run Dockerfile inside .build
This commit is contained in:
Christoph Schranz
parent
923eaf0f8e
commit
c539c52880
438
Dockerfile
438
Dockerfile
@ -1,438 +0,0 @@
|
|||||||
# Use NVIDIA CUDA as base image and run the same installation as in the other packages.
|
|
||||||
FROM nvidia/cuda:10.1-base-ubuntu18.04
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
#################### Dependency: jupyter/base-image ########################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
# Ubuntu 18.04 (bionic)
|
|
||||||
# https://hub.docker.com/_/ubuntu/?tab=tags&name=bionic
|
|
||||||
ARG ROOT_CONTAINER=ubuntu:bionic-20200112@sha256:bc025862c3e8ec4a8754ea4756e33da6c41cba38330d7e324abd25c8e0b93300
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
ARG NB_USER="jovyan"
|
|
||||||
ARG NB_UID="1000"
|
|
||||||
ARG NB_GID="100"
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# Install all OS dependencies for notebook server that starts but lacks all
|
|
||||||
# features (e.g., download as all possible file formats)
|
|
||||||
ENV DEBIAN_FRONTEND noninteractive
|
|
||||||
RUN apt-get update \
|
|
||||||
&& apt-get install -yq --no-install-recommends \
|
|
||||||
wget \
|
|
||||||
bzip2 \
|
|
||||||
ca-certificates \
|
|
||||||
sudo \
|
|
||||||
locales \
|
|
||||||
fonts-liberation \
|
|
||||||
run-one \
|
|
||||||
&& apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
||||||
|
|
||||||
RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
|
|
||||||
locale-gen
|
|
||||||
|
|
||||||
# Configure environment
|
|
||||||
ENV CONDA_DIR=/opt/conda \
|
|
||||||
SHELL=/bin/bash \
|
|
||||||
NB_USER=$NB_USER \
|
|
||||||
NB_UID=$NB_UID \
|
|
||||||
NB_GID=$NB_GID \
|
|
||||||
LC_ALL=en_US.UTF-8 \
|
|
||||||
LANG=en_US.UTF-8 \
|
|
||||||
LANGUAGE=en_US.UTF-8
|
|
||||||
ENV PATH=$CONDA_DIR/bin:$PATH \
|
|
||||||
HOME=/home/$NB_USER
|
|
||||||
|
|
||||||
# Copy a script that we will use to correct permissions after running certain commands
|
|
||||||
COPY fix-permissions /usr/local/bin/fix-permissions
|
|
||||||
RUN chmod a+rx /usr/local/bin/fix-permissions
|
|
||||||
|
|
||||||
# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
|
|
||||||
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
|
|
||||||
|
|
||||||
# Create NB_USER wtih name jovyan user with UID=1000 and in the 'users' group
|
|
||||||
# and make sure these dirs are writable by the `users` group.
|
|
||||||
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
|
|
||||||
sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
|
|
||||||
sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
|
|
||||||
useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
|
|
||||||
mkdir -p $CONDA_DIR && \
|
|
||||||
chown $NB_USER:$NB_GID $CONDA_DIR && \
|
|
||||||
chmod g+w /etc/passwd && \
|
|
||||||
fix-permissions $HOME && \
|
|
||||||
fix-permissions "$(dirname $CONDA_DIR)"
|
|
||||||
|
|
||||||
USER $NB_UID
|
|
||||||
WORKDIR $HOME
|
|
||||||
ARG PYTHON_VERSION=default
|
|
||||||
|
|
||||||
# Setup work directory for backward-compatibility
|
|
||||||
RUN mkdir /home/$NB_USER/work && \
|
|
||||||
fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
# Install conda as jovyan and check the md5 sum provided on the download site
|
|
||||||
ENV MINICONDA_VERSION=4.7.12.1 \
|
|
||||||
MINICONDA_MD5=81c773ff87af5cfac79ab862942ab6b3 \
|
|
||||||
CONDA_VERSION=4.7.12
|
|
||||||
|
|
||||||
RUN cd /tmp && \
|
|
||||||
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
|
|
||||||
echo "${MINICONDA_MD5} *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
|
|
||||||
/bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
|
|
||||||
rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
|
|
||||||
echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
|
|
||||||
conda config --system --prepend channels conda-forge && \
|
|
||||||
conda config --system --set auto_update_conda false && \
|
|
||||||
conda config --system --set show_channel_urls true && \
|
|
||||||
if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \
|
|
||||||
conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
|
|
||||||
conda install --quiet --yes conda && \
|
|
||||||
conda install --quiet --yes pip && \
|
|
||||||
conda update --all --quiet --yes && \
|
|
||||||
conda clean --all -f -y && \
|
|
||||||
rm -rf /home/$NB_USER/.cache/yarn && \
|
|
||||||
fix-permissions $CONDA_DIR && \
|
|
||||||
fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
# Install Tini
|
|
||||||
RUN conda install --quiet --yes 'tini=0.18.0' && \
|
|
||||||
conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
|
|
||||||
conda clean --all -f -y && \
|
|
||||||
fix-permissions $CONDA_DIR && \
|
|
||||||
fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
# Install Jupyter Notebook, Lab, and Hub
|
|
||||||
# Generate a notebook server config
|
|
||||||
# Cleanup temporary files
|
|
||||||
# Correct permissions
|
|
||||||
# Do all this in a single RUN command to avoid duplicating all of the
|
|
||||||
# files across image layers when the permissions change
|
|
||||||
RUN conda install --quiet --yes \
|
|
||||||
'notebook=6.0.3' \
|
|
||||||
'jupyterhub=1.1.0' \
|
|
||||||
'jupyterlab=1.2.5' && \
|
|
||||||
conda clean --all -f -y && \
|
|
||||||
npm cache clean --force && \
|
|
||||||
jupyter notebook --generate-config && \
|
|
||||||
rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
|
|
||||||
rm -rf /home/$NB_USER/.cache/yarn && \
|
|
||||||
fix-permissions $CONDA_DIR && \
|
|
||||||
fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
EXPOSE 8888
|
|
||||||
|
|
||||||
# Configure container startup
|
|
||||||
ENTRYPOINT ["tini", "-g", "--"]
|
|
||||||
CMD ["start-notebook.sh"]
|
|
||||||
|
|
||||||
# Copy local files as late as possible to avoid cache busting
|
|
||||||
COPY start.sh /usr/local/bin/
|
|
||||||
COPY start-notebook.sh /usr/local/bin/
|
|
||||||
COPY start-singleuser.sh /usr/local/bin/
|
|
||||||
COPY jupyter_notebook_config.py /etc/jupyter/
|
|
||||||
|
|
||||||
# Fix permissions on /etc/jupyter as root
|
|
||||||
USER root
|
|
||||||
RUN fix-permissions /etc/jupyter/
|
|
||||||
|
|
||||||
# Switch back to jovyan to avoid accidental container runs as root
|
|
||||||
USER $NB_UID
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
################# Dependency: jupyter/minimal-notebook #####################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# Install all OS dependencies for fully functional notebook server
|
|
||||||
RUN apt-get update && apt-get install -yq --no-install-recommends \
|
|
||||||
build-essential \
|
|
||||||
emacs \
|
|
||||||
git \
|
|
||||||
inkscape \
|
|
||||||
jed \
|
|
||||||
libsm6 \
|
|
||||||
libxext-dev \
|
|
||||||
libxrender1 \
|
|
||||||
lmodern \
|
|
||||||
netcat \
|
|
||||||
python-dev \
|
|
||||||
# ---- nbconvert dependencies ----
|
|
||||||
texlive-xetex \
|
|
||||||
texlive-fonts-recommended \
|
|
||||||
texlive-generic-recommended \
|
|
||||||
# Optional dependency
|
|
||||||
texlive-fonts-extra \
|
|
||||||
# ----
|
|
||||||
tzdata \
|
|
||||||
unzip \
|
|
||||||
nano \
|
|
||||||
&& apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
||||||
|
|
||||||
# Switch back to jovyan to avoid accidental container runs as root
|
|
||||||
USER $NB_UID
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
################# Dependency: jupyter/scipy-notebook #######################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
|
|
||||||
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 \
|
|
||||||
'beautifulsoup4=4.8.*' \
|
|
||||||
'conda-forge::blas=*=openblas' \
|
|
||||||
'bokeh=1.4.*' \
|
|
||||||
'cloudpickle=1.2.*' \
|
|
||||||
'cython=0.29.*' \
|
|
||||||
'dask=2.9.*' \
|
|
||||||
'dill=0.3.*' \
|
|
||||||
'h5py=2.10.*' \
|
|
||||||
'hdf5=1.10.*' \
|
|
||||||
'ipywidgets=7.5.*' \
|
|
||||||
'matplotlib-base=3.1.*' \
|
|
||||||
'numba=0.48.*' \
|
|
||||||
'numexpr=2.7.*' \
|
|
||||||
'pandas=0.25.*' \
|
|
||||||
'patsy=0.5.*' \
|
|
||||||
'protobuf=3.11.*' \
|
|
||||||
'scikit-image=0.16.*' \
|
|
||||||
'scikit-learn=0.22.*' \
|
|
||||||
'scipy=1.4.*' \
|
|
||||||
'seaborn=0.9.*' \
|
|
||||||
'sqlalchemy=1.3.*' \
|
|
||||||
'statsmodels=0.11.*' \
|
|
||||||
'sympy=1.5.*' \
|
|
||||||
'vincent=0.4.*' \
|
|
||||||
'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 && \
|
|
||||||
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
|
|
||||||
|
|
||||||
USER $NB_UID
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
################ Dependency: jupyter/datascience-notebook ##################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
|
|
||||||
# Set when building on Travis so that certain long-running build steps can
|
|
||||||
# be skipped to shorten build time.
|
|
||||||
ARG TEST_ONLY_BUILD
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# R pre-requisites
|
|
||||||
RUN apt-get update && \
|
|
||||||
apt-get install -y --no-install-recommends \
|
|
||||||
fonts-dejavu \
|
|
||||||
gfortran \
|
|
||||||
gcc && \
|
|
||||||
rm -rf /var/lib/apt/lists/*
|
|
||||||
|
|
||||||
# Julia dependencies
|
|
||||||
# install Julia packages in /opt/julia instead of $HOME
|
|
||||||
ENV JULIA_DEPOT_PATH=/opt/julia
|
|
||||||
ENV JULIA_PKGDIR=/opt/julia
|
|
||||||
ENV JULIA_VERSION=1.3.1
|
|
||||||
|
|
||||||
RUN mkdir /opt/julia-${JULIA_VERSION} && \
|
|
||||||
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 "faa707c8343780a6fe5eaf13490355e8190acf8e2c189b9e7ecbddb0fa2643ad *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 && \
|
|
||||||
fix-permissions $JULIA_PKGDIR
|
|
||||||
|
|
||||||
USER $NB_UID
|
|
||||||
|
|
||||||
# R packages including IRKernel which gets installed globally.
|
|
||||||
RUN conda install --quiet --yes \
|
|
||||||
'r-base=3.6.2' \
|
|
||||||
'r-caret=6.0*' \
|
|
||||||
'r-crayon=1.3*' \
|
|
||||||
'r-devtools=2.2*' \
|
|
||||||
'r-forecast=8.10*' \
|
|
||||||
'r-hexbin=1.28*' \
|
|
||||||
'r-htmltools=0.4*' \
|
|
||||||
'r-htmlwidgets=1.5*' \
|
|
||||||
'r-irkernel=1.1*' \
|
|
||||||
'r-nycflights13=1.0*' \
|
|
||||||
'r-plyr=1.8*' \
|
|
||||||
'r-randomforest=4.6*' \
|
|
||||||
'r-rcurl=1.98*' \
|
|
||||||
'r-reshape2=1.4*' \
|
|
||||||
'r-rmarkdown=2.1*' \
|
|
||||||
'r-rsqlite=2.1*' \
|
|
||||||
'r-shiny=1.3*' \
|
|
||||||
'r-tidyverse=1.3*' \
|
|
||||||
'rpy2=3.1*' \
|
|
||||||
&& \
|
|
||||||
conda clean --all -f -y && \
|
|
||||||
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")') && \
|
|
||||||
julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \
|
|
||||||
# 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/tensorflow-notebook ###################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
|
|
||||||
# Install Tensorflow
|
|
||||||
RUN pip install --quiet \
|
|
||||||
'tensorflow==2.1.0' && \
|
|
||||||
fix-permissions $CONDA_DIR && \
|
|
||||||
fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
########################## 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 ###############################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Update conda
|
|
||||||
RUN conda update -n base conda -y
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# Install elasticsearch libs
|
|
||||||
USER root
|
|
||||||
RUN apt-get update \
|
|
||||||
&& curl -sL https://repo1.maven.org/maven2/org/elasticsearch/elasticsearch-hadoop/6.8.1/elasticsearch-hadoop-6.8.1.jar
|
|
||||||
RUN pip install --no-cache-dir elasticsearch==7.1.0
|
|
||||||
|
|
||||||
# Install rpy2 to share data between Python and R
|
|
||||||
RUN conda install rpy2=2.9.4 plotly=4.4.1
|
|
||||||
RUN conda install -c conda-forge ipyleaflet
|
|
||||||
|
|
||||||
# Install important packages and Graphviz
|
|
||||||
RUN set -ex \
|
|
||||||
&& buildDeps=' \
|
|
||||||
graphviz==0.11 \
|
|
||||||
' \
|
|
||||||
&& apt-get update \
|
|
||||||
&& apt-get -y install htop apt-utils graphviz libgraphviz-dev \
|
|
||||||
&& pip install --no-cache-dir $buildDeps
|
|
||||||
|
|
||||||
# Install various extensions
|
|
||||||
RUN jupyter labextension install @jupyterlab/github
|
|
||||||
RUN jupyter labextension install jupyterlab-drawio
|
|
||||||
RUN jupyter labextension install jupyter-leaflet
|
|
||||||
RUN jupyter labextension install @jupyterlab/plotly-extension
|
|
||||||
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
|
|
||||||
RUN pip install --no-cache-dir jupyter-tabnine==1.0.2 && \
|
|
||||||
jupyter nbextension install --py jupyter_tabnine && \
|
|
||||||
jupyter nbextension enable --py jupyter_tabnine && \
|
|
||||||
jupyter serverextension enable --py jupyter_tabnine
|
|
||||||
RUN fix-permissions $CONDA_DIR
|
|
||||||
RUN conda install -c conda-forge jupyter_contrib_nbextensions && \
|
|
||||||
conda install -c conda-forge jupyter_nbextensions_configurator && \
|
|
||||||
jupyter nbextension enable codefolding/main
|
|
||||||
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
|
|
||||||
|
|
||||||
# Copying config and fix permissions
|
|
||||||
COPY jupyter_notebook_config.json /etc/jupyter/
|
|
||||||
RUN fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
# Switch back to jovyan to avoid accidental container runs as root
|
|
||||||
USER $NB_UID
|
|
||||||
@ -39,7 +39,7 @@ docker-compose (internally):
|
|||||||
|
|
||||||
```bash
|
```bash
|
||||||
./generate_Dockerfile.sh
|
./generate_Dockerfile.sh
|
||||||
docker build -t gpu-jupyter .
|
docker build -t gpu-jupyter .build/
|
||||||
docker run -d -p [port]:8888 gpu-jupyter
|
docker run -d -p [port]:8888 gpu-jupyter
|
||||||
```
|
```
|
||||||
|
|
||||||
|
|||||||
@ -2,7 +2,7 @@ version: "3.4"
|
|||||||
services:
|
services:
|
||||||
gpu-jupyter:
|
gpu-jupyter:
|
||||||
image: 127.0.0.1:$REGISTRY_PORT/gpu-jupyter
|
image: 127.0.0.1:$REGISTRY_PORT/gpu-jupyter
|
||||||
build: .
|
build: .build
|
||||||
ports:
|
ports:
|
||||||
- $JUPYTER_PORT:8888
|
- $JUPYTER_PORT:8888
|
||||||
volumes:
|
volumes:
|
||||||
|
|||||||
@ -2,7 +2,7 @@ version: "3.4"
|
|||||||
services:
|
services:
|
||||||
gpu-jupyter:
|
gpu-jupyter:
|
||||||
image: 127.0.0.1:5001/gpu-jupyter
|
image: 127.0.0.1:5001/gpu-jupyter
|
||||||
build: .
|
build: .build
|
||||||
ports:
|
ports:
|
||||||
- ${JUPYTER_PORT}:8888
|
- ${JUPYTER_PORT}:8888
|
||||||
volumes:
|
volumes:
|
||||||
|
|||||||
@ -1,35 +0,0 @@
|
|||||||
#!/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
|
|
||||||
@ -1,6 +0,0 @@
|
|||||||
|
|
||||||
{
|
|
||||||
"NotebookApp": {
|
|
||||||
"password": "sha1:e49e73b0eb0e:32edae7a5fd119045e699a0bd04f90819ca90cd6"
|
|
||||||
}
|
|
||||||
}
|
|
||||||
@ -1,55 +0,0 @@
|
|||||||
# 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))
|
|
||||||
@ -1,19 +0,0 @@
|
|||||||
#!/bin/bash
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
set -e
|
|
||||||
|
|
||||||
wrapper=""
|
|
||||||
if [[ "${RESTARTABLE}" == "yes" ]]; then
|
|
||||||
wrapper="run-one-constantly"
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [[ ! -z "${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 $wrapper jupyter lab "$@"
|
|
||||||
else
|
|
||||||
. /usr/local/bin/start.sh $wrapper jupyter notebook "$@"
|
|
||||||
fi
|
|
||||||
@ -1,43 +0,0 @@
|
|||||||
#!/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 $NOTEBOOK_ARGS "$@"
|
|
||||||
147
start.sh
147
start.sh
@ -1,147 +0,0 @@
|
|||||||
#!/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/$NB_USER" || ln -s /home/jovyan "/home/$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:GID of NB_USER to NB_UID:NB_GID if it does not match
|
|
||||||
if [ "$NB_UID" != $(id -u $NB_USER) ] || [ "$NB_GID" != $(id -g $NB_USER) ]; then
|
|
||||||
echo "Set user $NB_USER UID:GID to: $NB_UID:$NB_GID"
|
|
||||||
if [ "$NB_GID" != $(id -g $NB_USER) ]; then
|
|
||||||
groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
|
|
||||||
fi
|
|
||||||
userdel $NB_USER
|
|
||||||
useradd --home /home/$NB_USER -u $NB_UID -g $NB_GID -G 100 -l $NB_USER
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Enable sudo if requested
|
|
||||||
if [[ "$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
|
|
||||||
Loading…
Reference in New Issue
Block a user