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A GPU acceleration of 3-D Fourier reconstruction in cryo-EM

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14610%2F19%3A00109272" target="_blank" >RIV/00216224:14610/19:00109272 - isvavai.cz</a>

  • Result on the web

    <a href="https://journals.sagepub.com/doi/10.1177/1094342019832958" target="_blank" >https://journals.sagepub.com/doi/10.1177/1094342019832958</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1177/1094342019832958" target="_blank" >10.1177/1094342019832958</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    A GPU acceleration of 3-D Fourier reconstruction in cryo-EM

  • Original language description

    Cryo-electron microscopy is a popular method for macromolecules structure determination. Reconstruction of a 3-D volume from raw data obtained from a microscope is highly computationally demanding. Thus, acceleration of the reconstruction has a great practical value. In this article, we introduce a novel graphics processing unit (GPU)-friendly algorithm for direct Fourier reconstruction, one of the main computational bottlenecks in the 3-D volume reconstruction pipeline for some experimental cases (particularly those with a large number of images and a high internal symmetry). Contrary to the state of the art, our algorithm uses a gather memory pattern, improving cache locality and removing race conditions in parallel writing into the 3-D volume. We also introduce a finely tuned CUDA implementation of our algorithm, using auto-tuning to search for a combination of optimization parameters maximizing performance on a given GPU architecture. Our CUDA implementation is integrated in widely used software Xmipp, version 3.19, reaching 11.4× speedup compared to the original parallel CPU implementation using GPU with comparable power consumption. Moreover, we have reached 31.7× speedup using four GPUs and 2.14×–5.96× speedup compared to optimized GPU implementation based on a scatter memory pattern.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Result continuities

  • Project

    <a href="/en/project/EF16_013%2F0001802" target="_blank" >EF16_013/0001802: CERIT Scientific Cloud</a><br>

  • Continuities

    P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Others

  • Publication year

    2019

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    The International Journal of High Performance Computing Applications

  • ISSN

    1094-3420

  • e-ISSN

    1741-2846

  • Volume of the periodical

    33

  • Issue of the periodical within the volume

    5

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    12

  • Pages from-to

    948-959

  • UT code for WoS article

    000484527300014

  • EID of the result in the Scopus database

    2-s2.0-85062825004