PORTING AND BENCHMARKING OF THE AMBER MOLECULAR DYNAMICS SOFTWARE ON TERAGRID R

这个子项目是许多研究子项目中的一个 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来源获得了主要资金， 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。 我申请DAC奖作为teragrid漫游（30，000 SU），以帮助我在各种NSF资源上进一步开发AMBER分子动力学软件。这包括在所有NSF资源（包括Ranger）上测试和验证AMBER 10（2008年3月发布）。我计划继续开发并行经典分子动力学，同时也扩展AMBER 10中QM/MM实现的性能和可扩展性。在尽可能多的平台上进行测试对于确保软件的顺利发布至关重要。基准将通过AMBER网站向社区提供。此外，通过移植实现的任何性能改进都将被纳入发布代码中，以使整个AMBER社区从中受益。除上述目的外，DAC请求的目的还在于在各种机器上对AMBER 10代码进行初始测试和基准测试，以支持将于1月份提交的大型LRAC请求，该请求将于3月08日提交LRAC。

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. I am requesting a DAC award as teragrid roaming (30,000 SUs) in order to assist me in the further development of the AMBER molecular dyanmics software on various NSF resources. This includes testing and validation of AMBER 10 (due for release Mar 2008) on all NSF resources including Ranger. I plan to continue development of both parallel classical molecular dynamics but also to extend the performance and scalability of the QM/MM implementation in AMBER 10. The testing on as many platforms as possible is essential to ensuring a smooth release of the software. The benchmarks will be made available to the community via the AMBER website. In addition any performance improvements through porting will be incorporated in the release code for the entire AMBER community to benefit from. In addition to the above the purpose of this DAC request is also to do initial testing and benchmarking of the AMBER 10 code on various machines in order to support a large LRAC request that will be submitted in January for the March 08 LRAC.