add troubleshooting

Author: ErinWeisbart

documentation/CP-plugins-documentation/runcellpose.md

@@ -6,6 +6,13 @@ See [Using plugins - Using Docker](using_plugins.md/#using-docker-to-bypass-inst
 You can also this module using Cellpose installed to the same Python environment as CellProfiler.
 See [Using plugins - Installing dependencies](using_plugins.md/#installing-plugins-with-dependencies-using-cellprofiler-from-source) for more information on installing dependencies for CellProfiler plugins.
 
+## Troubleshooting
+
+If you are running RunCellpose in a docker and you get an error like this:
+`No such file or directory: '/Users/eweisbar/Documents/CPoutput/.cellprofiler_temp/c564a507-17e5-4256-837d-6e1d59892524/img/c564a507-17e5-4256-837d-6e1d59892524_seg.npy`
+It is likely an issue with running out of memory in the Docker.
+See [this Github issue](https://github.com/CellProfiler/CellProfiler-plugins/issues/243) for more information.
+
 ## Installing Cellpose in the same Python environment as CellProfiler
 
 We provide some information below about installations that have worked for us.
@@ -67,31 +74,36 @@ pip install mysqlclient==1.4.6 cellprofiler
 If you want to use a GPU to run the model (this is recommended for speed), you'll need a compatible version of PyTorch and a supported GPU.
 General instructions are available at this [link](https://pytorch.org/get-started/locally/).
 
-1. Your GPU should be visible in Device Manager under Display Adaptors. 
+1. Your GPU should be visible in Device Manager under Display Adaptors.
 If your GPU isn't there, you likely need to install drivers.
 [Here](https://www.nvidia.com/Download/Find.aspx) is where you can find NVIDIA GPU drivers if you need to install them.
 
-
 2. To test whether the GPU is configured correctly:
-  * Run `python` on the command line (i.e., in Command Prompt or Terminal) to start an interactive session
-  * Then run the following
-  ```
+
+* Run `python` on the command line (i.e., in Command Prompt or Terminal) to start an interactive session
+* Then run the following
+
+  ```bash
   import torch
   torch.cuda.is_available()
   ```
-  * If this returns `True`, you're all set
-  * If this returns `False`, you likely need to install/reinstall torch. See [here](https://pytorch.org/get-started/locally/) for your exact command.
-  * Exit the session with `exit()` then install torch if necessary
-  ```
+
+* If this returns `True`, you're all set
+* If this returns `False`, you likely need to install/reinstall torch. See [here](https://pytorch.org/get-started/locally/) for your exact command.
+* Exit the session with `exit()` then install torch if necessary
+
+  ```bash
   pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu113
   ```
-  If you have a previous version of torch installed, make sure to run `pip uninstall torch` first.
 
+  If you have a previous version of torch installed, make sure to run `pip uninstall torch` first.
 
 **NOTE**: You might get a warning like this:
-```
+
+```bash
 W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cudart64_110.dll'; dlerror: cudart64_110.dll not found
 2022-05-26 20:24:21.906286: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
 ```
+
 If you don't have a GPU, this is not a problem.
 If you do, your configuration is incorrect and you need to try reinstalling drivers and the correct version of CUDA for your system.