Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

J Struct Biol. 2011 Nov;176(2):250-3. doi: 10.1016/j.jsb.2011.07.017. Epub 2011 Aug 5.

Abstract

Iterative reconstruction algorithms are becoming increasingly important in electron tomography of biological samples. These algorithms, however, impose major computational demands. Parallelization must be employed to maintain acceptable running times. Graphics Processing Units (GPUs) have been demonstrated to be highly cost-effective for carrying out these computations with a high degree of parallelism. In a recent paper by Xu et al. (2010), a GPU implementation strategy was presented that obtains a speedup of an order of magnitude over a previously proposed GPU-based electron tomography implementation. In this technical note, we demonstrate that by making alternative design decisions in the GPU implementation, an additional speedup can be obtained, again of an order of magnitude. By carefully considering memory access locality when dividing the workload among blocks of threads, the GPU's cache is used more efficiently, making more effective use of the available memory bandwidth.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computer Storage Devices
  • Electron Microscope Tomography / methods*
  • Electronic Data Processing
  • Hemocyanins / ultrastructure
  • Image Processing, Computer-Assisted / instrumentation
  • Image Processing, Computer-Assisted / methods*

Substances

  • Hemocyanins
  • keyhole-limpet hemocyanin