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John Wiley & Sons Limited:1 Oldlands Way, Bognor Regis, P022 9SA United Kingdom:011 44 1243 779777, EMAIL: [email protected], INTERNET: http://www.wiley.co.uk, Fax: 011 44 1243 843232
Doi
Abstract
Coarse grain (CG) molecular models have been proposed to simulate complex sys-
tems with lower computational overheads and longer timescales with respect to atom-
istic level models. However, their acceleration on parallel architectures such as Graphic
Processing Units (GPU) 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 specic optimizations for
CG models, such as dedicated data structures to handle dierent bead type interac-
tions, 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 dierent GPU architectures as case studies
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