Fragment Molecular Orbital Method Adaptations for Heterogeneous Computing Platforms
- 作者：Sai Kiran Talamudupula ; Masha Sosonkina ; masha@scl.ameslab.gov ; Alexander Gaenko ; Michael W. Schmidt
- 关键词：Fragment Molecular Orbital method ; GAMESS ; algorithmic adaptations ; middleware ; heterogeneous computing platforms
- 刊名：Procedia Computer Science
- 出版年：2012
- 期刊代码：pc74_18770509
- 类别：cp
- 出版时间：2012
- 卷：9
- 期：Complete
- 页码：489-497
- 文件大小：595 K
摘要
Modern electronic structure calculations are characterized by unprecedented complexity and accuracy. They de-mand the full power of high-performance computing and must be in tune with the given architecture for superior efficiency. Thus, it is desirable to enable their static and dynamic adaptations using some external software (middle-ware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application.Building on the successful usage of the NICAN middleware with the computational chemistry package GAMESS, the work described in this paper links NICAN with the fragment molecular orbital (FMO) method to augment FMO with adaptive capabilities. Specifically, its fragment scheduling is performed, both statically and dynamically, based on current conditions within a heterogeneous computing environment. Significant execution time and throughput gains have been obtained with static adaptations, while the dynamic ones prevented FMO to abort calculations due to the insuffcient memory available at the runtime.