CHARACTERIZATION OF COARSE GRAIN MOLECULAR DYNAMIC SIMULATION PERFORMANCE ON GRAPHIC PROCESSING UNIT ARCHITECTURES

Ardita Shkurti, Andrea Acquaviva, Elisa Ficarra, Mario Orsi, Enrico Macii

2012

Abstract

Coarse grain (CG) molecular models have been proposed to simulate complex systems with lower computational overhead and longer timescales with respect to atomistic level timescales. 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 target, we implemented a GPU-accelerated version of a CG biomembrane simulator called BRAHMS, to which we apply specific optimizations for CG models, such as dedicated data structures to handle different bead type interactions. Moreover, we explore different GPU architectures to characterize the behavior of the optimized CG model.

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Paper Citation


in Harvard Style

Shkurti A., Acquaviva A., Ficarra E., Orsi M. and Macii E. (2012). CHARACTERIZATION OF COARSE GRAIN MOLECULAR DYNAMIC SIMULATION PERFORMANCE ON GRAPHIC PROCESSING UNIT ARCHITECTURES . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 339-342. DOI: 10.5220/0003790703390342


in Bibtex Style

@conference{bioinformatics12,
author={Ardita Shkurti and Andrea Acquaviva and Elisa Ficarra and Mario Orsi and Enrico Macii},
title={CHARACTERIZATION OF COARSE GRAIN MOLECULAR DYNAMIC SIMULATION PERFORMANCE ON GRAPHIC PROCESSING UNIT ARCHITECTURES},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={339-342},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003790703390342},
isbn={978-989-8425-90-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - CHARACTERIZATION OF COARSE GRAIN MOLECULAR DYNAMIC SIMULATION PERFORMANCE ON GRAPHIC PROCESSING UNIT ARCHITECTURES
SN - 978-989-8425-90-4
AU - Shkurti A.
AU - Acquaviva A.
AU - Ficarra E.
AU - Orsi M.
AU - Macii E.
PY - 2012
SP - 339
EP - 342
DO - 10.5220/0003790703390342