Addresses exascale computing challenges of COVID-19

The Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign (UIUC) is pleased to announce that it has established a oneAPI academic Center of Excellence (CoE) focusing on standards-based cross-architecture programming. The center will use oneAPI's heterogeneous programming model to accelerate computing for research conducted by life sciences application NAMD, which will help further the understanding of cellular processes at the molecular level to address challenges to human health.

NAMD is a parallel molecular dynamics code designed for high-performance simulation of biomolecular systems, particularly tuned for simulation of very large, cell-scale molecular systems. The NAMD simulation engine, together with its companion application VMD for visualization, setup, and analysis of simulation trajectories, provides a "computational microscope" that enables researchers to "see," in silico, the atomic-scale details of the molecular machinery that drive cellular processes. Major recent investigations enabled by NAMD include studies of the spike protein complex of the SARS-CoV-2 virus responsible for the COVID-19 pandemic. The supporting molecular dynamics simulations required billions of time steps performed on NSF and DOE supercomputer resources. In order to simulate one billion time steps within one week, the computation for each time step must be completed in under a millisecond, which necessitates effective use of CPUs and GPUs and efficient communication between them.

"Owing to algorithmic advances and hardware breakthroughs, we have come a very long way in simulation of biological systems and processes highly relevant to human health and disease. The expectation from simulation engines like NAMD is to provide molecular insight, which cannot be obtained otherwise, into key mechanisms and details that can be harvested to address major concerns in human health, as clearly exemplified by the current work performed at many labs on COVID-19 virus," says Emad Tajkhorshid, the Director of the NIH Center for Macromolecular Modeling and Bioinformatics and the Theoretical and Computational Biophysics Group at Illinois, the creator of NAMD and VMD. "A key element in our successful simulation of biological systems has been longer and faster simulations, achieved by maximal exploitation of available hardware technology in the best way possible, which also constitutes the main goal of the UIUC oneAPI CoE."

To achieve this, software developers at UIUC are working together with Intel engineers on oneAPI software optimizations. The use of oneAPI in NAMD will enable it to run on the Aurora supercomputer at Argonne National Laboratory, which will be one of the leaders in exascale computing. oneAPI's open standards will help software like NAMD leverage future heterogeneous computer architectures. "The need to maintain software for hardware accelerators from multiple vendors makes it increasingly important to have a portable programming model," says David Hardy, lead developer of NAMD.

As a oneAPI CoE, UIUC will lead innovations in developing portable HPC software solutions through the use of oneAPI technologies and provide instruction on best practices back to the community. The ongoing NAMD development by UIUC promises new breakthroughs for biomolecular research that will ultimately benefit human health and well-being.

"UIUC's pioneering work on oneAPI will allow scientists to focus on pushing the boundaries of science instead of struggling through the historical tradeoff between performance or the challenge of maintaining multiple code versions imposed by proprietary accelerated computing solutions," says Jeff McVeigh, Intel vice president of Datacenter XPU Products and Solutions.