Fixed version hashes and improved Dockerfiles readability. (8fe8ab08) · Commits · lofarit / containers

base/astro/Dockerfile

+129 −70

Original line number	Diff line number	Diff line
		FROM lofarit_base_exstras:latest
		FROM lofarit_base_extras:latest
		MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>
		ENV CONTAINER_NAME='lofarit_base_astro'

		#=============================
		# Switch to root for install
		#=============================
		USER root


		#=============================
		# Set install environment
		#=============================

		ENV J=40
		ENV INSTALLDIR=/opt/lofar
		ENV PYTHON_VERSION=2.7
		@@ -18,40 +25,44 @@ ENV BLAS_VERSION=3.8.0
		ENV BOOST_VERSION=1.69.0
		ENV CASACORE_VERSION=v2.4.1
		ENV # Leave at latest, release versions crash for some reason.
		ENV CASAREST_VERSION=latest
		# ENV CASAREST_VERSION=latest # Not used?
		ENV CFITSIO_VERSION=7.3.47
		ENV DPPP_VERSION=v4.2
		ENV DYSCO_VERSION=v1.2
		#export EVERYBEAM_VERSION=0cc64a81
		ENV EVERYBEAM_VERSION=master
		ENV EVERYBEAM_VERSION=1c22f47107187f21f6fb7c473c2c0c8a7e18b47c
		ENV FFTW_VERSION=3.5.8
		ENV HDF5_VERSION=1.10.5
		ENV IDG_VERSION=master
		#ENV IDG_VERSION=master # Not used?
		ENV LAPACK_VERSION=3.8.0
		ENV LOFAR_VERSION=3_2_18
		# Don't change LOSOTO2_VERSION. This is the last commit that plays nice with Python 2.
		ENV LOSOTO2_VERSION=c8fbd61
		ENV LOSOTO3_VERSION=latest
		#ENV LOSOTO3_VERSION=latest # Not used?
		ENV LSMTOOL_VERSION=v1.4.2
		ENV OPENBLAS_VERSION=3.8.0
		ENV PYBDSF_VERSION=master
		ENV PYBDSF_VERSION=380ea5f2adea122bbc081658a7105f891345d799
		ENV PYTHON_CASACORE_VERSION=v2.2.1
		ENV RMEXTRACT_VERSION=4c61232
		ENV SUPERLU_VERSION=5.2.1
		ENV WSCLEAN_VERSION=latest
		ENV WSCLEAN_VERSION=241ab7538624b840627ab027b40f88794db1a400
		ENV WCSLIB_VERSION=6.4
		ENV HDF5_USE_FILE_LOCKING=FALSE


		#=============================
		# Symlinks required for Fedora 31
		#=============================

		RUN ln -s /usr/lib64/libboost_python37.so /usr/lib64/libboost_python3.so && \
		ln -s /usr/lib64/libboost_numpy37.so /usr/lib64/libboost_numpy3.so && \
		ln -s /usr/lib64/libboost_python27.so /usr/lib64/libboost_python.so && \
		ln -s /usr/lib64/libboost_numpy27.so /usr/lib64/libboost_numpy.so && \
		ln -s /usr/lib64/libnsl.so.2.0.0 /usr/lib64/libnsl.so

		#
		# Setup the compiliong enviroment
		#

		#=============================
		# Setup the compiling env
		#=============================

		#ARG CFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
		#ARG CXXFLAGS="-std=c++11 -mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
		@@ -67,9 +78,9 @@ ARG PATH="/usr/lib64/openmpi/bin:$PATH"
		ARG OLD_PYTHONPATH=$PYTHONPATH


		#
		#=============================
		# Setup the Python environment.
		#
		#=============================

		COPY requirements3.txt $INSTALLDIR/requirements3.txt
		RUN pip --no-cache-dir install "virtualenv<20"
		@@ -83,45 +94,50 @@ RUN source $INSTALLDIR/pyenv-py2/bin/activate && export HDF5_VERSION=1.10.5 &
		pip install -r $INSTALLDIR/requirements.txt && pip install --no-deps "reproject==0.5.1"


		#
		#=============================
		# Install Montage
		#
		#=============================

		RUN mkdir -p /opt/montage && cd /opt/montage && wget https://github.com/Caltech-IPAC/Montage/archive/v6.0.tar.gz -O Montage_v6.0.tar.gz && \
		tar xf Montage_v6.0.tar.gz && cd Montage-6.0 && make -j $J

		#

		#=============================
		# Install difmap
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/difmap && cd $INSTALLDIR/difmap && \
		wget https://github.com/tikk3r/lofar-grid-hpccloud/blob/master/misc/difmap2.5e.tar.gz?raw=true -O difmap2.5e.tar.gz && \
		tar zxf difmap2.5e.tar.gz && cd uvf_difmap && \
		wget https://raw.githubusercontent.com/nealjackson/loop3_difmap/master/corplt.c -O difmap_src/corplt.c && \
		wget https://raw.githubusercontent.com/nealjackson/loop3_difmap/5e1409ec906f5a9b3c090076ca988d4fd2b7e6de/corplt.c -O difmap_src/corplt.c && \
		sed -i.bak -e '97d' configure && \
		sed -i.bak -e '97 i PGPLOT_LIB=/usr/lib64/libpgplot.so.5' configure && \
		./configure linux-i486-gcc && export PGPLOT_LIB=/usr/lib64/libpgplot.so.5 && export CFLAGS="-L/usr/lib64/libpgplot.so.5" && \
		./makeall
		RUN rm -rf $INSTALLDIR/difmap/*.tar.gz

		#

		#=============================
		# Install PyBDSF
		#
		#=============================

		#ARG CFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
		RUN mkdir -p ${INSTALLDIR}/pybdsf && cd ${INSTALLDIR}/pybdsf && git clone https://github.com/lofar-astron/pybdsf pybdsf
		RUN if [ "${PYBDSF_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/pybdsf/pybdsf && git checkout ${PYBDSF_VERSION}; fi

		RUN cd ${INSTALLDIR}/pybdsf/pybdsf && git checkout ${PYBDSF_VERSION}
		RUN cd ${INSTALLDIR}/pybdsf/pybdsf && python setup.py install
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/pybdsf/pybdsf


		#
		#=============================
		# Install CASAcore
		#
		#=============================

		# Casacore 2.4.1 does not seem to deal well with AVX512 instructions, so disable them if needed
		#export CFLAGS="-march=skylake -mtune=skylake -mno-avx512f"
		#export CXXFLAGS="-march=skylake -mtune=skylake -mno-avx512f"
		RUN mkdir -p ${INSTALLDIR}/casacore/build && mkdir -p ${INSTALLDIR}/casacore/data
		RUN cd $INSTALLDIR/casacore && git clone https://github.com/casacore/casacore.git src
		RUN if [ "${CASACORE_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/casacore/src && git checkout tags/${CASACORE_VERSION}; fi
		RUN cd ${INSTALLDIR}/casacore/src && git checkout tags/${CASACORE_VERSION}
		# Backport patch UVFITS for LOFAR. This is fixed in recent versions > May 26 2020
		# wget https://patch-diff.githubusercontent.com/raw/casacore/casacore/pull/1033.patch -O $INSTALLDIR/casacore/1033.patch
		# cd $INSTALLDIR/casacore/src && patch --fuzz 3 -p1 < $INSTALLDIR/casacore/1033.patch
		@@ -131,44 +147,50 @@ RUN cd ${INSTALLDIR}/casacore/build && cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR
		RUN cd ${INSTALLDIR}/casacore/build && make -s -j ${J} && make install
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/casacore/build && rm -rf $INSTALLDIR/casacore/src

		#

		#=============================
		# Install Python-CASAcore
		#
		#=============================

		RUN mkdir ${INSTALLDIR}/python-casacore && cd ${INSTALLDIR}/python-casacore && git clone https://github.com/casacore/python-casacore
		RUN if [ "$PYTHON_CASACORE_VERSION" != "latest" ]; then cd ${INSTALLDIR}/python-casacore/python-casacore && git checkout tags/${PYTHON_CASACORE_VERSION}; fi
		RUN cd ${INSTALLDIR}/python-casacore/python-casacore && git checkout tags/${PYTHON_CASACORE_VERSION}
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/python-casacore/python-casacore && python setup.py build_ext -I${INSTALLDIR}/casacore/include/:/usr/include/python2.7:/usr/include/cfitsio -L${INSTALLDIR}/casacore/lib/:/usr/lib64/ && python setup.py install #--prefix=${INSTALLDIR}/python-casacore/
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/python-casacore/python-casacore
		# and then reset the flags again if needed
		#export CFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"
		#export CXXFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"

		#

		#=============================
		# Install Dysco
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/dysco/build
		RUN cd $INSTALLDIR/dysco && git clone https://github.com/aroffringa/dysco.git src && cd src
		RUN if [ "$DYSCO_VERSION" != "latest" ]; then cd $INSTALLDIR/dysco/src && git checkout $DYSCO_VERSION; fi
		RUN cd $INSTALLDIR/dysco/src && git checkout $DYSCO_VERSION
		RUN cd $INSTALLDIR/dysco/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/dysco -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DPORTABLE=True ../src && make -s -j $J && make install
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/dysco/build && rm -rf $INSTALLDIR/dysco/src

		#

		#=============================
		# Install AOFlagger
		#
		#=============================

		RUN mkdir -p ${INSTALLDIR}/aoflagger/build && cd ${INSTALLDIR}/aoflagger && git clone git://git.code.sf.net/p/aoflagger/code aoflagger && cd ${INSTALLDIR}/aoflagger/aoflagger
		RUN if [ "${AOFLAGGER_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/aoflagger/aoflagger && git checkout tags/${AOFLAGGER_VERSION}; fi
		RUN cd ${INSTALLDIR}/aoflagger/aoflagger && git checkout tags/${AOFLAGGER_VERSION}
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/aoflagger/build && cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/aoflagger/ -DCASACORE_ROOT_DIR=${INSTALLDIR}/casacore -DBUILD_SHARED_LIBS=ON -DPORTABLE=True ../aoflagger
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/aoflagger/build && make -s -j ${J} && make install
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/aoflagger/aoflagger && rm -rf $INSTALLDIR/aoflagger/build && rm -rf $INSTALLDIR/aoflagger/src

		#

		#=============================
		# Install LOFAR
		#
		#=============================
		RUN mkdir -p ${INSTALLDIR}/lofar/build/gnucxx11_opt
		RUN if [ "${LOFAR_VERSION}" = "latest" ]; then cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/trunk src; fi
		RUN if [ "${LOFAR_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/tags/LOFAR-Release-${LOFAR_VERSION} src; fi
		RUN cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/trunk src
		RUN cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/tags/LOFAR-Release-${LOFAR_VERSION} src
		RUN cd $INSTALLDIR/lofar && svn update --depth=infinity $INSTALLDIR/lofar/src/CMake
		RUN cd $INSTALLDIR/lofar/ && wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/master/patches/lofar.patch && \
		RUN cd $INSTALLDIR/lofar/ && wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/cd33001869d8318ca1ee14e838ac40122c405260/patches/lofar.patch && \
		patch $INSTALLDIR/lofar/src/CMake/variants/GNUCXX11.cmake $PATCH_LOFAR && \
		cd ${INSTALLDIR}/lofar/build/gnucxx11_opt
		#cmake -DCMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/casacore:$INSTALLDIR/dysco -DBUILD_PACKAGES="StationResponse pystationresponse ParmDB pyparmdb Pipeline MS" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar/ -DUSE_LOG4CPLUS=OFF -DUSE_OPENMP=True ${INSTALLDIR}/lofar/src/
		@@ -179,78 +201,94 @@ ARG CXX=/usr/bin/g++
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/lofar/build/gnucxx11_opt && CC=/usr/bin/gcc && CXX=/usr/bin/g++ && cmake -DCMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/casacore:$INSTALLDIR/dysco -DBUILD_PACKAGES="Pipeline" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar/ -DUSE_LOG4CPLUS=OFF -DUSE_OPENMP=True -DBUILD_PYTHON3=OFF ${INSTALLDIR}/lofar/src/ && make -s -j $J && make install
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/lofar/build && rm -rf $INSTALLDIR/lofar/src

		#

		#=============================
		# Install msoverview separately
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/msoverview/src
		RUN cd $INSTALLDIR/msoverview/src && svn export https://svn.astron.nl/LOFAR/tags/LOFAR-Release-3_2_18/CEP/MS/src/msoverview.cc && \
		source $INSTALLDIR/pyenv-py2/bin/activate && gcc -I/opt/lofar/casacore/include/casacore/ -L/opt/lofar/casacore/lib msoverview.cc \
		-o $INSTALLDIR/lofar/bin/msoverview -lcasa_casa -lcasa_ms -lcasa_tables -lstdc++
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/msoverview

		#
		# Install the standalone StationResponse libraries.
		#

		#=============================
		# Install the standalone
		# StationResponse libraries.
		#=============================

		RUN mkdir -p $INSTALLDIR/LOFARBeam/build && cd $INSTALLDIR/LOFARBeam && git clone https://github.com/lofar-astron/LOFARBeam.git src
		RUN cd $INSTALLDIR/LOFARBeam && git checkout 5b5d80ff308784adbf00985293257b16afff86b2
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd $INSTALLDIR/LOFARBeam/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar ../src && make -j $J && make install
		RUN touch /opt/lofar/lofar/lib64/python2.7/site-packages/lofar/__init__.py
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/LOFARBeam/build && rm -rf $INSTALLDIR/LOFARBeam/src

		#
		#=============================
		# Install EveryBeam library
		#
		#=============================
		RUN mkdir -p $INSTALLDIR/EveryBeam/build && cd $INSTALLDIR/EveryBeam && git clone https://git.astron.nl/RD/EveryBeam.git src && \
		cd src && git checkout $EVERYBEAM_VERSION && \
		cd $INSTALLDIR/EveryBeam/build && \
		cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/EveryBeam ../src && \
		make -j $J && make install

		#
		#=============================
		# Install DPPP
		#
		#=============================
		RUN mkdir -p $INSTALLDIR/DPPP/build && git clone https://github.com/lofar-astron/DP3.git $INSTALLDIR/DPPP/src && \
		cd $INSTALLDIR/DPPP/src && git checkout tags/${DPPP_VERSION}
		RUN cd $INSTALLDIR/DPPP/build && cmake3 -DCMAKE_CXX_FLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS" -DCMAKE_INSTALL_PREFIX:PATH=$INSTALLDIR/DPPP -DLOFAR_STATION_RESPONSE_DIR:PATH=$INSTALLDIR/lofar/include -DLOFAR_STATION_RESPONSE_LIB:FILEPATH=$INSTALLDIR/lofar/lib/libstationresponse.so -DIDGAPI_LIBRARIES=$INSTALLDIR/idg/lib/libidg-api.so -DIDGAPI_INCLUDE_DIRS=$INSTALLDIR/idg/include -DAOFLAGGER_INCLUDE_DIR=$INSTALLDIR/aoflagger/include -DAOFLAGGER_LIB=$INSTALLDIR/aoflagger/lib/libaoflagger.so ../src && make -s -j $J && make install
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/DPPP/build && rm -rf $INSTALLDIR/DPPP/src



		############################################
		# Install Python packages for Python 2 now #
		############################################
		#

		#=============================
		# Install RMextract
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/RMextract/build && cd $INSTALLDIR/RMextract/build && git clone https://github.com/lofar-astron/RMextract.git src && \
		cd src && if [ "$RMEXTRACT_VERSION" != "latest" ]; then git checkout $RMEXTRACT_VERSION; fi
		cd src && git checkout $RMEXTRACT_VERSION
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd $INSTALLDIR/RMextract/build/src && python setup.py build --add-lofar-utils && \
		python setup.py install --add-lofar-utils && deactivate
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/RMextract

		#
		#=============================
		# Install LoSoTo
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/losoto/build && cd ${INSTALLDIR}/losoto/build && \
		git clone https://github.com/revoltek/losoto.git src && \
		cd src && if [ "$LOSOTO2_VERSION" != "latest" ]; then git checkout $LOSOTO2_VERSION; fi
		cd src && git checkout $LOSOTO2_VERSION
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/losoto/build/src && python setup.py build && \
		python setup.py install && deactivate
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/losoto

		#

		#=============================
		# Install LSMTool.
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/lsmtool && cd $INSTALLDIR/lsmtool && \
		git clone https://github.com/darafferty/LSMTool.git lsmtool && \
		cd $INSTALLDIR/lsmtool/lsmtool && \
		if [ "$LSMTOOL_VERSION" != "latest" ]; then git checkout $LSMTOOL_VERSION; fi
		git checkout $LSMTOOL_VERSION
		RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd $INSTALLDIR/lsmtool/lsmtool && python setup.py install && deactivate
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/lsmtool


		############################################
		# Install Python packages for Python 3 now #
		############################################
		#

		#=============================
		# Install LoSoTo
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/losoto/build && \
		cd $INSTALLDIR/losoto/build && \
		git clone https://github.com/revoltek/losoto.git src
		@@ -259,12 +297,17 @@ RUN cd $INSTALLDIR/losoto/build/src && source $INSTALLDIR/pyenv-py3/bin/activate
		python setup.py install && deactivate
		RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/losoto

		# Switch back to py2 to wrap up installation
		#

		##############################################
		# Switch back to py2 to wrap up installation #
		##############################################

		#=============================
		# Install-WSClean
		#
		#=============================

		RUN mkdir $INSTALLDIR/wsclean && cd ${INSTALLDIR}/wsclean && git clone https://gitlab.com/aroffringa/wsclean.git && \
		if [ "$WSCLEAN_VERSION" != "latest" ]; then cd ${INSTALLDIR}/wsclean/wsclean && git checkout $WSCLEAN_VERSION; fi
		cd ${INSTALLDIR}/wsclean/wsclean && git checkout $WSCLEAN_VERSION
		RUN cd ${INSTALLDIR}/wsclean/wsclean && mkdir build && cd build
		ARG CC=/usr/lib64/openmpi/bin/mpicc
		ARG CXX=/usr/lib64/openmpi/bin/mpic++
		@@ -272,26 +315,42 @@ RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/wsclean/wscle
		make -j ${J} && \
		make install && \
		cd $INSTALLDIR && rm -rf $INSTALLDIR/wsclean/wsclean
		#


		#=============================
		# Switch back to normal compilers
		#=============================

		ARG CC=/usr/bin/gcc
		ARG CXX=/usr/bin/g++
		#


		#=============================
		# Finaly cleanup of unnecessary stuff
		#
		#=============================

		ENV PYTHONPATH=$OLD_PYTHONPATH
		RUN rm -rf /var/cache/dnf/* && \
		rm -rf /var/cache/yum/* && \
		rm -rf /var/log/* && \
		dnf -y clean all

		#

		#=============================
		# init-lofar
		#
		#=============================

		RUN ln -s /opt/lofar/DPPP/bin/DPPP /opt/lofar/lofar/bin/NDPPP && \
		ln -s /opt/lofar/DPPP/bin/makesourcedb /opt/lofar/lofar/bin/makesourcedb &&\
		ln -s $INSTALLDIR/pyenv-py3/bin/h5plot /usr/bin/h5plot
		COPY files/post_init /tmp/post_init
		RUN cat /tmp/post_init >> $INSTALLDIR/init.sh
		RUN sed -e 's/\\\$/\$/g' /opt/lofar/init.sh


		#=============================
		# Switch back to metauser
		#=============================

		USER metauser

base/extras/Dockerfile

+27 −11

Original line number	Diff line number	Diff line
		FROM lofarit_base_system:latest
		MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>
		ENV CONTAINER_NAME='lofarit_base_exatras'

		#=============================
		# Switch to root for install
		#=============================
		USER root

		#
		# Set enviroment
		#

		#=============================
		# Set install environment
		#=============================

		ENV HDF5_VERSION=1.10.5
		ENV DEBIAN_FRONTEND=noninteractive

		RUN mkdir -p $INSTALLDIR

		ARG cpu_tune=generic
		ARG cpu_arch=x86-64
		ENV MTUNE=${cpu_tune}
		ENV MARCH=${cpu_arch}
		RUN echo "-march=${MARCH} -mtune=${MTUNE}"


		#=============================
		# Install HDF5
		#=============================

		RUN mkdir /opt/hdf5
		#COPY src/hdf5-${HDF5_VERSION}.tar.gz /opt/hdf5/hdf5-${HDF5_VERSION}.tar.gz
		RUN wget -O /opt/hdf5/hdf5-${HDF5_VERSION}.tar.gz https://www.ict.inaf.it/gitlab/lofarit/container-data/-/raw/master/software-packages/hdf5-${HDF5_VERSION}.tar.gz?inline=false
		@@ -32,10 +41,11 @@ RUN source /etc/profile && module load mpi/openmpi-x86_64 && \
		make -j $J && make install && \
		rm -fr /opt/hdf5/hdf5-${HDF5_VERSION}.tar.gz /opt/hdf5/hdf5-${HDF5_VERSION}

		#
		#

		#=============================
		# Install DS9
		#
		#=============================

		RUN mkdir -p $INSTALLDIR/ds9/bin
		#COPY src/ds9.fedora30.8.2.tar.gz /tmp
		RUN wget -O /tmp/ds9.fedora30.8.2.tar.gz https://www.ict.inaf.it/gitlab/lofarit/container-data/-/raw/master/software-packages/ds9.fedora30.8.2.tar.gz?inline=false
		@@ -45,13 +55,19 @@ RUN cd /tmp && \
		rm ds9*.tar.gz

		ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/hdf5/lib
		#


		#=============================
		# init-lofar
		#
		#=============================

		RUN echo export INSTALLDIR=$INSTALLDIR > $INSTALLDIR/init.sh
		RUN echo export LD_LIBRARY_PATH=$LD_LIBRARY_PATH >> $INSTALLDIR/init.sh


		# Set user lofar
		#=============================
		# Switch back to metauser
		#=============================

		USER metauser

base/system/Dockerfile

+20 −35

Original line number	Diff line number	Diff line
		FROM fedora:31
		MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>
		ENV CONTAINER_NAME='lofarit_base_system'

		#=============================
		# Switch to root for install
		#=============================
		USER root

		#

		#=============================
		# Set enviroment
		#
		#=============================

		ENV J=40
		ENV INSTALLDIR=/opt/lofar
		@@ -25,10 +30,14 @@ ENV SUPERLU_VERSION=5.2.1
		ENV WCSLIB_VERSION=6.4
		ENV DEBIAN_FRONTEND=noninteractive

		#

		#=============================
		# System installs
		#
		#=============================

		RUN dnf -y update

		# Common packages
		RUN dnf -y install dnf-plugins-core
		RUN dnf -y install https://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-$(rpm -E %fedora).noarch.rpm https://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-$(rpm -E %fedora).noarch.rpm
		RUN dnf -y install patch sudo yum-utils git svn wget vim nano emacs \
		@@ -41,49 +50,34 @@ RUN dnf -y install patch sudo yum-utils git svn wget vim nano emacs \
		libsigc++20-devel gtkmm30-devel lua lua-devel \
		pgplot python3-numpy-f2py perf qt5 rsync openmpi openmpi-devel htop mariadb-devel python3-pybind11 pybind11-devel


		#
		# Install Boost
		#
		RUN dnf -y install boost boost-devel boost-python2 boost-python2-devel boost-python3 boost-python3-devel

		#
		# Install FFTW
		#
		RUN dnf -y install fftw-devel fftw-libs

		# Install OpenBLAS
		#
		RUN dnf -y install blas-devel

		#
		# Install SuperLU
		#
		RUN dnf -y install SuperLU SuperLU-devel

		#
		# Install Armadillo
		#
		RUN dnf -y install armadillo armadillo-devel

		#
		# Install cfitsio
		#
		RUN dnf -y install cfitsio cfitsio-devel

		#
		# Install wcslib
		#
		RUN dnf -y install wcslib wcslib-devel hostname


		# Wrap up installation, remove unnecessary stuff.
		RUN dnf -y autoremove
		RUN dnf -y clean all

		#------------------------
		# Local User
		#------------------------
		#=============================
		# Create meta user
		#=============================

		# Add group. We chose GID 65527 to try avoiding conflicts.
		RUN groupadd -g 65527 metagroup
		@@ -104,18 +98,9 @@ RUN mv /home/metauser /metauser_home_vanilla
		RUN chmod 777 /home


		#----------------------
		# Entrypoint
		#----------------------

		# Copy entrypoint
		#COPY entrypoint.sh /

		# Give right permissions
		#RUN chmod 755 /entrypoint.sh
		#=============================
		# Switch to metauser
		#=============================

		# Set entrypoint
		#ENTRYPOINT ["/entrypoint.sh"]
		USER metauser

		# Set user lofar
		#USER metauser