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

这个由加州大学圣地亚哥分校的圣地亚哥超级计算机中心、佛罗里达大学的量子理论项目和工业合作伙伴NVIDIA Inc.合作的试点项目专注于开发创新的、全面的开源软件元素库，用于使用图形处理单元(GPU)加速生物分子的浓缩相分子动力学(MD)模拟。通过将MD技术移植到GPU，该项目使用户能够在不需要大量硬件或基础设施投资的情况下，在自己的本地计算中实现大幅增长，并有效利用NSF超级计算中心内的新机器提供的GPU加速。在Amber MD包内和作为开放源代码库开发和分发的软件元素正在提供关键的软件基础设施，以支持化学、生命科学、材料科学、环境和可再生能源研究领域的变革性研究。例如，仅在Amber软件中集成单GPU和多GPU加速就能使非常庞大和成熟的国内和国际用户群受益。从唯一的IP地址和500多个使用琥珀MD引擎的站点下载的琥珀工具包超过8,000次，这证明了这项工作影响的研究人员社区的范围。此外，正在制作的开源GPU MD加速库在多个领域产生了广泛的影响，而外联研讨会正在帮助培训下一代科学家，不仅是关于GPU MD加速库的使用和潜在好处，而且还包括现代MD模拟技术。该奖项由数字基础设施办公室、化学司和数学科学局多学科活动办公室共同资助。

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.