DEVELOPMENT OF ADVANCED COMPUTER HARDWARE AND SOFTWARE

随着适合大规模科学计算的并行计算机资源的可用性的增加，优化这些资源的使用是至关重要的。这些努力包括开发适用于大分子模拟的并行计算技术，以及开发并行计算机集群和相关软件，以低成本进行高效率模拟。目前的项目包括：- LoBoS：使用PC集群的高性能计算-并行QM/MM方法的开发-分子动力学并行算法的开发和评估-并行CHARMM的开发和支持-并行计算延迟容忍算法的开发LoBoS（货架上的许多盒子）和LoBoSII超级计算机已经使用商品PC设计和建造。与传统的超级计算机供应商产品相比，它们在性价比方面提供了10倍以上的改进。LoBoS最初采用的方法在某些应用中非常成功，每个节点有128个处理器和多个快速以太网连接。LoBoSII在可扩展性方面有了实质性的改进，因为使用千兆以太网的带宽提高了5倍，并且Linux内核中的TCP堆栈定制将延迟减少了一半。LoBoSII有200个Pentium II/III 450 MHz处理器，1.5 TB的磁盘空间和一个完全交换的千兆网络。LoBoS项目继续通过网络交换机、接口和高速存储设备的beta测试程序开发协作安排。集群管理和排队软件支持功能独特的实验室规模的集群已经开发和分发到几个学术网站。LoBoS项目已经为涉及计算化学工具的大多数应用程序在NIH产生了最强大的计算系统。它开辟了高性能计算的新领域，通过使用松散耦合的集群，在提高可靠性的同时继续降低成本。在集群上高效执行的应用程序的类别已经被描述，并且正在审查在硬件中支持延迟和带宽容忍算法的努力。- 并行，计算，高性能，CHARMM，LoBoS，分子动力学，模拟

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. Current projects include: - LoBoS: High performance computing using PC clusters - Development of parallel QM/MM methods - Development and evaluation of parallel algorithms for molecular dynamics - Development and support of parallel CHARMM - Development of Latency-tolerant algorithms for Parallel Computing The LoBoS (Lots of Boxes on Shelves) and LoBoSII supercomputers have been designed and constructed using commodity PCs. They provide a greater than 10-fold improvement in price/performance when compared with the traditional supercomputer vendors offerings. The initial approach taken for LoBoS had been very successful for certain applications with 128 processors and multiple fast Ethernet connections per node. LoBoSII is a substantial improvement in scalability due to a 5-fold improvement in bandwidth using Gigabit Ethernet and customizations of the TCP stack in the Linux kernel have reduced latency by half. LoBoSII has 200 PentiumII/III 450MHz processors, 1.5 Terabytes of disk space and a fully switched Gigabit network. The LoBoS project continues to develop collaborative arrangements through beta- test programs for network switches, interfaces and high-speed storage devices. Cluster management and queuing software supporting features unique to a laboratory-sized cluster has been developed and distributed to several academic sites. The LoBoS Project has produced the most capable computational system at the NIH for most applications involving computational chemistry tools. It has opened up a new realm of high performance computing which continues to drive the cost down while improving reliability through the use of loosely-coupled clusters. The classes of applications that execute efficiently on clusters have been characterized and efforts to support latency-and bandwidth-tolerant algorithms in hardware are under review. - parallel, computing, high performance, CHARMM, LoBoS, molecular dynamics, simulation