Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs

Zheming Jin; Jeffrey S. Vetter

doi:10.1109/SOCC58585.2023.10256881

Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Cas-OFFinder is a popular application for genome editing. Its OpenCL implementation searches potential off-target sites in parallel on a GPU. In this work, we describe our experience migrating the application from OpenCL to SYCL. Evaluating the performance of the OpenCL and SYCL applications using human genome sequences shows that the SYCL program could achieve performance portability on the target GPUs. Exploring the optimizations of the hotspot kernel in SYCL may further improve the performance of the application by 9% to 23%.

Original language	English
Title of host publication	Proceedings - 2023 IEEE 36th International System-on-Chip Conference, SOCC 2023
Editors	Jurgen Becker, Andrew Marshall, Tanja Harbaum, Amlan Ganguly, Fahad Siddiqui, Kieran McLaughlin
Publisher	IEEE Computer Society
ISBN (Electronic)	9798350300116
DOIs	https://doi.org/10.1109/SOCC58585.2023.10256881
State	Published - 2023
Event	36th IEEE International System-on-Chip Conference, SOCC 2023 - Santa Clara, United States Duration: Sep 5 2023 → Sep 8 2023

Publication series

Name	International System on Chip Conference
Volume	2023-September
ISSN (Print)	2164-1676
ISSN (Electronic)	2164-1706

Conference

Conference	36th IEEE International System-on-Chip Conference, SOCC 2023
Country/Territory	United States
City	Santa Clara
Period	09/5/23 → 09/8/23

Funding

The research used resources at the Experimental Computing Lab at Oak Ridge National Lab and was supported by the US Department of Energy Advanced Scientific Computing Research program under Contract No. DE-AC05-00OR22725.

Keywords

Programming model
heterogeneous computing
sequence analysis

Access to Document

10.1109/SOCC58585.2023.10256881

Cite this

Jin, Z., & Vetter, J. S. (2023). Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs. In J. Becker, A. Marshall, T. Harbaum, A. Ganguly, F. Siddiqui, & K. McLaughlin (Eds.), Proceedings - 2023 IEEE 36th International System-on-Chip Conference, SOCC 2023 (International System on Chip Conference; Vol. 2023-September). IEEE Computer Society. https://doi.org/10.1109/SOCC58585.2023.10256881

Jin, Zheming ; Vetter, Jeffrey S. / Experience Migrating OpenCL to SYCL : A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs. Proceedings - 2023 IEEE 36th International System-on-Chip Conference, SOCC 2023. editor / Jurgen Becker ; Andrew Marshall ; Tanja Harbaum ; Amlan Ganguly ; Fahad Siddiqui ; Kieran McLaughlin. IEEE Computer Society, 2023. (International System on Chip Conference).

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abstract = "Cas-OFFinder is a popular application for genome editing. Its OpenCL implementation searches potential off-target sites in parallel on a GPU. In this work, we describe our experience migrating the application from OpenCL to SYCL. Evaluating the performance of the OpenCL and SYCL applications using human genome sequences shows that the SYCL program could achieve performance portability on the target GPUs. Exploring the optimizations of the hotspot kernel in SYCL may further improve the performance of the application by 9% to 23%.",

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language = "English",

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Jin, Z & Vetter, JS 2023, Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs. in J Becker, A Marshall, T Harbaum, A Ganguly, F Siddiqui & K McLaughlin (eds), Proceedings - 2023 IEEE 36th International System-on-Chip Conference, SOCC 2023. International System on Chip Conference, vol. 2023-September, IEEE Computer Society, 36th IEEE International System-on-Chip Conference, SOCC 2023, Santa Clara, United States, 09/5/23. https://doi.org/10.1109/SOCC58585.2023.10256881

Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs. / Jin, Zheming; Vetter, Jeffrey S.
Proceedings - 2023 IEEE 36th International System-on-Chip Conference, SOCC 2023. ed. / Jurgen Becker; Andrew Marshall; Tanja Harbaum; Amlan Ganguly; Fahad Siddiqui; Kieran McLaughlin. IEEE Computer Society, 2023. (International System on Chip Conference; Vol. 2023-September).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Jin Z, Vetter JS. Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs. In Becker J, Marshall A, Harbaum T, Ganguly A, Siddiqui F, McLaughlin K, editors, Proceedings - 2023 IEEE 36th International System-on-Chip Conference, SOCC 2023. IEEE Computer Society. 2023. (International System on Chip Conference). doi: 10.1109/SOCC58585.2023.10256881

Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs

Abstract

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Keywords

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