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， 资源适合大规模科学计算，它是 这对优化这些资源的使用至关重要。这些努力包括 并行计算技术的发展适用于 大分子模拟和并行开发 计算机集群和相关软件， 低成本模拟。- LoBoS项目（大量的盒子上 Shelves）-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）已被 使用商用PC完成， 与传统的 超级计算机供应商的产品。这种方法已经 128处理器LoBoS I和LoBoS II非常成功， 随着更快的计算机和千兆以太网的发展， 交换机提供快速通信， 网络拓扑和通信路径。集群管理 和排队软件不断完善， 分布在5个站点。LoBoS项目已经产生了最快的 计算机系统在NIH。它开辟了一个新的境界， 不断降低成本的高性能计算 同时提高可靠性。该系统是使用商品 基于Intel的PC该系统的设计是为了生存的所有 "单点故障"问题。制定方法和 软件，使生产性地使用一般的并行机， 在大分子模拟中的使用仍然是一项正在进行的活动。的 全球通信方法，已成功地提供 CHARMM的高效全功能版本。这个平行版本 CHARMM已经扩展了LoBoS，几乎可以在任何 MIMD并行计算机平台。我们目前的发展努力 涉及一个可扩展的算法，承诺大大减少 对于非常大的MPP机器或大型 工作站群集。目前的项目包括： 并行QM/MM方法.并行的开发和支持 CHARMM-10万亿次GRAPE计算机的开发（在 RIKEN）用于大分子模拟-开发和 分子动力学的可扩展并行算法的评价- 一种高效的3. 维FFT计算-延迟容忍的开发 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 （~100ms）。因此，大多数算法的实际极限为8 到32个节点之前，效率变得不可接受的低。这项工作 利用消防队的方法来分发数据，因为它成为 有效，从而避免了大部分延迟问题。