Warning messages and TimeoutError: Cell execution timed out

[spring-haru]

[The File in Question]

I have 28 .ipynb and .md files for my JB, and one of them is called 12_Asymptotics.ipynb. It has 2125 lines, and contains a series of simulation. It takes about 18 minutes to finish executing the ipynb file.

[Problem]

After calling jb build to create my JB with all files, I get warning messages:

WARNING: Execution Failed: /Users/myname/Documents/My_Simulation/Python/JupyterBooks/book_etrics/docs/12_Asymptotics.ipynb
WARNING: Couldn't find cache key for notebook file docs/12_Asymptotics.ipynb. Outputs will not be inserted.
  Last execution failed with traceback saved in /Users/myname/Documents/My_Simulation/Python/JupyterBooks/book_etrics/_build/html/reports/12_Asymptotics.log

jb clean . —all does not help. I tried many times.

On the other hand, my JB seems to show all outputs (figures, equations, etc) of 12_Asymptotics.ipynb, despite that the error message says “Outputs will not be inserted”. Indeed, after calling

jb clean . —all
jb build .

the same warning messages are shown, but all outputs seem to be included in my JB.

On the other hand, after modifying the .ipynb file and excuting

jb clean .
jb build .

the same warning messages are shown and the 12_Asymptotics.ipynb part of my JB is NOT updated.

Below is the content of the 12_Asymtotics.log file, which says TimeoutError: Cell execution timed out.

Traceback (most recent call last):
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/jupyter_cache/executors/basic.py", line 157, in execute
    executenb(nb_bundle.nb, cwd=tmpdirname)
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 737, in executenb
    return ep.preprocess(nb, resources, km=km)[0]
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 405, in preprocess
    nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/nbconvert/preprocessors/base.py", line 69, in preprocess
    nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 438, in preprocess_cell
    reply, outputs = self.run_cell(cell, cell_index, store_history)
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 571, in run_cell
    if self._passed_deadline(deadline):
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 541, in _passed_deadline
    self._handle_timeout()
  File "/Users/myname/anaconda3/envs/JupyterBook/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 504, in _handle_timeout
    raise TimeoutError("Cell execution timed out")
TimeoutError: Cell execution timed out

[choldgraf]

Thanks for catching this - I believe @bmcfee had the same problem as well. We are working on a fix 👍 executablebooks/jupyter-cache#39

[chrisjsewell]

This should be closed in v0.8.0 😄, but feel free to re-open/open another issue if anything is outstanding: https://jupyterbook.org/reference/_changelog.html#v0-8-0-2020-09-01