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Commits on Source (7)
ddf2/DDFacet/
ddf2/killMS/
ddf2/keys
.DS_Store
.project
.pydevproject
FROM lofar/lofar-pipeline:LOFAR-Release-4_0_16
# Set non-interactive
ENV DEBIAN_FRONTEND noninteractive
# Always update when extending base images
RUN apt update
#------------------------
# Install deps
#------------------------
# Git, Curl, sudo and Nano
RUN apt-get install git curl sudo nano -y
#------------------------
# Lofar user
#------------------------
# Add group. We chose GID 65527 to try avoiding conflicts.
RUN groupadd -g 65527 lofar
# Add user. We chose UID 65527 to try avoiding conflicts.
RUN useradd lofar -d /home/lofar -u 65527 -g 65527 -m -s /bin/bash
# Add metuaser user to sudoers
RUN adduser lofar sudo
# No pass sudo (for everyone, actually)
COPY sudoers /etc/sudoers
# Setup home and input/output data directories
COPY data/input_data /input_data
COPY data/output_data /output_data
RUN chown lofar:lofar /home/lofar && chown -R lofar:lofar /input_data && chown -R lofar:lofar /output_data
# This is required mainly for Singularity
RUN mv /home/lofar /home/vanilla_lofar
RUN ln -s /tmp/lofarhome /home/lofar
RUN rm -rf /tmp/lofarhome
#----------------------
# Entrypoint
#----------------------
# Copy entrypoint
COPY entrypoint.sh /
# Give right permissions
RUN chmod 755 /entrypoint.sh
# Set entrypoint
ENTRYPOINT ["/entrypoint.sh"]
# Set user lofar
USER lofar
# Set container name
ENV CONTAINER_NAME='base4.0.16'
#!/bin/bash
docker build . -t lofarit/base4.0.16
Put here "calib" and "target" MS data (or link agains a folder containing them).
Directory for output data.
#!/bin/bash
# Exit on any error. More complex thing could be done in future
# (see https://stackoverflow.com/questions/4381618/exit-a-script-on-error)
set -e
echo ""
echo "[INFO] Executing entrypoint..."
#echo "[INFO] Sourcing env in /opt/lofarsoft/lofarinit.sh..."
#source /opt/lofarsoft/lofarinit.sh
echo "[INFO] Creating /tmp/lofarhome to be used as lofar home"
mkdir /tmp/lofarhome
echo "[INFO] Initialising /tmp/lofarhome with configuration files"
cp -aT /home/vanilla_lofar /tmp/lofarhome
echo "[INFO] Moving to /home/lofar and setting as home"
cd /home/lofar
export HOME=/home/lofar
echo "[INFO] Setting new prompt @$CONTAINER_NAME container"
echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@$CONTAINER_NAME@\h:\w\$ "' >> /tmp/lofarhome/.bashrc
# Set entrypoint command
if [ "x$@" == "x" ]; then
COMMAND="/bin/bash"
else
COMMAND="$@"
fi
# Start!
echo -n "[INFO] Will execute entrypoint command: "
echo $COMMAND
echo ""
echo "=============================================================="
echo ""
echo " Welcome to the LOFAR-IT $CONTAINER_NAME container!"
echo ""
echo "=============================================================="
echo ""
echo "You are now in /home/lofar with write access as user \"$(whoami)\"."
echo ""
echo "Remember that contents inside this container, unless stored"
echo "on a persistent volume mounted from you host machine, will"
echo "be wiped out when exiting the container."
echo ""
exec $COMMAND
#!/bin/bash
docker run --rm -v $PWD/data:/data -it lofarit/base4.0.16 /bin/bash
#
# This file MUST be edited with the 'visudo' command as root.
#
# Please consider adding local content in /etc/sudoers.d/ instead of
# directly modifying this file.
#
# See the man page for details on how to write a sudoers file.
#
Defaults env_reset
Defaults mail_badpass
Defaults secure_path="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
# Host alias specification
# User alias specification
# Cmnd alias specification
# User privilege specification
root ALL=(ALL:ALL) ALL
# Members of the admin group may gain root privileges
%admin ALL=(ALL) ALL
# Allow members of group sudo to execute any command
%sudo ALL=(ALL:ALL) NOPASSWD:ALL
# See sudoers(5) for more information on "#include" directives:
#includedir /etc/sudoers.d
FROM lofar/lofar-pipeline:LOFAR-Release-4_0_16
FROM lofarit/base4.0.16
USER root
# Package dependencies
COPY apt.sources.list /etc/apt/sources.list
......@@ -65,21 +67,48 @@ RUN ln -s /usr/bin/g++-$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
# Build DDF from source
#####################################################################
RUN mkdir /opt/DDFacet
# Copy DDFacet and SkyModel into the image
ADD DDFacet/DDFacet /opt/DDFacet/DDFacet
ADD DDFacet/SkyModel /opt/DDFacet/SkyModel
ADD DDFacet/MANIFEST.in /opt/DDFacet/MANIFEST.in
ADD DDFacet/setup.py /opt/DDFacet/setup.py
ADD DDFacet/setup.cfg /opt/DDFacet/setup.cfg
ADD DDFacet/README.rst /opt/DDFacet/README.rst
ADD DDFacet/pyproject.toml /opt/DDFacet/pyproject.toml
ADD DDFacet/.git /opt/DDFacet/.git
ADD DDFacet/.gitignore /opt/DDFacet/.gitignore
ADD DDFacet/.gitmodules /opt/DDFacet/.gitmodules
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
......@@ -89,17 +118,17 @@ 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
# Perform some basic tests
RUN DDF.py --help
RUN MakeMask.py --help
RUN MakeCatalog.py --help
......@@ -107,15 +136,30 @@ RUN MakeModel.py --help
RUN MaskDicoModel.py --help
RUN ClusterCat.py --help
#####################################################################
## killMs
# Get and build killMs
#####################################################################
ADD killMS /opt/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
# DDF-PIPELINE
#####################################################################
RUN pip3 install pyregion sshtunnel pymysql
RUN cd /opt; git clone https://github.com/mhardcastle/ddf-pipeline
......@@ -123,5 +167,12 @@ RUN sed -e "s|INSTALLDIR|/opt|" /opt/ddf-pipeline/misc/DDF.sh > /opt/DDFacet/ini
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'
#!/bin/bash
set -e
rm -rf DDFacet
rm -rf killMS
git clone https://github.com/cyriltasse/killMS.git
git checkout 0607798
git clone https://github.com/cyriltasse/DDFacet.git
git checkout e98968d
docker build . -t lofarit/ddfacet_ssd-py3_kms-lofar-release-4_0_16
#!/bin/bash
docker run --rm -v $PWD/data:/data -it lofarit/ddfacet_ssd-py3_kms-lofar-release-4_0_16 /bin/bash
#!/bin/bash
docker run --rm -v $PWD/data:/data -it lofarit/ddf2_base3.10 /bin/bash