PORTING AND TESTING THE DESMOND MOLECULAR DYNAMICS CODE

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 通过当前的启动分配，我们已经完成了 Desmond 2.2 到 Cray XT3 和 Altix 4700（Bigben 和 Pople）的初始移植，并将其提供给 PSC 的用户。我们现在请求更新此启动分配，以继续努力在这些平台上开发 Desmond。 Desmond 在 XT3 上的初始实现使用本机 MPI。我们现在想看看是否有可能在低级 Portals 网络接口上创建更高效​​的 Desmond 实现，就像 Infiniband 网络所做的那样。此外，随着 PSC 的用户开始使用 Desmond，我们预计将存在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. 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.