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MerBench: PGAS Benchmarks for High Performance Genome Assembly

Published: 12 November 2017 Publication History

Abstract

De novo genome assembly is one of the most important and challenging computational problems in modern genomics; further, it shares algorithms and communication patterns important to other graph analytic and irregular applications. Unlike simulations, it has no floating point arithmetic and is dominated by small memory transactions within and between computing nodes. In this work, we introduce MerBench, a compact set of PGAS benchmarks that capture the communication patterns of the parallel algorithms throughout HipMer, a parallel genome assembler pipeline that has been shown to scale to massive concurrencies. We also present results of these microbenchmarks on the Edison supercomputer and illustrate how these empirical results can be used to assess the scaling behavior of the pipeline.

References

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E. Georganas, A. Buluç, J. Chapman, S. Hofmeyr, C. Aluru, R. Egan, L. Oliker, D. Rokhsar, and K. Yelick, "Hipmer: an extreme-scale de novo genome assembler," in International Conference for High Performance Computing, Networking, Storage and Analysis (SC'15), 2015.
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  • (2023)Toward Reproducible Benchmarking of PGAS and MPI Communication Schemes2023 IEEE 29th International Conference on Parallel and Distributed Systems (ICPADS)10.1109/ICPADS60453.2023.00268(1959-1967)Online publication date: 17-Dec-2023
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cover image ACM Conferences
PAW17: Proceedings of the Second Annual PGAS Applications Workshop
November 2017
39 pages
ISBN:9781450351232
DOI:10.1145/3144779
Publication rights licensed to ACM. ACM acknowledges that this contribution was authored or co-authored by an employee, contractor or affiliate of the United States government. As such, the Government retains a nonexclusive, royalty-free right to publish or reproduce this article, or to allow others to do so, for Government purposes only.

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Publication History

Published: 12 November 2017

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View all
  • (2023)Toward Reproducible Benchmarking of PGAS and MPI Communication Schemes2023 IEEE 29th International Conference on Parallel and Distributed Systems (ICPADS)10.1109/ICPADS60453.2023.00268(1959-1967)Online publication date: 17-Dec-2023
  • (2022)Scalable irregular parallelism with GPUsProceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis10.5555/3571885.3571951(1-16)Online publication date: 13-Nov-2022
  • (2022)Scalable Irregular Parallelism with GPUs: Getting CPUs Out of the WaySC22: International Conference for High Performance Computing, Networking, Storage and Analysis10.1109/SC41404.2022.00055(1-16)Online publication date: Nov-2022
  • (2021)Designing Heterogeneous Systems: Large Scale Architectural Exploration Via Simulation : Invited Paper2021 IEEE/ACM Programming Environments for Heterogeneous Computing (PEHC)10.1109/PEHC54839.2021.00011(44-51)Online publication date: Nov-2021
  • (2020)Communication-Efficient Jaccard similarity for High-Performance Distributed Genome Comparisons2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS)10.1109/IPDPS47924.2020.00118(1122-1132)Online publication date: May-2020
  • (2020)The parallelism motifs of genomic data analysisPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences10.1098/rsta.2019.0394378:2166(20190394)Online publication date: 20-Jan-2020
  • (2018)Extreme scale de novo metagenome assemblyProceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis10.5555/3291656.3291670(1-13)Online publication date: 11-Nov-2018
  • (2018)Extreme scale de novo metagenome assemblyProceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis10.1109/SC.2018.00013(1-13)Online publication date: 11-Nov-2018

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