GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors - PubMed (original) (raw)

GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors

Xueming Li et al. J Struct Biol. 2010 Dec.

Abstract

Among all the factors that determine the resolution of a 3D reconstruction by single particle electron cryo-microscopy (cryoEM), the number of particle images used in the dataset plays a major role. More images generally yield better resolution, assuming the imaged protein complex is conformationally and compositionally homogeneous. To facilitate processing of very large datasets, we modified the computer program, FREALIGN, to execute the computationally most intensive procedures on Graphics Processing Units (GPUs). Using the modified program, the execution speed increased between 10 and 240-fold depending on the task performed by FREALIGN. Here we report the steps necessary to parallelize critical FREALIGN subroutines and evaluate its performance on computers with multiple GPUs.

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Figures

Figure 1

Figure 1. Implementing parallelization of FREALIGN

(A) Tree-structured parallel summation algorithm. The sums between every two pixels within the same block are computed in synchronization, and repeated until the final result is obtained. (B) Dividing and distributing subsets of the data on multiple GPUs for search and refinement. (C) Dividing and distributing subsets of the data on multiple GPUs for 3D reconstruction.

Figure 2

Figure 2. Speed enhancement factors of individual FREALIGN subroutines

Acceleration of individual subroutines with different image sizes: 56 × 56 to 500 × 500 pixels. For the measurement of the speed enhancement factors, only one GPU on system I was used.

Figure 3

Figure 3. Acceleration of search and refinement by GPU-enabled FREALIGN with various image sizes

(A) Search and (B) refinement. The accelerations factors were measured on a single GPU on System I vs. a single i7 CPU core on the same system. The corresponding execution times are listed in Supplementary Table 3 and 4. (C) Reconstruction. The acceleration factors were measured on 4 and 8 GPUs on System I and II, respectively, vs. a single CPU core on the same systems.

Figure 4

Figure 4. Acceleration of GPU-enabled FREALIGN on multiple GPUs

(A) Search, (B) refinement and (C) 3D reconstruction. Solid lines are the speed enhancement factors obtained for System I while dashed lines apply to System II. All corresponding data are listed in Supplementary Table 5.

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