Initial commit, local mode runs
This commit is contained in:
Christoph Schranz
parent
17f3f612dd
commit
87f2e77449
5
.gitignore
vendored
5
.gitignore
vendored
@ -102,3 +102,8 @@ venv.bak/
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# mypy
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.mypy_cache/
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# individual stuff
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/data
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*.save*
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20
add-to-swarm.sh
Executable file
20
add-to-swarm.sh
Executable file
@ -0,0 +1,20 @@
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#!/usr/bin/env bash
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cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
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if [[ -n "$1" ]]; then
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result=$(docker network ls)
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if [[ "$result" == *" $1 "* ]]; then
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echo "Adding gpu-jupyter to the swarm in the network $1."
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export JUPYTER_NETWORK=$1
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# echo $JUPYTER_NETWORK
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docker-compose -f docker-compose-swarm.yml build
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docker-compose -f docker-compose-swarm.yml push
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# docker stack deploy --compose-file docker-compose-swarm.yml gpu
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else
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echo "Could not find network $1. Please provide a valid docker network."
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fi
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else
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echo "Usage: $0 network"
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echo "Please set the network"
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fi
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36
docker-compose-swarm.yml
Executable file
36
docker-compose-swarm.yml
Executable file
@ -0,0 +1,36 @@
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version: "3.4"
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services:
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gpu-jupyter:
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image: 127.0.0.1:5001/gpu-jupyter
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build: ./src/
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ports:
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- 8848:8888
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volumes:
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- ./data:/home/jovyan/work
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environment:
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GRANT_SUDO: "yes"
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JUPYTER_ENABLE_LAB: "yes"
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# enable sudo permissions
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user:
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"root"
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networks:
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- default
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- $JUPYTER_NETWORK
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deploy:
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placement:
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constraints: [node.hostname == data-science]
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resources:
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limits:
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cpus: "4"
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memory: 8G
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replicas: 1
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update_config:
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parallelism: 2
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delay: 10s
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restart_policy:
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condition: on-failure
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networks:
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$JUPYTER_NETWORK:
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external:
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name: $JUPYTER_NETWORK
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28
docker-compose.yml
Executable file
28
docker-compose.yml
Executable file
@ -0,0 +1,28 @@
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version: "3.4"
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services:
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gpu-jupyter:
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image: 127.0.0.1:5001/gpu-jupyter
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build: ./src/
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ports:
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- 8848:8888
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volumes:
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- ./data:/home/jovyan/work
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environment:
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GRANT_SUDO: "yes"
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JUPYTER_ENABLE_LAB: "yes"
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# enable sudo permissions
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user:
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"root"
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deploy:
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placement:
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constraints: [node.hostname == data-science]
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resources:
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limits:
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cpus: "4"
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memory: 8G
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replicas: 1
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update_config:
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parallelism: 2
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delay: 10s
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restart_policy:
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condition: on-failure
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4
remove-from-swarm.sh
Executable file
4
remove-from-swarm.sh
Executable file
@ -0,0 +1,4 @@
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#!/usr/bin/env bash
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cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
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docker stack rm gpu_gpu-jupyter
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424
src/Dockerfile
Normal file
424
src/Dockerfile
Normal file
@ -0,0 +1,424 @@
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FROM nvidia/cuda:10.1-base-ubuntu18.04
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LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
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############################################################################
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#################### Dependency: jupyter/base-image ########################
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############################################################################
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ARG NB_USER="jovyan"
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ARG NB_UID="1000"
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ARG NB_GID="100"
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USER root
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# Install all OS dependencies for notebook server that starts but lacks all
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# features (e.g., download as all possible file formats)
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt-get update && apt-get -yq dist-upgrade \
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&& apt-get install -yq --no-install-recommends \
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wget \
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bzip2 \
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ca-certificates \
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sudo \
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locales \
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fonts-liberation \
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&& rm -rf /var/lib/apt/lists/*
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RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Configure environment
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ENV CONDA_DIR=/opt/conda \
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SHELL=/bin/bash \
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NB_USER=$NB_USER \
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NB_UID=$NB_UID \
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NB_GID=$NB_GID \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV PATH=$CONDA_DIR/bin:$PATH \
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HOME=/home/$NB_USER
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# Add a script that we will use to correct permissions after running certain commands
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ADD fix-permissions /usr/local/bin/fix-permissions
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# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
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RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
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# Create NB_USER wtih name jovyan user with UID=1000 and in the 'users' group
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# and make sure these dirs are writable by the `users` group.
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RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
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sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
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useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
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mkdir -p $CONDA_DIR && \
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chown $NB_USER:$NB_GID $CONDA_DIR && \
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chmod g+w /etc/passwd && \
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fix-permissions $HOME && \
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fix-permissions "$(dirname $CONDA_DIR)"
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USER $NB_UID
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WORKDIR $HOME
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# Setup work directory for backward-compatibility
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RUN mkdir /home/$NB_USER/work && \
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fix-permissions /home/$NB_USER
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# Install conda as jovyan and check the md5 sum provided on the download site
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ENV MINICONDA_VERSION=4.6.14 \
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CONDA_VERSION=4.7.10
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RUN cd /tmp && \
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wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
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echo "718259965f234088d785cad1fbd7de03 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
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/bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
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rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
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echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
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$CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
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$CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
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$CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
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$CONDA_DIR/bin/conda install --quiet --yes conda && \
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$CONDA_DIR/bin/conda update --all --quiet --yes && \
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conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
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conda clean --all -f -y && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Install Tini
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RUN conda install --quiet --yes 'tini=0.18.0' && \
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conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
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conda clean --all -f -y && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Install Jupyter Notebook, Lab, and Hub
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# Generate a notebook server config
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# Cleanup temporary files
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# Correct permissions
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# Do all this in a single RUN command to avoid duplicating all of the
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# files across image layers when the permissions change
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RUN conda install --quiet --yes \
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'notebook=6.0.0' \
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'jupyterhub=1.0.0' \
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'jupyterlab=1.0.4' && \
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conda clean --all -f -y && \
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npm cache clean --force && \
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jupyter notebook --generate-config && \
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rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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EXPOSE 8888
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# Configure container startup
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ENTRYPOINT ["tini", "-g", "--"]
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CMD ["start-notebook.sh"]
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# Add local files as late as possible to avoid cache busting
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COPY start.sh /usr/local/bin/
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COPY start-notebook.sh /usr/local/bin/
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COPY start-singleuser.sh /usr/local/bin/
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COPY jupyter_notebook_config.py /etc/jupyter/
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# Fix permissions on /etc/jupyter as root
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USER root
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RUN fix-permissions /etc/jupyter/
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############################################################################
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################# Dependency: jupyter/minimal-notebook #####################
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############################################################################
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# Install all OS dependencies for fully functional notebook server
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RUN apt-get update && apt-get install -yq --no-install-recommends \
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build-essential \
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emacs \
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git \
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inkscape \
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jed \
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libsm6 \
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libxext-dev \
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libxrender1 \
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lmodern \
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netcat \
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pandoc \
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python-dev \
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texlive-fonts-extra \
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texlive-fonts-recommended \
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texlive-generic-recommended \
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texlive-latex-base \
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texlive-latex-extra \
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texlive-xetex \
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tzdata \
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unzip \
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nano \
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&& rm -rf /var/lib/apt/lists/*
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############################################################################
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################# Dependency: jupyter/scipy-notebook #######################
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############################################################################
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# ffmpeg for matplotlib anim
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RUN apt-get update && \
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apt-get install -y --no-install-recommends ffmpeg && \
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rm -rf /var/lib/apt/lists/*
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USER $NB_UID
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# Install Python 3 packages
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RUN conda install --quiet --yes \
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'conda-forge::blas=*=openblas' \
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'ipywidgets=7.5*' \
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'pandas=0.24*' \
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'numexpr=2.6*' \
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'matplotlib-base=3.1.*' \
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'scipy=1.2*' \
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'seaborn=0.9*' \
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'scikit-learn=0.20*' \
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'scikit-image=0.14*' \
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'sympy=1.3*' \
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'cython=0.29*' \
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'patsy=0.5*' \
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'statsmodels=0.9*' \
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'cloudpickle=0.8*' \
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'dill=0.2*' \
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'dask=1.1.*' \
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'numba=0.42*' \
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'bokeh=1.0*' \
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'sqlalchemy=1.3*' \
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'hdf5=1.10*' \
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'h5py=2.9*' \
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'vincent=0.4.*' \
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'beautifulsoup4=4.7.*' \
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'protobuf=3.7.*' \
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'xlrd' && \
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conda clean --all -f -y && \
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# Activate ipywidgets extension in the environment that runs the notebook server
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jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
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# Also activate ipywidgets extension for JupyterLab
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# Check this URL for most recent compatibilities
|
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# https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
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jupyter labextension install @jupyter-widgets/jupyterlab-manager@^1.0.1 --no-build && \
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jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \
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jupyter lab build --dev-build=False && \
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npm cache clean --force && \
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rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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rm -rf /home/$NB_USER/.node-gyp && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Install facets which does not have a pip or conda package at the moment
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RUN cd /tmp && \
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git clone https://github.com/PAIR-code/facets.git && \
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cd facets && \
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jupyter nbextension install facets-dist/ --sys-prefix && \
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cd && \
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rm -rf /tmp/facets && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Import matplotlib the first time to build the font cache.
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ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
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RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
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fix-permissions /home/$NB_USER
|
||||
|
||||
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############################################################################
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||||
################ Dependency: jupyter/datascience-notebook ##################
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||||
############################################################################
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USER root
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||||
|
||||
# R pre-requisites
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||||
RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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||||
fonts-dejavu \
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||||
gfortran \
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gcc && \
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||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# Julia dependencies
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||||
# install Julia packages in /opt/julia instead of $HOME
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ENV JULIA_DEPOT_PATH=/opt/julia
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ENV JULIA_PKGDIR=/opt/julia
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||||
ENV JULIA_VERSION=1.1.0
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||||
|
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RUN mkdir /opt/julia-${JULIA_VERSION} && \
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cd /tmp && \
|
||||
wget -q https://julialang-s3.julialang.org/bin/linux/x64/`echo ${JULIA_VERSION} | cut -d. -f 1,2`/julia-${JULIA_VERSION}-linux-x86_64.tar.gz && \
|
||||
echo "80cfd013e526b5145ec3254920afd89bb459f1db7a2a3f21849125af20c05471 *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
|
||||
tar xzf julia-${JULIA_VERSION}-linux-x86_64.tar.gz -C /opt/julia-${JULIA_VERSION} --strip-components=1 && \
|
||||
rm /tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz
|
||||
RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
|
||||
|
||||
# Show Julia where conda libraries are \
|
||||
RUN mkdir /etc/julia && \
|
||||
echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \
|
||||
# Create JULIA_PKGDIR \
|
||||
mkdir $JULIA_PKGDIR && \
|
||||
chown $NB_USER $JULIA_PKGDIR && \
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||||
fix-permissions $JULIA_PKGDIR
|
||||
|
||||
USER $NB_UID
|
||||
|
||||
# R packages including IRKernel which gets installed globally.
|
||||
RUN conda install --quiet --yes \
|
||||
'rpy2=2.9*' \
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||||
'r-base=3.5.1' \
|
||||
'r-irkernel=0.8*' \
|
||||
'r-plyr=1.8*' \
|
||||
'r-devtools=1.13*' \
|
||||
'r-tidyverse=1.2*' \
|
||||
'r-shiny=1.2*' \
|
||||
'r-rmarkdown=1.11*' \
|
||||
'r-forecast=8.2*' \
|
||||
'r-rsqlite=2.1*' \
|
||||
'r-reshape2=1.4*' \
|
||||
'r-nycflights13=1.0*' \
|
||||
'r-caret=6.0*' \
|
||||
'r-rcurl=1.95*' \
|
||||
'r-crayon=1.3*' \
|
||||
'r-randomforest=4.6*' \
|
||||
'r-htmltools=0.3*' \
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||||
'r-sparklyr=0.9*' \
|
||||
'r-htmlwidgets=1.2*' \
|
||||
'r-hexbin=1.27*' && \
|
||||
conda clean --all -f -y && \
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||||
fix-permissions $CONDA_DIR && \
|
||||
fix-permissions /home/$NB_USER
|
||||
|
||||
# Add Julia packages. Only add HDF5 if this is not a test-only build since
|
||||
# it takes roughly half the entire build time of all of the images on Travis
|
||||
# to add this one package and often causes Travis to timeout.
|
||||
#
|
||||
# Install IJulia as jovyan and then move the kernelspec out
|
||||
# to the system share location. Avoids problems with runtime UID change not
|
||||
# taking effect properly on the .local folder in the jovyan home dir.
|
||||
RUN julia -e 'import Pkg; Pkg.update()' && \
|
||||
(test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
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||||
julia -e "using Pkg; pkg\"add Gadfly RDatasets IJulia InstantiateFromURL\"; pkg\"precompile\"" && \
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||||
# move kernelspec out of home \
|
||||
mv $HOME/.local/share/jupyter/kernels/julia* $CONDA_DIR/share/jupyter/kernels/ && \
|
||||
chmod -R go+rx $CONDA_DIR/share/jupyter && \
|
||||
rm -rf $HOME/.local && \
|
||||
fix-permissions $JULIA_PKGDIR $CONDA_DIR/share/jupyter
|
||||
|
||||
|
||||
############################################################################
|
||||
################ Dependency: jupyter/scipy-notebook ##################
|
||||
############################################################################
|
||||
|
||||
USER root
|
||||
|
||||
# ffmpeg for matplotlib anim
|
||||
RUN apt-get update && \
|
||||
apt-get install -y --no-install-recommends ffmpeg && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
USER $NB_UID
|
||||
|
||||
# Install Python 3 packages
|
||||
RUN conda install --quiet --yes \
|
||||
'conda-forge::blas=*=openblas' \
|
||||
'ipywidgets=7.5*' \
|
||||
'pandas=0.24*' \
|
||||
'numexpr=2.6*' \
|
||||
'matplotlib-base=3.1.*' \
|
||||
'scipy=1.2*' \
|
||||
'seaborn=0.9*' \
|
||||
'scikit-learn=0.20*' \
|
||||
'scikit-image=0.14*' \
|
||||
'sympy=1.3*' \
|
||||
'cython=0.29*' \
|
||||
'patsy=0.5*' \
|
||||
'statsmodels=0.9*' \
|
||||
'cloudpickle=0.8*' \
|
||||
'dill=0.2*' \
|
||||
'dask=1.1.*' \
|
||||
'numba=0.42*' \
|
||||
'bokeh=1.0*' \
|
||||
'sqlalchemy=1.3*' \
|
||||
'hdf5=1.10*' \
|
||||
'h5py=2.9*' \
|
||||
'vincent=0.4.*' \
|
||||
'beautifulsoup4=4.7.*' \
|
||||
'protobuf=3.7.*' \
|
||||
'xlrd' && \
|
||||
conda clean --all -f -y && \
|
||||
# Activate ipywidgets extension in the environment that runs the notebook server
|
||||
jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
|
||||
# Also activate ipywidgets extension for JupyterLab
|
||||
# Check this URL for most recent compatibilities
|
||||
# https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
|
||||
jupyter labextension install @jupyter-widgets/jupyterlab-manager@^1.0.1 --no-build && \
|
||||
jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \
|
||||
jupyter lab build --dev-build=False && \
|
||||
npm cache clean --force && \
|
||||
rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
|
||||
rm -rf /home/$NB_USER/.cache/yarn && \
|
||||
rm -rf /home/$NB_USER/.node-gyp && \
|
||||
fix-permissions $CONDA_DIR && \
|
||||
fix-permissions /home/$NB_USER
|
||||
|
||||
# Install facets which does not have a pip or conda package at the moment
|
||||
RUN cd /tmp && \
|
||||
git clone https://github.com/PAIR-code/facets.git && \
|
||||
cd facets && \
|
||||
jupyter nbextension install facets-dist/ --sys-prefix && \
|
||||
cd && \
|
||||
rm -rf /tmp/facets && \
|
||||
fix-permissions $CONDA_DIR && \
|
||||
fix-permissions /home/$NB_USER
|
||||
|
||||
# Import matplotlib the first time to build the font cache.
|
||||
ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
|
||||
RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
|
||||
fix-permissions /home/$NB_USER
|
||||
|
||||
|
||||
############################################################################
|
||||
############### Dependency: jupyter/tensorflow-notebook ####################
|
||||
############################################################################
|
||||
|
||||
# Install Tensorflow
|
||||
RUN conda install --quiet --yes \
|
||||
'tensorflow=1.13*' \
|
||||
'keras=2.2*' && \
|
||||
conda clean --all -f -y && \
|
||||
fix-permissions $CONDA_DIR && \
|
||||
fix-permissions /home/$NB_USER
|
||||
|
||||
# RUN pip install --upgrade tensorflow-gpu
|
||||
|
||||
############################################################################
|
||||
########################## Dependency: pytorch #############################
|
||||
############################################################################
|
||||
|
||||
# Install PyTorch dependencies
|
||||
RUN conda install --quiet --yes \
|
||||
pyyaml mkl mkl-include setuptools cmake cffi typing && \
|
||||
conda clean --all -f -y && \
|
||||
fix-permissions $CONDA_DIR && \
|
||||
fix-permissions /home/$NB_USER
|
||||
|
||||
# Install PyTorch
|
||||
RUN conda install -y -c pytorch \
|
||||
cudatoolkit=10.1 \
|
||||
'pytorch=1.3.1' \
|
||||
torchvision && \
|
||||
conda clean --all -f -y && \
|
||||
fix-permissions $CONDA_DIR && \
|
||||
fix-permissions /home/$NB_USER
|
||||
|
||||
############################################################################
|
||||
############################ Useful packages ###############################
|
||||
############################################################################
|
||||
|
||||
COPY jupyter_notebook_config.json /etc/jupyter/
|
||||
RUN fix-permissions /home/$NB_USER
|
||||
|
||||
# Switch back to jovyan to avoid accidental container runs as root
|
||||
USER $NB_UID
|
||||
35
src/fix-permissions
Executable file
35
src/fix-permissions
Executable file
@ -0,0 +1,35 @@
|
||||
#!/bin/bash
|
||||
# set permissions on a directory
|
||||
# after any installation, if a directory needs to be (human) user-writable,
|
||||
# run this script on it.
|
||||
# It will make everything in the directory owned by the group $NB_GID
|
||||
# and writable by that group.
|
||||
# Deployments that want to set a specific user id can preserve permissions
|
||||
# by adding the `--group-add users` line to `docker run`.
|
||||
|
||||
# uses find to avoid touching files that already have the right permissions,
|
||||
# which would cause massive image explosion
|
||||
|
||||
# right permissions are:
|
||||
# group=$NB_GID
|
||||
# AND permissions include group rwX (directory-execute)
|
||||
# AND directories have setuid,setgid bits set
|
||||
|
||||
set -e
|
||||
|
||||
for d in "$@"; do
|
||||
find "$d" \
|
||||
! \( \
|
||||
-group $NB_GID \
|
||||
-a -perm -g+rwX \
|
||||
\) \
|
||||
-exec chgrp $NB_GID {} \; \
|
||||
-exec chmod g+rwX {} \;
|
||||
# setuid,setgid *on directories only*
|
||||
find "$d" \
|
||||
\( \
|
||||
-type d \
|
||||
-a ! -perm -6000 \
|
||||
\) \
|
||||
-exec chmod +6000 {} \;
|
||||
done
|
||||
6
src/jupyter_notebook_config.json
Normal file
6
src/jupyter_notebook_config.json
Normal file
@ -0,0 +1,6 @@
|
||||
|
||||
{
|
||||
"NotebookApp": {
|
||||
"password": "sha1:e49e73b0eb0e:353c38d87d79527e57da1bba5f65046d0b376d95"
|
||||
}
|
||||
}
|
||||
55
src/jupyter_notebook_config.py
Normal file
55
src/jupyter_notebook_config.py
Normal file
@ -0,0 +1,55 @@
|
||||
# Copyright (c) Jupyter Development Team.
|
||||
# Distributed under the terms of the Modified BSD License.
|
||||
|
||||
from jupyter_core.paths import jupyter_data_dir
|
||||
import subprocess
|
||||
import os
|
||||
import errno
|
||||
import stat
|
||||
|
||||
c = get_config()
|
||||
c.NotebookApp.ip = '0.0.0.0'
|
||||
c.NotebookApp.port = 8888
|
||||
c.NotebookApp.open_browser = False
|
||||
|
||||
# https://github.com/jupyter/notebook/issues/3130
|
||||
c.FileContentsManager.delete_to_trash = False
|
||||
|
||||
# Generate a self-signed certificate
|
||||
if 'GEN_CERT' in os.environ:
|
||||
dir_name = jupyter_data_dir()
|
||||
pem_file = os.path.join(dir_name, 'notebook.pem')
|
||||
try:
|
||||
os.makedirs(dir_name)
|
||||
except OSError as exc: # Python >2.5
|
||||
if exc.errno == errno.EEXIST and os.path.isdir(dir_name):
|
||||
pass
|
||||
else:
|
||||
raise
|
||||
|
||||
# Generate an openssl.cnf file to set the distinguished name
|
||||
cnf_file = os.path.join(os.getenv('CONDA_DIR', '/usr/lib'), 'ssl', 'openssl.cnf')
|
||||
if not os.path.isfile(cnf_file):
|
||||
with open(cnf_file, 'w') as fh:
|
||||
fh.write('''\
|
||||
[req]
|
||||
distinguished_name = req_distinguished_name
|
||||
[req_distinguished_name]
|
||||
''')
|
||||
|
||||
# Generate a certificate if one doesn't exist on disk
|
||||
subprocess.check_call(['openssl', 'req', '-new',
|
||||
'-newkey', 'rsa:2048',
|
||||
'-days', '365',
|
||||
'-nodes', '-x509',
|
||||
'-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated',
|
||||
'-keyout', pem_file,
|
||||
'-out', pem_file])
|
||||
# Restrict access to the file
|
||||
os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
|
||||
c.NotebookApp.certfile = pem_file
|
||||
|
||||
# Change default umask for all subprocesses of the notebook server if set in
|
||||
# the environment
|
||||
if 'NB_UMASK' in os.environ:
|
||||
os.umask(int(os.environ['NB_UMASK'], 8))
|
||||
15
src/start-notebook.sh
Executable file
15
src/start-notebook.sh
Executable file
@ -0,0 +1,15 @@
|
||||
#!/bin/bash
|
||||
# Copyright (c) Jupyter Development Team.
|
||||
# Distributed under the terms of the Modified BSD License.
|
||||
|
||||
set -e
|
||||
|
||||
if [[ ! -z "${JUPYTERHUB_API_TOKEN}" ]]; then
|
||||
# launched by JupyterHub, use single-user entrypoint
|
||||
exec /usr/local/bin/start-singleuser.sh "$@"
|
||||
elif [[ ! -z "${JUPYTER_ENABLE_LAB}" ]]; then
|
||||
. /usr/local/bin/start.sh jupyter lab "$@"
|
||||
else
|
||||
. /usr/local/bin/start.sh jupyter notebook "$@"
|
||||
fi
|
||||
|
||||
44
src/start-singleuser.sh
Executable file
44
src/start-singleuser.sh
Executable file
@ -0,0 +1,44 @@
|
||||
#!/bin/bash
|
||||
# Copyright (c) Jupyter Development Team.
|
||||
# Distributed under the terms of the Modified BSD License.
|
||||
|
||||
set -e
|
||||
|
||||
# set default ip to 0.0.0.0
|
||||
if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then
|
||||
NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS"
|
||||
fi
|
||||
|
||||
# handle some deprecated environment variables
|
||||
# from DockerSpawner < 0.8.
|
||||
# These won't be passed from DockerSpawner 0.9,
|
||||
# so avoid specifying --arg=empty-string
|
||||
if [ ! -z "$NOTEBOOK_DIR" ]; then
|
||||
NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS"
|
||||
fi
|
||||
if [ ! -z "$JPY_PORT" ]; then
|
||||
NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS"
|
||||
fi
|
||||
if [ ! -z "$JPY_USER" ]; then
|
||||
NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS"
|
||||
fi
|
||||
if [ ! -z "$JPY_COOKIE_NAME" ]; then
|
||||
NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS"
|
||||
fi
|
||||
if [ ! -z "$JPY_BASE_URL" ]; then
|
||||
NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS"
|
||||
fi
|
||||
if [ ! -z "$JPY_HUB_PREFIX" ]; then
|
||||
NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS"
|
||||
fi
|
||||
if [ ! -z "$JPY_HUB_API_URL" ]; then
|
||||
NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
|
||||
fi
|
||||
if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then
|
||||
NOTEBOOK_BIN="jupyter labhub"
|
||||
else
|
||||
NOTEBOOK_BIN="jupyterhub-singleuser"
|
||||
fi
|
||||
|
||||
. /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS "$@"
|
||||
|
||||
152
src/start.sh
Executable file
152
src/start.sh
Executable file
@ -0,0 +1,152 @@
|
||||
#!/bin/bash
|
||||
# Copyright (c) Jupyter Development Team.
|
||||
# Distributed under the terms of the Modified BSD License.
|
||||
|
||||
set -e
|
||||
|
||||
# Exec the specified command or fall back on bash
|
||||
if [ $# -eq 0 ]; then
|
||||
cmd=( "bash" )
|
||||
else
|
||||
cmd=( "$@" )
|
||||
fi
|
||||
|
||||
run-hooks () {
|
||||
# Source scripts or run executable files in a directory
|
||||
if [[ ! -d "$1" ]] ; then
|
||||
return
|
||||
fi
|
||||
echo "$0: running hooks in $1"
|
||||
for f in "$1/"*; do
|
||||
case "$f" in
|
||||
*.sh)
|
||||
echo "$0: running $f"
|
||||
source "$f"
|
||||
;;
|
||||
*)
|
||||
if [[ -x "$f" ]] ; then
|
||||
echo "$0: running $f"
|
||||
"$f"
|
||||
else
|
||||
echo "$0: ignoring $f"
|
||||
fi
|
||||
;;
|
||||
esac
|
||||
done
|
||||
echo "$0: done running hooks in $1"
|
||||
}
|
||||
|
||||
run-hooks /usr/local/bin/start-notebook.d
|
||||
|
||||
# Handle special flags if we're root
|
||||
if [ $(id -u) == 0 ] ; then
|
||||
|
||||
# Only attempt to change the jovyan username if it exists
|
||||
if id jovyan &> /dev/null ; then
|
||||
echo "Set username to: $NB_USER"
|
||||
usermod -d /home/$NB_USER -l $NB_USER jovyan
|
||||
fi
|
||||
|
||||
# Handle case where provisioned storage does not have the correct permissions by default
|
||||
# Ex: default NFS/EFS (no auto-uid/gid)
|
||||
if [[ "$CHOWN_HOME" == "1" || "$CHOWN_HOME" == 'yes' ]]; then
|
||||
echo "Changing ownership of /home/$NB_USER to $NB_UID:$NB_GID with options '${CHOWN_HOME_OPTS}'"
|
||||
chown $CHOWN_HOME_OPTS $NB_UID:$NB_GID /home/$NB_USER
|
||||
fi
|
||||
if [ ! -z "$CHOWN_EXTRA" ]; then
|
||||
for extra_dir in $(echo $CHOWN_EXTRA | tr ',' ' '); do
|
||||
echo "Changing ownership of ${extra_dir} to $NB_UID:$NB_GID with options '${CHOWN_EXTRA_OPTS}'"
|
||||
chown $CHOWN_EXTRA_OPTS $NB_UID:$NB_GID $extra_dir
|
||||
done
|
||||
fi
|
||||
|
||||
# handle home and working directory if the username changed
|
||||
if [[ "$NB_USER" != "jovyan" ]]; then
|
||||
# changing username, make sure homedir exists
|
||||
# (it could be mounted, and we shouldn't create it if it already exists)
|
||||
if [[ ! -e "/home/$NB_USER" ]]; then
|
||||
echo "Relocating home dir to /home/$NB_USER"
|
||||
mv /home/jovyan "/home/$NB_USER"
|
||||
fi
|
||||
# if workdir is in /home/jovyan, cd to /home/$NB_USER
|
||||
if [[ "$PWD/" == "/home/jovyan/"* ]]; then
|
||||
newcwd="/home/$NB_USER/${PWD:13}"
|
||||
echo "Setting CWD to $newcwd"
|
||||
cd "$newcwd"
|
||||
fi
|
||||
fi
|
||||
|
||||
# Change UID of NB_USER to NB_UID if it does not match
|
||||
if [ "$NB_UID" != $(id -u $NB_USER) ] ; then
|
||||
echo "Set $NB_USER UID to: $NB_UID"
|
||||
usermod -u $NB_UID $NB_USER
|
||||
fi
|
||||
|
||||
# Set NB_USER primary gid to NB_GID (after making the group). Set
|
||||
# supplementary gids to NB_GID and 100.
|
||||
if [ "$NB_GID" != $(id -g $NB_USER) ] ; then
|
||||
echo "Add $NB_USER to group: $NB_GID"
|
||||
groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
|
||||
usermod -g $NB_GID -aG 100 $NB_USER
|
||||
fi
|
||||
|
||||
# Enable sudo if requested
|
||||
if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
|
||||
echo "Granting $NB_USER sudo access and appending $CONDA_DIR/bin to sudo PATH"
|
||||
echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook
|
||||
fi
|
||||
|
||||
# Add $CONDA_DIR/bin to sudo secure_path
|
||||
sed -r "s#Defaults\s+secure_path=\"([^\"]+)\"#Defaults secure_path=\"\1:$CONDA_DIR/bin\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
|
||||
|
||||
# Exec the command as NB_USER with the PATH and the rest of
|
||||
# the environment preserved
|
||||
run-hooks /usr/local/bin/before-notebook.d
|
||||
echo "Executing the command: ${cmd[@]}"
|
||||
exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}"
|
||||
else
|
||||
if [[ "$NB_UID" == "$(id -u jovyan)" && "$NB_GID" == "$(id -g jovyan)" ]]; then
|
||||
# User is not attempting to override user/group via environment
|
||||
# variables, but they could still have overridden the uid/gid that
|
||||
# container runs as. Check that the user has an entry in the passwd
|
||||
# file and if not add an entry.
|
||||
STATUS=0 && whoami &> /dev/null || STATUS=$? && true
|
||||
if [[ "$STATUS" != "0" ]]; then
|
||||
if [[ -w /etc/passwd ]]; then
|
||||
echo "Adding passwd file entry for $(id -u)"
|
||||
cat /etc/passwd | sed -e "s/^jovyan:/nayvoj:/" > /tmp/passwd
|
||||
echo "jovyan:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
|
||||
cat /tmp/passwd > /etc/passwd
|
||||
rm /tmp/passwd
|
||||
else
|
||||
echo 'Container must be run with group "root" to update passwd file'
|
||||
fi
|
||||
fi
|
||||
|
||||
# Warn if the user isn't going to be able to write files to $HOME.
|
||||
if [[ ! -w /home/jovyan ]]; then
|
||||
echo 'Container must be run with group "users" to update files'
|
||||
fi
|
||||
else
|
||||
# Warn if looks like user want to override uid/gid but hasn't
|
||||
# run the container as root.
|
||||
if [[ ! -z "$NB_UID" && "$NB_UID" != "$(id -u)" ]]; then
|
||||
echo 'Container must be run as root to set $NB_UID'
|
||||
fi
|
||||
if [[ ! -z "$NB_GID" && "$NB_GID" != "$(id -g)" ]]; then
|
||||
echo 'Container must be run as root to set $NB_GID'
|
||||
fi
|
||||
fi
|
||||
|
||||
# Warn if looks like user want to run in sudo mode but hasn't run
|
||||
# the container as root.
|
||||
if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
|
||||
echo 'Container must be run as root to grant sudo permissions'
|
||||
fi
|
||||
|
||||
# Execute the command
|
||||
run-hooks /usr/local/bin/before-notebook.d
|
||||
echo "Executing the command: ${cmd[@]}"
|
||||
exec "${cmd[@]}"
|
||||
fi
|
||||
|
||||
4
start-local.sh
Executable file
4
start-local.sh
Executable file
@ -0,0 +1,4 @@
|
||||
#!/usr/bin/env bash
|
||||
cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
|
||||
|
||||
docker-compose up --build -d
|
||||
4
stop-local.sh
Executable file
4
stop-local.sh
Executable file
@ -0,0 +1,4 @@
|
||||
#!/usr/bin/env bash
|
||||
cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
|
||||
|
||||
docker-compose down
|
||||
Loading…
Reference in New Issue
Block a user