TY - GEN
T1 - Porting and Benchmarking of BWAKIT Pipeline on OpenPOWER Architecture
AU - Kathiresan, Nagarajan
AU - Al-Ali, Rashid
AU - Jithesh, Puthen
AU - Narayanasamy, Ganesan
AU - Al-Ars, Zaid
N1 - Publisher Copyright:
© 2018, Springer Nature Switzerland AG.
PY - 2018
Y1 - 2018
N2 - Next Generation Sequencing (NGS) technology produces large volumes of genome data, which gets processed using various open source bioinformatics tools. The configuration and compilation of some bioinformatics tools (e.g. BWAKIT, root) is a challenging activity in its own right, not to mention the need to perform more elaborate porting activities for these applications on some architectures (e.g. IBM Power). The best practices of application porting should ensure (i) the semantics of the program or algorithm should not be changed, (ii) the output generated from the original source code and the modified source code (i.e., after porting) should be same even though the code is ported into different architectures and (iii) the output should be similar across different architectures after porting. Burrows-Wheeler Aligner (BWA) is the most popular genome mapping application used in the BWAKIT toolset. This BWAKIT provides pre-compiled binaries for x86_64 architecture and an end-to-end solution for genome mapping. In this paper, we show how to port various pre-built application binaries used in BWAKIT into OpenPOWER architecture and execute the BWAKIT pipeline successfully. Additionally, we demonstrate the validity of output results on OpenPOWER as well as present benchmarking results of BWAKIT applications that indicate the suitability of the highly multithreaded OpenPOWER architecture to execute these applications.
AB - Next Generation Sequencing (NGS) technology produces large volumes of genome data, which gets processed using various open source bioinformatics tools. The configuration and compilation of some bioinformatics tools (e.g. BWAKIT, root) is a challenging activity in its own right, not to mention the need to perform more elaborate porting activities for these applications on some architectures (e.g. IBM Power). The best practices of application porting should ensure (i) the semantics of the program or algorithm should not be changed, (ii) the output generated from the original source code and the modified source code (i.e., after porting) should be same even though the code is ported into different architectures and (iii) the output should be similar across different architectures after porting. Burrows-Wheeler Aligner (BWA) is the most popular genome mapping application used in the BWAKIT toolset. This BWAKIT provides pre-compiled binaries for x86_64 architecture and an end-to-end solution for genome mapping. In this paper, we show how to port various pre-built application binaries used in BWAKIT into OpenPOWER architecture and execute the BWAKIT pipeline successfully. Additionally, we demonstrate the validity of output results on OpenPOWER as well as present benchmarking results of BWAKIT applications that indicate the suitability of the highly multithreaded OpenPOWER architecture to execute these applications.
KW - BWAKIT
KW - Burrows-Wheeler Aligner
KW - Efficiency
KW - Genome mapping
KW - POWER architecture
KW - Parallelization
KW - Scalability
UR - http://www.scopus.com/inward/record.url?scp=85066112593&partnerID=8YFLogxK
U2 - 10.1007/978-3-030-02465-9_27
DO - 10.1007/978-3-030-02465-9_27
M3 - Conference contribution
AN - SCOPUS:85066112593
SN - 9783030024642
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 402
EP - 410
BT - High Performance Computing - ISC High Performance 2018 International Workshops, Revised Selected Papers
A2 - Weiland, Michèle
A2 - Alam, Sadaf
A2 - Yokota, Rio
A2 - Shalf, John
PB - Springer Verlag
T2 - International Conference on High Performance Computing, ISC High Performance 2018
Y2 - 28 June 2018 through 28 June 2018
ER -