Dockerfile

FROM lofarit/base4.0.16

USER root

# Package dependencies
COPY apt.sources.list /etc/apt/sources.list

# Support large mlocks
RUN echo "*        -   memlock     unlimited" > /etc/security/limits.conf

ENV DEBIAN_FRONTEND noninteractive
ENV DEBIAN_PRIORITY critical
ENV GNUCOMPILER 7
ENV DEB_SETUP_DEPENDENCIES \
    dpkg-dev \
    g++-$GNUCOMPILER \
    gcc-$GNUCOMPILER \
    libc-dev \
    cmake \
    gfortran-$GNUCOMPILER \
    git \
    wget \
    subversion

ENV DEB_DEPENCENDIES \
    python3-pip \
    libfftw3-dev \
    python3-numpy \
    libfreetype6 \
    libfreetype6-dev \
    libpng-dev \
    pkg-config \
    python3-dev \
    libboost-all-dev \
    libcfitsio-dev \
    libhdf5-dev \
    wcslib-dev \
    libatlas-base-dev \
    liblapack-dev \
    python3-tk \
    libreadline6-dev \
    subversion \
    liblog4cplus-dev \
    libhdf5-dev \
    libncurses5-dev \
    libsofa1-dev \
    flex \
    bison \
    libbison-dev \
    # Reference image generation dependencies
    make

RUN apt-get update
RUN apt-get install -y $DEB_SETUP_DEPENDENCIES
RUN apt-get install -y $DEB_DEPENCENDIES

ENV PATH /usr/local/bin:$PATH
ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH
ENV PYTHONPATH /usr/local/lib/python2.7/site-packages:$PYTHONPATH

# Latest GCC segfaults when compiling casacore
RUN rm /usr/bin/gcc /usr/bin/g++ /usr/bin/cpp /usr/bin/cc
RUN ln -s /usr/bin/gcc-$GNUCOMPILER /usr/bin/gcc
RUN ln -s /usr/bin/g++-$GNUCOMPILER /usr/bin/g++
RUN ln -s /usr/bin/gcc-$GNUCOMPILER /usr/bin/cc
RUN ln -s /usr/bin/g++-$GNUCOMPILER /usr/bin/cpp
RUN ln -s /usr/bin/gfortran-$GNUCOMPILER /usr/bin/gfortran


#####################################################################
# Add deployment keys
#####################################################################

RUN mkdir -p /root/.ssh/ 
COPY keys/lofarit_ddf2_rsa /root/.ssh/lofarit_ddf2_rsa
COPY keys/lofarit_killms_rsa /root/.ssh/lofarit_killms_rsa
RUN chmod 600 /root/.ssh/lofarit_ddf2_rsa && chmod 600 /root/.ssh/lofarit_killms_rsa


#####################################################################
# Get DDF from private repo
#####################################################################

# Add github key(s)
RUN ssh-keyscan github.com >> ~/.ssh/known_hosts

# Clone
RUN ssh-agent bash -c 'ssh-add /root/.ssh/lofarit_ddf2_rsa && cd /root/ && git clone git@github.com:cyriltasse/DDFacet'

# Checkout
RUN ssh-agent bash -c 'ssh-add /root/.ssh/lofarit_ddf2_rsa && cd /root/DDFacet && git pull && git checkout e98968d'



#####################################################################
# Build DDF from source
#####################################################################

RUN mkdir /opt/DDFacet

# Copy DDFacet and SkyModel into the image
RUN cp -a /root/DDFacet/DDFacet /opt/DDFacet/DDFacet && \
    cp -a /root/DDFacet/SkyModel /opt/DDFacet/SkyModel && \
    cp -a /root/DDFacet/MANIFEST.in /opt/DDFacet/MANIFEST.in && \
    cp -a /root/DDFacet/setup.py /opt/DDFacet/setup.py && \
    cp -a /root/DDFacet/setup.cfg /opt/DDFacet/setup.cfg && \
    cp -a /root/DDFacet/README.rst /opt/DDFacet/README.rst && \
    cp -a /root/DDFacet/pyproject.toml /opt/DDFacet/pyproject.toml && \
    cp -a /root/DDFacet/.git /opt/DDFacet/.git && \
    cp -a /root/DDFacet/.gitignore /opt/DDFacet/.gitignore && \
    cp -a /root/DDFacet/.gitmodules /opt/DDFacet/.gitmodules


# Finally install DDFacet
RUN rm -rf /opt/DDFacet/DDFacet/cbuild
RUN pip3 install -U pip setuptools wheel
RUN python3 -m pip install pybind11
RUN python3 -m pip install tensorflow==1.8.0
RUN python3 -m pip install -U "/opt/DDFacet/[dft-support,moresane-support,testing-requirements,fits-beam-support]"
RUN cd /opt/DDFacet/ && python3 setup.py build && cd /

# Set MeqTrees Cattery path to installation directory
ENV MEQTREES_CATTERY_PATH /usr/local/lib/python3.6/dist-packages/Cattery/
ENV PYTHONPATH $MEQTREES_CATTERY_PATH:$PYTHONPATH

RUN python3 -m pip install numpy==1.17.0

RUN python3 -c "import Siamese"
RUN python3 -c "import bdsf"

# Perform some basic tests
RUN DDF.py --help
RUN MakeMask.py --help
RUN MakeCatalog.py --help
RUN MakeModel.py --help
RUN MaskDicoModel.py --help
RUN ClusterCat.py --help


#####################################################################
# Get and build killMs
#####################################################################

# Clone
RUN ssh-agent bash -c 'ssh-add /root/.ssh/lofarit_killms_rsa && cd /opt/ && git clone git@github.com:cyriltasse/killMS'

# Checkout
RUN ssh-agent bash -c 'ssh-add /root/.ssh/lofarit_killms_rsa && cd /opt/killMS && git pull && git checkout 0607798'

RUN pip3 install /opt/killMS
RUN cd  /opt/killMS; python3 setup.py build


#####################################################################
# Remove deploymnet keys
#####################################################################

RUN rm -f /root/.ssh/lofarit_ddf2_rsa && rm -f /root/.ssh/lofarit_killms_rsa


#####################################################################
# DDF-PIPELINE
#####################################################################
RUN pip3 install pyregion sshtunnel pymysql
RUN  cd /opt; git clone https://github.com/mhardcastle/ddf-pipeline
RUN sed -e "s|INSTALLDIR|/opt|" /opt/ddf-pipeline/misc/DDF.sh > /opt/DDFacet/init.sh

RUN cd /opt && git clone https://www.ict.inaf.it/gitlab/lofarit/container-data.git


#####################################################################
# Switch back to lofar user and set env
#####################################################################

USER lofar

ENV DDF_PIPELINE_CATALOGS='/opt/container-data/bootstrap-cats/'
ENV CONTAINER_NAME='ddfacet_ssd-py3_kms-lofar-release-4_0_16'