A Workstation Cluster for High Performance Computing in Structural Biology

用于结构生物学高性能计算的工作站集群

• 批准号: 9423827
• 负责人: Klaus Schulten
• 金额: $ 27万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1995
• 资助国家: 美国
• 起止时间: 1995-08-01 至 1997-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9423827&HistoricalAwards=false
• 关键词: Workstation; Cluster; Performance; Computing; Structural

The objective of this proposal is to continue the development of a network of high performance workstations coupled through an Asynchronous Transfer Mode (ATM) switch for effective utilization in computational structural biology. The funds requested will complement (matching) funds to be obtained from Hewlett-Packard Comp. to build a cluster of sixteen (8 to be funded through NSF) Hewlett-Packard workstations based on PA-RISC 7200 processors, to acquire a communication backbone for this cluster (based either on an ATM or on fibre channel technology, which will be decided at the time of purchase), and to upgrade the ATM switch of an existing cluster of 16 workstations. The two clusters will be used: (1) for ongoing collaborative projects with experimental laboratories which involve very large scale modeling of supramolecular systems (membranes, phopspho lipase A2 - membrane complexes, polymerization of G-actin to F-actin and association of gene V protein with single stranded DNA, complexes of nuclear receptor proteins with DNA, light harvesting systems, and others); (2) for NMR protein structure/function studies; (3) for studies of electron transfer paths in redox proteins and for the prediction of protein structures (protein folding). One of the clusters will allow users to pool small numbers of workstations (1-4), the other will allow a pooling of 8-16 workstations. The peak power of a 16 workstation cluster will also be utilized for real time modeling. For effective parallel computing across the clusters molecular dynamics programs (namd, vmd) have been developed and are being further improved. The effort is funded through an NIH Resource grant and through an NSF Grand Challenge Applications Group grant. Real time modeling will be based on a new graphics program (vmd) for large screen stereo projections and 3D interactive devices. Besides the three principle investigators, sixteen experimental investigators will benefit from the computational resources sought in this proposal. Two computer science faculty members collaborate with us on molecular dynamics algorithms and parallel computing software. The computational work is partially funded through a grant from the Carver Charitable Trust which has provided six graduate students and two postdoctoral positions for projects between the computational group operating the clusters and experimental laboratories.

本建议的目的是继续发展的高性能工作站网络耦合通过异步传输模式（ATM）交换机在计算结构生物学的有效利用。 申请的资金将补充从惠普公司获得的（配套）资金，用于建立一个十六人的集群。（8个将通过NSF供资）基于PA-RISC 7200处理器的Hewlett-Packard工作站，以获得该群集的通信主干（采用自动柜员机或光纤通道技术，视购买时决定），以及升级现有16个工作站的自动柜员机交换机。 这两个集群将用于：（1）与实验室正在进行的合作项目，涉及超大规模的超分子系统建模（膜、磷酸脂酶A2 -膜复合物、G-肌动蛋白聚合成F-肌动蛋白和基因V蛋白与单链DNA的缔合、核受体蛋白与DNA的复合物、光捕获系统等）;（2）用于NMR蛋白质结构/功能研究;（3）用于氧化还原蛋白质中电子传递路径的研究和用于蛋白质结构（蛋白质折叠）的预测。 其中一个集群将允许用户汇集少量工作站（1-4），另一个将允许汇集8-16个工作站。 16工作站集群的峰值功率也将用于真实的时间建模。 为了有效的跨集群并行计算，分子动力学程序（namd，vmd）已经开发出来，并正在进一步改进。 这项工作是通过NIH资源赠款和NSF大挑战应用组赠款资助的。真实的时间建模将基于一个新的图形程序（vmd）的大屏幕立体投影和三维交互设备。 除了三位主要研究人员外，还有十六位实验研究人员将从计算资源中受益 在这个提案中寻求。 两名计算机科学教师与我们合作研究分子动力学算法和并行计算软件。 计算工作的部分资金来自卡弗慈善信托基金的赠款，该基金为操作集群的计算小组和实验实验室之间的项目提供了6名研究生和2个博士后职位。