Changes between Version 35 and Version 36 of Jupyter

Timestamp:

05/21/18 21:53:37 (6 years ago)

Author:

Jens Henrik Goebbert

Comment:

--

Jupyter

@@ -85 +85 @@
 but you can create your own specialized Jupyter kernel if you like (and need).
 
-==== Create your own specialized Jupyter-Kernel
+==== Setup your own specialized Jupyter-Kernel
 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:
 
-1. Create a new Python virtual environment in the directory $HOME/mykernel on JURECA
-{{{
-#!ShellExample
-
->> load modules
+Create a new Python virtual environment (e.g. in $HOME/**venv_mykernel**/) \\
+with a basic Jupyter kernel (e.g. in ${HOME}/.local/share/jupyter/kernels/**mykernel**)
+
+* LOAD modules
+{{{ #!ShellExample
 module --force purge
-module load Stages/Devel-2017a
+module load Stages/Devel-2018a
 module load GCCcore/.5.5.0
 module load Jupyter
-
->> create Python virtual environment in $HOME/mykernel
+}}}
+
+* CREATE Python virtual environment in $HOME/venv_mykernel
+{{{ #!ShellExample
 cd $HOME
-python -m venv mykernel
-
->> activate new Python virtual environment
-
+python -m venv venv_mykernel
+}}}
+
+* ACTIVATE new Python virtual environment
+{{{ #!ShellExample
+cd $HOME/venv_mykernel
+source bin/activate
+}}}
+
+* CREATE your personal Jupyter kernel
+{{{ #!ShellExample
+(venv) $ pip install ipykernel
+(venv) $ python $(which ipython) kernel install --user --name=mykernel
+}}}
+  This installs your personal Jupyter kernel in ${HOME}/.local/share/jupyter/kernels/mykernel
+
+Now, modify this basic jupyter kernel to suite your needs.
+
+* WRITE A SCRIPT (${HOME}/venv_mykernel/mykernel.sh) that does your setup followed by the IPython kernel launch:
+{{{ #!ShellExample
+#!/usr/bin/env bash
+
+module --force purge
+module load Stages/Devel-2018a
+module load GCCcore/.5.5.0
+module load Jupyter
+
+exec python -m ipykernel $@
+}}}
+
+* MODIFY the ${HOME}/.local/share/jupyter/kernels/mykernel/kernel.json file to call your script:
+{{{ #!ShellExample
+ "argv": [
+  "${HOME}/venv_mykernel/mykernel.sh",
+  "-f",
+  "{connection_file}"
+ ],
 }}}