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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

  • Czech description

Classification

  • Type

    D - Article in proceedings

  • CEP classification

    IN - Informatics

  • OECD FORD branch

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

  • e-ISSN

  • 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