Acquisition of a High Performance Parallel Computing Cluster for the Departments of Biology, Chemistry, Physics, and Mathematics and Computer Science at Clark University

在David Hibbett博士(PI)的指导下，克拉克大学与四名联合首席调查员(co-PI)一起获得了一笔赠款，题为“为克拉克大学生物、化学、物理、数学和计算机科学系获得高性能并行计算集群”。该提议的项目包括为克拉克大学的自然科学项目开发一个共享的计算学院。该仪器包括一个Beowulf类型的集群，具有32个相互连接的“节点”(单独的计算机)以及相关的存储设备、硬件和软件。该系统将在两年内开发，在供资期间的头两年每年购买一个集群。拟议的系统是根据对当前可供PI和共同PI使用的计算能力和所需计算能力的分析而设计的。PI和共同PI都有活跃的研究项目(包括研究生和本科生)，需要高性能的并行计算集群。拟议的仪器将用于不同的研究项目，包括：1)基于DNA序列的真菌进化研究(Hibbett，生物系)；2)液-固相变化研究(co-Pi H.Gould，物理系)；3)物体之间几何关系的算法分析(co-Pi L.han，数学和计算机科学系)；以及4)蛋白质建模和分子动力学(co-Pis R.布鲁塞尔韦勒和霍建华，化学系)。这些研究项目涉及机器人学、生物多样性保护、医学和其他应用学科。除了研究，PI和共同PI都参与了计算科学的集中，这为克拉克大学不同科学学科的本科生提供了计算应用方面的研究背景。这项建议的PI和Co-PI将在一些满足计算科学专业要求的本科课程中使用建议的仪器，包括计算机模拟实验室、分子进化与系统学、量子化学、生物分子核磁共振等。最后，拟议的集群将用于为地区高中教师举办的关于并行计算及其应用的年度讲习班。共享计算设施的开发代表了克拉克大学科学部门间的一项重大倡议。通过汇集资源，拟议的项目将为研究开发关键资源，否则各部门将无法获得这些资源。除了促进研究，拟议的并行计算集群将成为专注于计算科学的基石，这将促进对本科生进行跨学科的科学培训。拟议的仪器还将在为当地高中教师举办的并行计算技术暑期讲习班上发挥核心作用。这些研讨会是克拉克大学正在进行的社区外展工作的一部分。

A grant has been awarded to Clark University under the direction of Dr. David Hibbett(PI) with four co-Principal Investigators (co-PIs), titled "Acquisition of a HighPerformance Parallel Computing Cluster for the Departments of Biology, Chemistry,Physics, and Mathematics and Computer Science of Clark University". The proposedproject involves the development of a shared computational faculty for the naturalscience programs of Clark University. The instrumentation includes a Beowulf-type clusters, with 32 interconnected "nodes" (individual computers) and associated storage devices, hardware and software. The system will be developed over two years, with one cluster purchased in each of the first two years of the funding period. The proposed system was designed on the basis of an analysis of current and required computing capacity available to the PI and co-PIs. The PI and co-PIs all have active research programs (including graduate and undergraduate students) that require a high performance parallel computing cluster. The proposed instrumentation will be used in diverse research projects, including: 1) Evolutionary studies in fungi based on DNA sequences (Hibbett, Biology Dept.); 2) Studies of liquid-solid phase changes (co-PI H. Gould, Physics Dept.); 3) Algorithmic analyses of geometric relationships between objects (co-PI L. Han, Mathematics and Computer Science Dept.); and 4) Protein modeling and molecular dynamics (co-PIs R. Bruschweiler and S. Huo, Chemistry Dept.). These research projects are relevant to robotics, conservation of biodiversity, medicine, and other applied disciplines. In addition to research, the PI and co-PIs all participate in the Concentration in Computational Science, which provides a research-oriented background in computational applications for Clark University undergraduates majoring in diverse scientific disciplines. The PI and Co-PIs of this proposal will use the proposed instrumentation in a number of undergraduate courses that satisfy the Concentration in Computational Science, including Computer Simulation Laboratory, Molecular Evolution and Systematics, Quantum Chemistry, Biomolecular NMR, and others. Finally, the proposed cluster will be used in annual workshops on parallel computing and its applications that will be offered for area high school teachers. The development of a shared computational facility represents a significant interdepartmental initiative in the sciences at Clark. By pooling resources, the proposed project will develop critical resources for research that would be otherwise inaccessible to the individual Departments. In addition to enabling research, the proposed parallel computing cluster will become the cornerstone of the Concentration in Computational Science, which promotes interdisciplinary training for undergraduates in the sciences. The proposed instrumentation will also play a central role in summer workshops in parallel computing technology for local high school teachers. These workshops represent part of Clark University's ongoing community outreach efforts.