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Title: On the Impact of Widening Vector Registers on Sequence Alignment

Abstract

Vector extensions, such as SSE, have been part of the x86 since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.

Authors:
; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1340891
Report Number(s):
PNNL-SA-118504
KJ0402000
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Conference
Resource Relation:
Conference: 45th International Conference on Parallel Processing (ICPP 2016), August 15-19, 2016, Philadelphia, Pennsylvania, 506 - 515
Country of Publication:
United States
Language:
English
Subject:
Smitb-Waterman; Needleman-Wunsch; sequence alignment; SIMD; parasail

Citation Formats

Daily, Jeffrey A., Kalyanaraman, Anantharaman, Krishnamoorthy, Sriram, and Ren, Bin. On the Impact of Widening Vector Registers on Sequence Alignment. United States: N. p., 2016. Web. doi:10.1109/ICPP.2016.65.
Daily, Jeffrey A., Kalyanaraman, Anantharaman, Krishnamoorthy, Sriram, & Ren, Bin. On the Impact of Widening Vector Registers on Sequence Alignment. United States. doi:10.1109/ICPP.2016.65.
Daily, Jeffrey A., Kalyanaraman, Anantharaman, Krishnamoorthy, Sriram, and Ren, Bin. Thu . "On the Impact of Widening Vector Registers on Sequence Alignment". United States. doi:10.1109/ICPP.2016.65.
@article{osti_1340891,
title = {On the Impact of Widening Vector Registers on Sequence Alignment},
author = {Daily, Jeffrey A. and Kalyanaraman, Anantharaman and Krishnamoorthy, Sriram and Ren, Bin},
abstractNote = {Vector extensions, such as SSE, have been part of the x86 since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.},
doi = {10.1109/ICPP.2016.65},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Sep 22 00:00:00 EDT 2016},
month = {Thu Sep 22 00:00:00 EDT 2016}
}

Conference:
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