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Parallel Computer with High Memory Nodes

高内存节点并行计算机

基本信息

批准号：
8447324
负责人：
David W Piston
金额：
$ 59.75万
依托单位：
VANDERBILT UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-07-11 至 2014-07-10
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): We request funds to purchase 180 high-memory parallel computer nodes to support data and computationally intensive, NIH-funded, biomedical research at Vanderbilt University and Medical Center. The proposed system will facilitate many applications that require high memory/processor supercomputer performance at a small fraction of the cost. This system will be built aside our successful 4000-processor parallel computer known as the Advanced Computing Center for Research and Education (ACCRE) at Vanderbilt, which supports high-performance computing for research from elementary particle investigations using the Large Hadron Collider to model system genetics to human behavioral studies. Despite our successes with the existing cluster, many state-of-the-art biomedical computation projects have become memory hogs, and thus caused severe inefficiencies in our current system. These projects include macromolecular structure prediction, next-generation sequencing, multi-dimensional imaging, and proteomic identification. ACCRE users have access to the instrument and training through our established infrastructure. ACCRE is a grass-roots organization that was initially created by faculty from throughout the institution and later awarded the strong institutional support it enjoys today. It was initially established through a Major Research instrumentation Grant from NIH in 2004 along with Departments of Defense and Energy grants to the School of Engineering and Department of Physics. ACCRE was upgraded through another NIH Shared Instrumentation Grant awarded in 2009. ACCRE is managed by three co-directors, one each from the College of Arts and Science, School of Engineering, and School of Medicine (of which Dr. Piston is the co- director). In keeping with the tradition of bottom-up ownership of ACCRE, policy and procedures are set by the co-directors upon recommendations of the Faculty Advisory Board, which consists of 10 active PI users. The proposed parallel computer will be used directly by more than 20 NIH-funded researcher groups and its impact will reach many more investigators through outreach efforts of centralized facilities such as the Center for Structural Biology, the Center for Human Genetics Research, The Small Animal and Cell Imaging Resources, and the Proteomics Core Laboratory. In this manner, the equipment will support more than 100 NIH grants. The major users of the system have primary appointments in six different departments within the Vanderbilt University School of Medicine, College of Arts and Science, and School of Engineering. Research programs with unmet demand for high memory node computation are concentrated in structural biology, human genetics, imaging, and proteomics. These new high memory nodes will make it possible to carry out data and computationally intensive biomedical investigations otherwise not feasible thus significantly increasing the rate of scientific discovery in a variety of biomedical disciplins.

描述（由申请人提供）：我们请求资金购买180个高内存并行计算机节点，以支持范德比尔特大学和医学中心的数据和计算密集型、NIH资助的生物医学研究。所提出的系统将促进许多应用程序，需要高存储器/处理器的超级计算机性能的一小部分的成本。这个系统将建立在我们成功的4000处理器并行计算机称为高级计算中心的研究和教育（ACCRE）在范德比尔特，它支持高性能计算的研究，从基本粒子调查使用大型强子对撞机模型系统遗传学人类行为研究。尽管我们在现有的集群上取得了成功，但许多最先进的生物医学计算项目已经成为内存占用者，从而导致我们当前系统的效率严重低下。这些项目包括大分子结构预测、下一代测序、多维成像和蛋白质组学鉴定。 ACCRE用户可以通过我们的基础设施访问仪器和培训。ACCRE是一个基层组织，最初由整个机构的教师创建，后来获得了今天所享有的强大的机构支持。它最初是通过美国国立卫生研究院在2004年的主要研究仪器赠款沿着与国防部和能源部赠款工程学院和物理系。ACCRE通过2009年授予的另一项NIH共享仪器赠款进行了升级。ACCRE由三位联合主任管理，分别来自文理学院、工程学院和医学院（其中活塞博士是联合主任）。与ACCRE自下而上的所有权的传统保持一致，政策和程序由联合主任根据学院咨询委员会的建议制定，该委员会由10名活跃的PI用户组成。拟议中的并行计算机将由20多个NIH资助的研究小组直接使用，其影响将通过结构生物学中心、人类遗传学研究中心、小动物和细胞成像资源中心和蛋白质组学核心实验室等集中设施的外展工作而影响到更多的研究人员。通过这种方式，该设备将支持100多个NIH赠款。该系统的主要用户在范德比尔特大学医学院、艺术与科学学院和工程学院的六个不同部门中有主要的任命。对高内存节点计算需求未得到满足的研究项目集中在结构生物学、人类遗传学、成像和蛋白质组学。这些新的高内存节点将使进行数据和计算密集型生物医学调查成为可能，否则不可行，从而显着提高各种生物医学学科的科学发现率。