nvidia/cuda:10.2-base-ubuntu18.04

src/Dockerfile

@@ -1,463 +0,0 @@
-FROM nvidia/cuda:10.1-base-ubuntu18.04
-LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
-
-############################################################################
-#################### Dependency: jupyter/base-image ########################
-############################################################################
-
-ARG NB_USER="jovyan"
-ARG NB_UID="1000"
-ARG NB_GID="100"
-
-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 && apt-get -yq dist-upgrade \
- && apt-get install -yq --no-install-recommends \
-    wget \
-    bzip2 \
-    ca-certificates \
-    sudo \
-    locales \
-    fonts-liberation \
- && 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
-
-# Add a script that we will use to correct permissions after running certain commands
-ADD fix-permissions /usr/local/bin/fix-permissions
-
-# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
-RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
-
-# Create NB_USER wtih 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 $HOME && \
-    fix-permissions "$(dirname $CONDA_DIR)"
-
-USER $NB_UID
-WORKDIR $HOME
-
-# Setup work directory for backward-compatibility
-RUN mkdir /home/$NB_USER/work && \
-    fix-permissions /home/$NB_USER
-
-# Install conda as jovyan and check the md5 sum provided on the download site
-ENV MINICONDA_VERSION=4.6.14 \
-    CONDA_VERSION=4.7.10
-
-RUN cd /tmp && \
-    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
-    echo "718259965f234088d785cad1fbd7de03 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
-    /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
-    rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
-    echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
-    $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
-    $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
-    $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
-    $CONDA_DIR/bin/conda install --quiet --yes conda && \
-    $CONDA_DIR/bin/conda update --all --quiet --yes && \
-    conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
-    conda clean --all -f -y && \
-    rm -rf /home/$NB_USER/.cache/yarn && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-# Install Tini
-RUN conda install --quiet --yes 'tini=0.18.0' && \
-    conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
-    conda clean --all -f -y && \
-    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=6.0.0' \
-    'jupyterhub=1.0.0' \
-    'jupyterlab=1.0.4' && \
-    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"]
-
-# Add local files as late as possible to avoid cache busting
-COPY start.sh /usr/local/bin/
-COPY start-notebook.sh /usr/local/bin/
-COPY start-singleuser.sh /usr/local/bin/
-COPY jupyter_notebook_config.py /etc/jupyter/
-
-# Fix permissions on /etc/jupyter as root
-USER root
-RUN fix-permissions /etc/jupyter/
-
-############################################################################
-################# Dependency: jupyter/minimal-notebook #####################
-############################################################################
-
-# Install all OS dependencies for fully functional notebook server
-RUN apt-get update && apt-get install -yq --no-install-recommends \
-    build-essential \
-    emacs \
-    git \
-    inkscape \
-    jed \
-    libsm6 \
-    libxext-dev \
-    libxrender1 \
-    lmodern \
-    netcat \
-    pandoc \
-    python-dev \
-    texlive-fonts-extra \
-    texlive-fonts-recommended \
-    texlive-generic-recommended \
-    texlive-latex-base \
-    texlive-latex-extra \
-    texlive-xetex \
-    tzdata \
-    unzip \
-    nano \
-    && rm -rf /var/lib/apt/lists/*
-
-
-############################################################################
-################# Dependency: jupyter/scipy-notebook #######################
-############################################################################
-
-# ffmpeg for matplotlib anim
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ffmpeg && \
-    rm -rf /var/lib/apt/lists/*
-
-USER $NB_UID
-
-# Install Python 3 packages
-RUN conda install --quiet --yes \
-    'conda-forge::blas=*=openblas' \
-    'ipywidgets=7.5*' \
-    'pandas=0.24*' \
-    'numexpr=2.6*' \
-    'matplotlib-base=3.1.*' \
-    'scipy=1.2*' \
-    'seaborn=0.9*' \
-    'scikit-learn=0.20*' \
-    'scikit-image=0.14*' \
-    'sympy=1.3*' \
-    'cython=0.29*' \
-    'patsy=0.5*' \
-    'statsmodels=0.9*' \
-    'cloudpickle=0.8*' \
-    'dill=0.2*' \
-    'dask=1.1.*' \
-    'numba=0.42*' \
-    'bokeh=1.0*' \
-    'sqlalchemy=1.3*' \
-    'hdf5=1.10*' \
-    'h5py=2.9*' \
-    'vincent=0.4.*' \
-    'beautifulsoup4=4.7.*' \
-    'protobuf=3.7.*' \
-    'xlrd'  && \
-    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@^1.0.1 --no-build && \
-    jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \
-    jupyter lab build --dev-build=False && \
-    npm cache clean --force && \
-    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
-    rm -rf /home/$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
-RUN cd /tmp && \
-    git clone https://github.com/PAIR-code/facets.git && \
-    cd facets && \
-    jupyter nbextension install facets-dist/ --sys-prefix && \
-    cd && \
-    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
-
-
-############################################################################
-################ Dependency: jupyter/datascience-notebook ##################
-############################################################################
-
-USER root
-
-# R pre-requisites
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-    fonts-dejavu \
-    gfortran \
-    gcc && \
-    rm -rf /var/lib/apt/lists/*
-
-# Julia dependencies
-# install Julia packages in /opt/julia instead of $HOME
-ENV JULIA_DEPOT_PATH=/opt/julia
-ENV JULIA_PKGDIR=/opt/julia
-ENV JULIA_VERSION=1.1.0
-
-RUN mkdir /opt/julia-${JULIA_VERSION} && \
-    cd /tmp && \
-    wget -q https://julialang-s3.julialang.org/bin/linux/x64/`echo ${JULIA_VERSION} | cut -d. -f 1,2`/julia-${JULIA_VERSION}-linux-x86_64.tar.gz && \
-    echo "80cfd013e526b5145ec3254920afd89bb459f1db7a2a3f21849125af20c05471 *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
-    tar xzf julia-${JULIA_VERSION}-linux-x86_64.tar.gz -C /opt/julia-${JULIA_VERSION} --strip-components=1 && \
-    rm /tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz
-RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
-
-# Show Julia where conda libraries are \
-RUN mkdir /etc/julia && \
-    echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \
-    # Create JULIA_PKGDIR \
-    mkdir $JULIA_PKGDIR && \
-    chown $NB_USER $JULIA_PKGDIR && \
-    fix-permissions $JULIA_PKGDIR
-
-USER $NB_UID
-
-# R packages including IRKernel which gets installed globally.
-RUN conda install --quiet --yes \
-    'rpy2=2.9*' \
-    'r-base=3.5.1' \
-    'r-irkernel=0.8*' \
-    'r-plyr=1.8*' \
-    'r-devtools=1.13*' \
-    'r-tidyverse=1.2*' \
-    'r-shiny=1.2*' \
-    'r-rmarkdown=1.11*' \
-    'r-forecast=8.2*' \
-    'r-rsqlite=2.1*' \
-    'r-reshape2=1.4*' \
-    'r-nycflights13=1.0*' \
-    'r-caret=6.0*' \
-    'r-rcurl=1.95*' \
-    'r-crayon=1.3*' \
-    'r-randomforest=4.6*' \
-    'r-htmltools=0.3*' \
-    'r-sparklyr=0.9*' \
-    'r-htmlwidgets=1.2*' \
-    'r-hexbin=1.27*' && \
-    conda clean --all -f -y && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-# Add Julia packages. Only add HDF5 if this is not a test-only build since
-# it takes roughly half the entire build time of all of the images on Travis
-# to add this one package and often causes Travis to timeout.
-#
-# Install IJulia as jovyan and then move the kernelspec out
-# to the system share location. Avoids problems with runtime UID change not
-# taking effect properly on the .local folder in the jovyan home dir.
-RUN julia -e 'import Pkg; Pkg.update()' && \
-    (test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
-    julia -e "using Pkg; pkg\"add Gadfly RDatasets IJulia InstantiateFromURL\"; pkg\"precompile\"" && \ 
-    # move kernelspec out of home \
-    mv $HOME/.local/share/jupyter/kernels/julia* $CONDA_DIR/share/jupyter/kernels/ && \
-    chmod -R go+rx $CONDA_DIR/share/jupyter && \
-    rm -rf $HOME/.local && \
-    fix-permissions $JULIA_PKGDIR $CONDA_DIR/share/jupyter
-
-
-############################################################################
-################ Dependency: jupyter/scipy-notebook ##################
-############################################################################
-
-USER root
-
-# ffmpeg for matplotlib anim
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ffmpeg && \
-    rm -rf /var/lib/apt/lists/*
-
-USER $NB_UID
-
-# Install Python 3 packages
-RUN conda install --quiet --yes \
-    'conda-forge::blas=*=openblas' \
-    'ipywidgets=7.5*' \
-    'pandas=0.24*' \
-    'numexpr=2.6*' \
-    'matplotlib-base=3.1.*' \
-    'scipy=1.2*' \
-    'seaborn=0.9*' \
-    'scikit-learn=0.20*' \
-    'scikit-image=0.14*' \
-    'sympy=1.3*' \
-    'cython=0.29*' \
-    'patsy=0.5*' \
-    'statsmodels=0.9*' \
-    'cloudpickle=0.8*' \
-    'dill=0.2*' \
-    'dask=1.1.*' \
-    'numba=0.42*' \
-    'bokeh=1.0*' \
-    'sqlalchemy=1.3*' \
-    'hdf5=1.10*' \
-    'h5py=2.9*' \
-    'vincent=0.4.*' \
-    'beautifulsoup4=4.7.*' \
-    'protobuf=3.7.*' \
-    'xlrd'  && \
-    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@^1.0.1 --no-build && \
-    jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \
-    jupyter lab build --dev-build=False && \
-    npm cache clean --force && \
-    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
-    rm -rf /home/$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
-RUN cd /tmp && \
-    git clone https://github.com/PAIR-code/facets.git && \
-    cd facets && \
-    jupyter nbextension install facets-dist/ --sys-prefix && \
-    cd && \
-    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
-
-
-############################################################################
-############### Dependency: jupyter/tensorflow-notebook ####################
-############################################################################
-
-# Install Tensorflow
-RUN conda install --quiet --yes \
-    'tensorflow=1.13*' \
-    'keras=2.2*' && \
-    conda clean --all -f -y && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-# RUN pip install --upgrade tensorflow-gpu
-
-############################################################################
-########################## Dependency: pytorch #############################
-############################################################################
-
-# Install PyTorch 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
-
-# Install PyTorch
-RUN conda install -y -c pytorch \
-    cudatoolkit=10.1 \
-    'pytorch=1.3.1' \
-    torchvision && \
-    conda clean --all -f -y && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-############################################################################
-############################ Useful packages ###############################
-############################################################################
-
-# Update conda
-RUN conda update -n base conda -y
-
-# Install elasticsearch libs
-USER root
-RUN apt-get update \
- && curl -sL https://repo1.maven.org/maven2/org/elasticsearch/elasticsearch-hadoop/6.8.1/elasticsearch-hadoop-6.8.1.jar
-RUN pip install --no-cache-dir elasticsearch==7.1.0
-
-# Install rpy2 to share data between Python and R
-RUN conda install rpy2=2.9.4 plotly=4.4.1
-RUN conda install -c conda-forge ipyleaflet
-
-# 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 \
- && pip install --no-cache-dir $buildDeps
-
-# Install various extensions
-RUN jupyter labextension install @jupyterlab/github
-RUN jupyter labextension install jupyterlab-drawio
-RUN jupyter labextension install jupyter-leaflet
-RUN jupyter labextension install @jupyterlab/plotly-extension
-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 fix-permissions $CONDA_DIR
-RUN conda install -c conda-forge jupyter_contrib_nbextensions && \
-  conda install -c conda-forge jupyter_nbextensions_configurator && \
-  jupyter nbextension enable codefolding/main
-RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
-
-# Copying config and fix permissions
-COPY jupyter_notebook_config.json /etc/jupyter/
-RUN fix-permissions /home/$NB_USER
-
-# Switch back to jovyan to avoid accidental container runs as root
-USER $NB_UID

src/Dockerfile.header

@@ -1,3 +1,4 @@
 # Use NVIDIA CUDA as base image and run the same installation as in the other packages.
-FROM nvidia/cuda:10.1-base-ubuntu18.04
+# The version of cudatoolkit must match those of the base image, see Dockerfile.pytorch
+FROM nvidia/cuda:10.2-base-ubuntu18.04
 LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"

src/Dockerfile.pytorch

@@ -5,9 +5,9 @@ RUN conda install --quiet --yes \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER
 
-# Install PyTorch
+# Install PyTorch, version of cudatoolkit must match those of the base image
 RUN conda install -y -c pytorch \
-    cudatoolkit=10.1 \
+    cudatoolkit=10.2 \
     'pytorch=1.3.1' \
     torchvision && \
     conda clean --all -f -y && \