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利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 我请求获得TeraGrid漫游(30,000 SU)的DAC奖，以帮助我在NSF的各种资源上进一步开发琥珀分子动力学软件。这包括在包括游侠在内的所有NSF资源上测试和验证琥珀10(定于2008年3月发布)。我计划继续开发并行经典分子动力学，但也要扩展琥珀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是确保软件顺利发布的关键。这些基准将通过琥珀网站向社区提供。此外，通过移植进行的任何性能改进都将被合并到整个Amber社区的发布代码中，以便从中受益。除上述内容外，此DAC请求的目的也是在各种机器上对琥珀10代码进行初始测试和基准测试，以支持将于1月提交的大型LRAC请求，以参加2008年3月的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.