EVALUATING PERFORMANCE OPTIMIZATIONS OF LARGE-SCALE GENOMIC SEQUENCE SEARCH APPLICATIONS USING SST/MACRO

Tae-Hyuk Ahn, Damian Dechev, Heshan Lin, Helgi Adalsteinsson, Curtis Janssen

Abstract

The next decade will see a rapid evolution of HPC node architectures as power and cooling constraints are limiting increases in microprocessor clock speeds and constraining data movement. Future and current HPC applications will have to change and adapt as node architectures evolve. The application of advanced cycle accurate node architecture simulators will play a crucial role for the design and optimization of future data intensive applications. In this paper, we present our simulation-based framework for analyzing the scalability and performance of a number of critical optimizations of a massively parallel genomic search application, mpiBLAST, using an advanced macroscale simulator (SST/macro). In this paper we report the use of our framework for the evaluation of three potential improvements of mpiBLAST: enabling high-performance parallel output, an approach for caching database fragments in memory, and a methodology for pre-distributing database segments. In our experimental setup, we performed query sequence matching on the genome of the yellow fever mosquito, Aedes aegypti.

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Paper Citation


in Harvard Style

Ahn T., Dechev D., Lin H., Adalsteinsson H. and Janssen C. (2011). EVALUATING PERFORMANCE OPTIMIZATIONS OF LARGE-SCALE GENOMIC SEQUENCE SEARCH APPLICATIONS USING SST/MACRO . In Proceedings of 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH, ISBN 978-989-8425-78-2, pages 65-73. DOI: 10.5220/0003600200650073


in Bibtex Style

@conference{simultech11,
author={Tae-Hyuk Ahn and Damian Dechev and Heshan Lin and Helgi Adalsteinsson and Curtis Janssen},
title={EVALUATING PERFORMANCE OPTIMIZATIONS OF LARGE-SCALE GENOMIC SEQUENCE SEARCH APPLICATIONS USING SST/MACRO},
booktitle={Proceedings of 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,},
year={2011},
pages={65-73},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003600200650073},
isbn={978-989-8425-78-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,
TI - EVALUATING PERFORMANCE OPTIMIZATIONS OF LARGE-SCALE GENOMIC SEQUENCE SEARCH APPLICATIONS USING SST/MACRO
SN - 978-989-8425-78-2
AU - Ahn T.
AU - Dechev D.
AU - Lin H.
AU - Adalsteinsson H.
AU - Janssen C.
PY - 2011
SP - 65
EP - 73
DO - 10.5220/0003600200650073