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gpu-jupyter/.build/Dockerfile
Michael Pilosov 6766adb7fe add openssh-client to enable git clone via ssh 
I like to mount my .ssh and .gitconfig folders inside of containers, and was surprised to find myself unable to `git clone git@github.com: ...`, this addresses that. Adds about 7MB to docker image.
2020-08-08 12:29:37 -06:00

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# This adaptive Dockerfile is generated by 'generate-Dockerfile.sh' from parts within src/
# Use NVIDIA CUDA as base image and run the same installation as in the other packages.
# The version of cudatoolkit must match those of the base image, see Dockerfile.pytorch
FROM nvidia/cuda:10.1-base-ubuntu18.04
LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
# This is a concatenated Dockerfile, the maintainers of subsequent sections may vary.
RUN chmod 1777 /tmp && chmod 1777 /var/tmp
############################################################################
#################### Dependency: jupyter/base-image ########################
############################################################################
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
# Ubuntu 20.04 (focal)
# https://hub.docker.com/_/ubuntu/?tab=tags&name=focal
# OS/ARCH: linux/amd64
ARG ROOT_CONTAINER=ubuntu:focal-20200423@sha256:238e696992ba9913d24cfc3727034985abd136e08ee3067982401acdc30cbf3f
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"
# Fix DL4006
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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 \
openssh-client \
&& 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 $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/$NB_USER
# Install conda as jovyan and check the md5 sum provided on the download site
ENV MINICONDA_VERSION=4.8.2 \
MINICONDA_MD5=87e77f097f6ebb5127c77662dfc3165e \
CONDA_VERSION=4.8.2
WORKDIR /tmp
RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
echo "${MINICONDA_MD5} *Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
/bin/bash Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
rm Miniconda3-py37_${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 && \
conda config --system --set channel_priority strict && \
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=2.1.3' && \
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 start-notebook.sh 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
WORKDIR $HOME
############################################################################
################# 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-nox \
vim-tiny \
git \
inkscape \
jed \
libsm6 \
libxext-dev \
libxrender1 \
lmodern \
netcat \
python-dev \
# ---- nbconvert dependencies ----
texlive-xetex \
texlive-fonts-recommended \
texlive-plain-generic \
# 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 & dvipng for latex labels
RUN apt-get update && \
apt-get install -y --no-install-recommends ffmpeg dvipng && \
rm -rf /var/lib/apt/lists/*
USER $NB_UID
# Install Python 3 packages
RUN conda install --quiet --yes \
'beautifulsoup4=4.9.*' \
'conda-forge::blas=*=openblas' \
'bokeh=2.0.*' \
'bottleneck=1.3.*' \
'cloudpickle=1.4.*' \
'cython=0.29.*' \
'dask=2.15.*' \
'dill=0.3.*' \
'h5py=2.10.*' \
'hdf5=1.10.*' \
'ipywidgets=7.5.*' \
'ipympl=0.5.*'\
'matplotlib-base=3.2.*' \
# numba update to 0.49 fails resolving deps.
'numba=0.48.*' \
'numexpr=2.7.*' \
'pandas=1.0.*' \
'patsy=0.5.*' \
'protobuf=3.11.*' \
'pytables=3.6.*' \
'scikit-image=0.16.*' \
'scikit-learn=0.22.*' \
'scipy=1.4.*' \
'seaborn=0.10.*' \
'sqlalchemy=1.3.*' \
'statsmodels=0.11.*' \
'sympy=1.5.*' \
'vincent=0.4.*' \
'widgetsnbextension=3.5.*'\
'xlrd=1.2.*' \
&& \
conda clean --all -f -y && \
# Activate ipywidgets extension in the environment that runs the notebook server
jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
# Also activate ipywidgets extension for JupyterLab
# Check this URL for most recent compatibilities
# https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
jupyter labextension install @jupyter-widgets/jupyterlab-manager@^2.0.0 --no-build && \
jupyter labextension install @bokeh/jupyter_bokeh@^2.0.0 --no-build && \
jupyter labextension install jupyter-matplotlib@^0.7.2 --no-build && \
jupyter lab build -y && \
jupyter lab clean -y && \
npm cache clean --force && \
rm -rf "/home/${NB_USER}/.cache/yarn" && \
rm -rf "/home/${NB_USER}/.node-gyp" && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# Install facets which does not have a pip or conda package at the moment
WORKDIR /tmp
RUN git clone https://github.com/PAIR-code/facets.git && \
jupyter nbextension install facets/facets-dist/ --sys-prefix && \
rm -rf /tmp/facets && \
fix-permissions "${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
WORKDIR $HOME
############################################################################
################ 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
# Fix DL4006
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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 $HOME
ENV JULIA_DEPOT_PATH=/opt/julia
ENV JULIA_PKGDIR=/opt/julia
ENV JULIA_VERSION=1.4.1
WORKDIR /tmp
# hadolint ignore=SC2046
RUN mkdir "/opt/julia-${JULIA_VERSION}" && \
wget -q https://julialang-s3.julialang.org/bin/linux/x64/$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)"/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" && \
echo "fd6d8cadaed678174c3caefb92207a3b0e8da9f926af6703fb4d1e4e4f50610a *julia-${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 $NB_UID
# R packages including IRKernel which gets installed globally.
RUN conda install --quiet --yes \
'r-base=3.6.3' \
'r-caret=6.0*' \
'r-crayon=1.3*' \
'r-devtools=2.3*' \
'r-forecast=8.12*' \
'r-hexbin=1.28*' \
'r-htmltools=0.4*' \
'r-htmlwidgets=1.5*' \
'r-irkernel=1.1*' \
'r-nycflights13=1.0*' \
'r-plyr=1.8*' \
'r-randomforest=4.6*' \
'r-rcurl=1.98*' \
'r-reshape2=1.4*' \
'r-rmarkdown=2.1*' \
'r-rsqlite=2.2*' \
'r-shiny=1.4*' \
'r-tidyverse=1.3*' \
'rpy2=3.1*' \
&& \
conda clean --all -f -y && \
fix-permissions "${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"
WORKDIR $HOME
############################################################################
########################## Dependency: gpulibs #############################
############################################################################
LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
# Install Tensorflow, check compatibility here: https://www.tensorflow.org/install/gpu
# installation via conda leads to errors in version 4.8.2
#RUN conda install --quiet --yes \
# 'tensorflow-gpu=2.1*' \
# 'keras-gpu' && \
# fix-permissions $CONDA_DIR && \
# fix-permissions /home/$NB_USER
RUN pip install --upgrade pip && \
pip install --no-cache-dir "tensorflow-gpu>=2.1.*" && \
pip install --no-cache-dir keras
# Install PyTorch with dependencies
RUN conda install --quiet --yes \
pyyaml mkl mkl-include setuptools cmake cffi typing
# Check compatibility here: https://pytorch.org/get-started/locally/
RUN conda install --quiet --yes \
pytorch \
torchvision \
cudatoolkit=10.1 -c pytorch
# pip install torch_nightly -f https://download.pytorch.org/whl/nightly/cu90/torch_nightly.html && \
# Clean installation
RUN conda clean --all -f -y && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
############################################################################
############################ Useful packages ###############################
############################################################################
LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
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
RUN pip install --no-cache-dir ipyleaflet plotly==4.8.* "ipywidgets>=7.5"
# 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 fix-permissions $CONDA_DIR
RUN jupyter labextension install @jupyterlab/github
RUN jupyter labextension install jupyterlab-drawio
RUN jupyter labextension install jupyter-leaflet
RUN jupyter labextension install jupyterlab-plotly@4.8.1
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
RUN pip install --no-cache-dir jupyter-tabnine==1.0.2 && \
jupyter nbextension install --py jupyter_tabnine && \
jupyter nbextension enable --py jupyter_tabnine && \
jupyter serverextension enable --py jupyter_tabnine
RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
jupyter_nbextensions_configurator rise && \
jupyter nbextension enable codefolding/main
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
RUN fix-permissions /home/$NB_USER
# Switch back to jovyan to avoid accidental container runs as root
USER $NB_UID
# Copy jupyter_notebook_config.json
COPY jupyter_notebook_config.json /etc/jupyter/
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