Testing new paradigms for biomolecular simulation

Project Details

Project Lead
Peter Kasson 
Project Manager
Peter Kasson 
Project Members
Per Larsson  
Institution
University of Virginia, Departments of Molecular Physiology and of Biomedical Engineering  
Discipline
Biophysics (605) 

Abstract

Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. We are developing a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation. This framework combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring. Even for a small protein such as villin (9,864 atoms), Copernicus exhibits near-linear strong scaling from 1 to 5,376 AMD cores. We are now further testing and optimizing this framework for use on heterogeneous resource platforms such as FutureGrid.

Intellectual Merit

We are developing a software platform that combines traditional HPC and distributed-computing approaches to scale efficiently over many processor cores in heterogeneous architectures. This requires broad interdisciplinary collaboration between application scientists and supercomputing experts. The resulting package will allow any member of the community with sufficient computing power to perform calculations in a transparent and scalable manner.

Broader Impacts

This award will enable development of a next-generation computational platform to efficiently utilize the increasing number of processor cores for advances in biomolecular simulation. The software will be freely available under an open-source license.

Scale of Use

We can make effective use of every core we can get. Our framework takes advantage of fast interconnects when we have them but can also work with individual nodes.

Results

The first papers on this project have been submitted; references and details will be provided upon publication.