number	12
Issue Number	5
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-09-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Graphics processing units Instruction sets Radiation detectors Bioinformatics Indexes Frequency modulation Genomics Memory-Level Parallelism GPGPU Short Read Mapping FM-index Fine-Grain Parallelism memory-level parallelism bioinformatics short read mapping fine-grain parallelism
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

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