Petascale Molecular Dynamics Data Processing System

描述（申请人提供）：我们建议获得一个集成的计算机系统，用于大数据存储，高性能计算和最先进的可视化，该系统连接到国家超级计算中心的当前和下一代万亿次到千万亿次计算机，以支持膜过程的大规模和长时间生物分子模拟，生物纳米技术设备，细胞力学，细胞能量转换，和基因转录。100 TB的模拟数据集将存储在一个容量为204 TB的磁盘阵列上，并通过多个10千兆位/秒的网络访问。将通过两个大型共享内存（每个256千兆字节）服务器和图形处理单元加速（NVIDIA Teslas具有4 teraFLOP/s单精度浮点运算性能）实现对存储数据的高性能分析，相当于每个处理器数百个核心在设想的应用程序上的真实的性能。通过NVIDIA Quadro图形加速器（具有4 GB内存、teraFLOP/s浮点运算性能和102 GB/s内存带宽），该系统将驱动四个单用户可视化前端和一个最先进的980万像素多用户图形投影系统。该系统将支持伊利诺伊大学厄巴纳-香槟分校的NIH研究人员正在进行的实验-计算合作项目，以解决原子细节，涉及DNA解旋酶，脂蛋白组装，核糖体中的蛋白质合成，肌肉力量产生和弹性，电压门控离子通道，膜转运和生物能量学的单分子过程，以及纳米孔中的DNA单碱基对检测。这些项目在国家超级计算中心的万亿-千万亿次计算机上进行模拟，生成10-100 TB的数据，这些数据需要在本地存储，分析和可视化。数据中心的技术进步导致数据量增加了1,000倍，但必须配备足够的本地数据分析设备。拟议的制度就是为了达到这一目的。主要研究者指导NIH的大分子建模和生物信息学资源，该资源将操作该系统，是开发所需生物分子建模和分析软件的领导者，并且是新系统所采用技术的专家用户，特别是图形处理单元加速。 公共卫生相关性： 拟议的计算显微镜系统将有助于设计针对癌症、肌肉疾病、心血管疾病的治疗方法，对抗耐药性，并发现新药，例如，新的抗生素DNA、脂蛋白、蛋白质合成、肌肉功能和神经活动的实验通过计算机模拟来解释，这些模拟提供了身体分子机器的一个又一个视图。这些观点揭示了开发新的药物治疗所需的化学细节。

DESCRIPTION (provided by applicant): We propose to acquire an integrated computer system for large data storage, high-performance computation, and state-of-the-art visualization that links to present and next generation terascale- to-petascale computers at the national supercomputing centers to support large-scale and long- time biomolecular simulations of membrane processes, bionanotechnological devices, cell mechanics, cellular energy transformation, and gene transcription. Hundred-terabyte simulation datasets will be stored on a disk array with a capacity of 204 terabytes and accessed by multiple 10-gigabit/s networks. High-performance analysis of the stored data will be enabled through two large shared memory (256 gigabytes each) servers and through graphics processing unit acceleration (NVIDIA Teslas with 4 teraFLOP/s single precision floating point arithmetic performance) equivalent to hundreds of cores per processor in real performance on envisioned applications. Through NVIDIA Quadro graphics accelerators with 4 gigabytes of memory, teraFLOP/s floating point performance, and 102 gigabyte/s memory bandwidth, the system will drive four single-user visualization front ends and a state-of-the-art 9.8 million pixel multi-user graphics projection sys- tem. The system will support ongoing experimental-computational collaborative projects among NIH investigators at the University of Illinois at Urbana-Champaign to resolve, in atomic detail, single molecule processes involving DNA helicases, lipoprotein assembly, protein synthesis in the ribosome, muscle force generation and elasticity, voltage-gated ion channels, membrane trans- port, and bioenergetics, as well as DNA single base pair detection in nanopores. The projects carry out simulations on terascale-petascale computers at national supercomputing centers that generate 10-100 terabytes of data which need to be stored, analyzed, and visualized locally. Technological advances at the centers leading to 1,000-fold data size increases must be matched by adequate local data analysis equipment. The proposed system serves this purpose. The Principal Investigator directs the NIH Resource for Macromolecular Modeling and Bioinformatics that will operate the system, is a leader in developing the needed biomolecular modeling and analysis software, and is an expert user of the technologies employed by the new system, in particular graphics processing unit acceleration. PUBLIC HEALTH RELEVANCE: The proposed computational microscopy system will assist in devising treatments against cancers, muscle disorders, cardiovascular disorders, in fighting drug resistance, and in discovering new drugs, e.g., new antibiotics. Experiments on DNA, lipoproteins, protein synthesis, muscle function, and nerve activity are interpreted through computer simulations that provide a tom by a tom views of the body's molecular machines. These views reveal the chemical detail needed to develop new pharmacological treatments.