NDLI: SWAP-Assembler 2: Scalable Genome Assembler towards Millions of Cores -- Practice and Experience

Content Provider	IEEE Xplore Digital Library
Author	Jintao Meng Yanjie Wei Sangmin Seo Balaji, P.
Copyright Year	2015
Description	Author affiliation: Math. & Comput. Sci. Div., Argonne Nat. Lab., Chicago, IL, USA (Sangmin Seo; Balaji, P.) \|\| Center for High Performance Comput., Shenzhen Inst. of Adv. Technol., Shenzhen, China (Jintao Meng; Yanjie Wei)
Abstract	There is widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these huge sequencing data, which can be Tara bytes or even Peta bytes. Previously our assembly tool, SWAP-Assembler, can scale to 2048 cores on TianHe 1A for human Yanhuang genome. This work is to further scale SWAP-Assembler to millions of cores on Mira. SWAP-Assembler can be divided into 5 steps, and the most time consuming steps are input parallelization, kmer graph construction, graph simplification (edge merging). We optimize these three steps to keep the percentage of time usage in each step constant when the number of cores increases. For the input parallelization step, the input data is divided into virtual fragments with almost equal size, the begin position and end position for each fragment is automatically separated at the beginning symbol of reads. This data blocking strategy plays a central role in adjusting the data size to keep the communication and memory efficiency for the subsequent steps. In kmer graph construction, to prevent the communication efficiency degradation, the message size is kept constant (about 8k bytes) between any two processes by proportionally increasing the number of nucleotides to the number of processes in the input parallelization step in each round. The memory usage can be also benefited, as only a small part of the input data is processed in each round. Within graph simplification, the major improvement is to combine messages sending & receiving between its two neighbors into one loop in the communication protocol. After integrated with the above optimizations, the new assembly tool is denoted as SWAP-Assembler 2 or SWAP2 for short. In our experiment for 1k human genome dataset, the modified SWAP-Assembler 2 can scale to 16k cores with parallel efficiency of 70%.
Starting Page	769
Ending Page	772
File Size	254833
Page Count	4
File Format	PDF
ISBN	9781479980062
DOI	10.1109/CCGrid.2015.128
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-05-04
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Bioinformatics Genomics Bandwidth Assembly Optimization Sequential analysis Protocols performance optimization genome assembler parallel algorithms
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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