Troubleshooting: T20S extensive workflow patch motion correction failure


I have been trying to test my cryosparc install with the extensive workflow for T20S. The import worked fine, however the patch motion is giving me the following error:

[CPU: 197.5 MB]  Traceback (most recent call last):
  File "cryosparc2_worker/cryosparc2_compute/", line 85, in
  File "cryosparc2_master/cryosparc2_compute/jobs/motioncorrection/", line 363, in
AssertionError: Child process with PID 9312 has terminated unexpectedly!

I have followed previous threds with similar errors that seem to have been fixed through updating to more recent versions of cryosparc or with patches but I have these all up to date (Current version: v2.15.0+200728) but I am still getting this error.

For some additional information, I installed following quick installation instructions for a single workstation. The workstation has an AMD CPU with 3x2080Ti. I have recently installed CUDA 10.0 in addition to CUDA 8.0 but have carefully installed cryosparc with the cuda path to usr/local/cuda-10.0 so this shouldn’t be an issue. I did accidentally at one point install cuda 11 as some instructions on the nvidia website were a little unclear but as far as I’m aware I managed to purge this and autoremoved other dependencies so I don’t think this will be the issue.

Another error which may or may not be related occurred after I tried to run a 2D classification of some imported particles:

ImportError: cannot open shared object file: No such file or directory

Although this seems CUDA toolkit related as I have as part of cuda-10.0 so this is likely to be cuda related but not sure how to fix this either. I’m stumped and can’t get my install to work, help!

Hi @Lucy, assuming you have complete CUDA 10 installation, you may just have to re-install the CUDA-specific dependencies in the cryosparc2_worker folder. Here’s how you do that:

  1. Navigate to where you installed the cryosparc2_worker via command line
    cd /path/to/cryosparc2_worker
  2. Enter the following variables, changing the CUDA_PATH with the correct path (if it differs):
    export CUDA_PATH="/usr/local/cuda-10.0"
    export CUDA_INC_DIR="$CUDA_PATH/include"
  3. Re-run with your license ID:
    bash ./ --license "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" \
        --cudapath $CUDA_PATH

If you see any errors, please send over the output. If you see no errors, but the Patch Motion job still doesn’t work, I suggest you reinstall CUDA and retry the instructions above.

Let me know how that goes,