Troubleshooting - kreshuklab/plant-seg GitHub Wiki

  • If you stumble in the following error message:
AssertionError:
The NVIDIA driver on your system is too old (found version xxxx).
Please update your GPU driver by downloading and installing a new
version from the URL: http://www.nvidia.com/Download/index.aspx
Alternatively, go to: http://pytorch.org to install
a PyTorch version that has been compiled with your version
of the CUDA driver.

or:

    raise AssertionError("Torch not compiled with CUDA enabled")
AssertionError: Torch not compiled with CUDA enabled

It means that your cuda installation does not match the default in plantseg. You can check your current cuda version by typing in the terminal

cat /usr/local/cuda/version.txt

Then you can re-install the pytorch version compatible with your cuda by activating your plant-seg environment:

conda activate plant-seg

and

conda install -c pytorch torchvision cudatoolkit=<YOU_CUDA_VERSION> pytorch

e.g. for cuda 9.2

conda install -c pytorch torchvision cudatoolkit=9.2 pytorch

Alternatively one can create the plant-seg environment from scratch and ensuring the correct version of cuda/pytorch, by:

conda create -n plant-seg -c lcerrone -c abailoni -c cpape -c awolny -c conda-forge cudatoolkit=<YOU_CUDA_VERSION> plantseg
  • If you use plantseg from the GUI and you receive an error similar to:
RuntimeError: key : 'crop_volume' is missing, plant-seg requires 'crop_volume' to run

(or a similar message for any of the other keys) It might be that the last session configuration file got corrupted or is outdated. You should be able to solve it by removing the corrupted file config_gui_last.yaml.

If you have a standard installation of plantseg, you can remove it by executing on the terminal:

$ rm ~/.plantseg_models/configs/config_gui_last.yaml
  • If you use plantseg from the comand line and you receive an error similar to:
RuntimeError: key : 'crop_volume' is missing, plant-seg requires 'crop_volume' to run

Please make sure that your configuratiuon has the correct formatting and contains all required keys. An updated example can be found inside the directory examples, in this repository.

  • If when trying to execute the Lifted Multicut pipeline you receive an error like:
'cannot import name 'lifted_problem_from_probabilities' from 'elf.segmentation.features''

The solution is to re-install elf via

conda install -c conda-forge python-elf
  • PlantSeg is under active development so it may happen that the models/configuration files saved in ~/.plantseg_modes are outdated. In case of errors related to loading the configuration file, please close the PlantSeg app, remove ~/.plantseg_models directory and try again.