Changes between Version 41 and Version 42 of Jupyter


Ignore:
Timestamp:
05/22/18 10:36:48 (6 years ago)
Author:
Jens Henrik Goebbert
Comment:

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  • Jupyter

    v41 v42  
    7676
    7777==== Setup your own specialized Jupyter-Kernel
    78 The installed kernels might not suite your needs and you want to switch to a different software stage or want to load additional software modules. \\In that case you need to set up your own specialized Jupyter kernel.\\ This can be done in a few steps:
    79 
    80 Create a new Python virtual environment (e.g. in $HOME/**venv_mykernel**/) \\
    81 with a basic Jupyter kernel (e.g. in ${HOME}/.local/share/jupyter/kernels/**mykernel**)
    82 
    83 1. LOAD the modules you need and ensure Python3 is included!
     78The installed kernels might not suite your needs and you want to switch to a different software stage or want to load additional software modules. \\In that case you need to set up your own specialized Jupyter kernel.\\ This can be done in the terminal in a few steps on the supercomputer:
     79* LOAD the modules you need
     80  * start with ''module --force purge'' to remove any module which is already loaded
     81  * ensure this includes a recent Python 3.x (even if you are not planing to use Python)
     82  * example:
    8483{{{ #!ShellExample
    8584module --force purge
    … …  
    8988}}}
    9089
    91 2. CREATE Python virtual environment in $HOME/venv_mykernel
     90* CREATE a new Python virtual environment on the supercomputer
     91  * e.g. in ''$HOME/venv_mykernel/''
     92  * more: https://docs.python.org/3/library/venv.html
     93  * example:
    9294{{{ #!ShellExample
    9395cd $HOME
    9496python3 -m venv venv_mykernel
    9597}}}
    96   more: https://docs.python.org/3/library/venv.html
    97 
    98 3. ACTIVATE new Python virtual environment
     98
     99* ACTIVATE the new Python virtual environment (VENV) in your terminal
     100  * the loaded modules modify $PYTHONPATH (''python -m site'')
     101    * ensure(!!!) the first entry is the ''site-package'' directory of your VENV
     102    * ''export PYTHONPATH=<DIR-OF-VENV>/lib/python3.6/site-packages:${PYTHONPATH}''
     103  * example:
    99104{{{ #!ShellExample
    100105source ${HOME}/venv_mykernel/bin/activate
    101 export PYTHONPATH=${HOME}/venv_mykernel/lib/python3.6/site-packages:${PYTHONPATH}
    102 }}}
    103 
    104 4. CREATE your personal Jupyter kernel
     106(venv)$ export PYTHONPATH=${HOME}/venv_mykernel/lib/python3.6/site-packages:${PYTHONPATH}
     107}}}
     108
     109* PIMP your VENV
     110  * install ipykernel with ''pip''
     111  * install any other python software you need with ''pip''
     112  * example:
    105113{{{ #!ShellExample
    106114(venv) $ pip install ipykernel
     115(venv) $ <install whatever else you need in your Python virtual environment using pip>
     116}}}
     117
     118* INSTALL your personal Jupyter kernel
     119  * location of the new Jupyter kernel: ''${HOME}/.local/share/jupyter/kernels/mykernel/''
     120  * more: http://ipython.readthedocs.io/en/stable/install/kernel_install.html
     121  * example:
     122{{{ #!ShellExample
    107123(venv) $ python3 -m ipython kernel install --user --name=mykernel
    108 (venv) $ <install whatever else you need in your Python virtual environment using pip>
    109 }}}
    110   This installs your personal Jupyter kernel in ${HOME}/.local/share/jupyter/kernels/mykernel \\more: http://ipython.readthedocs.io/en/stable/install/kernel_install.html
     124}}}
    111125
    112126Now, modify this basic jupyter kernel to suite your needs.
    113127
    114 5. WRITE A SCRIPT (${HOME}/venv_mykernel/mykernel.sh) that does your setup followed by the IPython kernel launch:
    115   a. load the same modules as in (1)
    116   b. load the Python virtual environment as in (2)
     128* WRITE a script (e.g. ${HOME}/venv_mykernel/mykernel.sh)
     129  * that sets up your environment
     130    * load the same modules as in (1)
     131  * followed by the IPython kernel launch
     132    * load the Python virtual environment as in (2)
     133  * example:
    117134{{{ #!ShellExample
    118135#!/usr/bin/env bash
    … …  
    129146}}}
    130147
    131 6. MODIFY the ${HOME}/.local/share/jupyter/kernels/mykernel/kernel.json file to call your script:
     148* MODIFY the Jupyter kernel configuration file
     149  * located in ${HOME}/.local/share/jupyter/kernels/mykernel/kernel.json file
     150  * it must call your launch script:
     151  * example:
    132152{{{ #!ShellExample
    133153 "argv": [