PORTING AND TESTING THE DESMOND MOLECULAR DYNAMICS CODE

移植和测试 DEMOND 分子动力学代码

• 批准号: 8364288
• 负责人: JOEL R. STILES
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364288
• 关键词: Address; Biomedical Research; Code; Development; Funding; Grant; High Performance Computing; National Center for Research Resources; Performance; Principal Investigator; Research; Research Infrastructure; Resources; Source; Testing; United States National Institutes of Health; cost; improved; molecular dynamics

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.

该子项目是利用资源的众多研究子项目之一 由 NIH/NCRR 资助的中心拨款提供。子项目的主要支持 并且子项目的主要研究者可能是由其他来源提供的， 包括其他 NIH 来源。 子项目可能列出的总成本 代表子项目使用的中心基础设施的估计数量， NCRR 赠款不直接向子项目或子项目工作人员提供资金。 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。