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generate-Dockerfile.sh
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#!/usr/bin/env bash
cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
# Set the path of the generated Dockerfile
export DOCKERFILE=".build/Dockerfile"
export STACKS_DIR=".build/docker-stacks"
# please test the build of the commit in https://github.com/jupyter/docker-stacks/commits/master in advance
export HEAD_COMMIT="1387ff70e30635aa5e75c95cebee041f8d03acbf"
while [[ "$#" -gt 0 ]]; do case $1 in
-p|--pw|--password) PASSWORD="$2" && USE_PASSWORD=1; shift;;
-c|--commit) HEAD_COMMIT="$2"; shift;;
--no-datascience-notebook) no_datascience_notebook=1;;
--python-only) no_datascience_notebook=1;;
--no-useful-packages) no_useful_packages=1;;
-s|--slim) no_datascience_notebook=1 && no_useful_packages=1;;
-d|--devel) use_devel_image=1;;
-h|--help) HELP=1;;
*) echo "Unknown parameter passed: $1" && HELP=1;;
esac; shift; done
if [[ "$HELP" == 1 ]]; then
echo "Help for ./generate-Dockerfile.sh:"
echo "Usage: $0 [parameters]"
echo " -h|--help: Show this help."
echo " -p|--pw|--password: Set the password (and update in src/jupyter_notebook_config.json)"
echo " -c|--commit: Set the head commit of the jupyter/docker-stacks submodule (https://github.com/jupyter/docker-stacks/commits/master). default: $HEAD_COMMIT."
echo " --no-datascience-notebook|--python-only: Use not the datascience-notebook from jupyter/docker-stacks, don't install Julia and R."
echo " --no-useful-packages: Don't install the useful packages, specified in src/Dockerfile.usefulpackages"
echo " --slim: no useful packages and no datascience notebook."
echo " --devel: Use the devel version of the base image (Warning: might cause problems when used with a different base image)"
exit 21
fi
# Clone if docker-stacks doesn't exist, and set to the given commit or the default commit
ls $STACKS_DIR/README.md > /dev/null 2>&1 || (echo "Docker-stacks was not found, cloning repository" \
&& git clone https://github.com/jupyter/docker-stacks.git $STACKS_DIR)
echo "Set docker-stacks to commit '$HEAD_COMMIT'."
if [[ "$HEAD_COMMIT" == "latest" ]]; then
echo "WARNING, the latest commit of docker-stacks is used. This may result in version conflicts"
cd $STACKS_DIR && git pull && cd -
else
export GOT_HEAD="false"
cd $STACKS_DIR && git pull && git reset --hard "$HEAD_COMMIT" > /dev/null 2>&1 && cd - && export GOT_HEAD="true"
echo "$HEAD"
if [[ "$GOT_HEAD" == "false" ]]; then
echo "Error: The given sha-commit is invalid."
echo "Usage: $0 -c [sha-commit] # set the head commit of the docker-stacks submodule (https://github.com/jupyter/docker-stacks/commits/master)."
echo "Exiting"
exit 2
else
echo "Set head to given commit."
fi
fi
# Write the contents into the DOCKERFILE and start with the header
echo "# This Dockerfile is generated by 'generate-Dockerfile.sh' from elements within 'src/'
# **Please do not change this file directly!**
# To adapt this Dockerfile, adapt 'generate-Dockerfile.sh' or 'src/Dockerfile.usefulpackages'.
# More information can be found in the README under configuration.
" > $DOCKERFILE
if [[ "use_devel_image" == 1 ]]; then
echo "Using -devel base image"
cat src/Dockerfile.header | sed 's/runtime-ubuntu/devel-ubuntu/g' >> $DOCKERFILE
else
cat src/Dockerfile.header >> $DOCKERFILE
fi
echo "
############################################################################
#################### Dependency: jupyter/docker-stacks-foundation ########################
############################################################################
" >> $DOCKERFILE
cat $STACKS_DIR/docker-stacks-foundation/Dockerfile | grep -v 'BASE_CONTAINER' | grep -v 'FROM $ROOT_CONTAINER' >> $DOCKERFILE
# copy files that are used during the build:
cp $STACKS_DIR/docker-stacks-foundation/fix-permissions .build/
cp $STACKS_DIR/docker-stacks-foundation/start.sh .build/
cp $STACKS_DIR/docker-stacks-foundation/initial-condarc .build/
chmod 755 .build/*.sh
echo "
############################################################################
#################### Dependency: jupyter/base-notebook ########################
############################################################################
" >> $DOCKERFILE
cat $STACKS_DIR/base-notebook/Dockerfile | grep -v 'BASE_CONTAINER' | grep -v 'FROM $ROOT_CONTAINER' >> $DOCKERFILE
# copy files that are used during the build:
cp $STACKS_DIR/base-notebook/jupyter_server_config.py .build/
cp $STACKS_DIR/base-notebook/start-notebook.sh .build/
cp $STACKS_DIR/base-notebook/start-singleuser.sh .build/
chmod 755 .build/*.sh
echo "
############################################################################
################# Dependency: jupyter/minimal-notebook #####################
############################################################################
" >> $DOCKERFILE
cat $STACKS_DIR/minimal-notebook/Dockerfile | grep -v BASE_CONTAINER | grep -v 'Rprofile' >> $DOCKERFILE
echo "
############################################################################
################# Dependency: jupyter/scipy-notebook #######################
############################################################################
" >> $DOCKERFILE
cat $STACKS_DIR/scipy-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE
# install Julia and R if not excluded or spare mode is used
if [[ "$no_datascience_notebook" != 1 ]]; then
echo "
############################################################################
################ Dependency: jupyter/datascience-notebook ##################
############################################################################
" >> $DOCKERFILE
echo "
# Add R mimetype option to specify how the plot returns from R to the browser
COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
" >> $DOCKERFILE
cat $STACKS_DIR/datascience-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE
cp $STACKS_DIR/minimal-notebook/Rprofile.site .build/
else
echo "Set 'no-datascience-notebook' = 'python-only', not installing the datascience-notebook with Julia and R."
fi
# Note that the following step also installs the cudatoolkit, which is
# essential to access the GPU.
echo "
############################################################################
########################## Dependency: gpulibs #############################
############################################################################
" >> $DOCKERFILE
cat src/Dockerfile.gpulibs >> $DOCKERFILE
# install useful packages if not excluded or spare mode is used
if [[ "$no_useful_packages" != 1 ]]; then
echo "
############################################################################
############################ Useful packages ###############################
############################################################################
" >> $DOCKERFILE
cat src/Dockerfile.usefulpackages >> $DOCKERFILE
else
echo "Set 'no-useful-packages', not installing stuff within src/Dockerfile.usefulpackages."
fi
# Copy the demo notebooks and change permissions
cp -r extra/Getting_Started data
chmod -R 755 data/
# set password
if [[ "$USE_PASSWORD" == 1 ]]; then
echo "Set password to given input"
SALT="3b4b6378355"
HASHED=$(echo -n ${PASSWORD}${SALT} | sha1sum | awk '{print $1}')
unset PASSWORD # delete variable PASSWORD
# build jupyter_notebook_config.json
echo "{
\"NotebookApp\": {
\"password\": \"sha1:$SALT:$HASHED\"
}
}" > src/jupyter_notebook_config.json
fi
cp src/jupyter_notebook_config.json .build/
echo >> $DOCKERFILE
echo "# Copy jupyter_notebook_config.json" >> $DOCKERFILE
echo "COPY jupyter_notebook_config.json /etc/jupyter/" >> $DOCKERFILE
# Set environment variables
export JUPYTER_UID=$(id -u)
export JUPYTER_GID=$(id -g)
#cp $(find $(dirname $DOCKERFILE) -type f | grep -v $STACKS_DIR | grep -v .gitkeep) .
echo
echo "The GPU Dockerfile was generated successfully in file ${DOCKERFILE}."
echo "To start the GPU-based Juyterlab instance, run:"
echo " docker build -t gpu-jupyter .build/ # will take a while"
echo " docker run --gpus all -d -it -p 8848:8888 -v $(pwd)/data:/home/jovyan/work -e GRANT_SUDO=yes -e JUPYTER_ENABLE_LAB=yes -e NB_UID=$(id -u) -e NB_GID=$(id -g) --user root --restart always --name gpu-jupyter_1 gpu-jupyter"