90 lines
3.1 KiB
Docker
Executable File
90 lines
3.1 KiB
Docker
Executable File
ARG DOCKER_NOTEBOOK_IMAGE
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ARG DISPLAY
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FROM $DOCKER_NOTEBOOK_IMAGE
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ARG JUPYTERHUB_VERSION
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#any additional installations go here.
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RUN export DISPLAY=$DISPLAY
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USER root
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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vim \
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htop \
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fonts-dejavu \
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tzdata \
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gfortran \
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gcc
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# finish off with MPI dependencies (only required if not installing fenics)
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#RUN sudo apt-get install mpich libmpich-dev -y
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RUN rm -rf /var/lib/apt/lists/*
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USER jovyan
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RUN conda update --all
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RUN conda install fenics
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# If you do not need parallelism, delete the following.
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RUN python3 -m pip install ipyparallel mpi4py
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RUN ipython profile create --parallel --profile=mpi
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RUN ipython profile create --parallel --profile=default
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RUN echo "c.IPClusterEngines.engine_launcher_class = 'MPIEngineSetLauncher'" >> /home/jovyan/.ipython/profile_mpi/ipcluster_config.py
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# Python 2 environment
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RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml ipyparallel mpi4py scipy pyDOE
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RUN /opt/conda/envs/python2/bin/ipython profile create --parallel --profile=mpi
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USER root
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# Create a global kernelspec in the image and modify it so that it properly activates
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# the python2 conda environment.
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RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
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$CONDA_DIR/envs/python2/bin/kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json
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USER $NB_UID
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# Jupyterhub and memory monitoring
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RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse && \
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jupyter labextension install --minimize=False jupyterlab-topbar-extension && \
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jupyter labextension install --minimize=False jupyterlab-system-monitor && \
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npm cache clean --force && \
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rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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rm -rf /home/$NB_USER/.node-gyp && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# R environment
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USER root
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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libapparmor1 \
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libedit2 \
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lsb-release \
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psmisc \
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libssl1.0.0 \
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;
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# You can use rsession from rstudio's desktop package as well.
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ENV RSTUDIO_PKG=rstudio-server-1.1.463-amd64.deb
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RUN wget -q http://download2.rstudio.org/${RSTUDIO_PKG}
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RUN dpkg -i ${RSTUDIO_PKG}
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RUN rm ${RSTUDIO_PKG}
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RUN conda install -c r r-shiny && conda clean -tipsy
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RUN apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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USER $NB_USER
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# The desktop package uses /usr/lib/rstudio/bin
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RUN python3 -m pip install jupyter-rsession-proxy
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RUN python3 -m pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy
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RUN jupyter labextension install jupyterlab-server-proxy
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ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
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ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib"
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#ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib"
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# USER SETTINGS
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USER jovyan
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RUN echo "export EDITOR=/usr/bin/vim" >> /home/jovyan/.bashrc
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