Performance Optimization for the Trinity RNA-Seq Assembler

Michael Wagner (), Ben Fulton and Robert Henschel
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Michael Wagner: Barcelona Supercomputing Center
Ben Fulton: Scientific Applications and Performance Tuning Indiana University
Robert Henschel: Scientific Applications and Performance Tuning Indiana University

Chapter Chapter 3 in Tools for High Performance Computing 2015, 2016, pp 29-40 from Springer

Abstract: Abstract Utilizing the enormous computing resources of high performance computing systems is anything but a trivial task. Performance analysis tools are designed to assist developers in this challenging task by helping to understand the application behavior and identify critical performance issues. In this paper we share our efforts and experiences in analyzing and optimizing Trinity, a well-established framework for the de novo reconstruction of transcriptomes from RNA-seq reads. Thereby, we try to reflect all aspects of the ongoing performance engineering: the identification of optimization targets, the code improvements resulting in 22 % overall runtime reduction, as well as the challenges we encountered getting there.

Keywords: Poor Scaling; Parallel Region; Runtime Behavior; High Performance Computing System; OpenMP Thread (search for similar items in EconPapers)
Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-319-39589-0_3

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DOI: 10.1007/978-3-319-39589-0_3

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