grosse
/
jupyterlab-datascience-gpu
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
jupyterlab-datascience-gpu/Dockerfile

393 lines
14 KiB
Docker
Raw Blame History

ARG NVIDIA_IMAGE=nvcr.io/nvidia/tensorflow:22.12-tf2-py3
FROM ${NVIDIA_IMAGE}
############################################################################
#################### Dependency: jupyter/base-image ########################
############################################################################
#### copied from https://github.com/jupyter/docker-stacks/tree/main/docker-stacks-foundation
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
# Ubuntu 22.04 (jammy)
# https://hub.docker.com/_/ubuntu/tags?page=1&name=jammy
ARG ROOT_CONTAINER=ubuntu:22.04
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root
# Install all OS dependencies for notebook server that starts but lacks all
# features (e.g., download as all possible file formats)
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update --yes && \
# - apt-get upgrade is run to patch known vulnerabilities in apt-get packages as
# the ubuntu base image is rebuilt too seldom sometimes (less than once a month)
apt-get upgrade --yes && \
apt-get install --yes --no-install-recommends \
# - bzip2 is necessary to extract the micromamba executable.
bzip2 \
ca-certificates \
locales \
sudo \
# - tini is installed as a helpful container entrypoint that reaps zombie
# processes and such of the actual executable we want to start, see
# https://github.com/krallin/tini#why-tini for details.
tini \
wget && \
apt-get clean && rm -rf /var/lib/apt/lists/* && \
echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
locale-gen
# Configure environment
ENV CONDA_DIR=/opt/conda \
SHELL=/bin/bash \
NB_USER="${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/${NB_USER}"
EXPOSE 8888
# Configure container startup
ENTRYPOINT ["tini", "-g", "--"]
CMD ["start-notebook.sh"]
# Copy local files as late as possible to avoid cache busting
COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
COPY jupyter_server_config.py /etc/jupyter/
# Fix permissions on /etc/jupyter as root
USER root
# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
/etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
fix-permissions /etc/jupyter/
# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
http${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}"
################ 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>"
#tensorflow 2.10.1 requires keras<2.11,>=2.10.0, but you have keras 2.11.0
# 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==2.11.0"
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
############################################################################
############################ 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>=4.14.3" "ipywidgets>=7.5"
RUN conda install -c conda-forge nodejs
# Install important packages and Graphviz
RUN set -ex \
&& buildDeps=' \
graphviz==0.19.1 \
' \
&& apt-get update \
&& apt-get -y install htop apt-utils iputils-ping graphviz libgraphviz-dev openssh-client \
&& pip install --no-cache-dir $buildDeps
# Install various extensions
RUN fix-permissions $CONDA_DIR
# RUN jupyter labextension install @jupyterlab/github
# RUN pip install jupyterlab-git
RUN pip install jupyterlab-drawio
RUN jupyter nbextension enable --py --sys-prefix ipyleaflet
RUN jupyter labextension install jupyterlab-plotly
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager plotlywidget
# RUN pip install --no-cache-dir jupyter-tabnine --user && \
# jupyter nbextension install --py jupyter_tabnine --user && \
# jupyter nbextension enable --py jupyter_tabnine --user && \
# jupyter serverextension enable --py jupyter_tabnine --user
RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
jupyter_nbextensions_configurator rise
# jupyter nbextension enable codefolding/main
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
RUN fix-permissions /home/$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/
Reference in New Issue View Git Blame Copy Permalink