mm/jupyterhub-deploy-docker
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updated default singleuser.

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mathematicalmichael 2019-01-21 13:11:09 -07:00
parent dc4c7c0d36
commit 91e18a9b41
2 changed files with 23 additions and 54 deletions
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3
jupyterhub_config.py
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@ -72,7 +72,7 @@ c.DockerSpawner.extra_create_kwargs.update({ 'command': spawn_cmd })
# Memory limit
c.Spawner.mem_limit = '2G' # RAM limit
#c.Spawner.cpu_limit = 0.1
c.Spawner.cpu_limit = 0.0001
# Connect containers to this Docker network
network_name = '%s-network'%hub_name
@ -89,7 +89,6 @@ notebook_dir = os.environ.get('DOCKER_NOTEBOOK_DIR') or '/home/jovyan/work'
c.DockerSpawner.notebook_dir = notebook_dir
# Mount the real user's Docker volume on the host to the notebook user's
# notebook directory in the container
c.DockerSpawner.volumes = { 'hub-user-{username}': notebook_dir }
# volume_driver is no longer a keyword argument to create_container()

74
singleuser/Dockerfile
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@ -6,17 +6,25 @@ ARG JUPYTERHUB_VERSION
USER root
RUN apt-get update && \
apt-get install -y vim && \
apt-get install -y gcc && \
apt-get install -y --no-install-recommends \
vim \
htop \
fonts-dejavu \
tzdata \
gfortran \
gcc && \
rm -rf /var/lib/apt/lists/*
USER jovyan
RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse jupyter-rsession-proxy
RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse
RUN conda install -c conda-forge fenics
RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml && \
conda clean -tipsy
RUN python3 -m pip install ipyparallel
RUN ipython profile create --parallel --profile=mpi
RUN echo "c.IPClusterEngines.engine_launcher_class = 'MPIEngineSetLauncher'" >> /home/jovyan/.ipython/profile_mpi/ipcluster_config.py
RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml
USER root
@ -25,45 +33,6 @@ USER root
RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
$CONDA_DIR/envs/python2/bin/kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json
# R pre-requisites
RUN apt-get update && \
apt-get install -y --no-install-recommends \
fonts-dejavu \
tzdata \
gfortran \
gcc && \
rm -rf /var/lib/apt/lists/*
USER $NB_UID
# R packages
RUN conda install --quiet --yes \
'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 -tipsy && \
fix-permissions $CONDA_DIR
RUN conda install rstudio && \
fix-permissions $CONDA_DIR
USER root
RUN apt-get update && \
@ -81,16 +50,17 @@ ENV RSTUDIO_PKG=rstudio-server-1.0.136-amd64.deb
RUN wget -q http://download2.rstudio.org/${RSTUDIO_PKG}
RUN dpkg -i ${RSTUDIO_PKG}
RUN rm ${RSTUDIO_PKG}
RUN conda install -c r r-shiny && conda clean -tipsy
RUN apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN python3 -m pip install jupyterhub jupyter-rsession-proxy \
&& jupyter labextension install jupyterlab-server-proxy
USER $NB_USER
# The desktop package uses /usr/lib/rstudio/bin
RUN python3 -m pip install jupyter-rsession-proxy
RUN python3 -m pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy
RUN jupyter labextension install jupyterlab-server-proxy
ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
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"
#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"
USER jovyan
RUN python3 -m pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy
# The desktop package uses /usr/lib/rstudio/bin
ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
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"