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en:services:application_services:jupyter:start [2019/08/02 11:03]
bwegman1 [Installing additional python modules]
en:services:application_services:jupyter:start [2019/10/08 14:22] (current)
bwegman1
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 Jupyter-Hub is the portal users log in to and start and manage their notebooks and associated files. Jupyter-Hub is the portal users log in to and start and manage their notebooks and associated files.
  
-Please note that you can also use [[https://​info.gwdg.de/​docs/​doku.php?​id=en:​services:​application_services:​high_performance_computing:​jupyter|Jupyter on our SCC]] if you do need direct access to data on the SCC and have medium to high compute resource requirements.+Please note that you can also use [[https://​info.gwdg.de/​docs/​doku.php?​id=en:​services:​application_services:​jupyter:hpc|Jupyter on our SCC]] if you do need direct access to data on the SCC and have medium to high compute resource requirements.
  
 ===== How to use Jupyter / Jupyter-Hub?​ ===== ===== How to use Jupyter / Jupyter-Hub?​ =====
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 Prefixing the installation with the TEMP variable makes pip use that location for this one installation. Prefixing the installation with the TEMP variable makes pip use that location for this one installation.
 +
 +=== Notebook fails to start after package installation or update, error 500 ===
 +
 +If every notebook fails to start after a package installation or upgrade (error 500) the issue can be resolved by renaming the folder ''​.local'':​
 +<code bash>
 +mv -v .local/ .local.gwdg-disable
 +</​code>​
 +This deactivates all additionally installed packages. The notebook should start again normally.
 +
 +==== Installation of additional packages and environments via Conda ====
 +
 +Management of software packages and environments with Conda requires a terminal session started from the notebook server. The terminal ist available after login via ''​New -> Terminal''​.
 +
 +Before working with ''​conda''​ commands the necessary conda functions need to be loaded (<​b>​mind the dot at the beginning!</​b>​):​
 +<code bash>
 +. /​opt/​conda/​etc/​profile.d/​conda.sh
 +</​code>​
 +
 +=== Creating a new environment ===
 +
 +The following describes the creation of a new, simple environment ''​wikidoku'',​ the installation of the package ''​jinja2''​ as an example and how to make the environment available in the kernel selection of the notebook.
 +
 +Creating and activating the environment:​
 +<code bash>
 +conda create -y --prefix ./wikidoku
 +conda activate ./wikidoku
 +</​code>​
 +
 +As an example the package ''​jinja2''​ will be installed next. This is the step to install the desired software packages from various Conda channels.
 +<code bash>
 +conda install -y jinja2
 +</​code>​
 +
 +Next the new environment will be registered with the notebook. Terms for ''​--name''​ and ''​--display-name''​ (optional) can be chosen freely, the later being shown in the kernel selection of the notebook. The second command lists all known environments. ​ The last command exists the environment.
 +<code bash>
 +python3 -m ipykernel install --user --name wikidoku --display-name "​Python (wikidoku)"​
 +jupyter kernelspec list
 +conda deactivate
 +</​code>​
 +
 +If installation of the kernel fails with the message ''/​usr/​bin/​python:​ No module named ipykernel''​ the additional package ''​jupyter''​ needs to be installed and installation of the kernel repeated:
 +<code bash>
 +python3 -m pip install jupyter
 +</​code>​
 +
 +=== Selecting the new environment ===
 +
 +== Restarting of the notebook server ==
 +
 +After installation of a new environment it is recommended to restart the notebook server. Leave all existing terminals and close all open notebooks. In the Jupyter overview page click on ''​Control Panel''​ and stop the server by clicking ''​Stop My Server''​ and restart it with ''​Start My Server''​.
 +
 +Via ''​New ->''​ a new notebook with the new environment can be started. In existing notebooks the kernel can be changed after starting the notebook and selecting ''​Kernel -> Change Kernel''​.
 +
 +=== Installing additional kernels in an Conda environment ===
 +
 +Installing a new, independent Python kernel für the current environment is possible. As an example an older Python 2.7 kernel will be installed next.
 +
 +A new environment needs to be created and activated as per the steps above.
 +Next follows the installation of the kernel, the ''​jupyter''​ module for that kernel and finally the kernel is made available for selection in the kernel list.
 +<code bash>
 +conda install -y python=2.7
 +python3 -m pip install jupyter
 +python3 -m ipykernel install --user --name oldpython --display-name "​Python 2.7 (oldpython)"​
 +</​code>​
 +
 +The new kernel is now available for new and existing notebooks after restarting the notebook server.
 +The current kernel version can be queried from within Python:
 +<code python>
 +import sys
 +print (sys.version)
 +</​code>​
 +
 +=== Removing an environment ===
 +
 +In order to remove an environment it has to be de-registered from the notebook server and then its files removed (optional but recommended). We list the installed kernels, de-register and remove the environment'​s files:
 +
 +<code bash>
 +jupyter kernelspec list
 +jupyter kernelspec remove wikidoku
 +rm -rf ./wikidoku
 +</​code>​
 +
 ==== Installing additional R packages==== ==== Installing additional R packages====
 <​code>​ <​code>​