Presenter: David Hardy, University of Illinois at Urbana-Champaign
Co-Authors: Eric Bohm, University of Illinois at Urbana-Champaign; Ke Yue, Intel Corporation; Wei Jiang, Argonne National Laboratory
Intel eXtreme Performance Users Group (IXPUG) Annual Conference 2025 Technical Talk
Abstract: Molecular dynamics simulations serve as a bridge between structural data and biological function, offering an atomic-scale view of the mechanistic foundations of life. The parallel molecular dynamics application NAMD is capable of scaling simulations to tens of thousands of CPU cores and thousands of GPUs, providing a high-performance "computational microscope" to biomedical researchers that can leverage the capabilities of the Aurora supercomputer. The NAMD team in collaboration with Intel has been developing a oneAPI/SYCL code path to fully exploit the Intel Ponte Vecchio GPUs that power Aurora. In this presentation, we will review the past NAMD SYCL development efforts, show NAMD scaling benchmarks on Aurora, and discuss our ongoing work to improve single- and multi-node performance.
Slides: https://www.ixpug.org/resources/scaling-molecular-dynamics-simulations-on-aurora-with-namd