Development of Advanced Computer Hardware and Software

先进计算机硬件和软件的开发

• 批准号: 6109192
• 负责人: Bernard R Brooks
• 金额: --
• 依托单位: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6109192
• 关键词: chemical models; computer simulation; computer system design /evaluation; macromolecule; parallel processing

With the increased availability of parallel computer resources amenable to large scale scientific computing, it is essential to optimize the use of these resources. The efforts include the development of parallel computing techniques suitable for macromolecular simulation and the development of a parallel computer cluster and related software for high-efficiency simulations at low cost. - The LoBoS project (Lots of Boxes on Shelves) - Massively Parallel Computing using Off-The-Shelf Personal Computers LoBoS I (Lots of Boxes on Shelves) has been completed using commodity PCs to provide a greater than 10-fold improvement in price/performance when compared with the primary supercomputer vendor's offerings. This approach has been very successful with 128 processor LoBoS I and LoBoS II is now being developed with faster computers and gigabit ethernet switches to provide rapid communication with an improved network topology and communications paths. Cluster management and queuing software continue to be refined and have been distributed to 5 sites. The LoBoS project has produced the fastest computational system at the NIH. It opens up a new realm of high performance computing which continues to drive the cost down while improving reliability. This system is created using commodity priced Intel based PCs. The system has been designed to survive all "single point of failure"problems. Development of methods and software to make productive use of general parallel machines for use in macromolecular simulations is still an ongoing activity. The global communication approach, has been successful in providing an efficient full feature version of CHARMM. This parallel version of CHARMM has been extended LoBoS to run on almost any MIMD parallel computer platform. Our current development effort involves a scalable algorithm that promises to greatly reduce the communication cost for very large MPP machines or for large workstation clusters. Current projects include: - Development of parallel QM/MM methods - Development and support of parallel CHARMM - Development of a 10 teraflop GRAPE computer (at RIKEN) for macromolecular simulation - Development and evaluation of scalable parallel algorithms for molecular dynamics - Development of an efficient communication scheme for 3 dimensional FFT calculations - Development of Latency-tolerant algorithms for Parallel Computing LoBoS' off-the-shelf components include Fast Ethernet network components which has a high latency (~100ms). Consequently, most algorithms have a practical limit of 8 to 32 nodes before efficiency becomes unacceptably low. This work utilizes the Fire Brigade method for distributing data as it becomes valid, thereby avoiding most of the latency issues.

随着并行计算机可用性的提高 适合大规模科学计算的资源，它是 对优化这些资源的使用至关重要。这些努力包括 适合于计算机的并行计算技术的发展 大分子模拟与并行软件的开发 高效的计算机集群及相关软件 以低成本进行模拟。-Lobos项目(上有很多盒子 货架)-使用现成的大规模并行计算 个人电脑Lobos I(货架上有很多盒子)已经被 使用商用PC完成，可提供超过10倍的 性价比与 主要超级计算机供应商的产品。这一方法一直是 使用128处理器的Lobos I非常成功，而Lobos II现在 正在开发速度更快的计算机和千兆以太网 交换机可提供改进的快速通信 网络拓扑和通信路径。集群管理 和排队软件继续改进，并已 分布在5个站点。Lobos项目产生了最快的 美国国立卫生研究院的计算机系统。它开辟了高等教育的新境界 继续压低成本的性能计算 同时提高了可靠性。这个系统是使用商品创建的 定价基于英特尔的PC。该系统被设计成能够经受住所有 “单点故障”问题。方法和方法的发展 高效利用通用并行机的软件 在大分子模拟中的使用仍然是一项正在进行的活动。这个 全球通信方法，已经成功地提供了 一个高效的全功能版本的CHARMM。此平行版本 已将LOBOS扩展为在几乎所有 MIMD并行计算机平台。我们目前的开发工作 涉及一种可伸缩的算法，该算法承诺大大减少 超大型MPP机器或大型MPP机器的通信成本 工作站集群。目前的项目包括：-开发 并行QM/MM方法--并行的发展和支持 CHARMM--10万亿次浮点GRAPE计算机的开发(在 RIKEN)用于大分子模拟-开发和 分子动力学可扩展并行算法的评价-- 为3开发一种高效的通信方案 量纲FFT计算--延迟容限的发展 并行计算LOBOS现成组件的算法 包括具有高延迟快速以太网网络组件 (~100毫秒)。因此，大多数算法的实际限制是8 到32个节点，然后效率变得低到无法接受的程度。这部作品 使用消防队方法在数据变为 有效，从而避免了大多数延迟问题。