Acceleration of dRMSD Calculation and Efficient Usage of GPU Caches
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F15%3A00083460" target="_blank" >RIV/00216224:14330/15:00083460 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1109/HPCSim.2015.7237020" target="_blank" >http://dx.doi.org/10.1109/HPCSim.2015.7237020</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1109/HPCSim.2015.7237020" target="_blank" >10.1109/HPCSim.2015.7237020</a>
Alternative languages
Result language
angličtina
Original language name
Acceleration of dRMSD Calculation and Efficient Usage of GPU Caches
Original language description
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 computationusing 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.
Czech name
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Czech description
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Classification
Type
D - Article in proceedings
CEP classification
IN - Informatics
OECD FORD branch
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Result continuities
Project
<a href="/en/project/EE2.3.30.0037" target="_blank" >EE2.3.30.0037: Employment of Best Young Scientists for International Cooperation Empowerment</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Article name in the collection
Proceedings of IEEE International Conference on High Performance Computing & Simulation
ISBN
9781467378123
ISSN
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e-ISSN
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Number of pages
8
Pages from-to
47-54
Publisher name
IEEE
Place of publication
neuveden
Event location
Amsterdam, The Nederlands
Event date
Jan 1, 2015
Type of event by nationality
WRD - Celosvětová akce
UT code for WoS article
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