add hint to restart JupyterLab after kernel creation

18bab2db · Tim Kreuzer · d51c96d8 · 18bab2db
Commit 18bab2db authored 2 years ago by Tim Kreuzer
--- a/03-HowTos/Create_JupyterKernel_general.ipynb
+++ b/03-HowTos/Create_JupyterKernel_general.ipynb
@@ -427,6 +427,13 @@
    "ls ${KERNEL_SPECS_DIR} # double check"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* 3.4 - You can select the new kernel in the top right corner of your notebook. The kernel icon will be added to your launcher, once you've restarted the JupyterLab"
+   ]
+  },
  {
   "cell_type": "markdown",
   "metadata": {},

 %% Cell type:markdown id: tags:

 ![header.png](attachment:9f53dcb1-00d6-4245-955a-b527f1540865.png)
 <h5 style="text-align: right">Author: <a href="mailto:j.goebbert@fz-juelich.de?subject=Jupyter-JSC%20documentation">Jens Henrik Göbbert</a></h5>
 <h5><a href="../index.ipynb">Index</a></h5>
 <h1 style="text-align: center">Create your own Jupyter Kernel</h1>

 %% Cell type:markdown id: tags:

 Often the standard kernel do not provide all features you need for your work. This might be that certain modules are not loaded or packages are not installed.
 With your own kernel you can overcome that problem easily and define your own environment, in which you work.

 This notebook shows you how you can build your own kernel for a **python environment**.

 -------------------------

 %% Cell type:markdown id: tags:

 ## Building your own Jupyter kernel is a three step process
 1. Create/Pimp new virtual Python environment
   * venv
 2. Create/Edit launch script for the Jupyter kernel
   * kernel.sh
 3. Create/Edit Jupyter kernel configuration
   * kernel.json

 %% Cell type:markdown id: tags:

 ### Settings

 %% Cell type:markdown id: tags:

 * Set kernel name
  - must be lower case
  - change if you like

 %% Cell type:code id: tags:

 ``` bash
 # INPUT NEEDED:
 KERNEL_NAME=${USER}_kernel

 export KERNEL_NAME=$(echo "${KERNEL_NAME}" | awk '{print tolower($0)}')
 echo ${KERNEL_NAME} # double check
 ```

 %% Cell type:markdown id: tags:

 * List directories where JupyterLab will search for kernels

 %% Cell type:code id: tags:

 ``` bash
 # JUPYTER SEARCH PATH (for kernels-directory)
 echo "jupyter search paths for kernels-directories"
 if [ -z $JUPYTER_PATH ]; then
  echo "$HOME/.local/share/jupyter"
 else
  tr ':' '\n' <<< "$JUPYTER_PATH"
 fi
 ```

 %% Cell type:markdown id: tags:

 <div class="alert alert-block alert-info">
 <b>Attention:</b>
 Please choose 'private kernel' if you are unsure.</br>
 Using 'project kernel's need to be enabled for your project first by our Jupyter-JSC admins.
 </div>

 * Set kernel type
    - private kernel = "\${HOME}/.local/"
    - project kernel = "\${PROJECT}/.local/"
    - other kernel    = "\<your-path\>" (ensure it is part of $JUPYTER_PATH or your kernel will not be found by JuypterLab)

 %% Cell type:code id: tags:

 ``` bash
 # INPUT NEEDED:
 export KERNEL_TYPE=private # private, project or other
 export KERNEL_SPECS_PREFIX=${HOME}/.local

 ###################
 # project kernel
 if [ "${KERNEL_TYPE}" == "project" ]; then
  export KERNEL_SPECS_PREFIX=${PROJECT}/.local
  echo "project kernel"
 # private kernel
 elif [ "${KERNEL_TYPE}" == "private" ]; then
  export KERNEL_SPECS_PREFIX=${HOME}/.local
  echo "private kernel"
 else
  if [ ! -d "$KERNEL_SPECS_PREFIX" ]; then
    echo "ERROR: please create directory $KERNEL_SPECS_PREFIX"
  fi
  echo "other kernel"
 fi
 export KERNEL_SPECS_DIR=${KERNEL_SPECS_PREFIX}/share/jupyter/kernels

 # check if kernel name is unique
 if [ -d "${KERNEL_SPECS_DIR}/${KERNEL_NAME}" ]; then
  echo "ERROR: Kernel already exists in ${KERNEL_SPECS_DIR}/${KERNEL_NAME}"
  echo "       Rename kernel name or remove directory."
 fi

 echo ${KERNEL_SPECS_DIR}/${KERNEL_NAME} # double check
 ```

 %% Cell type:markdown id: tags:

 * Set directory for kernels virtual environment
  - change if you like

 %% Cell type:code id: tags:

 ``` bash
 # INPUT NEEDED:
 export KERNEL_VENVS_DIR=${PROJECT}/${USER}/jupyter/kernels

 ###################
 mkdir -p ${KERNEL_VENVS_DIR}
 if [ "${KERNEL_TYPE}" != "private" ] && [ "${KERNEL_TYPE}" != "other" ]; then
  echo "Please check the permissions and ensure your project partners have read/execute permissions:"
  namei -l ${KERNEL_VENVS_DIR}
 fi

 echo ${KERNEL_VENVS_DIR} # double check
 ls -lt ${KERNEL_VENVS_DIR}
 ```

 %% Cell type:markdown id: tags:

 ---

 %% Cell type:markdown id: tags:

 ## 1. Create/Pimp new virtual Python environment

 %% Cell type:markdown id: tags:

 * 1.1 - Load basic Python module

 %% Cell type:code id: tags:

 ``` bash
 module -q purge
 module -q use $OTHERSTAGES
 module -q load Stages/2020    2> /dev/null # any stage can be used
 module -q load GCCcore/.9.3.0 2> /dev/null
 module -q load Python/3.8.5                # only Python is required
 module list # double check
 ```

 %% Cell type:markdown id: tags:

 * 1.2 - Load extra modules you need for your kernel

 %% Cell type:code id: tags:

 ``` bash
 # module load <module you need>
 ```

 %% Cell type:markdown id: tags:

 * 1.3 - Create and activate a virtual environment for the kernel
 and ensure python packages installed in the virtual environment are always prefered

 %% Cell type:code id: tags:

 ``` bash
 if [ -d "${KERNEL_VENVS_DIR}/${KERNEL_NAME}" ]; then
  echo "ERROR: Directory for virtual environment already ${KERNEL_VENVS_DIR}/${KERNEL_NAME}"
  echo "       Rename kernel name or remove directory."
 else
  python -m venv --system-site-packages ${KERNEL_VENVS_DIR}/${KERNEL_NAME}
  source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate
  export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:${PYTHONPATH}
  echo ${VIRTUAL_ENV} # double check
 fi
 ```

 %% Cell type:markdown id: tags:

 * 1.4 - Install Python libraries required for communication with Jupyter

 %% Cell type:code id: tags:

 ``` bash
 which pip
 if [ -z "${VIRTUAL_ENV}" ]; then
  echo "ERROR: Virtual environment not successfully initialized."
 else
  pip install --ignore-installed ipykernel
  ls ${VIRTUAL_ENV}/lib/python3.8/site-packages/ # double check
 fi
 ```

 %% Cell type:markdown id: tags:

 * 1.5 - Install whatever else you need in your Python virtual environment (using pip)

 %% Cell type:code id: tags:

 ``` bash
 #pip install <python-package you need>
 ```

 %% Cell type:markdown id: tags:

 ---

 %% Cell type:markdown id: tags:

 ## 2. Create/Edit launch script for the Jupyter kernel

 %% Cell type:markdown id: tags:

 * 2.1 - Create launch script, which loads your Python virtual environment and starts the ipykernel process inside:

 <div class="alert alert-block alert-info">
 <b>Attention:</b>
 You MUST load the exactly the same modules as you did above for your virtual Python environment.
 </div>

 %% Cell type:code id: tags:

 ``` bash
 echo '#!/bin/bash'"

 # Load basic Python module
 module purge
 module use "'$OTHERSTAGES'"
 module load Stages/2020
 module load GCCcore/.9.3.0
 module load Python/3.8.5

 # Load extra modules you need for your kernel (as you did in step 1.2)
 #module load <module you need>

 # Activate your Python virtual environment
 source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate

 # Ensure python packages installed in the virtual environment are always prefered
 export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:"'${PYTHONPATH}'"

 exec python -m ipykernel "'$@' > ${VIRTUAL_ENV}/kernel.sh
 chmod +x ${VIRTUAL_ENV}/kernel.sh

 cat ${VIRTUAL_ENV}/kernel.sh # double check
 ```

 %% Cell type:markdown id: tags:

 ---

 %% Cell type:markdown id: tags:

 ## 3. Create/Edit Jupyter kernel configuration

 %% Cell type:markdown id: tags:

 * 3.1 - Create Jupyter kernel configuration directory and files

 %% Cell type:code id: tags:

 ``` bash
 python -m ipykernel install --name=${KERNEL_NAME} --prefix ${VIRTUAL_ENV}
 export VIRTUAL_ENV_KERNELS=${VIRTUAL_ENV}/share/jupyter/kernels
 ```

 %% Cell type:markdown id: tags:

 * 3.2 - Adjust kernel.json file

 %% Cell type:code id: tags:

 ``` bash
 mv ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json.orig

 echo '{
  "argv": [
    "'${KERNEL_VENVS_DIR}/${KERNEL_NAME}/kernel.sh'",
    "-m",
    "ipykernel_launcher",
    "-f",
    "{connection_file}"
  ],
  "display_name": "'${KERNEL_NAME}'",
  "language": "python"
 }' > ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json

 cat ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json # double check
 ```

 %% Cell type:markdown id: tags:

 * 3.3 - Create link to kernel specs

 %% Cell type:code id: tags:

 ``` bash
 mkdir -p ${KERNEL_SPECS_DIR}
 cd ${KERNEL_SPECS_DIR}
 ln -s ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME} .

 echo -e "\n\nThe new kernel '${KERNEL_NAME}' was added to your kernels in '${KERNEL_SPECS_DIR}/'\n"
 ls ${KERNEL_SPECS_DIR} # double check
 ```

 %% Cell type:markdown id: tags:

+* 3.4 - You can select the new kernel in the top right corner of your notebook. The kernel icon will be added to your launcher, once you've restarted the JupyterLab
+
+%% Cell type:markdown id: tags:
+
 ---

 %% Cell type:markdown id: tags:

 ## 4. Cleanup

 %% Cell type:code id: tags:

 ``` bash
 deactivate
 ```