diff --git a/src/Dockerfile b/src/Dockerfile deleted file mode 100644 index ceac7e7..0000000 --- a/src/Dockerfile +++ /dev/null @@ -1,463 +0,0 @@ -FROM nvidia/cuda:10.1-base-ubuntu18.04 -LABEL maintainer="Christoph Schranz " - -############################################################################ -#################### 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 diff --git a/src/Dockerfile.header b/src/Dockerfile.header index 1e5d21d..1a5d9ba 100644 --- a/src/Dockerfile.header +++ b/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 " diff --git a/src/Dockerfile.pytorch b/src/Dockerfile.pytorch index 439b1b1..f3eec75 100644 --- a/src/Dockerfile.pytorch +++ b/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 && \