JUPYTER

JUPYTER
Description: Produce documents with Jupyter Notebook App
SHARCNET Package information: see JUPYTER software page in web portal
Full list of SHARCNET supported software

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