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Single-particle 3D reconstruction from cryo-electron microscopy images on GPU

Guangming Tan, Ziyu Guo, Mingyu Chen, Dan Meng
Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Science, Beijing, China
Proceedings of the 23rd international conference on Supercomputing, ICS ’09

@conference{tan2009single,

   title={Single-particle 3d reconstruction from cryo-electron microscopy images on GPU},

   author={Tan, G. and Guo, Z. and Chen, M. and Meng, D.},

   booktitle={Proceedings of the 23rd international conference on Supercomputing},

   pages={380–389},

   year={2009},

   organization={ACM}

}

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Single-particle 3D reconstruction from cryo-electron microscopy (cryo-EM) images is a kernel application of biological molecules analysis, as the computational requirement of which is now beyond PetaFlop for a high-resolution 3D structure. In this paper, we quantitatively analyze the workload, computational intensity and memory performance of the application, parallelize it on an emerging multicore architecture GPU-CUDA. Further we apply a percolation technique to decouple computation with memory operations and orchestrate thread-data mapping to reduce the overhead off-chip memory operations. Finally we tested our optimization strategy on a popular open-source package EMAN to GPU-CUDA, which achieves a relative speedup of about 10X to the original CPU-only EMAN. The experimental results also show that the proposed percolation programming greatly improves utilization of memory bandwidth and floating-point units.
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