PORTING AND TESTING THE DESMOND MOLECULAR DYNAMICS CODE

该子项目是利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 通过我们目前的启动分配，我们已经完成了Desmond 2.2到Cray XT 3和Altix 4700（Bigben和Pople）的初始端口，并在PSC向用户提供这些端口。我们现在要求更新此启动分配，以继续我们在这些平台上开发Desmond的努力。Desmond在XT 3上的初始实现使用原生MPI。我们现在想看看在底层门户网络接口上创建一个更有效的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提供给PSC资源用户的改进或额外功能。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.