← 研踪 PaperTrailarXiv:2611.06207 · v1
Performance Portability of Out-of-Kernel Optimizations on GPUs: A Molecular Docking Case Study
首次提交 2026-11-04 17:21
版本更新 2026-11-04 17:21
雷达观测 2026-11-05 11:10
摘要
Achieving performance portability is challenging for irregular scientific applications built as repeated multi-kernel GPU pipelines, because throughput depends on out-of-kernel decisions as much as on kernel efficiency. Using molecular docking as a representative case study, we propose an out-of-kernel tuning methodology that treats batching policy, worker concurrency, and per-worker memory allocation as explicit optimization parameters, replacing backend-dependent occupancy-driven choices with a more portable execution strategy based on explicit resource bounds. We implement this methodology in the muDock mini-app under a manager/worker execution model where multiple host workers share a GPU through independent streams. We then evaluate the methodology on NVIDIA, AMD, and Intel GPUs across CUDA, HIP, and SYCL implementations. Across all evaluated platform/backend pairs, the memory-bounded formulation exceeds the peak throughput of the occupancy-guided baseline. The fully tuned methodology improves the end-to-end throughput on all tested configurations, achieving an average speedup of 1.53x over the baseline.
作者备注：11 pages, 5 figures, 1 table
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v1 · 2026-11-04 17:21 · 最新观测版本
Performance Portability of Out-of-Kernel Optimizations on GPUs: A Molecular Docking Case Study
Achieving performance portability is challenging for irregular scientific applications built as repeated multi-kernel GPU pipelines, because throughput depends on out-of-kernel decisions as much as on kernel efficiency. Using molecular docking as a representative case study, we propose an out-of-kernel tuning methodology that treats batching policy, worker concurrency, and per-worker memory allocation as explicit optimization parameters, replacing backend-dependent occupancy-driven choices with a more portable execution strategy based on explicit resource bounds. We implement this methodology in the muDock mini-app under a manager/worker execution model where multiple host workers share a GPU through independent streams. We then evaluate the methodology on NVIDIA, AMD, and Intel GPUs across CUDA, HIP, and SYCL implementations. Across all evaluated platform/backend pairs, the memory-bounded formulation exceeds the peak throughput of the occupancy-guided baseline. The fully tuned methodology improves the end-to-end throughput on all tested configurations, achieving an average speedup of 1.53x over the baseline.
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