Paper Info
Title
Pursuing Coordinated Trajectory Progression and Efficient Resource Utilization of GPU-Enabled Molecular Dynamics Simulations
Abstract
To address the challenge of pursuing coordinated trajectory progression and efficient resource utilization of GPU-enabled molecular dynamics (MD) simulations on nondedicated high-end clusters, our work aims to supplement, rather than rewrite, existing workflow and resource managers. To this end, we propose a companion module that complements workflow managers and a wrapper module that supports resource managers. We model the maximum utilization of our approach in comparison to the traditional common approach for two molecular simulations: a sodium dodecyl sulfate (SDS) system with dynamically variable job runtimes and a carbon nanotube system with hardware and application failures. In light of our solution, we estimate increased utilization in both simulations. These findings implicitly assure a more coordinated progression of long trajectories across GPUs on a cluster's nodes.
Year
DOI
Venue
2014
10.1109/MDAT.2013.2284203
IEEE Design & Test of Computers
Keywords
Field
DocType
companion module,sds system,maximum utilization model,graphics processing unit,dynamically variable job runtimes,resource utilization,gpu-enabled molecular dynamics simulations,graphics processing units,workflow manager,resource allocation,biology computing,molecular biophysics,nondedicated high-end clusters,md simulations,coordinated trajectory progression,wrapper module,carbon nanotube system,sodium dodecyl sulfate system,application failure,resource manager,hardware failure
Resource management,Cluster (physics),Computer science,Resource allocation,Molecular dynamics,Computer engineering,Workflow,Trajectory,Distributed computing,Embedded system
Journal
Volume
Issue
ISSN
31
SP1
2168-2356
Citations 
PageRank 
References 
1
0.37
7
Authors
6
Name
Order
Citations
PageRank
S. Schlachter151.97
S. Herbein250.83
Shuching Ou310.71
J. S. Logan410.37
Sandeep Patel510712.96
michela taufer635253.04