Developing Synthetic Applications Benchmarks on Composable Cyberinfrastructure: A Study of Scaling Molecular Dynamics Applications on GPUs
Richard E Lawrence, Dhruva K. Chakravorty, Zhenhua He, Francis Dang, Lisa M. Pérez, Wesley A. Brashear, Honggao Liu · Practice and Experience in Advanced Research Computing · 2023
The potential for infinite scaling, improved performance, and better sharing of computing resources motivates researchers to adapt to composable infrastructures. Measuring performance on these systems requires an assessment of how the composed configuration itself affects performance which goes beyond traditional scaling approaches. We emphasize the subtle relationship between the nature of the calculation and the configuration of the composable infrastructure. New application benchmarking strategies are explored to inform the optimal configurations and best computing practices for composable systems. Realistic molecular dynamics research workflows are employed as benchmarks for composed GPU systems to develop a benchmarking strategy that yields recognizable and informative results. We employ the practices on a realistic case for a molecular dynamics research workflow on a composed GPU system. We discuss the identification of computational bottlenecks and establish a need for new benchmark performance suites that can help researchers articulate optimum compositions for composable infrastructure.