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gpu-jupyter/.build/Dockerfile

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# 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:10.1-cudnn7-runtime-ubuntu18.04
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: 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-gpu>=2.1.*" && \
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 $CONDA_DIR
RUN jupyter labextension install @jupyterlab/github
RUN jupyter labextension install jupyterlab-drawio
RUN jupyter labextension install jupyter-leaflet
RUN jupyter labextension install jupyterlab-plotly@4.8.1
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
RUN pip install --no-cache-dir jupyter-tabnine==1.0.2 && \
jupyter nbextension install --py jupyter_tabnine && \
jupyter nbextension enable --py jupyter_tabnine && \
jupyter serverextension enable --py jupyter_tabnine
RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
jupyter_nbextensions_configurator rise && \
jupyter nbextension enable codefolding/main
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
RUN fix-permissions /home/$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/
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