NAMD Molecular Dynamics Simulations

Molecular dynamics simulations with NAMD serve as a bridge between structural data and biological function, providing a “computational microscope” that offers an atomic-scale view of the mechanistic foundations of life. This talk will discuss the use of oneAPI in NAMD to support Intel PVC GPUs for fast, scalable simulations on ALCF Aurora and TACC Stampede 3 supercomputers. Development has included porting CUDA kernels to SYCL, using oneDPL for collective primitives, and using oneMKL for math library support. An ongoing challenge is how to best maintain the different code paths in NAMD to support GPU acceleration for different device architectures.