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）：我们要求资金购买180个高内存平行的计算机节点，以支持范德比尔特大学和医学中心的数据和计算密集，NIH资助的生物医学研究。所提出的系统将促进许多需要以一小部分成本的应用程序的应用程序/处理器超级计算机性能。该系统将被构建为我们成功的4000个处理器并联计算机，称为Vanderbilt的高级研究和教育计算中心，该计算中心支持高性能计算，用于从基本粒子研究中使用大型强子碰撞器对人类行为研究模拟系统遗传学的基础粒子研究。尽管我们在现有集群中取得了成功，但许多最新的生物医学计算项目已成为记忆猪，因此在我们当前的系统中导致严重的效率低下。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识别。 Accre用户可以通过我们已建立的基础设施访问该工具和培训。 Accre是一个基层组织，最初是由整个机构中的教师创建的，后来授予了今天所享有的强大机构支持。它最初是通过NIH于2004年与工程学院和物理系的国防和能源赠款部门一起建立的。 Accre通过了2009年授予的另一项NIH共享工具赠款进行了升级。CACCRE由三个联合导演管理，一名来自艺术与科学学院，工程学院和医学院（Piston博士是合作社）。为了符合自下而上的承认所有权的传统，政策和程序是由教师顾问委员会的建议设定的，由10位活跃的PI用户组成。拟议的平行计算机将直接由20多个由NIH资助的研究人员使用，其影响将通过集中式设施的外展工作（例如结构生物学中心，人类遗传学研究中心，小动物和细胞成像资源，小动物和细胞成像中心）以及蛋白质组学核心实验室来吸引更多研究人员。通过这种方式，设备将为100多个NIH赠款提供支持。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任命。对高记忆节点计算的需求未满足的研究计划集中在结构生物学，人类遗传学，成像和蛋白质组学。这些新的高记忆节点将使进行数据和计算密集型生物医学研究否则不可行，从而显着提高了各种生物医学科段的科学发现率。