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Commit 4f9210b4 authored by Andre Offringa's avatar Andre Offringa
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Base dockerfile on Ubuntu 20.04

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2 merge requests!69Change the name of the pre-calibrated output MS,!58Base dockerfile on Ubuntu 20.04
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Docker/Dockerfile
+ 222
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View file @ 4f9210b4
FROM lofareosc/lofar-pipeline:latest
USER root
FROM ubuntu:20.04 as builder
ARG portable=True
RUN export DEBIAN_FRONTEND=noninteractive && \
apt-get update && \
apt-get install -y \
bison \
build-essential \
casacore-data \
casacore-dev \
cmake \
flex \
gfortran \
git \
libblas-dev \
libcfitsio-dev \
libfftw3-dev \
libgsl-dev \
liblapack-dev \
liblua5.3-dev \
libhdf5-serial-dev \
libboost-filesystem-dev \
libboost-system-dev \
libboost-date-time-dev \
libboost-program-options-dev \
libboost-test-dev \
libgtkmm-3.0-dev \
libncurses5-dev \
libpng-dev \
libpython3-dev \
pkg-config \
python3-numpy \
wcslib-dev \
wget && \
mkdir -p /src/
WORKDIR /src/
RUN \
git clone https://github.com/lofar-astron/LofarStMan --depth 1 && \
mkdir LofarStMan/build && \
cd LofarStMan/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=${portable} && \
make install -j`nproc`
RUN \
git clone https://github.com/aroffringa/dysco.git --depth 1 && \
mkdir dysco/build && \
cd dysco/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=${portable} && \
make install -j`nproc`
# IDG doesn't work with --depth 1, because it needs all branches to
# determine its version :-(
RUN \
git clone https://git.astron.nl/RD/idg.git && \
mkdir idg/build && \
cd idg/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ && \
make install -j`nproc`
RUN \
git clone https://gitlab.com/aroffringa/aoflagger.git --depth 1 && \
mkdir aoflagger/build && \
cd aoflagger/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=${portable} && \
make install -j`nproc`
RUN \
apt-get install -y libboost-python-dev libboost-numpy-dev && \
git clone https://github.com/lofar-astron/LOFARBeam.git --depth 1 && \
mkdir LOFARBeam/build && \
cd LOFARBeam/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ && \
make install -j`nproc`
RUN \
git clone https://git.astron.nl/RD/EveryBeam.git --depth 1 && \
mkdir EveryBeam/build && \
cd EveryBeam/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ && \
make install -j`nproc`
# We currently checkout a specific version of DP3 because there's
# currently a bug in the solver in the master branch. Once this is
# solved we should again use master, and the clone cmd should be changed
# back to:
# git clone https://git.astron.nl/RD/DP3.git --depth 1 && \
RUN \
git clone https://git.astron.nl/RD/DP3.git && \
cd DP3 && git checkout 1eadf43fee5ac76f48611fdd1fd464ebda8c0b6d && cd .. && \
mkdir DP3/build && \
cd DP3/build && \
cmake ../ \
-DCMAKE_INSTALL_PREFIX=/usr/local/ \
-DPORTABLE=${portable} \
-DAOFlagger_DIR=/usr/local/ && \
make install -j`nproc`
RUN \
git clone https://gitlab.com/aroffringa/wsclean.git --depth 1 && \
mkdir wsclean/build && \
cd wsclean/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=${portable} && \
make install -j`nproc`
#---------------------------------------------------------------------------
# The image is now rebuild without adding the source, to get a smaller image
# Further binary and/or Python dependencies are also added here.
#---------------------------------------------------------------------------
FROM ubuntu:20.04 as runner
COPY --from=builder /usr/local/ /usr/local
RUN chmod +rx /usr/local/bin/*
SHELL ["/bin/bash", "-c"]
RUN export DEBIAN_FRONTEND=noninteractive && \
apt-get update && \
apt-get install -y \
bison \
git \
casacore-data \
casacore-tools \
flex \
gfortran \
libboost-date-time1.71 \
libboost-filesystem1.71 \
libboost-numpy1.71 \
libboost-program-options1.71 \
libboost-python1.71 \
libboost-system1.71 \
libboost-test1.71 \
libcasa-casa4 \
libcasa-fits4 \
libcasa-measures4 \
libcasa-ms4 \
libcasa-tables4 \
libcfitsio8 \
libfftw3-3 \
libgsl23 \
liblua5.3-0 \
libncurses5 \
libgtkmm-3.0 \
libhdf5-cpp-103 \
libpng16-16 \
nodejs \
pybind11-dev \
python3 \
python3-casacore \
python3-h5py \
python3-matplotlib \
python3-numpy \
python3-pip \
python3-scipy \
python3-sphinx \
tar \
wget \
wcslib-dev && \
rm -rf /var/lib/apt/lists/*
ARG TOIL_VERSION=3.20.0
ARG CASACORE_TAG=master
ARG LSMTool_TAG=master
ARG LoSoTo_TAG=master
ARG STMAN_TAG=master
ARG Dysco_TAG=master
ARG LofarBeam_TAG=master
ARG DP3_TAG=master
ARG IDG_TAG=master
ARG Everybeam_TAG
ARG AOFlagger_TAG
ARG RMextract_TAG=master
ARG WSClean_TAG
LABEL \
casacore.version.tag=${CASACORE_TAG} \
toil.version=${TOIL_VERSION} \
LSMTool.version.tag=${LSMTool_TAG} \
LoSoTo.version.tag=${LoSoTo_TAG} \
STMAN.version.tag=${STMAN_TAG} \
Dysco.version.tag=${Dysco_TAG} \
LOFARBeam.version.tag=${LofarBeam_TAG} \
DP3.version.tag=${DP3_TAG} \
IDG.version.tag=${IDG_TAG} \
Everybeam.version.tag=${Everybeam_TAG} \
AOFlagger.version.tag=${AOFlagger_TAG} \
RMextract.version.tag=${RMextract_TAG} \
WSClean.version.tag=${WSClean_TAG}
ENV PREFACTOR_VERSION='master' \
PREFACTOR_NAME=prefactor \
LC_ALL=C.UTF-8 \
PREFACTOR_DATA_ROOT=/usr/local/share/prefactor \
PYTHONPATH="/usr/local/bin:${PYTHONPATH}"
PYTHONPATH="/usr/local/bin:/usr/local/lib/python3.8/site-packages"
RUN \
apt-get update && \
apt-get install -y vim wget casacore-tools && \
rm -rf /var/cache/apt
RUN \
pip3 install --upgrade pip && \
pip3 install h5py
RUN \
pip3 install --upgrade pip && \
git clone https://github.com/lofar-astron/prefactor.git ${PREFACTOR_NAME} && \
# Install WSRT Measures (extra casacore data)
# Note: The file on the ftp site is updated daily. When warnings regarding leap
# seconds appear, ignore them or regenerate the docker image.
wget -q -O /WSRT_Measures.ztar ftp://ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar \
&& cd /var/lib/casacore/data \
&& tar xfz /WSRT_Measures.ztar \
&& rm /WSRT_Measures.ztar && \
\
# Install cwtool & cwl-runner
python3 -m pip install --upgrade pip && \
python3 -m pip install cwltool cwl-runner && \
\
# Install Prefactor
git clone https://github.com/lofar-astron/prefactor.git ${PREFACTOR_NAME} --branch ${PREFACTOR_VERSION} --depth 1 && \
cd ${PREFACTOR_NAME} && \
git checkout ${PREFACTOR_VERSION} && \
git pull && \
pip3 install --upgrade $PWD && \
cd .. && \
rm -rfv ${PREFACTOR_NAME}
rm -rfv ${PREFACTOR_NAME} && \
\
# A user 'lofaruser' is added (this might be legacy -- not sure this is
# still relevant).
mkdir /home/lofaruser/ && \
groupadd -r lofaruser && \
useradd --no-log-init -r -g lofaruser lofaruser && \
chown lofaruser:lofaruser /home/lofaruser && \
\
# Try to run the compiled tools to make sure they run without
# a problem (e.g. no missing libraries).
aoflagger --version && \
DP3 --version && \
wsclean --version
USER lofaruser
WORKDIR /home/lofaruser
USER lofaruser
Docker/Dockerfile-base deleted 100644 → 0
+ 0
− 213
View file @ 3381dbfb
FROM kernsuite/base:6 as builder
SHELL ["/bin/bash", "-c"]
RUN export DEBIAN_FRONTEND=noninteractive && \
apt-get update && \
apt-get install -y \
gfortran \
flex \
bison \
wcslib-dev \
libncurses5-dev \
casacore-data \
casacore-dev \
libboost-python-dev \
libcfitsio-dev \
python-dev \
python3-numpy \
libcasa* \
cmake \
build-essential \
liblua5.3-dev \
libhdf5-serial-dev \
libarmadillo-dev \
libboost-filesystem-dev \
libboost-system-dev \
libboost-date-time-dev \
libboost-numpy-dev \
libboost-signals-dev \
libboost-program-options-dev \
libboost-test-dev \
pybind11-dev \
libxml2-dev \
libpng-dev \
pkg-config \
libgtkmm-3.0-dev \
git \
wget \
libfftw3-dev \
libgsl-dev
RUN mkdir -p /src/
WORKDIR /src/
RUN \
git clone https://github.com/lofar-astron/LofarStMan && \
mkdir LofarStMan/build && \
cd LofarStMan/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True && \
make install -j`nproc --all`
RUN \
git clone https://github.com/aroffringa/dysco.git && \
mkdir dysco/build && \
cd dysco/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True && \
make install -j`nproc --all`
RUN \
git clone https://git.astron.nl/RD/idg.git && \
mkdir idg/build && \
cd idg/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ && \
make install -j`nproc --all`
RUN \
git clone https://gitlab.com/aroffringa/aoflagger.git && \
mkdir aoflagger/build && \
cd aoflagger/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPYTHON_EXECUTABLE=/usr/bin/python3.6 -DPORTABLE=True && \
make install -j`nproc --all`
RUN \
git clone https://github.com/lofar-astron/LOFARBeam.git && \
mkdir LOFARBeam/build && \
cd LOFARBeam/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPYTHON_EXECUTABLE=/usr/bin/python3.6 && \
make install -j`nproc --all`
RUN \
git clone https://git.astron.nl/RD/EveryBeam.git && \
mkdir EveryBeam/build && \
cd EveryBeam/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ && \
make install -j`nproc --all`
RUN \
git clone https://git.astron.nl/RD/DP3.git && \
mkdir DP3/build && \
cd DP3/build && \
cmake ../ \
-DCMAKE_INSTALL_PREFIX=/usr/local/ \
-DPYTHON_EXECUTABLE=/usr/bin/python3.6 \
-DPORTABLE=True \
-DAOFlagger_DIR=/usr/local/ && \
make install -j`nproc --all`
RUN \
git clone https://gitlab.com/aroffringa/wsclean.git && \
mkdir wsclean/build && \
cd wsclean/build && \
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True && \
make install -j`nproc --all`
#---------------------------------------------------------------------------
# The image is now rebuild without adding the source, to get a smaller image
# Further binary and/or Python dependencies are also added here.
#---------------------------------------------------------------------------
FROM kernsuite/base:6 as runner
COPY --from=builder /usr/local/ /usr/local
RUN chmod +rx /usr/local/bin/*
SHELL ["/bin/bash", "-c"]
RUN export DEBIAN_FRONTEND=noninteractive && \
apt-get update && \
apt-get install -y \
casacore-data \
wcslib-dev \
libarmadillo8 \
bison \
libncurses5 \
flex \
libboost-date-time1.65.1 \
libboost-filesystem1.65.1 \
libboost-numpy1.65.1 \
libboost-python1.65.1 \
libboost-program-options1.65.1 \
libboost-system1.65.1 \
libboost-signals1.65.1 \
libboost-test1.65.1 \
libboost-python1.65-dev \
libstationresponse3 \
liblua5.3-dev \
libcasa-* \
pybind11-dev \
libcfitsio5 \
libcfitsio-dev \
libgtkmm-3.0 \
libfftw3-3 \
libhdf5-cpp-100 \
libpng16-16 \
libxml2 \
python3.7 \
python3-casacore \
dysco \
python3-numpy \
python3-scipy && \
rm -rf /var/lib/apt/lists/*
ARG CASACORE_TAG=master
LABEL casacore.version.tag=${CASACORE_TAG}
ARG TOIL_VERSION=3.20.0
LABEL toil.version=${TOIL_VERSION}
ARG LSMTool_TAG=master
LABEL LSMTool.version.tag=${LSMTool_TAG}
ARG LoSoTo_TAG=master
LABEL LoSoTo.version.tag=${LoSoTo_TAG}
ARG STMAN_TAG=master
LABEL STMAN.version.tag=${STMAN_TAG}
ARG Dysco_TAG=master
LABEL Dysco.version.tag=${Dysco_TAG}
ARG LofarBeam_TAG=master
LABEL LOFARBeam.version.tag=${LofarBeam_TAG}
ARG DP3_TAG=master
LABEL DP3.version.tag=${DP3_TAG}
ARG IDG_TAG=master
LABEL IDG.version.tag=${IDG_TAG}
ARG Everybeam_TAG
LABEL Everybeam.version.tag=${Everybeam_TAG}
ARG Aoflagger_TAG
LABEL Aoflagger.version.tag=${Aoflagger_TAG}
ARG RMextract_TAG
LABEL RMextract.version.tag=${RMExtract_TAG}
ARG wsclean_TAG
LABEL wsclean.version.tag=${wsclean_TAG}
RUN \
apt-get --allow-releaseinfo-change update -y && \
apt-get install -y nodejs python3-pip git gfortran && \
python3 \
-m pip install cwltool cwl-runner \
-e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool" \
"toil[cwl]"==${TOIL_VERSION} \
matplotlib && \
python3 \
-m pip install \
-e "git+https://github.com/revoltek/losoto.git@${LoSoTo_TAG}#egg=LoSoTo" \
ipython "git+https://github.com/lofar-astron/RMextract.git@${RMextract_TAG}#egg=RMextract"
RUN \
mkdir /home/lofaruser/ && \
groupadd -r lofaruser && \
useradd --no-log-init -r -g lofaruser lofaruser && \
chown lofaruser:lofaruser /home/lofaruser
WORKDIR /home/lofaruser
USER lofaruser
ENV PYTHONPATH=/usr/local/lib/python3.6/site-packages/
Docker/build_docker.sh
+ 1
− 4
View file @ 4f9210b4
......@@ -3,8 +3,5 @@ set -e
DOCKER_TAG=latest
docker build ${PWD} -f Dockerfile-base -t lofareosc/lofar-pipeline:${DOCKER_TAG}
docker push lofareosc/lofar-pipeline:${DOCKER_TAG}
docker build --no-cache ${PWD} -t lofareosc/prefactor3-cwl:${DOCKER_TAG}
docker build ${PWD} -f Dockerfile -t lofareosc/prefactor3-cwl:${DOCKER_TAG}
docker push lofareosc/prefactor3-cwl:${DOCKER_TAG}
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