Document Detail


Acceleration of coarse grain molecular dynamics on GPU architectures.
MedLine Citation:
PMID:  23280763     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Coarse grain (CG) molecular models have been proposed to simulate complex systems with lower computational overheads and longer timescales with respect to atomistic level models. However, their acceleration on parallel architectures such as graphic processing units (GPUs) presents original challenges that must be carefully evaluated. The objective of this work is to characterize the impact of CG model features on parallel simulation performance. To achieve this, we implemented a GPU-accelerated version of a CG molecular dynamics simulator, to which we applied specific optimizations for CG models, such as dedicated data structures to handle different bead type interactions, obtaining a maximum speed-up of $14$ on the NVIDIA GTX480 GPU with Fermi architecture. We provide a complete characterization and evaluation of algorithmic and simulated system features of CG models impacting the achievable speed-up and accuracy of results, using three different GPU architectures as case studies. © 2012 Wiley Periodicals, Inc.
Authors:
Ardita Shkurti; Mario Orsi; Enrico Macii; Elisa Ficarra; Andrea Acquaviva
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-12-28
Journal Detail:
Title:  Journal of computational chemistry     Volume:  -     ISSN:  1096-987X     ISO Abbreviation:  J Comput Chem     Publication Date:  2012 Dec 
Date Detail:
Created Date:  2013-1-2     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9878362     Medline TA:  J Comput Chem     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
Affiliation:
Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy C.so Duca degli Abruzzi 24, Turin 10129, Italy.
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