High-performance genome sorting program

被引：1

作者：

Kasilov, Vasily ^{[1
]}

Drobintsev, Pavel ^{[1
]}

Voinov, Nikita ^{[1
]}

机构：

[1] Peter Great St Petersburg Polytech Univ, Polytech Skaya 29, St Petersburg 195251, Russia

来源：

10TH INTERNATIONAL YOUNG SCIENTISTS CONFERENCE IN COMPUTATIONAL SCIENCE (YSC2021) | 2021年 / 193卷

关键词：

genome; sorting algorithm; alignment; BAM and SAM files; OpenMP; HPC;

D O I：

10.1016/j.procs.2021.10.048

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

This paper is devoted to the practical application of parallel sorting algorithms and parallel input-output methods for the problem of genome alignment. The paper considers different approaches to the implementation of such algorithms, taking into account the capabilities of high-performance systems. Main purpose of the work is to develop a genome sorting program, the efficiency of which significantly exceeds the efficiency of free software analogues. The genome sorting program is implemented for a supercomputer using the C++ language and the OpenMP and OpenMPI. The developed program demonstrates a significant increase in the speed of operation (up to 10 times) compared to free software analogues due to massive parallel data input and output. Different approaches for data input/output parallelization and data processing considered in the paper can be applied in other subject areas. (C) 2021 The Authors. Published by Elsevier B.V.

引用

页码：464 / 473

页数：10

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