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@inproceedings{1306977,
author = {Filipovič, Jiří and Plhák, Jan and Střelák, David},
address = {neuveden},
booktitle = {Proceedings of IEEE International Conference on High Performance Computing & Simulation},
doi = {http://dx.doi.org/10.1109/HPCSim.2015.7237020},
editor = {Waleed Smari},
keywords = {RMSD; GPU; code optimization; cache},
howpublished = {tištěná verze "print"},
language = {eng},
location = {neuveden},
isbn = {978-1-4673-7812-3},
pages = {47-54},
publisher = {IEEE},
title = {Acceleration of dRMSD Calculation and Efficient Usage of GPU Caches},
year = {2015}
}
TY - JOUR
ID - 1306977
AU - Filipovič, Jiří - Plhák, Jan - Střelák, David
PY - 2015
TI - Acceleration of dRMSD Calculation and Efficient Usage of GPU Caches
PB - IEEE
CY - neuveden
SN - 9781467378123
KW - RMSD
KW - GPU
KW - code optimization
KW - cache
N2 - In this paper, we introduce the GPU acceleration of dRMSD algorithm, used to compare different structures of a molecule. Comparing to multithreaded CPU implementation, we have reached 13.4x speedup in clustering and 62.7x speedup in 1:1 dRMSD computation using mid-end GPU. The dRMSD computation exposes strong memory locality and thus is compute-bound. Along with conservative implementation using shared memory, we have decided to implement variants of the algorithm using GPU caches to maintain memory locality. Our implementation using cache reaches 96.5 % and 91.6 % of shared memory performance on Fermi and Maxwell, respectively. We have identified several performance pitfalls related to cache blocking in compute-bound codes and suggested optimization techniques to improve the performance.
ER -
FILIPOVIČ, Jiří, Jan PLHÁK a David STŘELÁK. Acceleration of dRMSD Calculation and Efficient Usage of GPU Caches. In Waleed Smari. \textit{Proceedings of IEEE International Conference on High Performance Computing \&{} Simulation}. neuveden: IEEE, 2015, s.~47-54. ISBN~978-1-4673-7812-3. Dostupné z: https://dx.doi.org/10.1109/HPCSim.2015.7237020.
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