Update troubleshooting doc, remove from README, fix #206

README.md

@@ -301,77 +301,8 @@ the boundary signal, we could leverage the fact that one cell contains only one
 segmentation strategy and obtain improved segmentation. This workflow is now available in all PlantSeg interfaces.
 
 ## Troubleshooting
-* 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 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-It might be that the last session configuration file got corrupted or is outdated.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 command 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 configuration 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](https://github.com/constantinpape/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.
+See [troubleshooting](https://hci-unihd.github.io/plant-seg/chapters/getting_started/troubleshooting) for a list of common issues and their solutions.
 
 ## Tests
 In order to run tests make sure that `pytest` is installed in your conda environment. You can run your tests

docs/chapters/getting_started/troubleshooting.md

@@ -1,6 +1,30 @@
-# Troubleshooting
+# Troubleshooting  <!-- omit in toc -->
 
-* If you stumble in the following error message:
+- [`Could not load library libcudnn_ops_infer.so.8.`](#could-not-load-library-libcudnn_ops_inferso8)
+- [`NVIDIA driver on your system is too old` or `Torch not compiled with CUDA enabled`](#nvidia-driver-on-your-system-is-too-old-or-torch-not-compiled-with-cuda-enabled)
+- [`RuntimeError: key : KEY_NAME is missing, plant-seg requires KEY_NAME to run`](#runtimeerror-key--key_name-is-missing-plant-seg-requires-key_name-to-run)
+- [`cannot import name 'lifted_problem_from_probabilities'`](#cannot-import-name-lifted_problem_from_probabilities)
+- [Other issues](#other-issues)
+
+----
+
+#### `Could not load library libcudnn_ops_infer.so.8.`
+
+If you stumble in the following error message:
+```
+Could not load library libcudnn_ops_infer.so.8. Error: libcudnn_ops_infer.so.8: cannot open shared object file: No such file or directory
+```
+
+Just install `cudnn` by running:
+```
+$ mamba install -c conda-forge cudnn
+```
+
+----
+
+#### `NVIDIA driver on your system is too old` or `Torch not compiled with CUDA enabled`
+
+If you stumble in the following error message:
 ```
 AssertionError:
 The NVIDIA driver on your system is too old (found version xxxx).
@@ -35,10 +59,14 @@ 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
+conda create -n plant-seg -c lcerrone -c abailoni -c cpape -c conda-forge cudatoolkit=<YOU_CUDA_VERSION> plantseg
 ```
 
-* If you use plantseg from the GUI and you receive an error similar to:
+----
+
+#### `RuntimeError: key : KEY_NAME is missing, plant-seg requires KEY_NAME to run`
+
+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
 ```
@@ -51,15 +79,19 @@ If you have a standard installation of plantseg, you can remove it by executing
 $ rm ~/.plantseg_models/configs/config_gui_last.yaml
 ```
 
-* If you use plantseg from the comand line and you receive an error similar to:
+If you use plantseg from the command 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.
+Please make sure that your configuration 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'`
+
+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''
 ```
@@ -68,6 +100,10 @@ The solution is to re-install [elf](https://github.com/constantinpape/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`
+----
+
+#### Other issues
+
+* 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.
+remove `~/.plantseg_models` directory and try again.