Development Of Advanced Computer Hardware And Software

随着可用于大规模科学计算的并行计算机资源的增加，优化这些资源的使用是至关重要的。主要工作包括正在开发适合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，以便以低成本进行高效率的模拟。 目前的项目包括： -LOBOS：使用PC集群的高性能计算，LobosV -开发并行QM/MM方法、副本/路径 -为PC集群开发生物信息学工具 -开发和支持并行CHARMM -电子显微镜应用的EMAP方法的开发和并行化。 -SGMD的实现和并行化，以实现高效的构象搜索。 LOBOS(货架上有很多盒子)，LobosV超级计算机是用商用PC设计和建造的。与传统的超级计算机供应商的产品相比，它们在性价比上提高了10倍以上。早期的Lobos系统证明了这种方法的有效性，并且在技术和Linux脚本的开发中是必不可少的。Lobos V是一个实质性的改进，因为已经使用了140多个2 GHz处理器。LOBOS项目已经在美国国立卫生研究院为大多数涉及计算化学工具(http://www.lobos.nh.gov/).)的应用产生了能力最强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继续降低成本，同时提高可靠性。为个人计算机集群环境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。群集非常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)。这项工作是我们支持NHLBI生物信息学核心设施的努力的一部分。作为复制/路径QM/MM方法发展的一部分，我们创造了一种新的方法来并行化这些涉及MPI集群的大规模量子计算部分。 在CHARMM中创建了一个新的EMAP模块，用于电子显微镜应用。用一种新的核加权拟合相关方法确定了大分子络合物的结构。我们已经做出努力，使这些应用程序能够在Lobos集群上高效运行。同样，SGMD的高效实现和快速构象搜索的并行化使该方法获得了更广泛的适用性。

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.