Thanks again for your reply. Unfortunately, I didn’t get any wiser from the output. I get:
$ jupyter nbconvert --ExecutePreprocessor.timeout=600 --to notebook --execute diffusion.h.ipynb
[NbConvertApp] Converting notebook diffusion.h.ipynb to notebook
[NbConvertApp] Executing notebook with kernel: root
[NbConvertApp] ERROR | Timeout waiting for execute reply (600s).
Traceback (most recent call last):
File "/usr/local/bin/jupyter-nbconvert", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/dist-packages/jupyter_core/application.py", line 266, in launch_instance
return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 325, in start
self.convert_notebooks()
File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 493, in convert_notebooks
self.convert_single_notebook(notebook_filename)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 464, in convert_single_notebook
output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 393, in export_single_notebook
output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 174, in from_filename
return self.from_file(f, resources=resources, **kw)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 192, in from_file
return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/notebook.py", line 31, in from_notebook_node
nb_copy, resources = super(NotebookExporter, self).from_notebook_node(nb, resources, **kw)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 134, in from_notebook_node
nb_copy, resources = self._preprocess(nb_copy, resources)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 311, in _preprocess
nbc, resc = preprocessor(nbc, resc)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/base.py", line 47, in __call__
return self.preprocess(nb, resources)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 262, in preprocess
nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/base.py", line 69, in preprocess
nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 280, in preprocess_cell
reply, outputs = self.run_cell(cell, cell_index)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 348, in run_cell
exec_reply = self._wait_for_reply(msg_id, cell)
File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 337, in _wait_for_reply
raise exception("Cell execution timed out")
RuntimeError: Cell execution timed out
I’m pretty sure the cell that it is trying to execute is the one that causes the crash in the first play
Btw, the compiled binary of the same code I’m trying to run in the notebook finishes within 1 second…
Ahmad