diff --git a/singleuser/Dockerfile b/singleuser/Dockerfile index 64ce801..9d83749 100755 --- a/singleuser/Dockerfile +++ b/singleuser/Dockerfile @@ -16,28 +16,35 @@ RUN apt-get update && \ gfortran \ gcc -# finish off with MPI dependencies -RUN sudo apt-get install mpich libmpich-dev -y && rm -rf /var/lib/apt/lists/* +# finish off with MPI dependencies (only required if not installing fenics) +#RUN sudo apt-get install mpich libmpich-dev -y && rm -rf /var/lib/apt/lists/* -RUN conda update --all && conda install fenics USER jovyan +RUN conda update --all +RUN conda install fenics -RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse +RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse && \ + jupyter labextension install jupyterlab-topbar-extension && \ + jupyter labextension install jupyterlab-system-monitor +# If you do not need parallelism, delete the following. RUN python3 -m pip install ipyparallel mpi4py RUN ipython profile create --parallel --profile=mpi +RUN ipython profile create --parallel --profile=default RUN echo "c.IPClusterEngines.engine_launcher_class = 'MPIEngineSetLauncher'" >> /home/jovyan/.ipython/profile_mpi/ipcluster_config.py +# Python 2 environment USER root RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml ipyparallel mpi4py RUN /opt/conda/envs/python2/bin/ipython profile create --parallel --profile=mpi - # Create a global kernelspec in the image and modify it so that it properly activates # the python2 conda environment. RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \ $CONDA_DIR/envs/python2/bin/kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json + +# R environment USER root RUN apt-get update && \ @@ -68,5 +75,7 @@ ENV PATH="${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 SETTINGS USER jovyan RUN echo "export EDITOR=/usr/bin/vim" >> /home/jovyan/.bashrc