Performance Portability of Out-of-Kernel Optimizations on GPUs: A Molecular Docking Case Study

Abstract: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. Submission history Access Paper: View PDF HTML (experimental) TeX Source Additional Features Audio Summary Current browse context: References & Citations Google Scholar Semantic Scholar Bookmark Institution arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.