From a4d55736980f3919bdff8fee8a184973a097d60a Mon Sep 17 00:00:00 2001
From: Christoph Schranz <christoph.schranz@salzburgresearch.at>
Date: Mon, 22 Jun 2020 13:26:01 +0200
Subject: [PATCH] feature: set sparse Dockerfile with Python interpreter only

---
 .build/Dockerfile                          | 260 ++++++---------------
 .build/docker-stacks                       |   2 +-
 .build/start-notebook.sh                   |  10 +-
 .build/start-singleuser.sh                 |  22 +-
 .build/start.sh                            |   2 +-
 README.md                                  |  89 ++++---
 extra/Getting_Started/GPU-processing.ipynb | 100 ++++----
 generate-Dockerfile.sh                     |  47 ++--
 src/Dockerfile.gpulibs                     |  16 +-
 src/Dockerfile.header                      |   2 +-
 10 files changed, 232 insertions(+), 318 deletions(-)

diff --git a/.build/Dockerfile b/.build/Dockerfile
index c4111bf..b49bd40 100755
--- a/.build/Dockerfile
+++ b/.build/Dockerfile
@@ -2,7 +2,7 @@
 # The version of cudatoolkit must match those of the base image, see Dockerfile.pytorch
 FROM nvidia/cuda:10.1-base-ubuntu18.04
 LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
-# The maintainers of subsequent sections may vary
+# This is a concatenated Dockerfile, the maintainers of subsequent sections may vary.
 
 ############################################################################
 #################### Dependency: jupyter/base-image ########################
@@ -11,15 +11,19 @@ LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
 
-# Ubuntu 18.04 (bionic)
-# https://hub.docker.com/_/ubuntu/?tab=tags&name=bionic
-ARG ROOT_CONTAINER=ubuntu:bionic-20200112@sha256:bc025862c3e8ec4a8754ea4756e33da6c41cba38330d7e324abd25c8e0b93300
+# Ubuntu 20.04 (focal)
+# https://hub.docker.com/_/ubuntu/?tab=tags&name=focal
+# OS/ARCH: linux/amd64
+ARG ROOT_CONTAINER=ubuntu:focal-20200423@sha256:238e696992ba9913d24cfc3727034985abd136e08ee3067982401acdc30cbf3f
 
 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
 
 # Install all OS dependencies for notebook server that starts but lacks all
@@ -68,7 +72,7 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
     chown $NB_USER:$NB_GID $CONDA_DIR && \
     chmod g+w /etc/passwd && \
     fix-permissions $HOME && \
-    fix-permissions "$(dirname $CONDA_DIR)"
+    fix-permissions $CONDA_DIR
 
 USER $NB_UID
 WORKDIR $HOME
@@ -79,19 +83,20 @@ RUN mkdir /home/$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=4.7.12.1 \
-    MINICONDA_MD5=81c773ff87af5cfac79ab862942ab6b3 \
-    CONDA_VERSION=4.7.12
+ENV MINICONDA_VERSION=4.8.2 \
+    MINICONDA_MD5=87e77f097f6ebb5127c77662dfc3165e \
+    CONDA_VERSION=4.8.2
 
-RUN cd /tmp && \
-    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
-    echo "${MINICONDA_MD5} *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 && \
+WORKDIR /tmp
+RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
+    echo "${MINICONDA_MD5} *Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
+    /bin/bash Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
+    rm Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
     echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
     conda config --system --prepend channels conda-forge && \
     conda config --system --set auto_update_conda false && \
     conda config --system --set show_channel_urls true && \
+    conda config --system --set channel_priority strict && \
     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 && \
@@ -118,7 +123,7 @@ RUN conda install --quiet --yes 'tini=0.18.0' && \
 RUN conda install --quiet --yes \
     'notebook=6.0.3' \
     'jupyterhub=1.1.0' \
-    'jupyterlab=1.2.5' && \
+    'jupyterlab=2.1.3' && \
     conda clean --all -f -y && \
     npm cache clean --force && \
     jupyter notebook --generate-config && \
@@ -134,9 +139,7 @@ ENTRYPOINT ["tini", "-g", "--"]
 CMD ["start-notebook.sh"]
 
 # Copy 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 start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
 COPY jupyter_notebook_config.py /etc/jupyter/
 
 # Fix permissions on /etc/jupyter as root
@@ -146,6 +149,8 @@ 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 #####################
 ############################################################################
@@ -160,7 +165,8 @@ USER root
 # Install all OS dependencies for fully functional notebook server
 RUN apt-get update && apt-get install -yq --no-install-recommends \
     build-essential \
-    emacs \
+    emacs-nox \
+    vim-tiny \
     git \
     inkscape \
     jed \
@@ -173,7 +179,7 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \
     # ---- nbconvert dependencies ----
     texlive-xetex \
     texlive-fonts-recommended \
-    texlive-generic-recommended \
+    texlive-plain-generic \
     # Optional dependency
     texlive-fonts-extra \
     # ----
@@ -196,40 +202,45 @@ LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
 
 USER root
 
-# ffmpeg for matplotlib anim
+# ffmpeg for matplotlib anim & dvipng for latex labels
 RUN apt-get update && \
-    apt-get install -y --no-install-recommends ffmpeg && \
+    apt-get install -y --no-install-recommends ffmpeg dvipng && \
     rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID
 
 # Install Python 3 packages
 RUN conda install --quiet --yes \
-    'beautifulsoup4=4.8.*' \
+    'beautifulsoup4=4.9.*' \
     'conda-forge::blas=*=openblas' \
-    'bokeh=1.4.*' \
-    'cloudpickle=1.2.*' \
+    'bokeh=2.0.*' \
+    'bottleneck=1.3.*' \
+    'cloudpickle=1.4.*' \
     'cython=0.29.*' \
-    'dask=2.9.*' \
+    'dask=2.15.*' \
     'dill=0.3.*' \
     'h5py=2.10.*' \
     'hdf5=1.10.*' \
     'ipywidgets=7.5.*' \
-    'matplotlib-base=3.1.*' \
+    'ipympl=0.5.*'\
+    'matplotlib-base=3.2.*' \
+    # numba update to 0.49 fails resolving deps.
     'numba=0.48.*' \
     'numexpr=2.7.*' \
-    'pandas=0.25.*' \
+    'pandas=1.0.*' \
     'patsy=0.5.*' \
     'protobuf=3.11.*' \
+    'pytables=3.6.*' \
     'scikit-image=0.16.*' \
     'scikit-learn=0.22.*' \
     'scipy=1.4.*' \
-    'seaborn=0.9.*' \
+    'seaborn=0.10.*' \
     'sqlalchemy=1.3.*' \
     'statsmodels=0.11.*' \
     'sympy=1.5.*' \
     'vincent=0.4.*' \
-    'xlrd' \
+    'widgetsnbextension=3.5.*'\
+    'xlrd=1.2.*' \
     && \
     conda clean --all -f -y && \
     # Activate ipywidgets extension in the environment that runs the notebook server
@@ -237,121 +248,34 @@ RUN conda install --quiet --yes \
     # 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 && \
+    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 $CONDA_DIR/share/jupyter/lab/staging && \
-    rm -rf /home/$NB_USER/.cache/yarn && \
-    rm -rf /home/$NB_USER/.node-gyp && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
+    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 && \
+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
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
 
 # Import matplotlib the first time to build the font cache.
-ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
+ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
+
 RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
-    fix-permissions /home/$NB_USER
+    fix-permissions "/home/${NB_USER}"
 
 USER $NB_UID
 
-############################################################################
-################ Dependency: jupyter/datascience-notebook ##################
-############################################################################
-
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
-
-# Set when building on Travis so that certain long-running build steps can
-# be skipped to shorten build time.
-ARG TEST_ONLY_BUILD
-
-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 $HOME
-ENV JULIA_DEPOT_PATH=/opt/julia
-ENV JULIA_PKGDIR=/opt/julia
-ENV JULIA_VERSION=1.3.1
-
-RUN mkdir /opt/julia-${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 "faa707c8343780a6fe5eaf13490355e8190acf8e2c189b9e7ecbddb0fa2643ad *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 \
-    'r-base=3.6.2' \
-    'r-caret=6.0*' \
-    'r-crayon=1.3*' \
-    'r-devtools=2.2*' \
-    'r-forecast=8.10*' \
-    'r-hexbin=1.28*' \
-    'r-htmltools=0.4*' \
-    'r-htmlwidgets=1.5*' \
-    'r-irkernel=1.1*' \
-    'r-nycflights13=1.0*' \
-    'r-plyr=1.8*' \
-    'r-randomforest=4.6*' \
-    'r-rcurl=1.98*' \
-    'r-reshape2=1.4*' \
-    'r-rmarkdown=2.1*' \
-    'r-rsqlite=2.1*' \
-    'r-shiny=1.3*' \
-    'r-tidyverse=1.3*' \
-    'rpy2=3.1*' \
-    && \
-    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 IJulia\"; 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
+WORKDIR $HOME
 
 ############################################################################
 ########################## Dependency: gpulibs #############################
@@ -359,12 +283,16 @@ RUN julia -e 'import Pkg; Pkg.update()' && \
 
 LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
 
-# Install Tensorflow, check compatibility here: https://www.tensorflow.org/install/gpu 
-RUN conda install --quiet --yes \
-    'tensorflow-gpu=2.1*' \
-    'keras-gpu' && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
+# Install Tensorflow, check compatibility here: https://www.tensorflow.org/install/gpu
+# installation via conda leads to errors in version 4.8.2
+#RUN conda install --quiet --yes \
+#    'tensorflow-gpu=2.1*' \
+#    'keras-gpu' && \
+#    fix-permissions $CONDA_DIR && \
+#    fix-permissions /home/$NB_USER
+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 \
@@ -382,57 +310,5 @@ RUN conda clean --all -f -y && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER
 
-############################################################################
-############################ Useful packages ###############################
-############################################################################
-
-LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
-
-# Update conda
-RUN conda update -n base conda -y
-
-USER root
-
-# 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 $CONDA_DIR
-RUN conda install -c conda-forge jupyter_contrib_nbextensions && \
-  conda install -c conda-forge jupyter_nbextensions_configurator && \
-  conda install -c conda-forge rise && \
-  jupyter nbextension enable codefolding/main
-RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
-
-RUN fix-permissions /home/$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/
diff --git a/.build/docker-stacks b/.build/docker-stacks
index c1c3293..04f7f60 160000
--- a/.build/docker-stacks
+++ b/.build/docker-stacks
@@ -1 +1 @@
-Subproject commit c1c32938438151c7e2a22b5aa338caba2ec01da2
+Subproject commit 04f7f60d34a674a2964d96a6cb97c57a7870a828
diff --git a/.build/start-notebook.sh b/.build/start-notebook.sh
index ed6d066..f893af1 100755
--- a/.build/start-notebook.sh
+++ b/.build/start-notebook.sh
@@ -6,14 +6,14 @@ set -e
 
 wrapper=""
 if [[ "${RESTARTABLE}" == "yes" ]]; then
-  wrapper="run-one-constantly"
+    wrapper="run-one-constantly"
 fi
 
 if [[ ! -z "${JUPYTERHUB_API_TOKEN}" ]]; then
-  # launched by JupyterHub, use single-user entrypoint
-  exec /usr/local/bin/start-singleuser.sh "$@"
+    # launched by JupyterHub, use single-user entrypoint
+    exec /usr/local/bin/start-singleuser.sh "$@"
 elif [[ ! -z "${JUPYTER_ENABLE_LAB}" ]]; then
-  . /usr/local/bin/start.sh $wrapper jupyter lab "$@"
+    . /usr/local/bin/start.sh $wrapper jupyter lab "$@"
 else
-  . /usr/local/bin/start.sh $wrapper jupyter notebook "$@"
+    . /usr/local/bin/start.sh $wrapper jupyter notebook "$@"
 fi
diff --git a/.build/start-singleuser.sh b/.build/start-singleuser.sh
index 8cb8cae..0c8f7ad 100755
--- a/.build/start-singleuser.sh
+++ b/.build/start-singleuser.sh
@@ -6,7 +6,7 @@ set -e
 
 # set default ip to 0.0.0.0
 if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then
-  NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS"
+    NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS"
 fi
 
 # handle some deprecated environment variables
@@ -14,30 +14,26 @@ fi
 # These won't be passed from DockerSpawner 0.9,
 # so avoid specifying --arg=empty-string
 if [ ! -z "$NOTEBOOK_DIR" ]; then
-  NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS"
+    NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS"
 fi
 if [ ! -z "$JPY_PORT" ]; then
-  NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS"
+    NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS"
 fi
 if [ ! -z "$JPY_USER" ]; then
-  NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS"
+    NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS"
 fi
 if [ ! -z "$JPY_COOKIE_NAME" ]; then
-  NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS"
+    NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS"
 fi
 if [ ! -z "$JPY_BASE_URL" ]; then
-  NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS"
+    NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS"
 fi
 if [ ! -z "$JPY_HUB_PREFIX" ]; then
-  NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS"
+    NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS"
 fi
 if [ ! -z "$JPY_HUB_API_URL" ]; then
-  NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
-fi
-if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then
-  NOTEBOOK_BIN="jupyter labhub"
-else
-  NOTEBOOK_BIN="jupyterhub-singleuser"
+    NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
 fi
+NOTEBOOK_BIN="jupyterhub-singleuser"
 
 . /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS "$@"
diff --git a/.build/start.sh b/.build/start.sh
index da6905b..b293197 100755
--- a/.build/start.sh
+++ b/.build/start.sh
@@ -93,7 +93,7 @@ if [ $(id -u) == 0 ] ; then
     fi
 
     # Add $CONDA_DIR/bin to sudo secure_path
-    sed -r "s#Defaults\s+secure_path=\"([^\"]+)\"#Defaults secure_path=\"\1:$CONDA_DIR/bin\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
+    sed -r "s#Defaults\s+secure_path\s*=\s*\"?([^\"]+)\"?#Defaults secure_path=\"\1:$CONDA_DIR/bin\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
 
     # Exec the command as NB_USER with the PATH and the rest of
     # the environment preserved
diff --git a/README.md b/README.md
index d91b383..1286404 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 
 First of all, thanks to [docker-stacks](https://github.com/jupyter/docker-stacks) 
 for creating and maintaining a robost  Python, R and Julia toolstack for Data Analytics/Science 
-applications. This project uses the NVIDIA CUDA image as a basis image and installs their 
+applications. This project uses the NVIDIA CUDA image as the base image and installs their 
 toolstack on top of it to enable GPU calculations in the Jupyter notebooks. 
 The image of this repository is available on [Dockerhub](https://hub.docker.com/r/cschranz/gpu-jupyter).
 
@@ -21,13 +21,34 @@ The image of this repository is available on [Dockerhub](https://hub.docker.com/
 
 ## Requirements
 
-1.  Install [Docker](https://www.docker.com/community-edition#/download) version **1.10.0+**
+1.  A NVIDIA GPU
+2.  Install [Docker](https://www.docker.com/community-edition#/download) version **1.10.0+**
  and [Docker Compose](https://docs.docker.com/compose/install/) version **1.6.0+**.
-2.  A NVIDIA GPU
-3.  Get access to use your GPU via the CUDA drivers, check out this 
+3.  Get access to your GPU via CUDA drivers within Docker containers. Therfore, check out this 
 [medium article](https://medium.com/@christoph.schranz/set-up-your-own-gpu-based-jupyterlab-e0d45fcacf43).
     The CUDA toolkit is not required on the host system, as it will be deployed 
-    in [NVIDIA-docker](https://github.com/NVIDIA/nvidia-docker).
+    in [NVIDIA-docker](https://github.com/NVIDIA/nvidia-docker). 
+    You can be sure that you can access your GPU within Docker, 
+    if the command `docker run --runtime nvidia nvidia/cuda:10.1-base-ubuntu18.04 nvidia-smi`
+    returns a result similar to this one:
+    ```bash
+    Mon Jun 22 09:06:28 2020       
+    +-----------------------------------------------------------------------------+
+    | NVIDIA-SMI 440.82       Driver Version: 440.82       CUDA Version: 10.1     |
+    |-------------------------------+----------------------+----------------------+
+    | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
+    | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
+    |===============================+======================+======================|
+    |   0  GeForce RTX 207...  Off  | 00000000:01:00.0  On |                  N/A |
+    |  0%   46C    P8     9W / 215W |    424MiB /  7974MiB |      6%      Default |
+    +-------------------------------+----------------------+----------------------+
+                                                                                   
+    +-----------------------------------------------------------------------------+
+    | Processes:                                                       GPU Memory |
+    |  GPU       PID   Type   Process name                             Usage      |
+    |=============================================================================|
+    +-----------------------------------------------------------------------------+
+    ```
 4. Clone the Repository or pull the image from 
     [Dockerhub](https://hub.docker.com/repository/docker/cschranz/gpu-jupyter):
     ```bash
@@ -37,29 +58,45 @@ The image of this repository is available on [Dockerhub](https://hub.docker.com/
 
 ## Quickstart
 
-First of all, it is necessary to generate the `Dockerfile` based on the latest toolstack of 
-[hub.docker.com/u/jupyter](https://hub.docker.com/u/jupyter).
-As soon as you have access to your GPU locally (it can be tested via a Tensorflow or PyTorch 
-directly on the host node), you can run these commands to start the jupyter notebook via 
-docker-compose (internally):
-
-  ```bash
-  ./generate-Dockerfile.sh
-  docker build -t gpu-jupyter .build/
-  docker run -d -p [port]:8888 gpu-jupyter
-  ``` 
-
-Alternatively, you can configure the environment in `docker-compose.yml` and run 
-this to deploy the `GPU-Jupyter` via docker-compose (under-the-hood):
-
-  ```bash
-  ./generate-Dockerfile.sh
-  ./start-local.sh -p 8888  # where -p stands for the port of the service
-  ```
-  
-Both options will run *GPU-Jupyter* by default on [localhost:8888](http://localhost:8888) with the default 
+First of all, it is necessary to generate the `Dockerfile` based on the
+[docker-stacks](https://github.com/jupyter/docker-stacks).
+As soon as you have access to your GPU within Docker containers 
+(make sure the command `docker run --runtime nvidia nvidia/cuda:10.1-base-ubuntu18.04 nvidia-smi` shows your
+GPU statistics), you can generate a Dockerfile and build it via docker-compose.
+The two commands will start *GPU-Jupyter* on [localhost:1234](http://localhost:1234) with the default 
 password `asdf`.
 
+  ```bash
+  ./generate-Dockerfile.sh
+  ./start-local.sh -p 1234  # where -p stands for the port, default 8888
+  ``` 
+
+## Parameter
+
+The script `generate-Dockerfile.sh` has multiple parameters:
+
+* `-c|--commit`: specify a commit or `"latest"` for the `docker-stacks`, the default commit is a working one.
+
+* `-s|--slim`: Generate a slim Dockerfile. 
+As some installations are not needed by everyone, there is the possibility to skip some installations 
+to reduce the size of the image.
+Here the `docker-stack` `scipy-notebook` is used instead of `datascience-notebook` that comes with Julia and R. 
+Moreover, none of the packages within `src/Dockerfile.usefulpackages` is installed.
+
+* `--no-datascience-notebook`: As the name suggests, the `docker-stack` `datascience-notebook` is not installed
+on top of the `scipy-notebook`, but the packages within `src/Dockerfile.usefulpackages` are.
+
+* `--no-useful-packages`: On top of the `docker-stack` `datascience-notebook`, the essential `gpulibs` are installed
+but not the packages within `src/Dockerfile.usefulpackages`.
+
+
+The script `start-local.sh` is a wrapper for a quick configuration of the underlying `docker-compose.yml`.
+It is equal to these commands:
+
+  ```bash
+  docker build -t gpu-jupyter .build/
+  docker run -d -p [port]:8888 gpu-jupyter
+  ```
 
 ## Tracing
   
diff --git a/extra/Getting_Started/GPU-processing.ipynb b/extra/Getting_Started/GPU-processing.ipynb
index 016359a..77b3513 100644
--- a/extra/Getting_Started/GPU-processing.ipynb
+++ b/extra/Getting_Started/GPU-processing.ipynb
@@ -27,15 +27,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Wed Mar 11 07:16:17 2020       \n",
+      "Mon Jun 22 11:24:08 2020       \n",
       "+-----------------------------------------------------------------------------+\n",
-      "| NVIDIA-SMI 440.48.02    Driver Version: 440.48.02    CUDA Version: 10.2     |\n",
+      "| NVIDIA-SMI 440.82       Driver Version: 440.82       CUDA Version: 10.2     |\n",
       "|-------------------------------+----------------------+----------------------+\n",
       "| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |\n",
       "| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |\n",
       "|===============================+======================+======================|\n",
-      "|   0  GeForce RTX 207...  Off  | 00000000:01:00.0 Off |                  N/A |\n",
-      "|  0%   42C    P8     1W / 215W |   1788MiB /  7974MiB |      0%      Default |\n",
+      "|   0  GeForce RTX 207...  Off  | 00000000:01:00.0  On |                  N/A |\n",
+      "|  0%   49C    P0    38W / 215W |    430MiB /  7974MiB |      5%      Default |\n",
       "+-------------------------------+----------------------+----------------------+\n",
       "                                                                               \n",
       "+-----------------------------------------------------------------------------+\n",
@@ -87,10 +87,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "WARNING:tensorflow:From <ipython-input-3-d1bfbb527297>:3: is_gpu_available (from tensorflow.python.framework.test_util) is deprecated and will be removed in a future version.\n",
-      "Instructions for updating:\n",
-      "Use `tf.config.list_physical_devices('GPU')` instead.\n",
-      "True\n"
+      "[PhysicalDevice(name='/physical_device:XLA_GPU:0', device_type='XLA_GPU')]\n"
      ]
     },
     {
@@ -101,30 +98,20 @@
        " memory_limit: 268435456\n",
        " locality {\n",
        " }\n",
-       " incarnation: 8034786465358909470,\n",
+       " incarnation: 12436949185972503812,\n",
        " name: \"/device:XLA_CPU:0\"\n",
        " device_type: \"XLA_CPU\"\n",
        " memory_limit: 17179869184\n",
        " locality {\n",
        " }\n",
-       " incarnation: 13772661904993777233\n",
+       " incarnation: 9674938692146126962\n",
        " physical_device_desc: \"device: XLA_CPU device\",\n",
-       " name: \"/device:GPU:0\"\n",
-       " device_type: \"GPU\"\n",
-       " memory_limit: 5480775680\n",
-       " locality {\n",
-       "   bus_id: 1\n",
-       "   links {\n",
-       "   }\n",
-       " }\n",
-       " incarnation: 8336380964433791501\n",
-       " physical_device_desc: \"device: 0, name: GeForce RTX 2070 SUPER, pci bus id: 0000:01:00.0, compute capability: 7.5\",\n",
        " name: \"/device:XLA_GPU:0\"\n",
        " device_type: \"XLA_GPU\"\n",
        " memory_limit: 17179869184\n",
        " locality {\n",
        " }\n",
-       " incarnation: 4817022749254415174\n",
+       " incarnation: 7870544216044264725\n",
        " physical_device_desc: \"device: XLA_GPU device\"]"
       ]
      },
@@ -136,7 +123,7 @@
    "source": [
     "import tensorflow as tf\n",
     "from tensorflow.python.client import device_lib\n",
-    "print(tf.test.is_gpu_available(cuda_only=True))\n",
+    "print(tf.config.list_physical_devices('XLA_GPU'))\n",
     "device_lib.list_local_devices()"
    ]
   },
@@ -148,11 +135,11 @@
     {
      "data": {
       "text/plain": [
-       "tensor([[0.1091, 0.0178, 0.2500],\n",
-       "        [0.1409, 0.9612, 0.0325],\n",
-       "        [0.8944, 0.3869, 0.9657],\n",
-       "        [0.8131, 0.5454, 0.2587],\n",
-       "        [0.6570, 0.0147, 0.1361]])"
+       "tensor([[0.0399, 0.1738, 0.2486],\n",
+       "        [0.7464, 0.1461, 0.8991],\n",
+       "        [0.7264, 0.9835, 0.8844],\n",
+       "        [0.4544, 0.8331, 0.8435],\n",
+       "        [0.0109, 0.0689, 0.2997]])"
       ]
      },
      "execution_count": 4,
@@ -202,7 +189,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "248 ms ± 174 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "276 ms ± 9.97 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
      ]
     }
    ],
@@ -236,13 +223,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "78.2 ms ± 250 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
+      "82.1 ms ± 1.85 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
-    "# Calculate the projection matrix of x\n",
+    "# Calculate the projection matrix of x on the CPU\n",
     "H = x.mm( (x.t().mm(x)).inverse() ).mm(x.t())"
    ]
   },
@@ -262,16 +249,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "tensor([[0.0962, 0.3125, 0.7327, 0.5982, 0.4624],\n",
-      "        [0.4655, 0.4890, 0.9603, 0.4339, 0.0524],\n",
-      "        [0.9294, 0.9639, 0.6312, 0.1752, 0.7721],\n",
-      "        [0.5533, 0.3656, 0.9329, 0.8796, 0.9513],\n",
-      "        [0.4949, 0.0972, 0.2892, 0.7570, 0.2847]], device='cuda:0')\n",
-      "tensor([[0.0962, 0.3125, 0.7327, 0.5982, 0.4624],\n",
-      "        [0.4655, 0.4890, 0.9603, 0.4339, 0.0524],\n",
-      "        [0.9294, 0.9639, 0.6312, 0.1752, 0.7721],\n",
-      "        [0.5533, 0.3656, 0.9329, 0.8796, 0.9513],\n",
-      "        [0.4949, 0.0972, 0.2892, 0.7570, 0.2847]], dtype=torch.float64)\n"
+      "tensor([[0.2854, 0.3384, 0.6473, 0.0433, 0.5640],\n",
+      "        [0.3960, 0.0449, 0.6597, 0.5347, 0.8402],\n",
+      "        [0.0048, 0.9231, 0.0311, 0.2545, 0.0409],\n",
+      "        [0.6506, 0.8651, 0.7558, 0.1086, 0.8135],\n",
+      "        [0.1083, 0.0039, 0.6049, 0.3596, 0.1359]], device='cuda:0')\n",
+      "tensor([[0.2854, 0.3384, 0.6473, 0.0433, 0.5640],\n",
+      "        [0.3960, 0.0449, 0.6597, 0.5347, 0.8402],\n",
+      "        [0.0048, 0.9231, 0.0311, 0.2545, 0.0409],\n",
+      "        [0.6506, 0.8651, 0.7558, 0.1086, 0.8135],\n",
+      "        [0.1083, 0.0039, 0.6049, 0.3596, 0.1359]], dtype=torch.float64)\n"
      ]
     }
    ],
@@ -295,12 +282,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "11.4 ms ± 60.2 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "11.4 ms ± 28.8 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
+    "# Calculate the projection matrix of x on the GPU\n",
     "H = x.mm( (x.t().mm(x)).inverse() ).mm(x.t())"
    ]
   },
@@ -341,11 +329,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "tensor([[0.4303, 0.7364, 0.1235, 0.7786, 0.7036],\n",
-      "        [0.3256, 0.4515, 0.7994, 0.9814, 0.7705],\n",
-      "        [0.2292, 0.5194, 0.4354, 0.3964, 0.5804],\n",
-      "        [0.8855, 0.5156, 0.9321, 0.9555, 0.4150],\n",
-      "        [0.0640, 0.0665, 0.1170, 0.9547, 0.2668]], device='cuda:0')\n"
+      "tensor([[0.1101, 0.7887, 0.0641, 0.1327, 0.1681],\n",
+      "        [0.7914, 0.7248, 0.7731, 0.2662, 0.4908],\n",
+      "        [0.2451, 0.3568, 0.4006, 0.2099, 0.5212],\n",
+      "        [0.6195, 0.5120, 0.5212, 0.7321, 0.2272],\n",
+      "        [0.2374, 0.4540, 0.0868, 0.9393, 0.1561]], device='cuda:0')\n"
      ]
     }
    ],
@@ -376,11 +364,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "tensor([[1.0966e-03, 3.5866e-04, 4.0044e-04, 3.2466e-04, 2.3044e-04],\n",
-      "        [3.5866e-04, 9.7424e-04, 2.8649e-04, 8.2904e-04, 2.0482e-04],\n",
-      "        [4.0044e-04, 2.8649e-04, 5.4179e-04, 1.2729e-04, 9.4659e-05],\n",
-      "        [3.2466e-04, 8.2904e-04, 1.2729e-04, 1.3005e-03, 6.6951e-06],\n",
-      "        [2.3044e-04, 2.0482e-04, 9.4659e-05, 6.6950e-06, 1.3420e-03]],\n",
+      "tensor([[ 6.4681e-04, -1.5392e-05,  3.3608e-04,  2.1025e-04,  8.0912e-05],\n",
+      "        [-1.5392e-05,  5.0718e-04, -1.1769e-04, -2.3084e-05, -2.3264e-04],\n",
+      "        [ 3.3608e-04, -1.1769e-04,  6.9678e-04,  2.2663e-04, -1.8900e-04],\n",
+      "        [ 2.1025e-04, -2.3084e-05,  2.2663e-04,  6.0036e-04,  2.7787e-04],\n",
+      "        [ 8.0912e-05, -2.3264e-04, -1.8900e-04,  2.7787e-04,  1.4208e-03]],\n",
       "       device='cuda:0')\n"
      ]
     }
@@ -399,11 +387,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "tensor([[1.0966e-03, 3.5866e-04, 4.0044e-04, 3.2466e-04, 2.3044e-04],\n",
-      "        [3.5866e-04, 9.7424e-04, 2.8649e-04, 8.2904e-04, 2.0482e-04],\n",
-      "        [4.0044e-04, 2.8649e-04, 5.4179e-04, 1.2729e-04, 9.4659e-05],\n",
-      "        [3.2466e-04, 8.2904e-04, 1.2729e-04, 1.3005e-03, 6.6951e-06],\n",
-      "        [2.3044e-04, 2.0482e-04, 9.4659e-05, 6.6950e-06, 1.3420e-03]],\n",
+      "tensor([[ 6.4681e-04, -1.5392e-05,  3.3608e-04,  2.1025e-04,  8.0912e-05],\n",
+      "        [-1.5392e-05,  5.0718e-04, -1.1769e-04, -2.3084e-05, -2.3264e-04],\n",
+      "        [ 3.3608e-04, -1.1769e-04,  6.9678e-04,  2.2663e-04, -1.8900e-04],\n",
+      "        [ 2.1025e-04, -2.3084e-05,  2.2663e-04,  6.0036e-04,  2.7787e-04],\n",
+      "        [ 8.0912e-05, -2.3264e-04, -1.8900e-04,  2.7787e-04,  1.4208e-03]],\n",
       "       dtype=torch.float64)\n"
      ]
     }
diff --git a/generate-Dockerfile.sh b/generate-Dockerfile.sh
index 09717be..535c4df 100755
--- a/generate-Dockerfile.sh
+++ b/generate-Dockerfile.sh
@@ -4,10 +4,14 @@ cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
 # Set the path of the generated Dockerfile
 export DOCKERFILE=".build/Dockerfile"
 export STACKS_DIR=".build/docker-stacks"
-export HEAD_COMMIT="c1c32938438151c7e2a22b5aa338caba2ec01da2"
+# please test the build of the commit in https://github.com/jupyter/docker-stacks/commits/master in advance
+export HEAD_COMMIT="04f7f60d34a674a2964d96a6cb97c57a7870a828"
 
 while [[ "$#" -gt 0 ]]; do case $1 in
   -c|--commit) HEAD_COMMIT="$2"; shift;;
+  --no-datascience-notebook) no_datascience_notebook=1;;
+  --no-useful-packages) no_useful_packages=1;;
+  -s|--slim) no_datascience_notebook=1 && no_useful_packages=1;;
   *) echo "Unknown parameter passed: $1" &&
     echo "Usage: $0 -c [sha-commit] # set the head commit of the docker-stacks submodule
     (https://github.com/jupyter/docker-stacks/commits/master). default: $HEAD_COMMIT."; exit 1;;
@@ -23,11 +27,12 @@ if [[ "$HEAD_COMMIT" == "latest" ]]; then
   cd $STACKS_DIR && git pull && cd -
 else
   export GOT_HEAD="false"
-  cd $STACKS_DIR && git reset --hard "$HEAD_COMMIT" > /dev/null 2>&1  && cd - && export GOT_HEAD="true"
+  cd $STACKS_DIR && git pull && git reset --hard "$HEAD_COMMIT" > /dev/null 2>&1  && cd - && export GOT_HEAD="true"
   echo "$HEAD"
   if [[ "$GOT_HEAD" == "false" ]]; then
-    echo "Given sha-commit is invalid."
+    echo "Error: The given sha-commit is invalid."
     echo "Usage: $0 -c [sha-commit] # set the head commit of the docker-stacks submodule (https://github.com/jupyter/docker-stacks/commits/master)."
+    echo "Exiting"
     exit 2
   else
     echo "Set head to given commit."
@@ -66,13 +71,17 @@ echo "
 " >> $DOCKERFILE
 cat $STACKS_DIR/scipy-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE
 
-echo "
-############################################################################
-################ Dependency: jupyter/datascience-notebook ##################
-############################################################################
-" >> $DOCKERFILE
-cat $STACKS_DIR/datascience-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE
-
+# install Julia and R if not excluded or spare mode is used
+if [[ "$no_datascience_notebook" != 1 ]]; then
+  echo "
+  ############################################################################
+  ################ Dependency: jupyter/datascience-notebook ##################
+  ############################################################################
+  " >> $DOCKERFILE
+  cat $STACKS_DIR/datascience-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE
+else
+  echo "Set 'no-datascience-notebook', not installing the datascience-notebook with Julia and R."
+fi
 
 # Note that the following step also installs the cudatoolkit, which is
 # essential to access the GPU.
@@ -83,13 +92,17 @@ echo "
 " >> $DOCKERFILE
 cat src/Dockerfile.gpulibs >> $DOCKERFILE
 
-
-echo "
-############################################################################
-############################ Useful packages ###############################
-############################################################################
-" >> $DOCKERFILE
-cat src/Dockerfile.usefulpackages >> $DOCKERFILE
+# install useful packages if not excluded or spare mode is used
+if [[ "$no_useful_packages" != 1 ]]; then
+  echo "
+  ############################################################################
+  ############################ Useful packages ###############################
+  ############################################################################
+  " >> $DOCKERFILE
+  cat src/Dockerfile.usefulpackages >> $DOCKERFILE
+else
+  echo "Set 'no-useful-packages', not installing stuff within src/Dockerfile.usefulpackages."
+fi
 
 # Copy the demo notebooks and change permissions
 cp -r extra/Getting_Started data
diff --git a/src/Dockerfile.gpulibs b/src/Dockerfile.gpulibs
index 088a9bd..339f37c 100644
--- a/src/Dockerfile.gpulibs
+++ b/src/Dockerfile.gpulibs
@@ -1,11 +1,15 @@
 LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
 
-# Install Tensorflow, check compatibility here: https://www.tensorflow.org/install/gpu 
-RUN conda install --quiet --yes \
-    'tensorflow-gpu=2.1*' \
-    'keras-gpu' && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
+# Install Tensorflow, check compatibility here: https://www.tensorflow.org/install/gpu
+# installation via conda leads to errors in version 4.8.2
+#RUN conda install --quiet --yes \
+#    'tensorflow-gpu=2.1*' \
+#    'keras-gpu' && \
+#    fix-permissions $CONDA_DIR && \
+#    fix-permissions /home/$NB_USER
+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 \
diff --git a/src/Dockerfile.header b/src/Dockerfile.header
index ca9ce65..e8c9dfd 100644
--- a/src/Dockerfile.header
+++ b/src/Dockerfile.header
@@ -2,4 +2,4 @@
 # The version of cudatoolkit must match those of the base image, see Dockerfile.pytorch
 FROM nvidia/cuda:10.1-base-ubuntu18.04
 LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
-# The maintainers of subsequent sections may vary
+# This is a concatenated Dockerfile, the maintainers of subsequent sections may vary.