PORTING AND TESTING THE DESMOND MOLECULAR DYNAMICS CODE

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 使用我们当前的启动分配，我们已经完成了从Desmond 2.2到Cray XT3和Altix 4700(Bigben And Pople)的初始端口，并将这些端口提供给PSC的用户。我们现在请求续订此启动分配，以继续努力在这些平台上开发Desmond。Desmond在XT3上的初始实施使用本机MPI。我们现在想研究在低级门户网络接口上创建更高效的Desmond实现的可能性，就像在Infiniband网络上所做的那样。此外，随着PSC的用户开始使用Desmond，我们预计将会有一些尚未发现的性能问题需要解决。此外，Desmond正在积极开发中，可能会包括我们希望向PSC资源用户提供的改进或附加功能。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. With our current Startup allocation we have completed the initial port of Desmond 2.2 to the Cray XT3 and Altix 4700 (Bigben and Pople) and made these available to users at the PSC. We now request a renewal of this Startup allocation to continue our efforts to develop Desmond on these platforms. The initial implementation of Desmond on the XT3 uses native MPI. We would now like to look at the possibility of creating an even more efficient implementation of Desmond on the low-level Portals network interface, as had been done with Infiniband networks. In addition, as users at PSC start using Desmond we anticipate that there will be some as yet undiscovered performance issues that will have to be addressed. Also, Desmond is under active development and will likely include improved or additional capabilities that we will want to provide to users of PSC resources.