481 lines
17 KiB
Docker
Executable File
481 lines
17 KiB
Docker
Executable File
# This Dockerfile is generated by 'generate-Dockerfile.sh' from elements within 'src/'
|
|
|
|
# **Please do not change this file directly!**
|
|
# To adapt this Dockerfile, adapt 'generate-Dockerfile.sh' or 'src/Dockerfile.usefulpackages'.
|
|
# More information can be found in the README under configuration.
|
|
|
|
|
|
# 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:11.2.0-runtime-ubuntu20.04
|
|
LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
|
|
# 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-20201106@sha256:4e4bc990609ed865e07afc8427c30ffdddca5153fd4e82c20d8f0783a291e241
|
|
|
|
|
|
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
|
|
|
|
# ---- Miniforge installer ----
|
|
# Default values can be overridden at build time
|
|
# (ARGS are in lower case to distinguish them from ENV)
|
|
# Check https://github.com/conda-forge/miniforge/releases
|
|
# Conda version
|
|
ARG conda_version="4.9.2"
|
|
# Miniforge installer patch version
|
|
ARG miniforge_patch_number="0"
|
|
# Miniforge installer architecture
|
|
ARG miniforge_arch="x86_64"
|
|
# Python implementation to use
|
|
# can be either Miniforge3 to use Python or Miniforge-pypy3 to use PyPy
|
|
ARG miniforge_python="Miniforge3"
|
|
|
|
# Miniforge archive to install
|
|
ARG miniforge_version="${conda_version}-${miniforge_patch_number}"
|
|
# Miniforge installer
|
|
ARG miniforge_installer="${miniforge_python}-${miniforge_version}-Linux-${miniforge_arch}.sh"
|
|
# Miniforge checksum
|
|
ARG miniforge_checksum="6321775eb2c02d7f51d3a9004ce0be839099f126f4099c781531428536669560"
|
|
|
|
# Install all OS dependencies for notebook server that starts but lacks all
|
|
# features (e.g., download as all possible file formats)
|
|
ENV DEBIAN_FRONTEND noninteractive
|
|
RUN apt-get update \
|
|
&& apt-get install -yq --no-install-recommends \
|
|
wget \
|
|
ca-certificates \
|
|
sudo \
|
|
locales \
|
|
fonts-liberation \
|
|
run-one \
|
|
&& apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
|
|
RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
|
|
locale-gen
|
|
|
|
# Configure environment
|
|
ENV CONDA_DIR=/opt/conda \
|
|
SHELL=/bin/bash \
|
|
NB_USER=$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/$NB_USER \
|
|
CONDA_VERSION="${conda_version}" \
|
|
MINIFORGE_VERSION="${miniforge_version}"
|
|
|
|
# Copy a script that we will use to correct permissions after running certain commands
|
|
COPY fix-permissions /usr/local/bin/fix-permissions
|
|
RUN chmod a+rx /usr/local/bin/fix-permissions
|
|
|
|
# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
|
|
# hadolint ignore=SC2016
|
|
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
|
|
# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
|
|
echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
|
|
|
|
# Create NB_USER with 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 $NB_UID
|
|
ARG PYTHON_VERSION=default
|
|
|
|
# Setup work directory for backward-compatibility
|
|
RUN mkdir "/home/$NB_USER/work" && \
|
|
fix-permissions "/home/$NB_USER"
|
|
|
|
# Install conda as jovyan and check the sha256 sum provided on the download site
|
|
WORKDIR /tmp
|
|
|
|
# Prerequisites installation: conda, pip, tini
|
|
RUN wget --quiet "https://github.com/conda-forge/miniforge/releases/download/${miniforge_version}/${miniforge_installer}" && \
|
|
echo "${miniforge_checksum} *${miniforge_installer}" | sha256sum --check && \
|
|
/bin/bash "${miniforge_installer}" -f -b -p $CONDA_DIR && \
|
|
rm "${miniforge_installer}" && \
|
|
# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
|
|
echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
|
|
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_VERSION}" \
|
|
'pip' \
|
|
'tini=0.18.0' && \
|
|
conda update --all --quiet --yes && \
|
|
conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
|
|
conda clean --all -f -y && \
|
|
rm -rf /home/$NB_USER/.cache/yarn && \
|
|
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=6.1.6' \
|
|
'jupyterhub=1.3.0' \
|
|
'jupyterlab=2.2.9' && \
|
|
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/
|
|
# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
|
|
COPY jupyter_notebook_config.py /etc/jupyter/
|
|
|
|
# Fix permissions on /etc/jupyter as root
|
|
USER root
|
|
|
|
# Prepare upgrade to JupyterLab V3.0 #1205
|
|
RUN sed -re "s/c.NotebookApp/c.ServerApp/g" \
|
|
/etc/jupyter/jupyter_notebook_config.py > /etc/jupyter/jupyter_server_config.py
|
|
|
|
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 \
|
|
vim-tiny \
|
|
git \
|
|
inkscape \
|
|
libsm6 \
|
|
libxext-dev \
|
|
libxrender1 \
|
|
lmodern \
|
|
netcat \
|
|
# ---- nbconvert dependencies ----
|
|
texlive-xetex \
|
|
texlive-fonts-recommended \
|
|
texlive-plain-generic \
|
|
# ----
|
|
tzdata \
|
|
unzip \
|
|
nano-tiny \
|
|
&& apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
|
|
# Create alternative for nano -> nano-tiny
|
|
RUN update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
|
|
|
|
# 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+cm-super for latex labels
|
|
RUN apt-get update && \
|
|
apt-get install -y --no-install-recommends ffmpeg dvipng cm-super && \
|
|
apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
|
|
USER $NB_UID
|
|
|
|
# Install Python 3 packages
|
|
RUN conda install --quiet --yes \
|
|
'beautifulsoup4=4.9.*' \
|
|
'conda-forge::blas=*=openblas' \
|
|
'bokeh=2.2.*' \
|
|
'bottleneck=1.3.*' \
|
|
'cloudpickle=1.6.*' \
|
|
'cython=0.29.*' \
|
|
'dask=2020.12.*' \
|
|
'dill=0.3.*' \
|
|
'h5py=3.1.*' \
|
|
'ipywidgets=7.6.*' \
|
|
'ipympl=0.5.*'\
|
|
'matplotlib-base=3.3.*' \
|
|
'numba=0.52.*' \
|
|
'numexpr=2.7.*' \
|
|
'pandas=1.1.*' \
|
|
'patsy=0.5.*' \
|
|
'protobuf=3.14.*' \
|
|
'pytables=3.6.*' \
|
|
'scikit-image=0.18.*' \
|
|
'scikit-learn=0.24.*' \
|
|
'scipy=1.5.*' \
|
|
'seaborn=0.11.*' \
|
|
'sqlalchemy=1.3.*' \
|
|
'statsmodels=0.12.*' \
|
|
'sympy=1.7.*' \
|
|
'vincent=0.4.*' \
|
|
'widgetsnbextension=3.5.*'\
|
|
'xlrd=1.2.*' \
|
|
&& \
|
|
conda clean --all -f -y && \
|
|
# Activate ipywidgets extension in the environment that runs the notebook server
|
|
jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
|
|
# Also activate ipywidgets extension for JupyterLab
|
|
# Check this URL for most recent compatibilities
|
|
# https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
|
|
jupyter labextension install @jupyter-widgets/jupyterlab-manager@^2.0.0 --no-build && \
|
|
jupyter labextension install @bokeh/jupyter_bokeh@^2.0.0 --no-build && \
|
|
jupyter labextension install jupyter-matplotlib@^0.7.2 --no-build && \
|
|
jupyter lab build -y && \
|
|
jupyter lab clean -y && \
|
|
npm cache clean --force && \
|
|
rm -rf "/home/${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
|
|
|
|
# Julia installation
|
|
# Default values can be overridden at build time
|
|
# (ARGS are in lower case to distinguish them from ENV)
|
|
# Check https://julialang.org/downloads/
|
|
ARG julia_version="1.5.3"
|
|
# SHA256 checksum
|
|
ARG julia_checksum="f190c938dd6fed97021953240523c9db448ec0a6760b574afd4e9924ab5615f1"
|
|
|
|
# R pre-requisites
|
|
RUN apt-get update && \
|
|
apt-get install -y --no-install-recommends \
|
|
fonts-dejavu \
|
|
gfortran \
|
|
gcc && \
|
|
apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
|
|
# Julia dependencies
|
|
# install Julia packages in /opt/julia instead of $HOME
|
|
ENV JULIA_DEPOT_PATH=/opt/julia \
|
|
JULIA_PKGDIR=/opt/julia \
|
|
JULIA_VERSION="${julia_version}"
|
|
|
|
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 "${julia_checksum} *julia-${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 $NB_UID
|
|
|
|
# R packages including IRKernel which gets installed globally.
|
|
RUN conda install --quiet --yes \
|
|
'r-base=4.0.3' \
|
|
'r-caret=6.0*' \
|
|
'r-crayon=1.3*' \
|
|
'r-devtools=2.3*' \
|
|
'r-forecast=8.13*' \
|
|
'r-hexbin=1.28*' \
|
|
'r-htmltools=0.5*' \
|
|
'r-htmlwidgets=1.5*' \
|
|
'r-irkernel=1.1*' \
|
|
'r-nycflights13=1.0*' \
|
|
'r-randomforest=4.6*' \
|
|
'r-rcurl=1.98*' \
|
|
'r-rmarkdown=2.6*' \
|
|
'r-rsqlite=2.2*' \
|
|
'r-shiny=1.5*' \
|
|
'r-tidyverse=1.3*' \
|
|
'rpy2=3.3*' && \
|
|
conda clean --all -f -y && \
|
|
fix-permissions "${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 pip install --upgrade pip && \
|
|
pip install --no-cache-dir "tensorflow==2.3.2" && \
|
|
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 && \
|
|
RUN pip install --no-cache-dir torchviz
|
|
|
|
|
|
# Clean installation
|
|
RUN conda clean --all -f -y && \
|
|
fix-permissions $CONDA_DIR && \
|
|
fix-permissions /home/$NB_USER
|
|
|
|
############################################################################
|
|
############################ Useful packages ###############################
|
|
############################################################################
|
|
|
|
LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
|
|
|
|
USER root
|
|
|
|
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 openssh-client \
|
|
&& pip install --no-cache-dir $buildDeps
|
|
|
|
# Install various extensions
|
|
RUN fix-permissions $CONDA_DIR
|
|
RUN jupyter labextension install @jupyterlab/github
|
|
RUN jupyter labextension install jupyterlab-drawio
|
|
RUN jupyter labextension install jupyter-leaflet
|
|
RUN jupyter labextension install jupyterlab-plotly@4.8.1
|
|
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
|
|
RUN pip install --no-cache-dir jupyter-tabnine==1.1.0 --user && \
|
|
jupyter nbextension install --py jupyter_tabnine --user && \
|
|
jupyter nbextension enable --py jupyter_tabnine --user && \
|
|
jupyter serverextension enable --py jupyter_tabnine --user
|
|
RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
|
|
jupyter_nbextensions_configurator rise
|
|
# jupyter nbextension enable codefolding/main
|
|
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
|
|
|
|
RUN fix-permissions /home/$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/
|