Fragment Molecular Orbital Method Adaptations for Heterogeneous Computing Platforms

TitleFragment Molecular Orbital Method Adaptations for Heterogeneous Computing Platforms
Publication TypeBook Chapter
Year of Publication2012
AuthorsTalamudupula SK, Sosonkina M, Gaenko A, Schmidt MW
EditorAli H, Shi Y, Khazanchi D, Lees M, VanAlbada GD, Dongarra J, Sloot PMA
Book TitleProceedings of the International Conference on Computational Science, ICCS 2012
CityAmsterdam
PublisherElsevier Science Bv
Volume9
Pages489-497
Series TitleProcedia Computer Science
ISBN Number1877-0509
Accession NumberWOS:000306288400051
Keywordsalgorithmic adaptations, Fragment Molecular Orbital method, gamess, heterogeneous computing platforms, large systems, middleware, SCHEME
Abstract

Modern electronic structure calculations are characterized by unprecedented complexity and accuracy. They demand 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 (middleware), 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 insufficient memory available at the runtime.

URL<Go to ISI>://WOS:000306288400051
DOI10.1016/j.procs.2012.04.052