Index of /examples/jupyter_notebook/batch_notebook

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Running Python notebooks through the batch system

module load python3/3.8.10

#  Here are 4 ways you can run a Jupyter Notebook in a batch job.

# 1.
# convert notebook to a script that can be run as a batch job. This
# can be done within a batch job or beforehand.
jupyter nbconvert --to script notebook_name.ipynb
# Now run the script
python notebook_name.py

# 2.
# execute the notebook directly. Results are saved within the
# notebook exactly the way they would be if run from within
# Jupyter. 
jupyter nbconvert --to notebook --execute notebook_name.ipynb

# 3.
# execute the notebook as in step 2 and then convert it to a pdf
# Load the pandoc  and texlive modules
module load pandoc/2.5
module load texlive/2021
jupyter nbconvert  --to pdf notebook_name.ipynb  

# 4.
# Again, execute the notebook as in step 2 then convert it
# to an HTML doc. This requires the module loads from part 3.
#Or if you want to save it into HTML format then: 
jupyter nbconvert --to html notebook_name.ipynb