Grid, Public and GPU Computing for the Tree of Life

生命之树的网格、公共和 GPU 计算

• 批准号: 0755048
• 负责人: Michael Cummings
• 金额: $ 131.57万
• 依托单位: University of Maryland, College Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-15 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0755048&HistoricalAwards=false
• 关键词: Grid; Public; GPU; Computing; Tree

The University of Maryland College Park is awarded a grant to create tools that expand the computing power freely available to all ATOL (Assembling the Tree of Life), and other phylogenetic researchers. The central idea is to combine Grid and GPU (graphics processing unit) computing to take better advantage of a diversity of computing resources, particularly existing desktop processing capacity available through public-computing. The main product will be a Grid system, customized for phylogenetic tree search and accessed through a user-friendly web interface, that links thousands of individual computers world-wide. The likelihood-based tree search program GARLI (Genetic Algorithm for Rapid Likelihood Inference), will serve as the initial model application during development. The new system is intended to allow analyses that far transcend what one can do on a single desktop computer or moderate-sized cluster. For example, it should become possible to carry out extensive bootstrap analyses in little more time than is now required for a single tree search. The project will also exploit a second under-utilized resource inside desktop computers, namely the graphics processing unit (GPU), which can do many scientific calculations faster than the central processing unit (CPU). A free, open-source library (C/C++) for maximum likelihood calculations using parallel CPU/GPU processing will be developed. GARLI versions will be developed that take advantage of major GPU platforms. Subsequent development will extend to other likelihood-intensive methods (e.g., Bayesian analysis). Five participating ATOL projects will help test the new tools, and publish a collaborative evaluation of the performance of the new system across the diverse phylogenetic problems they represent. The project will be a joint effort with Bowie State University, Coppin State College, and the University of Kansas Center for Research, Inc.

马里兰大学学院公园分校获得了一笔拨款，用于创建工具，以扩展所有ATOL（组装生命之树）和其他系统发育研究人员免费使用的计算能力。其核心思想是将网格和GPU（图形处理单元）计算结合起来，以更好地利用各种计算资源，特别是通过公共计算提供的现有桌面处理能力。主要产品将是一个网格系统，为系统发育树搜索定制，并通过用户友好的网络界面访问，连接全球数千台个人计算机。基于似然的树搜索程序GARLI（快速似然推理遗传算法）将作为开发过程中的初始模型应用程序。新系统的目的是允许进行远远超出单个台式计算机或中等规模集群所能做的分析。例如，应该可以在比现在单个树搜索所需的时间稍长一点的时间内执行广泛的自举分析。该项目还将利用台式计算机内部第二个未充分利用的资源，即图形处理单元（GPU），它可以比中央处理单元（CPU）更快地进行许多科学计算。将开发一个免费的、开源的库（C/ c++），用于使用并行CPU/GPU处理的最大似然计算。GARLI版本将利用主要的GPU平台进行开发。后续的开发将扩展到其他可能性密集的方法（例如，贝叶斯分析）。五个参与的ATOL项目将帮助测试新工具，并发布对新系统在不同系统发育问题上的性能的协作评估。该项目将由Bowie州立大学、Coppin州立学院和堪萨斯大学研究中心共同努力。