init

.woodpecker.yml

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+pipeline:
+  publish-container:
+    image: woodpeckerci/plugin-docker-buildx
+    secrets: [ docker_username, docker_password ]
+    group: docker
+    settings:
+      registry: https://git.sandbox.iuk.hdm-stuttgart.de
+      repo: git.sandbox.iuk.hdm-stuttgart.de/grosse/jupyterlab-datascience-gpu
+      dockerfile: Dockerfile
+      tags: latest

Dockerfile

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+ARG NVIDIA_IMAGE=nvcr.io/nvidia/tensorflow:22.12-tf2-py3
+
+FROM ${NVIDIA_IMAGE}
+
+#### copied from https://github.com/jupyter/docker-stacks/tree/main/docker-stacks-foundation
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+# Ubuntu 22.04 (jammy)
+# https://hub.docker.com/_/ubuntu/tags?page=1&name=jammy
+ARG ROOT_CONTAINER=ubuntu:22.04
+
+
+LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
+ARG NB_USER="jovyan"
+ARG NB_UID="1000"
+ARG NB_GID="100"
+
+# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
+# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+USER root
+
+# Install all OS dependencies for notebook server that starts but lacks all
+# features (e.g., download as all possible file formats)
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update --yes && \
+    # - apt-get upgrade is run to patch known vulnerabilities in apt-get packages as
+    #   the ubuntu base image is rebuilt too seldom sometimes (less than once a month)
+    apt-get upgrade --yes && \
+    apt-get install --yes --no-install-recommends \
+    # - bzip2 is necessary to extract the micromamba executable.
+    bzip2 \
+    ca-certificates \
+    locales \
+    sudo \
+    # - tini is installed as a helpful container entrypoint that reaps zombie
+    #   processes and such of the actual executable we want to start, see
+    #   https://github.com/krallin/tini#why-tini for details.
+    tini \
+    wget && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* && \
+    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+# Configure environment
+ENV CONDA_DIR=/opt/conda \
+    SHELL=/bin/bash \
+    NB_USER="${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/${NB_USER}"
+
+# Download and install Micromamba, and initialize Conda prefix.
+#   <https://github.com/mamba-org/mamba#micromamba>
+#   Similar projects using Micromamba:
+#     - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
+#     - repo2docker: <https://github.com/jupyterhub/repo2docker>
+# Install Python, Mamba and jupyter_core
+# Cleanup temporary files and remove Micromamba
+# Correct permissions
+# Do all this in a single RUN command to avoid duplicating all of the
+# files across image layers when the permissions change
+COPY --chown="${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' \
+        'jupyter_core' && \
+    rm micromamba && \
+    # Pin major.minor version of python
+    mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
+    mamba clean --all -f -y && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+# Configure container startup
+ENTRYPOINT ["tini", "-g", "--"]
+CMD ["start.sh"]
+
+# Copy local files as late as possible to avoid cache busting
+COPY start.sh /usr/local/bin/
+
+# Switch back to jovyan to avoid accidental container runs as root
+USER ${NB_UID}
+
+WORKDIR "${HOME}"
+
+################ copied from https://github.com/iot-salzburg/gpu-jupyter/tree/master/src
+
+# LABEL authors="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
+RUN pip install --upgrade pip && \
+    pip install --no-cache-dir "tensorflow==2.10.1"
+RUN pip install --upgrade pip && \
+    pip install --no-cache-dir keras==2.11.0
+
+# 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 torchvision torchaudio torchviz --extra-index-url https://download.pytorch.org/whl/cu116
+
+ENV CUDA_PATH=/opt/conda/
+
+USER root
+
+# Install nvtop to monitor the gpu tasks
+RUN apt-get update && \
+    apt-get install -y cmake libncurses5-dev libncursesw5-dev git && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN git clone https://github.com/Syllo/nvtop.git /run/nvtop && \
+    mkdir -p /run/nvtop/build && cd /run/nvtop/build && \
+    (cmake .. -DNVML_RETRIEVE_HEADER_ONLINE=True 2> /dev/null || echo "cmake was not successful") && \
+    (make 2> /dev/null || echo "make was not successful") && \
+    (make install 2> /dev/null || echo "make install was not successful") && \
+    cd /tmp && rm -rf /tmp/nvtop
+
+RUN fix-permissions /home/$NB_USER
+
+USER $NB_UID

fix-permissions

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+#!/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

initital-condarc

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+# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
+
+auto_update_conda: false
+show_channel_urls: true
+channels:
+  - conda-forge

start.sh

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+#!/bin/bash
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+set -e
+
+# The _log function is used for everything this script wants to log. It will
+# always log errors and warnings, but can be silenced for other messages
+# by setting JUPYTER_DOCKER_STACKS_QUIET environment variable.
+_log () {
+    if [[ "$*" == "ERROR:"* ]] || [[ "$*" == "WARNING:"* ]] || [[ "${JUPYTER_DOCKER_STACKS_QUIET}" == "" ]]; then
+        echo "$@"
+    fi
+}
+_log "Entered start.sh with args:" "$@"
+
+# The run-hooks function looks for .sh scripts to source and executable files to
+# run within a passed directory.
+run-hooks () {
+    if [[ ! -d "${1}" ]] ; then
+        return
+    fi
+    _log "${0}: running hooks in ${1} as uid / gid: $(id -u) / $(id -g)"
+    for f in "${1}/"*; do
+        case "${f}" in
+            *.sh)
+                _log "${0}: running script ${f}"
+                # shellcheck disable=SC1090
+                source "${f}"
+                ;;
+            *)
+                if [[ -x "${f}" ]] ; then
+                    _log "${0}: running executable ${f}"
+                    "${f}"
+                else
+                    _log "${0}: ignoring non-executable ${f}"
+                fi
+                ;;
+        esac
+    done
+    _log "${0}: done running hooks in ${1}"
+}
+
+# A helper function to unset env vars listed in the value of the env var
+# JUPYTER_ENV_VARS_TO_UNSET.
+unset_explicit_env_vars () {
+    if [ -n "${JUPYTER_ENV_VARS_TO_UNSET}" ]; then
+        for env_var_to_unset in $(echo "${JUPYTER_ENV_VARS_TO_UNSET}" | tr ',' ' '); do
+            echo "Unset ${env_var_to_unset} due to JUPYTER_ENV_VARS_TO_UNSET"
+            unset "${env_var_to_unset}"
+        done
+        unset JUPYTER_ENV_VARS_TO_UNSET
+    fi
+}
+
+
+# Default to starting bash if no command was specified
+if [ $# -eq 0 ]; then
+    cmd=( "bash" )
+else
+    cmd=( "$@" )
+fi
+
+# NOTE: This hook will run as the user the container was started with!
+run-hooks /usr/local/bin/start-notebook.d
+
+# If the container started as the root user, then we have permission to refit
+# the jovyan user, and ensure file permissions, grant sudo rights, and such
+# things before we run the command passed to start.sh as the desired user
+# (NB_USER).
+#
+if [ "$(id -u)" == 0 ] ; then
+    # Environment variables:
+    # - NB_USER: the desired username and associated home folder
+    # - NB_UID: the desired user id
+    # - NB_GID: a group id we want our user to belong to
+    # - NB_GROUP: a group name we want for the group
+    # - GRANT_SUDO: a boolean ("1" or "yes") to grant the user sudo rights
+    # - CHOWN_HOME: a boolean ("1" or "yes") to chown the user's home folder
+    # - CHOWN_EXTRA: a comma separated list of paths to chown
+    # - CHOWN_HOME_OPTS / CHOWN_EXTRA_OPTS: arguments to the chown commands
+
+    # Refit the jovyan user to the desired the user (NB_USER)
+    if id jovyan &> /dev/null ; then
+        if ! usermod --home "/home/${NB_USER}" --login "${NB_USER}" jovyan 2>&1 | grep "no changes" > /dev/null; then
+            _log "Updated the jovyan user:"
+            _log "- username: jovyan       -> ${NB_USER}"
+            _log "- home dir: /home/jovyan -> /home/${NB_USER}"
+        fi
+    elif ! id -u "${NB_USER}" &> /dev/null; then
+        _log "ERROR: Neither the jovyan user or '${NB_USER}' exists. This could be the result of stopping and starting, the container with a different NB_USER environment variable."
+        exit 1
+    fi
+    # Ensure the desired user (NB_USER) gets its desired user id (NB_UID) and is
+    # a member of the desired group (NB_GROUP, NB_GID)
+    if [ "${NB_UID}" != "$(id -u "${NB_USER}")" ] || [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
+        _log "Update ${NB_USER}'s UID:GID to ${NB_UID}:${NB_GID}"
+        # Ensure the desired group's existence
+        if [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
+            groupadd --force --gid "${NB_GID}" --non-unique "${NB_GROUP:-${NB_USER}}"
+        fi
+        # Recreate the desired user as we want it
+        userdel "${NB_USER}"
+        useradd --home "/home/${NB_USER}" --uid "${NB_UID}" --gid "${NB_GID}" --groups 100 --no-log-init "${NB_USER}"
+    fi
+
+    # Move or symlink the jovyan home directory to the desired users home
+    # directory if it doesn't already exist, and update the current working
+    # directory to the new location if needed.
+    if [[ "${NB_USER}" != "jovyan" ]]; then
+        if [[ ! -e "/home/${NB_USER}" ]]; then
+            _log "Attempting to copy /home/jovyan to /home/${NB_USER}..."
+            mkdir "/home/${NB_USER}"
+            if cp -a /home/jovyan/. "/home/${NB_USER}/"; then
+                _log "Success!"
+            else
+                _log "Failed to copy data from /home/jovyan to /home/${NB_USER}!"
+                _log "Attempting to symlink /home/jovyan to /home/${NB_USER}..."
+                if ln -s /home/jovyan "/home/${NB_USER}"; then
+                    _log "Success creating symlink!"
+                else
+                    _log "ERROR: Failed copy data from /home/jovyan to /home/${NB_USER} or to create symlink!"
+                    exit 1
+                fi
+            fi
+        fi
+        # Ensure the current working directory is updated to the new path
+        if [[ "${PWD}/" == "/home/jovyan/"* ]]; then
+            new_wd="/home/${NB_USER}/${PWD:13}"
+            _log "Changing working directory to ${new_wd}"
+            cd "${new_wd}"
+        fi
+    fi
+
+    # Optionally ensure the desired user get filesystem ownership of it's home
+    # folder and/or additional folders
+    if [[ "${CHOWN_HOME}" == "1" || "${CHOWN_HOME}" == "yes" ]]; then
+        _log "Ensuring /home/${NB_USER} is owned by ${NB_UID}:${NB_GID} ${CHOWN_HOME_OPTS:+(chown options: ${CHOWN_HOME_OPTS})}"
+        # shellcheck disable=SC2086
+        chown ${CHOWN_HOME_OPTS} "${NB_UID}:${NB_GID}" "/home/${NB_USER}"
+    fi
+    if [ -n "${CHOWN_EXTRA}" ]; then
+        for extra_dir in $(echo "${CHOWN_EXTRA}" | tr ',' ' '); do
+            _log "Ensuring ${extra_dir} is owned by ${NB_UID}:${NB_GID} ${CHOWN_EXTRA_OPTS:+(chown options: ${CHOWN_EXTRA_OPTS})}"
+            # shellcheck disable=SC2086
+            chown ${CHOWN_EXTRA_OPTS} "${NB_UID}:${NB_GID}" "${extra_dir}"
+        done
+    fi
+
+    # Update potentially outdated environment variables since image build
+    export XDG_CACHE_HOME="/home/${NB_USER}/.cache"
+
+    # Prepend ${CONDA_DIR}/bin to sudo secure_path
+    sed -r "s#Defaults\s+secure_path\s*=\s*\"?([^\"]+)\"?#Defaults secure_path=\"${CONDA_DIR}/bin:\1\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
+
+    # Optionally grant passwordless sudo rights for the desired user
+    if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == "yes" ]]; then
+        _log "Granting ${NB_USER} passwordless sudo rights!"
+        echo "${NB_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers.d/added-by-start-script
+    fi
+
+    # NOTE: This hook is run as the root user!
+    run-hooks /usr/local/bin/before-notebook.d
+
+    unset_explicit_env_vars
+    _log "Running as ${NB_USER}:" "${cmd[@]}"
+    exec sudo --preserve-env --set-home --user "${NB_USER}" \
+        PATH="${PATH}" \
+        PYTHONPATH="${PYTHONPATH:-}" \
+        "${cmd[@]}"
+        # Notes on how we ensure that the environment that this container is started
+        # with is preserved (except vars listed in JUPYTER_ENV_VARS_TO_UNSET) when
+        # we transition from running as root to running as NB_USER.
+        #
+        # - We use `sudo` to execute the command as NB_USER. What then
+        #   happens to the environment will be determined by configuration in
+        #   /etc/sudoers and /etc/sudoers.d/* as well as flags we pass to the sudo
+        #   command. The behavior can be inspected with `sudo -V` run as root.
+        #
+        #   ref: `man sudo`    https://linux.die.net/man/8/sudo
+        #   ref: `man sudoers` https://www.sudo.ws/man/1.8.15/sudoers.man.html
+        #
+        # - We use the `--preserve-env` flag to pass through most environment
+        #   variables, but understand that exceptions are caused by the sudoers
+        #   configuration: `env_delete` and `env_check`.
+        #
+        # - We use the `--set-home` flag to set the HOME variable appropriately.
+        #
+        # - To reduce the default list of variables deleted by sudo, we could have
+        #   used `env_delete` from /etc/sudoers. It has higher priority than the
+        #   `--preserve-env` flag and the `env_keep` configuration.
+        #
+        # - We preserve PATH and PYTHONPATH explicitly. Note however that sudo
+        #   resolves `${cmd[@]}` using the "secure_path" variable we modified
+        #   above in /etc/sudoers.d/path. Thus PATH is irrelevant to how the above
+        #   sudo command resolves the path of `${cmd[@]}`. The PATH will be relevant
+        #   for resolving paths of any subprocesses spawned by `${cmd[@]}`.
+
+# The container didn't start as the root user, so we will have to act as the
+# user we started as.
+else
+    # Warn about misconfiguration of: granting sudo rights
+    if [[ "${GRANT_SUDO}" == "1" || "${GRANT_SUDO}" == "yes" ]]; then
+        _log "WARNING: container must be started as root to grant sudo permissions!"
+    fi
+
+    JOVYAN_UID="$(id -u jovyan 2>/dev/null)"  # The default UID for the jovyan user
+    JOVYAN_GID="$(id -g jovyan 2>/dev/null)"  # The default GID for the jovyan user
+
+    # Attempt to ensure the user uid we currently run as has a named entry in
+    # the /etc/passwd file, as it avoids software crashing on hard assumptions
+    # on such entry. Writing to the /etc/passwd was allowed for the root group
+    # from the Dockerfile during build.
+    #
+    # ref: https://github.com/jupyter/docker-stacks/issues/552
+    if ! whoami &> /dev/null; then
+        _log "There is no entry in /etc/passwd for our UID=$(id -u). Attempting to fix..."
+        if [[ -w /etc/passwd ]]; then
+            _log "Renaming old jovyan user to nayvoj ($(id -u jovyan):$(id -g jovyan))"
+
+            # We cannot use "sed --in-place" since sed tries to create a temp file in
+            # /etc/ and we may not have write access. Apply sed on our own temp file:
+            sed --expression="s/^jovyan:/nayvoj:/" /etc/passwd > /tmp/passwd
+            echo "${NB_USER}:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
+            cat /tmp/passwd > /etc/passwd
+            rm /tmp/passwd
+
+            _log "Added new ${NB_USER} user ($(id -u):$(id -g)). Fixed UID!"
+
+            if [[ "${NB_USER}" != "jovyan" ]]; then
+                _log "WARNING: user is ${NB_USER} but home is /home/jovyan. You must run as root to rename the home directory!"
+            fi
+        else
+            _log "WARNING: unable to fix missing /etc/passwd entry because we don't have write permission. Try setting gid=0 with \"--user=$(id -u):0\"."
+        fi
+    fi
+
+    # Warn about misconfiguration of: desired username, user id, or group id.
+    # A misconfiguration occurs when the user modifies the default values of
+    # NB_USER, NB_UID, or NB_GID, but we cannot update those values because we
+    # are not root.
+    if [[ "${NB_USER}" != "jovyan" && "${NB_USER}" != "$(id -un)" ]]; then
+        _log "WARNING: container must be started as root to change the desired user's name with NB_USER=\"${NB_USER}\"!"
+    fi
+    if [[ "${NB_UID}" != "${JOVYAN_UID}" && "${NB_UID}" != "$(id -u)" ]]; then
+        _log "WARNING: container must be started as root to change the desired user's id with NB_UID=\"${NB_UID}\"!"
+    fi
+    if [[ "${NB_GID}" != "${JOVYAN_GID}" && "${NB_GID}" != "$(id -g)" ]]; then
+        _log "WARNING: container must be started as root to change the desired user's group id with NB_GID=\"${NB_GID}\"!"
+    fi
+
+    # Warn if the user isn't able to write files to ${HOME}
+    if [[ ! -w /home/jovyan ]]; then
+        _log "WARNING: no write access to /home/jovyan. Try starting the container with group 'users' (100), e.g. using \"--group-add=users\"."
+    fi
+
+    # NOTE: This hook is run as the user we started the container as!
+    run-hooks /usr/local/bin/before-notebook.d
+    unset_explicit_env_vars
+    _log "Executing the command:" "${cmd[@]}"
+    exec "${cmd[@]}"
+fi