Development Of Advanced Computer Hardware And Software

先进计算机硬件和软件的开发

• 批准号: 6690471
• 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/6690471
• 关键词: chemical models; computer program /software; computer simulation; computer system design /evaluation; computer system hardware; informatics; macromolecule; model design /development; molecular dynamics; parallel processing; quantum chemistry; structural biology

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 primary efforts include the ongoing 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, LobosV - Development of parallel QM/MM methods, Replica/Path - Development of bioinformatics tools for PC clusters - Development and support of parallel CHARMM - Development and parallelization of the EMAP method for electron microscopy applications. - Implementation and parallelization of SGMD for efficient conformational search. The LoBoS (Lots of Boxes on Shelves), LobosV 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 vendor's offerings. The early LoBoS systems demonstrated the effectiveness of this approach and were essential in the development of techniques and linux scripts. LoBoS V is a substantial improvement in that over 140 2GHz processors have been employed. The LoBoS Project has produced the most capable computational systems at the NIH for most applications involving computational chemistry tools (http://www.lobos.nh.gov/). 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 main effort in developing new bioinformatics tools for the PC cluster environment is the development of a new architecture for the integration of disparate biological databases and for the distribution of compute-intensive tasks. Clusters are uniquely suited to large database applications since each compute node has its own disk (maximizing IO) and its workload may be configured to be independent of other nodes (maximizing efficiency). This work was part of our efforts to support the NHLBI Bioinformatics Core Facility. As part of the development of the Replica/Path QM/MM method, we have created a novel way to parallelize these large scale quantum part of these calculations involving MPI clusters. A new EMAP module have been created in CHARMM for electron microscopy applications. This approach is used to determine structures of large complexes using a novel core-weighting fitting correlation method. An effort has been made to allow these applications to perform efficiently on the Lobos clusters. Similarly, the efficient implementation and parallelzation of SGMD for rapid conformational searching has allowed this method to gain wider applicability.

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。主要的努力包括正在进行的适合于大分子模拟的并行计算技术的开发，以及用于低成本高效率模拟的并行计算机集群和相关软件的开发。 目前的项目包括： - LoBoS：使用PC集群的高性能计算，LobosV - 并行QM/MM方法的开发，并行QM/MM方法的开发 - PC集群生物信息学工具的开发 - 并行CHARMM的开发与支持 - EMAP方法在电子显微镜应用中的发展和并行化。 - SGMD的实现和并行化以实现高效的构象搜索。 Lobos V超级计算机（Lobos V）是使用商用PC设计和建造的。与传统的超级计算机供应商的产品相比，它们在性价比方面提供了10倍以上的改进。早期的LoBoS系统证明了这种方法的有效性，并且在技术和Linux脚本的开发中至关重要。LoBoS V是一个实质性的改进，已经使用了超过140个2GHz处理器。LoBoS项目已经在NIH为涉及计算化学工具的大多数应用产生了最有能力的计算系统（http：//www.lobos.nh.gov/）。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PC集群环境下开发新的生物信息学工具的主要努力是开发一种新的体系结构，用于整合不同的生物数据库和分配计算密集型任务。集群特别适合大型数据库应用程序，因为每个计算节点都有自己的磁盘（最大化IO），并且其工作负载可以配置为独立于其他节点（最大化效率）。这项工作是我们努力支持NHLBI生物信息学核心设施的一部分。作为量子/路径QM/MM方法开发的一部分，我们已经创建了一种新的方法来并行化这些涉及MPI集群的计算的大规模量子部分。 一个新的EMAP模块已经创建在CHARMM电子显微镜的应用。这种方法是用来确定使用一种新的核心加权拟合相关方法的大型复杂的结构。已经做出了努力，使这些应用程序在Lobos集群上有效地执行。同样，SGMD的高效实现和并行化的快速构象搜索，使这种方法获得更广泛的适用性。