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July 3, 2023 15:57
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Install Jupyter kernel in custom conda environment on JUWELS
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## Install a kernel for the picongpu analysis environment | |
## | |
## Before runnign this script, see JSC documentation at | |
## (https://docs.jupyter-jsc.fz-juelich.de/github/FZJ-JSC/jupyter-jsc-notebooks/blob/documentation/index.ipynb) -> 'Install kernel with conda' | |
## | |
## The steps performed here are only the lsat ones after installing an own conda environment. | |
## | |
CONDA_TARGET_DIR=/p/project/<PROJECTNAME>/<USERNAME>/miniconda3 | |
CONDA_ENV=picongpu | |
echo '#!/bin/bash | |
# module purge # optional to disable the external environment, necessary, if python version is different | |
# Activate your Python virtual environment | |
source '"${CONDA_TARGET_DIR}"'/bin/activate '"${CONDA_ENV}"' | |
# Ensure python packages installed in conda are always prefered, not necessary if module purge is used | |
export PYTHONPATH=${CONDA_PREFIX}/lib/python3.10/site-packages:${PYTHONPATH} | |
exec python -m ipykernel $@' > ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh | |
chmod +x ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh | |
mkdir -p $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV} | |
echo '{ | |
"argv": [ | |
"'"${CONDA_TARGET_DIR}"'/envs/'"${CONDA_ENV}"'/kernel.sh", | |
"-f", | |
"{connection_file}" | |
], | |
"display_name": "conda_'"${CONDA_ENV}"'", | |
"language": "python" | |
}' > $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}/kernel.json |
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