Afzal A, Hager G, Wellein G (2025)
Publication Language: English
Publication Status: Submitted
Publication Type: Conference contribution, Original article
Future Publication Type: Conference contribution
Publication year: 2025
Publisher: Euro-Par 2025: Parallel Processing Workshops Volume in the Springer Lecture Notes in Computer Science (LNCS) series.
Book Volume: 16294 and 16295
Conference Proceedings Title: Euro-Par 2025: Parallel Processing Workshops Volume in the Springer Lecture Notes in Computer Science (LNCS) series.
Event location: Dresden, Germany
DOI: 10.48550/arXiv.2412.08792
Molecular dynamics simulations are essential tools in computational biophysics, but their performance depend heavily on hardware choices and configuration. In this work, we presents a comprehensive performance analysis of four NVIDIA GPU accelerators -- A40, A100, L4, and L40 -- using six representative GROMACS biomolecular workloads alongside two synthetic benchmarks: Pi Solver (compute bound) and STREAM Triad (memory bound). We investigate how performance scales with GPU graphics clock frequency and how workloads respond to power capping. The two synthetic benchmarks define the extremes of frequency scaling: Pi Solver shows ideal compute scalability, while STREAM Triad reveals memory bandwidth limits -- framing GROMACS's performance in context. Our results reveal distinct frequency scaling behaviors: Smaller GROMACS systems exhibit strong frequency sensitivity, while larger systems saturate quickly, becoming increasingly memory bound. Under power capping, performance remains stable until architecture- and workload-specific thresholds are reached, with high-end GPUs like the A100 maintaining near-maximum performance even under reduced power budgets. Our findings provide practical guidance for selecting GPU hardware and optimizing GROMACS performance for large-scale MD workflows under power constraints.
APA:
Afzal, A., Hager, G., & Wellein, G. (2025). GROMACS Unplugged: How Power Capping and Frequency Shapes Performance on GPUs. In Euro-Par 2025: Parallel Processing Workshops Volume in the Springer Lecture Notes in Computer Science (LNCS) series.. Dresden, Germany: Euro-Par 2025: Parallel Processing Workshops Volume in the Springer Lecture Notes in Computer Science (LNCS) series..
MLA:
Afzal, Ayesha, Georg Hager, and Gerhard Wellein. "GROMACS Unplugged: How Power Capping and Frequency Shapes Performance on GPUs." Proceedings of the 31st International European Conference on Parallel and Distributed Computing (Euro-Par 2025), Dresden, Germany Euro-Par 2025: Parallel Processing Workshops Volume in the Springer Lecture Notes in Computer Science (LNCS) series., 2025.
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