diff --git a/002-Methods/003-Visualization/001-InSitu/001-Catalyst/build_ParaViewKernel.sh b/002-Methods/003-Visualization/001-InSitu/001-Catalyst/build_ParaViewKernel.sh deleted file mode 100755 index 3fd97b4ee035e2df8d576a4646bb6a487c373397..0000000000000000000000000000000000000000 --- a/002-Methods/003-Visualization/001-InSitu/001-Catalyst/build_ParaViewKernel.sh +++ /dev/null @@ -1,119 +0,0 @@ -# INPUT NEEDED: -export KERNEL_NAME="paraviewkernel5.8" -export KERNEL_TYPE="private" # private or project -export KERNEL_VENVS_DIR=~/jupyter/kernels -export LOAD_PARAVIEW_COMMAND="module load ParaView/5.8.0-EGL-opengl-Python-3.6.8" -export LOAD_JUPYTER_COMMAND="module load Jupyter/2019a-devel-Python-3.6.8" -export UNLOAD_VTK_COMMAND="module unload VTK" - - -echo "Kernel Name:" -echo ${KERNEL_NAME} -echo "Kernel Type:" -echo ${KERNEL_TYPE} -echo "Kernel venvs dir:" -echo ${KERNEL_VENVS_DIR} # double check - - -################### -# private kernel -if [ ${KERNEL_TYPE} == "private" ]; then - export KERNEL_SPECS_PREFIX=${HOME}/.local - echo "private kernel" -# project kernel -else - export KERNEL_SPECS_PREFIX=${PROJECT}/.local - echo "project kernel" -fi -export KERNEL_SPECS_DIR=${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 - - - -################### -mkdir -p ${KERNEL_VENVS_DIR} -if [ ${KERNEL_TYPE} != "private" ]; then - echo "Please check the permissions and ensure your project partners have read/execute permissions:" - namei -l ${KERNEL_VENVS_DIR} -fi - - -module -q purge -module -q use $OTHERSTAGES -module -q load Stages/Devel-2019a 2> /dev/null # any stage can be used -module -q load GCCcore/.8.3.0 2> /dev/null -module -q load Python/3.6.8 # only Python is required -#module -q load GCC/8.3.0 -#module -q load ParaStationMPI/5.2.2-1 -#module -q load ParaView/5.7.0-EGL-opengl-Python-3.6.8 - -module list # double check - - -python -m venv --system-site-packages ${KERNEL_VENVS_DIR}/${KERNEL_NAME} -source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate -export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.6/site-packages:${PYTHONPATH} -echo ${VIRTUAL_ENV} # double check - -which pip -#pip install --ignore-installed ipykernel -ls ${VIRTUAL_ENV}/lib/python3.6/site-packages/ # double check - - -echo "#!/bin/bash - -# Load required modules -module purge -module use "'$OTHERSTAGES'" -module load Stages/Devel-2019a -module load GCCcore/.8.3.0 -module load Python/3.6.8 - -# Load extra modules you need for your kernel (as you did in step 1.2) -module load GCC/8.3.0 -module load ParaStationMPI/5.2.2-1 -${LOAD_PARAVIEW_COMMAND} -${LOAD_JUPYTER_COMMAND} -${UNLOAD_VTK_COMMAND} -module list - -# 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=${VIRTUAL_ENV}/lib/python3.6/site-packages:"'${PYTHONPATH}'" -echo ${PYTHONPATH} - -exec python -m ipykernel "'$@' > ${VIRTUAL_ENV}/kernel.sh -chmod +x ${VIRTUAL_ENV}/kernel.sh - -python -m ipykernel install --name=${KERNEL_NAME} --prefix ${VIRTUAL_ENV} -export VIRTUAL_ENV_KERNELS=${VIRTUAL_ENV}/share/jupyter/kernels - -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 - -cd ${KERNEL_SPECS_DIR} -ln -s ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME} . -ls ${KERNEL_SPECS_DIR} # double check - - -deactivate