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

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Authors

STŘELÁK David SORZANO Carlos Óscar S. CARAZO José María FILIPOVIČ Jiří

Type Article in Periodical
Magazine / Source The International Journal of High Performance Computing Applications
MU Faculty or unit

Institute of Computer Science

Citation
Web https://journals.sagepub.com/doi/10.1177/1094342019832958
Doi http://dx.doi.org/10.1177/1094342019832958
Keywords Cryo-EM; GPU; CUDA; 3-D Fourier reconstruction; auto-tuning
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.
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