Collaborative Research SI2-SSE: Comprehensive Sustained Innovation in Acceleration of Molecular Dynamics Simulation and Analysis on Graphical Processing Units.

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This collaborative pilot project between the San Diego Supercomputer Center at the University of California San Diego, the Quantum Theory Project at the University of Florida and industrial partners NVIDIA Inc. is focused on developing innovative, comprehensive open source software element libraries for accelerating condensed phase Molecular Dynamics (MD) simulations of biomolecules using Graphics Processing Units (GPU). By porting MD techniques to GPUs this project is enabling users to both attain substantial increases in their own local calculations without the need for substantial investment in hardware or infrastructure, and to make effective use of GPU acceleration provided by new machines within the NSF supercomputing centers. The software elements being developed and distributed both within the AMBER MD package and as open source libraries are providing critical software infrastructure in support of transformative research in the fields of chemistry, life science, materials science, environmental and renewable energy research.The software elements being created in this project have very broad impact. For example, the integration of single and multi-GPU acceleration within the AMBER software alone benefits a very large and established national and international user base. Over 8,000 downloads of the AMBER Tools package from unique IP addresses and more than 500 sites which use the AMBER MD engine testify to the scope of the community of researchers this work impacts. Additionally the open source GPU MD acceleration libraries being produced provide broad impact across multiple domains while outreach workshops are helping to train the next generation of scientists not just in the use and potential benefits of GPU MD acceleration libraries but also in modern MD simulation techniques.This award is co-funded by the Office of Cyberinfrastructure, the Division of Chemistry and the Office of Multidisciplinary Activites of the Directorate of Mathematical Sciences.