Supported Applications


  • Description

    a version of FREALIGN modified to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup.

  • Usage Notes

    1) At least two NVIDIA GPUs (required by the reconstruction). NVIDIA GeForce GTX295 or better is recommended.

    2) It is strongly recommended that the graphic card used GPU computing by FREALIGN does not connect to any monitor. CUDA has a 5 sec executing time limit and the GPU connected to a monitor may be unstable.

    3) The box size of particle images should be smaller than 500 pixels.

    4) The original FREALIGN integrates both alignment and reconstruction into a single executable file. In the current GPU version of FREALIGN, the two functions are separated and compiled into two separate executable files. The source codes are kept in two separate folders: src_ref and src_rec. Otherwise, the usage of the GPU-enabled FREALIGN is exactly same as the original FREALIGN.

    5) Because the multithread processing has been embedded, a single FREALIGN process will occupy all the available GPU resources in one computer. So each computer or cluster node can run only one FREALIGN job.

  • Primary Citation*

    X. Li, N. Grigorieff, and Y. Cheng. 2010. GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors. J Struct Biol. 172(3): 407-412.

    • *Full citation information available through

  • Categories

    Electron Microscopy

  • Default Versions

    Linux 64:  8.06-20110514

  • Developers

    Yifan Cheng.