Administrative and Computational Core Facility

管理和计算核心设施

• 批准号: 7466197
• 负责人: Jere P Segrest
• 金额: $ 15.05万
• 依托单位: UNIVERSITY OF ALABAMA AT BIRMINGHAM
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-05-01 至 2013-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7466197
• 关键词: Advisory Committees; Atherosclerosis; Bite; Computers; Core Facility; Engineering; Evolution; Expenditure; Extramural Activities; Faculty; Fostering; Genes; High Performance Computing; Home environment; Individual; Information Sciences; Linux; Mathematics; Memory; Modeling; Performance; Price; Program Research Project Grants; Publishing; Quality Control; Rate; Research; Research Personnel; Resources; Role; Schedule; Schools; Scientist; Services; Site Visit; Solutions; Speed; System; Time; Travel; Update; Work; computing resources; design; particle; programs; structural biology; supercomputer

A.ADMINISTRATION. The Program Project Grant Director, Dr. Segrest, is Director of the Atherosclerosis Research Unit (ARU), the administrative home for the program project. He also is Director of the Center for Computational and Structural Biology at UAB. He will be responsible for planning of the overall direction of the program and for quality control. One of the major roles of the Director will be to foster interactions and to stimulate new ideas and directions within and between the various projects and core units. Systems management support and programming support for the Program Project will be provided by Martin Jones, MS. Mr. Jones manages the computing section of the ARU and assists investigators with programming solutions. He also provides assistance in troubleshooting, pricing, and computer replacement/upgrading. He is also currently working on two research problems: i) He is updating the "Wheel Programs" suite (consisting of the programs Locate, Wheel, Helnet, and Combo) to use a more portable and usable interface. He is also working to make these programs more readily available. (See http://www.aru.uab.edu/ resources.html) ii) He is working with Dr. Gilbert Weinstein of the Department of Mathematics at UAB to computationally model the dynamic physical and differential geometric evolution of HDL-like disc particles. Most of the clerical and desktop publishing services, correspondence, etc. will be provided by LaDonna Bangham. She will prepare and submit purchase orders, track expenditures, and make the travel arrangements for the program faculty. She provides support for faculty and staff involved in all aspects of the PPG. Ms. Bangham will be responsible for coordination of the travel arrangements for the PPG External advisory Committee and external speakers for the ARU Scientific Seminars. An ARU Internal Advisory Committee, independent of the program project investigators, provides periodic scientific and administrative advice to the Director of the program project/ARU. The PPG Internal Advisory Committee will meet monthly to provide information and advice to the Director. The PPG External Advisory Committee will consist of four extramural scientists to be appointed to overlapping three year terms who will perform a site visit yearly to review individual components of the program project for the Director. B.COMPUTATION Shared high performance computing facility used by this PPG. The primary computational resource for Project 1 of this PPG is a single rack UAB Blue Gene. The UAB Blue Gene, an IBM Blue Gene/L, is a uniquely designed massively parallel supercomputer. A single Blue Gene/ L rack has 1024 nodes, each node having two processors and 512MB of main memory. The 2048 processors in the Blue Gene/L rack are tightly integrated in one form factor using five proprietary high-speed interconnection networks, producing a peak performance of 5.6 Teraflops. There are 13 Terabytes of disk storage available to this cluster. The Segrest group is currently scheduled for 50% minimum usage of the UAB Blue Gene, with on-demand utilization of 100% of the 2048 processors of the UAB Blue Gene. Secondary Computing resources are provided by three commodity clusters. Coosa: A DELL Xeon 64-bit Linux HPC Cluster that consists of a 128-node DELL PE1425 computer that has dual Xeon 3.6GHz processors with either 2GB or 6GB of memory per node. There are 4 Terabytes of disk storage available to this cluster. This cluster is rated at more than 1 Teraflops computing capacity Cheaha: A Verari Opteron 64-bit Linux HPC Cluster that consists of a 64-node dual AMD Opteron 242 computer with 2GB of memory each node. Both Coosa and Cheaha clusters use Gigabit Ethernet inter-node network connections. Olympus: A 128-node (256- processor), 1.4Teraflop-rated grid node that is similar to Coosa The Coosa and Cheaha clusters, as well as the DAB Blue Gene, are supported by Dr. Bharat Soni's group in the School of Engineering. Olympus support is provided Dr. Tony Skjellum's department - Computer and Information Sciences. The Segrest research group is flexibly scheduled for 264 (64-bit) cpu from these clusters at any one time.

A.ADMINISTRATION.该计划项目赠款主任，博士Segrest，是Atherecommunications的主任 研究单位（ARU），该计划项目的行政家园。他也是该中心的主任， 计算和结构生物学在UAB。他将负责规划 程序和质量控制。主任的主要作用之一是促进互动， 在各个项目和核心单位内部和之间提出新的想法和方向。 Martin将为该计划项目提供系统管理支持和编程支持 琼斯先生管理ARU的计算部分，并协助调查人员进行编程 解决方案他还提供故障排除、定价和计算机更换/升级方面的帮助。 他目前还在研究两个问题：i）他正在更新“车轮程序”套件 （由Locate、Wheel、Helnet和Combo程序组成），以使用更便携和可用的界面。 他也在努力使这些项目更容易获得。(See http://www.aru.uab.edu/ resources.html）ii）他正在与UAB数学系的吉尔伯特温斯坦博士合作， 计算模拟HDL样盘颗粒的动态物理和微分几何演化。 大多数文书和桌面出版服务、通信等将由LaDonna提供 班汉她将准备和提交采购订单，跟踪支出，并作出旅行安排 for the program程序faculty教师.她为参与PPG各个方面的教职员工提供支持。 女士Bangham将负责协调PPG外部顾问的旅行安排 委员会和ARU科学研讨会的外部发言人。 ARU内部咨询委员会独立于项目调查人员，定期提供 科学和行政建议的项目/ARU主任。PPG内部咨询 委员会将每月举行会议，向主任提供资料和意见。 PPG外部咨询委员会将由四名校外科学家组成，他们将被任命为重叠的 为期三年，每年进行一次现场访问，以审查该计划的各个组成部分 导演的项目。 B.COMPUTATION 共享高性能计算 这是PPG使用的设备。 主要计算资源 对于本PPG的项目1， 装上UAB蓝色基因。UAB蓝色 IBM Blue Gene/L是一款 独特设计的大规模并行 超级计算机一个蓝色基因/ L机架有1024个节点，每个节点 具有两个处理器和512 MB 主内存。2048处理器 在蓝色基因/L机架是 紧密集成在一个外形中 使用五个专有的高速 互连网络，生成 5.6 Teraflops的峰值性能。 有13 TB的磁盘存储空间 可用于此群集。的 Segrest集团目前计划使用50%的UAB蓝色基因，按需利用 UAB蓝色基因2048个处理器的100%。 次级计算资源由三个商品集群提供。 Coosa：DELL Xeon 64位Linux HPC群集，由128节点DELL PE 1425计算机组成， 双至强3.6 GHz处理器，每个节点配备2 GB或6 GB内存。有4 TB的磁盘 此群集可用的存储。该集群的计算能力超过1 Teraflops Cheaha：Verari Opteron 64位Linux HPC群集，由64节点双AMD Opteron 242计算机组成 每个节点有2GB内存。 Coosa和Cheaha集群都使用千兆以太网节点间网络连接。 Olympus：一个128节点（256处理器）、1.4Teraflop等级的网格节点，类似于Coosa Coosa和Cheaha集群以及DAB Blue基因得到了Bharat Soni博士小组的支持， 工程学院奥林巴斯支持提供博士托尼Skjellum的部门-计算机和 信息科学。Segrest研究组从这些集群中灵活调度264（64位）CPU 在任何一个时间。