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@article{1505476,
author = {Střelák, David and Sorzano, Carlos Óscar S. and Carazo, José María and Filipovič, Jiří},
article_number = {5},
doi = {http://dx.doi.org/10.1177/1094342019832958},
keywords = {Cryo-EM; GPU; CUDA; 3-D Fourier reconstruction; auto-tuning},
language = {eng},
issn = {1094-3420},
journal = {The International Journal of High Performance Computing Applications},
title = {A GPU acceleration of 3-D Fourier reconstruction in cryo-EM},
url = {https://journals.sagepub.com/doi/10.1177/1094342019832958},
volume = {33},
year = {2019}
}
TY - JOUR
ID - 1505476
AU - Střelák, David - Sorzano, Carlos Óscar S. - Carazo, José María - Filipovič, Jiří
PY - 2019
TI - A GPU acceleration of 3-D Fourier reconstruction in cryo-EM
JF - The International Journal of High Performance Computing Applications
VL - 33
IS - 5
SP - 948-959
EP - 948-959
PB - SAGE Publishing
SN - 10943420
KW - Cryo-EM
KW - GPU
KW - CUDA
KW - 3-D Fourier reconstruction
KW - auto-tuning
UR - https://journals.sagepub.com/doi/10.1177/1094342019832958
L2 - https://journals.sagepub.com/doi/10.1177/1094342019832958
N2 - 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.
ER -
STŘELÁK, David, Carlos Óscar S. SORZANO, José María CARAZO a Jiří FILIPOVIČ. A GPU acceleration of 3-D Fourier reconstruction in cryo-EM. \textit{The International Journal of High Performance Computing Applications}. SAGE Publishing, 2019, roč.~33, č.~5, s.~948-959. ISSN~1094-3420. Dostupné z: https://dx.doi.org/10.1177/1094342019832958.
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