MRI: Acquisition of Linux Cluster and Workstation Network for Biophysics, Mathematics, and Computer Science Research

MRI：收购 Linux 集群和工作站网络用于生物物理、数学和计算机科学研究

• 批准号: 0116202
• 负责人: Ralph Meeker
• 金额: $ 7.13万
• 依托单位: Benedictine University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-09-01 至 2004-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0116202&HistoricalAwards=false
• 关键词: MRI; Acquisition; Linux; Cluster; Workstation

A grant has been awarded to Dr. Ralph Meeker at Benedictine University to acquire a multi-processor Linux computer system and a network of computer workstations with stereo viewing capability for research in biophysics, mathematics, and computer science. Faculty and undergraduate students conducting biophysics research will perform molecular modeling simulations of protein binding and use the stereo workstations to analyze and visualize the results. Faculty and undergraduate students conducting mathematics research will use computer algebra software to study group cohomology and to make extensions to modular representation theory. The research in biophyiscs and algebra will provide data for Dr. Meeker and his students to measure the performance of the multi-processor computer system for both molecular modeling and computer-based algebra software as a function of the configuration of the computer system.Large-scale scientific computations, traditionally performed at reasonable speeds on specialized, expensive supercomputers or very slowly on engineering workstations, are being performed more and more on inexpensive Linux-based clusters of computers using a Linux variant to provide the cluster support. Rapid improvement in the performance of Pentium central processors, coupled with the stability and performance of the Linux operating system, has made it possible to assemble a networked cluster of personal computers at a fraction of the cost of a supercomputer. The equipment to be acquired with this grant includes a Linux multiprocessor computer system configured as an interconnected cluster with 16 separate computers. When assembling a Linux-based computer cluster for use in high-performance computing, one must take into account not only the raw computing power of the individual central processing units, but also system requirements in terms of memory and the network interconnection between the computers. This research project will measure the performance of the Linux-based cluster for both molecular modeling and computer-based algebra software as a function of the individual computers' memory configuration, the total number of clustered computers available for processing, the number of processors per computer in single-processor and dual-processor configurations, the number of simultaneous users, and what price/performance improvements are obtained from using dual-processor motherboards instead of single-processor motherboards. A network of computer workstations will provide researchers access to the cluster computer system. Three of the workstations will incorporate stereo viewing screens for visualization of three-dimensional molecular models of biological interest. Here is a brief description of the typical steps involved in this kind of modeling project. Identify a pair of molecules that are known to interact as a key step in a physiological process. If the molecules are large, and typically they are, the three-dimensional structure must be known or have a reasonable homology model from which to generate spatial coordinates and sequence regions of the molecules that interact. Results of x-ray studies conducted by other researchers can be used to determine this information. The molecules are then modeled by bringing them together, calculating the minimum of their molecular energy, and running through molecular dynamic calculations to identify possible binding orientations and their associated energies. For the mathematics research, the first stage of this research program will be analysis of data collected on the cohomology rings of the groups of order 64. The data analysis will yield insight on which groups of order 128 should provide "interesting" cohomology rings to compute. Results of this research will contribute to three areas of science: biophysics, mathematics, and computer science. The biophysics research is particularly useful in determining the binding of a fibrinogen chain to the integrin receptor of platelet cells, an essential step in blood clotting. The mathematics computational work should help distinguish irreducible abstract algebraic modules from other more complex modules by compiling a library of these basic algebraic building blocks. The computer science research will characterize the performance of a low-cost, high-performance computer system in computationally intensive applications to biophysics and mathematics. The involvement of the undergraduate students in these projects over the years have resulted in a number of undergraduate research papers and several who are now pursuing advanced degrees in science.

本笃会大学的 Ralph Meeker 博士获得了一笔赠款，用于购买多处理器 Linux 计算机系统和具有立体观看功能的计算机工作站网络，用于生物物理学、数学和计算机科学的研究。进行生物物理学研究的教师和本科生将进行蛋白质结合的分子建模模拟，并使用立体工作站来分析和可视化结果。进行数学研究的教师和本科生将使用计算机代数软件来研究群上同调并对模表示理论进行扩展。生物物理学和代数方面的研究将为米克博士和他的学生提供数据，以测量多处理器计算机系统在分子建模和基于计算机的代数软件方面的性能，作为计算机系统配置的函数。大规模科学计算传统上是在专门的、昂贵的超级计算机上以合理的速度执行，或者在工程工作站上非常缓慢地执行，现在越来越多地在廉价的基于 Linux 的计算机集群上执行，使用 Linux 变体来提供集群支持。奔腾中央处理器性能的快速提高，加上Linux操作系统的稳定性和性能，使得以超级计算机成本的一小部分组装个人计算机网络集群成为可能。通过这笔赠款获得的设备包括一个 Linux 多处理器计算机系统，该系统配置为由 16 台独立计算机组成的互连集群。在组装用于高性能计算的基于Linux的计算机集群时，不仅必须考虑各个中央处理单元的原始计算能力，还必须考虑内存和计算机之间的网络互连方面的系统要求。该研究项目将测量基于 Linux 的分子建模和基于计算机的代数软件集群的性能，作为单个计算机的内存配置、可用于处理的集群计算机总数、每台计算机的处理器数量的函数在单处理器和双处理器配置中，同时用户的数量，以及使用双处理器主板而不是单处理器主板可以获得哪些性价比改进。计算机工作站网络将为研究人员提供对集群计算机系统的访问。其中三个工作站将配备立体观看屏幕，用于可视化具有生物学意义的三维分子模型。以下是此类建模项目所涉及的典型步骤的简要描述。 识别一对已知相互作用的分子，这是生理过程中的关键步骤。如果分子很大（通常情况下是这样），则必须知道三维结构或具有合理的同源模型，从中生成相互作用的分子的空间坐标和序列区域。其他研究人员进行的 X 射线研究的结果可用于确定此信息。然后通过将分子放在一起、计算其分子能量的最小值并通过分子动力学计算来识别可能的结合方向及其相关能量来对分子进行建模。对于数学研究，该研究计划的第一阶段将分析在 64 阶群的上同调环上收集的数据。数据分析将深入了解哪些 128 阶群应提供“有趣的”上同调环来计算。这项研究的结果将有助于三个科学领域：生物物理学、数学和计算机科学。生物物理学研究对于确定纤维蛋白原链与血小板细胞整合素受体的结合特别有用，这是血液凝固的重要步骤。数学计算工作应该通过编译这些基本代数构建块的库来帮助区分不可约抽象代数模块与其他更复杂的模块。计算机科学研究将表征低成本、高性能计算机系统在生物物理学和数学计算密集型应用中的性能。多年来，本科生对这些项目的参与已经产生了许多本科生研究论文，还有一些学生现在正在攻读科学高级学位。