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Troubleshoot

Pipeline crash

If the coppafisher pipeline is crashing, first read the error message. If there is a suggestion about how to fix the issue in the config, try changing the config variable and run the pipeline again. If the suggestion does not make sense to you, feel free to reach out to the developer(s) for help or create an issue on GitHub!

If you find any mysterious crash during filter or registration with an error message that traces back to the joblib python package, disable joblib entirely by adding

[filter]
num_cores = 1

for the filter stage and

[register]
flow_cores = 1

for the registration stage.

Memory crash at OMP

Try reducing subset_pixels in the OMP config. This will cause OMP to compute on fewer pixels at time. It has a minimal effect on compute times, but will lower the RAM/VRAM usage. By default, the subset pixel number is found on the fly based on the PC's hardware, you can see this by looking at the pipeline.log file and searching for subset_pixels.