Dockerfile

FROM debian:bullseye


# install Octopus 12.1 on Debian implimented from fangohr/octopus-in-spack
ARG DOCKER_USER

######### Octopus Setup #########
# Convenience tools (up to emacs)
# Libraries that octopus needs (up to procps)
# and optional dependencies (starting from libnetcdf-dev)
RUN apt-get -y update && apt-get -y install autoconf \ 
    build-essential \
    emacs \ 
    g++ \ 
    gcc \ 
    gfortran \ 
    git \ 
    libatlas-base-dev  \
    libblas-dev \ 
    libboost-dev \ 
    libcgal-dev \
    libelpa-dev \
    libetsf-io-dev \ 
    libfftw3-dev \ 
    libgmp-dev \ 
    libgsl-dev \ 
    liblapack-dev \ 
    libmpfr-dev \ 
    libnetcdff-dev \ 
    libnlopt-dev \ 
    libopenmpi-dev \
    libscalapack-mpi-dev  \
    libspfft-dev \ 
    libtool \ 
    libxc-dev \ 
    libyaml-dev \ 
    likwid \ 
    nano \ 
    pkg-config  \
    procps \ 
    time \ 
    vim \ 
    wget \ 
    && rm -rf /var/lib/apt/lists/*

# Mimic the host uid and gid from host to container to enable write support to mounted volumes
RUN groupadd cfel -g 3512 # group for CFEL
RUN useradd $DOCKER_USER --create-home --shell /bin/bash -g 3512 -u 52351
USER $DOCKER_USER

# Build Octopus

WORKDIR /home/$DOCKER_USER
RUN wget -O oct.tar.gz https://octopus-code.org/down.php?file=12.1/octopus-12.1.tar.gz && tar xfvz oct.tar.gz && rm oct.tar.gz
WORKDIR /home/$DOCKER_USER/octopus-12.1

RUN autoreconf -i
RUN ./configure 

# Which optional dependencies are missing?
RUN cat config.log | grep WARN > octopus-configlog-warnings
RUN cat octopus-configlog-warnings

# all in one line to make image smaller
USER root
RUN make && make install && make clean && make distclean
USER $DOCKER_USER

RUN octopus --version > octopus-version
RUN octopus --version

# The next command returns an error code as some tests fail
# RUN make check-short

RUN mkdir -p /home/$DOCKER_USER/octopus-examples
COPY --chown=$DOCKER_USER:cfel examples /home/$DOCKER_USER/octopus-examples

# Instead of tests, run two short examples
RUN cd /home/$DOCKER_USER/octopus-examples/h-atom && octopus
RUN cd /home/$DOCKER_USER/octopus-examples/he && octopus
RUN cd /home/$DOCKER_USER/octopus-examples/recipe && octopus

######### Postopus Setup #########
USER root
RUN apt-get -y update && apt-get -y install python3 \
            python3-pip \
            ffmpeg \
            libsm6 \
            libxext6 \
            && rm -rf /var/lib/apt/lists/*  

USER $DOCKER_USER
EXPOSE 8888

# Mount the host directory containing the  src as a volume in the container
RUN mkdir -p /home/$DOCKER_USER/io
USER root
RUN chown -R $DOCKER_USER:cfel /home/$DOCKER_USER/io

USER $DOCKER_USER
RUN pip install --no-cache jupyterlab && \
    pip install --no-cache git+https://gitlab.com/octopus-code/postopus.git && \
    pip install --no-cache "holoviews[recommended]" 

# CD to directory where we mount the host file system
WORKDIR /home/$DOCKER_USER/io

# RUN jupyter lab --LabApp.token='' --ip=${HOSTNAME} > /dev/null 2>&1 &  disown
# use 'start-jupyter-lab.sh' script from inside container
CMD bash -l