JUPYTER |
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Description: Produce documents with Jupyter Notebook App |
SHARCNET Package information: see JUPYTER software page in web portal |
Full list of SHARCNET supported software |
Contents
Introduction
Provide Jupyter Notebook App on a sharcnet fedora visualization workstation.
Version
Jupyter is in the default path, no module must be loaded to use it. Only one version is currently installed.
Usage
Cluster
Jupyter is not installed on the clusters.
Interactive
Jupiter is not intended to be used on the command line apart for installation of environments as described in the below Notes section.
Graphical
Run command line:
jupyter notebook
This package is best run with noVNC or vncviewer https://www.sharcnet.ca/help/index.php/Remote_Graphical_Connections.
Notes
Getting Some Help
jupyter notebook --help
Create Jupyter Notebooks
Follow the below sections to make additional environments available to Jupiter Notebook. The conda approach is used for setting up python 2, 3 and r virtual environments as described in https://ipython.readthedocs.io/en/latest/install/kernel_install.html ...
Step 1)
[roberpj@vdi-fedora23:~] python -V Python 2.7.11 [roberpj@vdi-fedora23:] export PATH=/usr/local/miniconda/3/bin:$PATH [roberpj@vdi-fedora23:] conda create -n ipykernel_py2 python=2 ipykernel Proceed ([y]/n)? y [roberpj@vdi-fedora23:~] source activate ipykernel_py2 (ipykernel_py2) [roberpj@vdi-fedora23:~] python -V Python 2.7.12 :: Continuum Analytics, Inc.
Step 2)
(ipykernel_py2) [roberpj@vdi-fedora23:~] python -m ipykernel install --user Installed kernelspec python2 in /home/roberpj/.local/share/jupyter/kernels/python2
Python 2 should now appear under "New" pulldown (on rhs ) when we run the app:
[roberpj@vdi-fedora23:~] jupyter notebook
To uninstall do something like ...
[roberpj@vdi-fedora23:~] conda uninstall -n ipykernel_py2 ipykernel
Python 3 Environment
Step1)
[roberpj@vdi-fedora23:~] python -V Python 2.7.11 [roberpj@vdi-fedora23:~] export PATH=/usr/local/miniconda/3/bin:$PATH [roberpj@vdi-fedora23:~] conda create -n ipykernel_py3 python=3 ipykernel Proceed ([y]/n)? y [roberpj@vdi-fedora23:~] source activate ipykernel_py3 (ipykernel_py3) [roberpj@vdi-fedora23:~] python -V Python 3.5.2 :: Continuum Analytics, Inc.
Step 2)
(ipykernel_py3) [roberpj@vdi-fedora23:~] python -m ipykernel install --user Installed kernelspec python3 in /home/roberpj/.local/share/jupyter/kernels/python3
Python 3 should now appear under the "New" pulldown when we run the app in the Notebooks section:
[roberpj@vdi-fedora23:~] jupyter notebook
R Environment
Step 1)
[roberpj@vdi-fedora23:~] R --version R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" [roberpj@vdi-fedora23:~] export PATH=/usr/local/miniconda/3/bin:$PATH [roberpj@vdi-fedora23:~] conda create -n r anaconda [roberpj@vdi-fedora23:~] source activate r (r) [roberpj@vdi-fedora23:~] conda install -c r r (r) [roberpj@vdi-fedora23:~] conda install -c r r-essentials (r) [roberpj@vdi-fedora23:~] conda install -c r r-irkernel (r) [roberpj@vdi-fedora23:~] R --version R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Step 2)
[roberpj@vdi-fedora23:~] R > IRkernel::installspec() [InstallKernelSpec] Installed kernelspec ir in /home/roberpj/.local/share/jupyter/kernels/ir
R should appear under the "New" pulldown in the Notebooks section when jupyter is started:
[roberpj@vdi-fedora23:~] jupyter notebook
ASIDE notice we so far now have created these 3 directories:
[roberpj@vdi-fedora23:/work/roberpj/python/envs] ls ipykernel_py2 ipykernel_py3 r
Octave Environment
Coming soon ...
Haskell Environment
Coming soon ...
Deactivating An Environment
As an example we can deactivate the r environment by doing:
(r) [roberpj@vdi-fedora23:~] source deactivate [roberpj@vdi-fedora23:~]
Removing Packages
Ideally use conda, python and r to cleanly uninstall all packages if one wants remove everything and start over. Otherwise remove the installation directories directly with great case by doing something like the following:
rm -rf ~/.jupyter/ ~/.local/share/jupyter /work/$USER/python/envs $XDG_RUNTIME_DIR/jupyter*
References
o Homepage: http://jupyter.org/
o Release: http://jupyter.readthedocs.io/en/latest/releases/content-releases.html
o Forum: http://jupyter.org/community.html