Dockerfile

# 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 cuda must match those of the packages installed in src/Dockerfile.gpulibs
FROM nvidia/cuda:11.6.2-cudnn8-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

# install apt-utils in header to fix warnings in docker-stacks
RUN apt-get update && \
    apt-get -y install apt-utils

############################################################################
#################### 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
ARG ROOT_CONTAINER=ubuntu:focal


LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"

# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
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 --yes && \
    # - apt-get upgrade is run to patch known vulnerabilities in apt-get packages as
    #   the ubuntu base image is rebuilt too seldom sometimes (less than once a month)
    apt-get upgrade --yes && \
    apt-get install --yes --no-install-recommends \
    # - bzip2 is necessary to extract the micromamba executable.
    bzip2 \
    ca-certificates \
    fonts-liberation \
    locales \
    # - pandoc is used to convert notebooks to html files
    #   it's not present in arm64 ubuntu image, so we install it here
    pandoc \
    # - run-one - a wrapper script that runs no more
    #   than one unique  instance  of  some  command with a unique set of arguments,
    #   we use `run-one-constantly` to support `RESTARTABLE` option
    run-one \
    sudo \
    # - tini is installed as a helpful container entrypoint that reaps zombie
    #   processes and such of the actual executable we want to start, see
    #   https://github.com/krallin/tini#why-tini for details.
    tini \
    wget && \
    apt-get clean && rm -rf /var/lib/apt/lists/* && \
    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
# 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 -l -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}

# Pin python version here, or set it to "default"
ARG PYTHON_VERSION=3.10

# Setup work directory for backward-compatibility
RUN mkdir "/home/${NB_USER}/work" && \
    fix-permissions "/home/${NB_USER}"

# Download and install Micromamba, and initialize Conda prefix.
#   <https://github.com/mamba-org/mamba#micromamba>
#   Similar projects using Micromamba:
#     - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
#     - repo2docker: <https://github.com/jupyterhub/repo2docker>
# Install Python, Mamba, Jupyter Notebook, Lab, and Hub
# Generate a notebook server config
# Cleanup temporary files and remove Micromamba
# Correct permissions
# Do all this in a single RUN command to avoid duplicating all of the
# files across image layers when the permissions change
COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
WORKDIR /tmp
RUN set -x && \
    arch=$(uname -m) && \
    if [ "${arch}" = "x86_64" ]; then \
        # Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
        arch="64"; \
    fi && \
    wget -qO /tmp/micromamba.tar.bz2 \
        "https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
    tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
    rm /tmp/micromamba.tar.bz2 && \
    PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
    if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
    # Install the packages
    ./micromamba install \
        --root-prefix="${CONDA_DIR}" \
        --prefix="${CONDA_DIR}" \
        --yes \
        "${PYTHON_SPECIFIER}" \
        'mamba' \
        'notebook' \
        'jupyterhub' \
        'jupyterlab' && \
    rm micromamba && \
    # Pin major.minor version of python
    mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
    jupyter notebook --generate-config && \
    mamba clean --all -f -y && \
    npm cache clean --force && \
    jupyter lab clean && \
    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_server_config.py /etc/jupyter/

# Fix permissions on /etc/jupyter as root
USER root

# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
    /etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
    fix-permissions /etc/jupyter/

# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
HEALTHCHECK  --interval=15s --timeout=3s --start-period=5s --retries=3 \
    CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
    http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1

# 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.
ARG OWNER=jupyter

LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"

# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

USER root

# Install all OS dependencies for fully functional notebook server
RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    # Common useful utilities
    git \
    nano-tiny \
    tzdata \
    unzip \
    vim-tiny \
    # Inkscape is installed to be able to convert SVG files
    inkscape \
    # git-over-ssh
    openssh-client \
    # less is needed to run help in R
    # see: https://github.com/jupyter/docker-stacks/issues/1588
    less \
    # nbconvert dependencies
    # https://nbconvert.readthedocs.io/en/latest/install.html#installing-tex
    texlive-xetex \
    texlive-fonts-recommended \
    texlive-plain-generic && \
    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.
ARG OWNER=jupyter

LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"

# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

USER root

RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    # for cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
    build-essential \
    # for latex labels
    cm-super \
    dvipng \
    # for matplotlib anim
    ffmpeg && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

USER ${NB_UID}

# Install Python 3 packages
RUN mamba install --quiet --yes \
    'altair' \
    'beautifulsoup4' \
    'bokeh' \
    'bottleneck' \
    'cloudpickle' \
    'conda-forge::blas=*=openblas' \
    'cython' \
    'dask' \
    'dill' \
    'h5py' \
    'ipympl'\
    'ipywidgets' \
    'matplotlib-base' \
    'numba' \
    'numexpr' \
    'pandas' \
    'patsy' \
    'protobuf' \
    'pytables' \
    'scikit-image' \
    'scikit-learn' \
    'scipy' \
    'seaborn' \
    'sqlalchemy' \
    'statsmodels' \
    'sympy' \
    'widgetsnbextension'\
    'xlrd' && \
    mamba clean --all -f -y && \
    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: gpulibs #############################
############################################################################

LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"

# Install Tensorflow, check compatibility here:
# https://www.tensorflow.org/install/source#gpu
# installation via conda leads to errors in version 4.8.2
USER ${NB_UID}
RUN pip install --upgrade pip && \
    pip install --no-cache-dir tensorflow==2.10.1 keras==2.10 && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

# Install PyTorch with 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}"

# Check compatibility here:
# https://pytorch.org/get-started/locally/
# Installation via conda leads to errors installing cudatoolkit=11.1
# RUN pip install --no-cache-dir torch==1.13.1 torchvision==0.14.1 torchaudio==0.13.1  && \
#     torchviz==0.0.2 --extra-index-url https://download.pytorch.org/whl/cu116
RUN set -ex \
 && buildDeps=' \
    torch==1.13.1 \
    torchvision==0.14.1 \
    torchaudio==0.13.1 \
    torchviz==0.0.2 \
' \
 && pip install --no-cache-dir $buildDeps --extra-index-url https://download.pytorch.org/whl/cu116 \
 && fix-permissions "${CONDA_DIR}" \
 && fix-permissions "/home/${NB_USER}"

USER root
ENV CUDA_PATH=/opt/conda/

# Install nvtop to monitor the gpu tasks
RUN apt-get update && \
    apt-get install -y --no-install-recommends cmake libncurses5-dev libncursesw5-dev git && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

# reinstall nvcc with cuda-nvcc to install ptax
USER $NB_UID
RUN conda install -c nvidia cuda-nvcc -y && \
    conda clean --all -f -y && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

USER root
RUN ln -s /opt/conda/bin/ptxas /usr/bin/ptxas

USER $NB_UID

  ############################################################################
  ############################ Useful packages ###############################
  ############################################################################
  
LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"

USER root

# Install useful packages and Graphviz
RUN apt-get update \
 && apt-get -y install --no-install-recommends htop apt-utils iputils-ping graphviz libgraphviz-dev openssh-client \
 && apt-get clean && rm -rf /var/lib/apt/lists/*

USER $NB_UID
RUN set -ex \
 && buildDeps=' \
    graphviz==0.19.1 \
    pytest==7.2.2 \
' \
 && pip install --no-cache-dir $buildDeps \
 && fix-permissions "${CONDA_DIR}" \
 && fix-permissions "/home/${NB_USER}"

# upgrade jupyter-server for compatibility
RUN pip install --no-cache-dir --upgrade \
    distributed==2023.3.0 \
    jupyter-server==2.4 \
    # fix permissions of conda
 && fix-permissions "${CONDA_DIR}" \
 && fix-permissions "/home/${NB_USER}"

RUN pip install --no-cache-dir \
    # install extension manager
    jupyter_contrib_nbextensions==0.7.0 \
    jupyter_nbextensions_configurator==0.6.1 \
    # install git extension
    jupyterlab-git==0.41.0 \
    # install plotly extension
    plotly==5.13.1 \
    # install drawio and graphical extensions
    jupyterlab-drawio==0.9.0 \
    rise==5.7.1 \
    ipyleaflet==0.17.2 \
    ipywidgets==8.0.4 \
    # install spell checker
    jupyterlab-spellchecker==0.7.3 && \
    # fix permissions of conda
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

# Switch back to jovyan to avoid accidental container runs as root
USER $NB_UID