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

2023 IEEE 36th International System-on-Chip Conference (SOCC)(2023)

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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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Key words
Programming model,heterogeneous computing,sequence analysis
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