393 lines
14 KiB
Docker
393 lines
14 KiB
Docker
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ARG NVIDIA_IMAGE=nvcr.io/nvidia/tensorflow:22.12-tf2-py3
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FROM ${NVIDIA_IMAGE}
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############################################################################
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#################### Dependency: jupyter/base-image ########################
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############################################################################
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#### copied from https://github.com/jupyter/docker-stacks/tree/main/docker-stacks-foundation
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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# Ubuntu 22.04 (jammy)
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# https://hub.docker.com/_/ubuntu/tags?page=1&name=jammy
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ARG ROOT_CONTAINER=ubuntu:22.04
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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ARG NB_USER="jovyan"
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ARG NB_UID="1000"
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ARG NB_GID="100"
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# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
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# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
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SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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# Install all OS dependencies for notebook server that starts but lacks all
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# features (e.g., download as all possible file formats)
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt-get update --yes && \
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# - apt-get upgrade is run to patch known vulnerabilities in apt-get packages as
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# the ubuntu base image is rebuilt too seldom sometimes (less than once a month)
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apt-get upgrade --yes && \
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apt-get install --yes --no-install-recommends \
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# - bzip2 is necessary to extract the micromamba executable.
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bzip2 \
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ca-certificates \
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locales \
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sudo \
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# - tini is installed as a helpful container entrypoint that reaps zombie
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# processes and such of the actual executable we want to start, see
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# https://github.com/krallin/tini#why-tini for details.
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tini \
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wget && \
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apt-get clean && rm -rf /var/lib/apt/lists/* && \
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echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Configure environment
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ENV CONDA_DIR=/opt/conda \
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SHELL=/bin/bash \
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NB_USER="${NB_USER}" \
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NB_UID=${NB_UID} \
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NB_GID=${NB_GID} \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV PATH="${CONDA_DIR}/bin:${PATH}" \
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HOME="/home/${NB_USER}"
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# Copy a script that we will use to correct permissions after running certain commands
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COPY fix-permissions /usr/local/bin/fix-permissions
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RUN chmod a+rx /usr/local/bin/fix-permissions
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# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
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# hadolint ignore=SC2016
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RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
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# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
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echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
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# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
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# and make sure these dirs are writable by the `users` group.
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RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
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sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
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useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
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mkdir -p "${CONDA_DIR}" && \
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chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
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chmod g+w /etc/passwd && \
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fix-permissions "${HOME}" && \
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fix-permissions "${CONDA_DIR}"
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USER ${NB_UID}
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# Pin python version here, or set it to "default"
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ARG PYTHON_VERSION=3.10
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# Setup work directory for backward-compatibility
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RUN mkdir "/home/${NB_USER}/work" && \
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fix-permissions "/home/${NB_USER}"
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# Download and install Micromamba, and initialize Conda prefix.
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# <https://github.com/mamba-org/mamba#micromamba>
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# Similar projects using Micromamba:
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# - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
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# - repo2docker: <https://github.com/jupyterhub/repo2docker>
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# Install Python, Mamba and jupyter_core
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# Cleanup temporary files and remove Micromamba
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# Correct permissions
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# Do all this in a single RUN command to avoid duplicating all of the
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# files across image layers when the permissions change
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COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
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WORKDIR /tmp
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RUN set -x && \
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arch=$(uname -m) && \
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if [ "${arch}" = "x86_64" ]; then \
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# Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
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arch="64"; \
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fi && \
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wget -qO /tmp/micromamba.tar.bz2 \
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"https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
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tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
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rm /tmp/micromamba.tar.bz2 && \
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PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
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if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
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# Install the packages
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./micromamba install \
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--root-prefix="${CONDA_DIR}" \
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--prefix="${CONDA_DIR}" \
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--yes \
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"${PYTHON_SPECIFIER}" \
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'mamba' \
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'jupyter_core' && \
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rm micromamba && \
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# Pin major.minor version of python
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mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
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mamba clean --all -f -y && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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EXPOSE 8888
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# Configure container startup
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ENTRYPOINT ["tini", "-g", "--"]
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CMD ["start-notebook.sh"]
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# Copy local files as late as possible to avoid cache busting
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COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
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# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
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COPY jupyter_server_config.py /etc/jupyter/
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# Fix permissions on /etc/jupyter as root
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USER root
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# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
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RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
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/etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
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fix-permissions /etc/jupyter/
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# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
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# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
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# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
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HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
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CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
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http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
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# Switch back to jovyan to avoid accidental container runs as root
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USER ${NB_UID}
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WORKDIR "${HOME}"
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############################################################################
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################# Dependency: jupyter/minimal-notebook #####################
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############################################################################
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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ARG OWNER=jupyter
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
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# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
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SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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# Install all OS dependencies for fully functional notebook server
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RUN apt-get update --yes && \
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apt-get install --yes --no-install-recommends \
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# Common useful utilities
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git \
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nano-tiny \
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tzdata \
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unzip \
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vim-tiny \
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# Inkscape is installed to be able to convert SVG files
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inkscape \
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# git-over-ssh
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openssh-client \
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# less is needed to run help in R
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# see: https://github.com/jupyter/docker-stacks/issues/1588
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less \
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# nbconvert dependencies
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# https://nbconvert.readthedocs.io/en/latest/install.html#installing-tex
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texlive-xetex \
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texlive-fonts-recommended \
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texlive-plain-generic && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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# Create alternative for nano -> nano-tiny
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RUN update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
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# Switch back to jovyan to avoid accidental container runs as root
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USER ${NB_UID}
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############################################################################
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################# Dependency: jupyter/scipy-notebook #######################
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############################################################################
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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ARG OWNER=jupyter
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
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# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
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SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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RUN apt-get update --yes && \
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apt-get install --yes --no-install-recommends \
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# for cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
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build-essential \
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# for latex labels
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cm-super \
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dvipng \
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# for matplotlib anim
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ffmpeg && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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USER ${NB_UID}
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# Install Python 3 packages
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RUN mamba install --quiet --yes \
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'altair' \
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'beautifulsoup4' \
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'bokeh' \
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'bottleneck' \
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'cloudpickle' \
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'conda-forge::blas=*=openblas' \
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'cython' \
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'dask' \
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'dill' \
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'h5py' \
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'ipympl'\
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'ipywidgets' \
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'matplotlib-base' \
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'numba' \
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'numexpr' \
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'pandas' \
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'patsy' \
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'protobuf' \
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'pytables' \
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'scikit-image' \
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'scikit-learn' \
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'scipy' \
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'seaborn' \
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'sqlalchemy' \
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'statsmodels' \
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'sympy' \
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'widgetsnbextension'\
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'xlrd' && \
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mamba clean --all -f -y && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Install facets which does not have a pip or conda package at the moment
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WORKDIR /tmp
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RUN git clone https://github.com/PAIR-code/facets.git && \
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jupyter nbextension install facets/facets-dist/ --sys-prefix && \
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rm -rf /tmp/facets && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Import matplotlib the first time to build the font cache.
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ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
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RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
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fix-permissions "/home/${NB_USER}"
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USER ${NB_UID}
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WORKDIR "${HOME}"
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################ copied from https://github.com/iot-salzburg/gpu-jupyter/tree/master/src
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# LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
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#tensorflow 2.10.1 requires keras<2.11,>=2.10.0, but you have keras 2.11.0
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# Install Tensorflow, check compatibility here:
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# https://www.tensorflow.org/install/source#gpu
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# installation via conda leads to errors in version 4.8.2
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RUN pip install --upgrade pip && \
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pip install --no-cache-dir "tensorflow==2.11.0"
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RUN pip install --upgrade pip && \
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pip install --no-cache-dir keras==2.11.0
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# Install PyTorch with dependencies
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RUN conda install --quiet --yes \
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pyyaml mkl mkl-include setuptools cmake cffi typing && \
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conda clean --all -f -y && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Check compatibility here:
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# https://pytorch.org/get-started/locally/
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# Installation via conda leads to errors installing cudatoolkit=11.1
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RUN pip install --no-cache-dir torch torchvision torchaudio torchviz --extra-index-url https://download.pytorch.org/whl/cu116
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ENV CUDA_PATH=/opt/conda/
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USER root
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# Install nvtop to monitor the gpu tasks
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RUN apt-get update && \
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apt-get install -y cmake libncurses5-dev libncursesw5-dev git && \
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rm -rf /var/lib/apt/lists/*
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RUN git clone https://github.com/Syllo/nvtop.git /run/nvtop && \
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mkdir -p /run/nvtop/build && cd /run/nvtop/build && \
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(cmake .. -DNVML_RETRIEVE_HEADER_ONLINE=True 2> /dev/null || echo "cmake was not successful") && \
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(make 2> /dev/null || echo "make was not successful") && \
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(make install 2> /dev/null || echo "make install was not successful") && \
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cd /tmp && rm -rf /tmp/nvtop
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RUN fix-permissions /home/$NB_USER
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USER $NB_UID
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############################################################################
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############################ Useful packages ###############################
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############################################################################
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LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
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USER root
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RUN pip install --no-cache-dir ipyleaflet "plotly>=4.14.3" "ipywidgets>=7.5"
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|
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RUN conda install -c conda-forge nodejs
|
||
|
|
# Install important packages and Graphviz
|
||
|
|
RUN set -ex \
|
||
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|
&& buildDeps=' \
|
||
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|
graphviz==0.19.1 \
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||
|
|
' \
|
||
|
|
&& apt-get update \
|
||
|
|
&& apt-get -y install htop apt-utils iputils-ping graphviz libgraphviz-dev openssh-client \
|
||
|
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&& pip install --no-cache-dir $buildDeps
|
||
|
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|
||
|
|
# Install various extensions
|
||
|
|
RUN fix-permissions $CONDA_DIR
|
||
|
|
|
||
|
|
# RUN jupyter labextension install @jupyterlab/github
|
||
|
|
# RUN pip install jupyterlab-git
|
||
|
|
RUN pip install jupyterlab-drawio
|
||
|
|
RUN jupyter nbextension enable --py --sys-prefix ipyleaflet
|
||
|
|
|
||
|
|
RUN jupyter labextension install jupyterlab-plotly
|
||
|
|
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager plotlywidget
|
||
|
|
# RUN pip install --no-cache-dir jupyter-tabnine --user && \
|
||
|
|
# jupyter nbextension install --py jupyter_tabnine --user && \
|
||
|
|
# jupyter nbextension enable --py jupyter_tabnine --user && \
|
||
|
|
# jupyter serverextension enable --py jupyter_tabnine --user
|
||
|
|
RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
|
||
|
|
jupyter_nbextensions_configurator rise
|
||
|
|
# jupyter nbextension enable codefolding/main
|
||
|
|
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
|
||
|
|
|
||
|
|
RUN fix-permissions /home/$NB_USER
|
||
|
|
|
||
|
|
|
||
|
|
## add sandbox plugins
|
||
|
|
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-theme
|
||
|
|
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-data-pool
|
||
|
|
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-training
|
||
|
|
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-synthetic-data
|
||
|
|
|
||
|
|
# 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/
|