How to stop the running cell if interupt kernel does not work in Jupyter Notebook

Question

I\'m using Jupyter Notebook for a while. Often when I tried to stop a cell execution, interrupting kernel did not work. In this case, what else can I do, other than just closing

Answer 1

If the iPython kernel did not die, you might be able to inject Python code into it that saves important data using pyrasite. You need to install and run pyrasite as root, i.e. with sudo python -m pip install pyrasite or python3 as needed. Then you need to figure out the process id (PID) of the iPython kernel (e.g. via htop or ps aux | grep ipython), say 3873. Then, write a script that saves the state for example to a pickle in a file inject.py, say, it is a Pandas dataframe df in the global scope:

df.to_pickle("rescued_df.pkl")

Finally, and inject it into the process as follows:

sudo pyrasite 3873 inject.py

You may need to enable dtrace first like so:

echo 0 | sudo tee /proc/sys/kernel/yama/ptrace_scope