Commit 306c8f75 authored by Jens Henrik Goebbert's avatar Jens Henrik Goebbert
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update notebook

parent bf68ae88
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
![jsc-logo.jpg](attachment:67258d94-84e6-4a0c-ae8f-c74332ec082e.jpg) ![jsc-logo.jpg](attachment:67258d94-84e6-4a0c-ae8f-c74332ec082e.jpg)
Author: [Jens Henrik Göbbert](mailto:j.goebbert@fz-juelich.de) Author: [Jens Henrik Göbbert](mailto:j.goebbert@fz-juelich.de)
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%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
# Create your own Jupyter Kernel # Create your own Jupyter Kernel
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. 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. 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**. This notebook shows you how you can build your own kernel for a **python environment**.
------------------------- -------------------------
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Building your own Jupyter kernel is a three step process ## Building your own Jupyter kernel is a three step process
1. Create/Pimp new virtual Python environment 1. Create/Pimp new virtual Python environment
* venv * venv
2. Create/Edit launch script for the Jupyter kernel 2. Create/Edit launch script for the Jupyter kernel
* kernel.sh * kernel.sh
3. Create/Edit Jupyter kernel configuration 3. Create/Edit Jupyter kernel configuration
* kernel.json * kernel.json
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Settings ### Settings
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* Set kernel name * Set kernel name
- must be lower case - must be lower case
- change if you like - change if you like
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
# INPUT NEEDED: # INPUT NEEDED:
KERNEL_NAME=${USER}_kernel KERNEL_NAME=${USER}_kernel
export KERNEL_NAME=$(echo "${KERNEL_NAME}" | awk '{print tolower($0)}') export KERNEL_NAME=$(echo "${KERNEL_NAME}" | awk '{print tolower($0)}')
echo ${KERNEL_NAME} # double check echo ${KERNEL_NAME} # double check
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* List directories where JupyterLab will search for kernels * List directories where JupyterLab will search for kernels
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
# JUPYTER SEARCH PATH (for kernels-directory) # JUPYTER SEARCH PATH (for kernels-directory)
echo "jupyter search paths for kernels-directories" echo "jupyter search paths for kernels-directories"
if [ -z $JUPYTER_PATH ]; then if [ -z $JUPYTER_PATH ]; then
echo "$HOME/.local/share/jupyter" echo "$HOME/.local/share/jupyter"
else else
tr ':' '\n' <<< "$JUPYTER_PATH" tr ':' '\n' <<< "$JUPYTER_PATH"
fi fi
``` ```
%% Cell type:markdown id: tags: %% 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 * Set kernel type
- private kernel = "\${HOME}/.local/" - private kernel = "\${HOME}/.local/"
- project kernel = "\${PROJECT}/.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) - other kernel = "\<your-path\>" (ensure it is part of $JUPYTER_PATH or your kernel will not be found by JuypterLab)
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
# INPUT NEEDED: # INPUT NEEDED:
export KERNEL_TYPE=private # private, project or other export KERNEL_TYPE=private # private, project or other
export KERNEL_SPECS_PREFIX=${HOME}/.local export KERNEL_SPECS_PREFIX=${HOME}/.local
################### ###################
# project kernel # project kernel
if [ "${KERNEL_TYPE}" == "project" ]; then if [ "${KERNEL_TYPE}" == "project" ]; then
export KERNEL_SPECS_PREFIX=${PROJECT}/.local export KERNEL_SPECS_PREFIX=${PROJECT}/.local
echo "project kernel" echo "project kernel"
# private kernel # private kernel
elif [ "${KERNEL_TYPE}" == "private" ]; then elif [ "${KERNEL_TYPE}" == "private" ]; then
export KERNEL_SPECS_PREFIX=${HOME}/.local export KERNEL_SPECS_PREFIX=${HOME}/.local
echo "private kernel" echo "private kernel"
else else
if [ ! -d "$KERNEL_SPECS_PREFIX" ]; then if [ ! -d "$KERNEL_SPECS_PREFIX" ]; then
echo "ERROR: please create directory $KERNEL_SPECS_PREFIX" echo "ERROR: please create directory $KERNEL_SPECS_PREFIX"
fi fi
echo "other kernel" echo "other kernel"
fi fi
export KERNEL_SPECS_DIR=${KERNEL_SPECS_PREFIX}/share/jupyter/kernels export KERNEL_SPECS_DIR=${KERNEL_SPECS_PREFIX}/share/jupyter/kernels
# check if kernel name is unique # check if kernel name is unique
if [ -d "${KERNEL_SPECS_DIR}/${KERNEL_NAME}" ]; then if [ -d "${KERNEL_SPECS_DIR}/${KERNEL_NAME}" ]; then
echo "ERROR: Kernel already exists in ${KERNEL_SPECS_DIR}/${KERNEL_NAME}" echo "ERROR: Kernel already exists in ${KERNEL_SPECS_DIR}/${KERNEL_NAME}"
echo " Rename kernel name or remove directory." echo " Rename kernel name or remove directory."
fi fi
echo ${KERNEL_SPECS_DIR}/${KERNEL_NAME} # double check echo ${KERNEL_SPECS_DIR}/${KERNEL_NAME} # double check
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* Set directory for kernels virtual environment * Set directory for kernels virtual environment
- change if you like - change if you like
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
# INPUT NEEDED: # INPUT NEEDED:
export KERNEL_VENVS_DIR=${PROJECT}/${USER}/jupyter/kernels export KERNEL_VENVS_DIR=${PROJECT}/${USER}/jupyter/kernels
################### ###################
mkdir -p ${KERNEL_VENVS_DIR} mkdir -p ${KERNEL_VENVS_DIR}
if [ "${KERNEL_TYPE}" != "private" ] && [ "${KERNEL_TYPE}" != "other" ]; then if [ "${KERNEL_TYPE}" != "private" ] && [ "${KERNEL_TYPE}" != "other" ]; then
echo "Please check the permissions and ensure your project partners have read/execute permissions:" echo "Please check the permissions and ensure your project partners have read/execute permissions:"
namei -l ${KERNEL_VENVS_DIR} namei -l ${KERNEL_VENVS_DIR}
fi fi
echo ${KERNEL_VENVS_DIR} # double check echo ${KERNEL_VENVS_DIR} # double check
ls -lt ${KERNEL_VENVS_DIR} ls -lt ${KERNEL_VENVS_DIR}
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
--- ---
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## 1. Create/Pimp new virtual Python environment ## 1. Create/Pimp new virtual Python environment
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 1.1 - Load required modules * 1.1 - Load basic Python module
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
module -q purge module -q purge
module -q use $OTHERSTAGES module -q use $OTHERSTAGES
module -q load Stages/2020 2> /dev/null # any stage can be used module -q load Stages/2020 2> /dev/null # any stage can be used
module -q load GCCcore/.9.3.0 2> /dev/null module -q load GCCcore/.9.3.0 2> /dev/null
module -q load Python/3.8.5 # only Python is required module -q load Python/3.8.5 # only Python is required
module list # double check module list # double check
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 1.2 - Load extra modules you need for your kernel * 1.2 - Load extra modules you need for your kernel
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
# module load <module you need> # module load <module you need>
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 1.3 - Create and activate a virtual environment for the kernel * 1.3 - Create and activate a virtual environment for the kernel
and ensure python packages installed in the virtual environment are always prefered and ensure python packages installed in the virtual environment are always prefered
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
if [ -d "${KERNEL_VENVS_DIR}/${KERNEL_NAME}" ]; then if [ -d "${KERNEL_VENVS_DIR}/${KERNEL_NAME}" ]; then
echo "ERROR: Directory for virtual environment already ${KERNEL_VENVS_DIR}/${KERNEL_NAME}" echo "ERROR: Directory for virtual environment already ${KERNEL_VENVS_DIR}/${KERNEL_NAME}"
echo " Rename kernel name or remove directory." echo " Rename kernel name or remove directory."
else else
python -m venv --system-site-packages ${KERNEL_VENVS_DIR}/${KERNEL_NAME} python -m venv --system-site-packages ${KERNEL_VENVS_DIR}/${KERNEL_NAME}
source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate
export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:${PYTHONPATH} export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:${PYTHONPATH}
echo ${VIRTUAL_ENV} # double check echo ${VIRTUAL_ENV} # double check
fi fi
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 1.4 - Install Python libraries required for communication with Jupyter * 1.4 - Install Python libraries required for communication with Jupyter
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
which pip which pip
if [ -z "${VIRTUAL_ENV}" ]; then if [ -z "${VIRTUAL_ENV}" ]; then
echo "ERROR: Virtual environment not successfully initialized." echo "ERROR: Virtual environment not successfully initialized."
else else
pip install --ignore-installed ipykernel pip install --ignore-installed ipykernel
ls ${VIRTUAL_ENV}/lib/python3.8/site-packages/ # double check ls ${VIRTUAL_ENV}/lib/python3.8/site-packages/ # double check
fi fi
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 1.5 - Install whatever else you need in your Python virtual environment (using pip) * 1.5 - Install whatever else you need in your Python virtual environment (using pip)
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
#pip install <python-package you need> #pip install <python-package you need>
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
--- ---
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## 2. Create/Edit launch script for the Jupyter kernel ## 2. Create/Edit launch script for the Jupyter kernel
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 2.1 - Create launch script, which loads your Python virtual environment and starts the ipykernel process inside: * 2.1 - Create launch script, which loads your Python virtual environment and starts the ipykernel process inside:
<div class="alert alert-block alert-info">
<b>Attention:</b>
You MUST load the exactly the same modules as you did above for your virtual Python environment.
</div>
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
echo '#!/bin/bash'" echo '#!/bin/bash'"
# Load required modules # Load basic Python module
module purge module purge
module use "'$OTHERSTAGES'" module use "'$OTHERSTAGES'"
module load Stages/2020 module load Stages/2020
module load GCCcore/.9.3.0 module load GCCcore/.9.3.0
module load Python/3.8.5 module load Python/3.8.5
# Load extra modules you need for your kernel (as you did in step 1.2) # Load extra modules you need for your kernel (as you did in step 1.2)
#module load <module you need> #module load <module you need>
# Activate your Python virtual environment # Activate your Python virtual environment
source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate
# Ensure python packages installed in the virtual environment are always prefered # Ensure python packages installed in the virtual environment are always prefered
export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:"'${PYTHONPATH}'" export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:"'${PYTHONPATH}'"
exec python -m ipykernel "'$@' > ${VIRTUAL_ENV}/kernel.sh exec python -m ipykernel "'$@' > ${VIRTUAL_ENV}/kernel.sh
chmod +x ${VIRTUAL_ENV}/kernel.sh chmod +x ${VIRTUAL_ENV}/kernel.sh
cat ${VIRTUAL_ENV}/kernel.sh # double check cat ${VIRTUAL_ENV}/kernel.sh # double check
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
--- ---
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## 3. Create/Edit Jupyter kernel configuration ## 3. Create/Edit Jupyter kernel configuration
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 3.1 - Create Jupyter kernel configuration directory and files * 3.1 - Create Jupyter kernel configuration directory and files
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
python -m ipykernel install --name=${KERNEL_NAME} --prefix ${VIRTUAL_ENV} python -m ipykernel install --name=${KERNEL_NAME} --prefix ${VIRTUAL_ENV}
export VIRTUAL_ENV_KERNELS=${VIRTUAL_ENV}/share/jupyter/kernels export VIRTUAL_ENV_KERNELS=${VIRTUAL_ENV}/share/jupyter/kernels
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 3.2 - Adjust kernel.json file * 3.2 - Adjust kernel.json file
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
mv ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json.orig mv ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json.orig
echo '{ echo '{
"argv": [ "argv": [
"'${KERNEL_VENVS_DIR}/${KERNEL_NAME}/kernel.sh'", "'${KERNEL_VENVS_DIR}/${KERNEL_NAME}/kernel.sh'",
"-m", "-m",
"ipykernel_launcher", "ipykernel_launcher",
"-f", "-f",
"{connection_file}" "{connection_file}"
], ],
"display_name": "'${KERNEL_NAME}'", "display_name": "'${KERNEL_NAME}'",
"language": "python" "language": "python"
}' > ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json }' > ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json
cat ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json # double check cat ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json # double check
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* 3.3 - Create link to kernel specs * 3.3 - Create link to kernel specs
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
mkdir -p ${KERNEL_SPECS_DIR} mkdir -p ${KERNEL_SPECS_DIR}
cd ${KERNEL_SPECS_DIR} cd ${KERNEL_SPECS_DIR}
ln -s ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME} . 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" echo -e "\n\nThe new kernel '${KERNEL_NAME}' was added to your kernels in '${KERNEL_SPECS_DIR}/'\n"
ls ${KERNEL_SPECS_DIR} # double check ls ${KERNEL_SPECS_DIR} # double check
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
--- ---
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## 4. Cleanup ## 4. Cleanup
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` bash ``` bash
deactivate deactivate
``` ```
......
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