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Cloned from https://github.com/neurolabusc/gpu_test/ on 22nd October 2021 Commit: ff28eeb7f906564c67801f143a9a1da6e979a171

About

Graphics cards (GPU) can dramatically accelerate some stages of brain imaging processing. In particular, the FSL tools Bedpostx, Eddy and Probtrackx are all commonly used for diffusion analyses and can be dramatically accelerations using an NVidia GPU that supports the CUDA language. While the performance benefits are huge, setting up these systems can be tricky. This repository contains minimal datasets and scripts for testing these tools.

These sample datasets are only designed to validate the installation of these tools. They are not designed to showcase the performance benefits of GPU acceleration. Specifically, the datasets are designed to be small allowing for fast download and testing. Typical datasets are much larger and more computationally intensive. Several of these tests are probably constrained by memory speeds or the required CPU-based serial processing stages that precede and follow the parallel processing of the GPU.

Scripts

  • btest for CUDA accelerated Bedpostx

    • The script runme_gpu.sh will run Bedpostx_GPU.
    • If the script fails to run, make sure your version of Bedpostx_GPU matches your version of CUDA.

  • etest for CUDA accelerated Eddy

    • Since there are different versions of Eddy for different generations of CUDA (e.g. eddy_cuda9.1 only works with CUDA 9.1), the shell script assumes that the executable sym-link eddy_cuda exists. In theory, the FSL installer should create this for you, but this requires CUDA is setup prior to installing FSL. If this is not the case, this repository includes the installer script from FSL 6.0.4, which you can run sudo ./configure_eddy.sh -f /usr/local/fsl. In my experience, this can fail if you have multiple versions of CUDA installed. As an alternative, I include the script configure_eddy_cr.sh which you can run (e.g. ./configure_eddy.sh) and it will suggest a command you can run to create the symbolic link (e.g. sudo ln -s /usr/local/fsl/bin/eddy_cuda9.1 /usr/local/fsl/bin/eddy_cuda.

  • ptest for CUDA accelerated Probtrackx

  • The script runme_gpu.sh will run Probtrackx_GPU.

  • If the script fails to run, make sure your version of Probtrackx_GPU matches your version of CUDA.

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