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Commit 20a8ba84 authored by Giuliano Taffoni's avatar Giuliano Taffoni
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vlbi pipeline

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FROM morgan1971/vlbi-base:0.0.1
MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>
ENV CONTAINER_NAME='lovarVLBISoftware'
USER root
ENV J=40
ENV INSTALLDIR=/opt/lofar
ENV PYTHON_VERSION=2.7
# Path to where the patch for python-casacore's setup is stored.
ENV PYTHON_CASACORE_PATCH=$INSTALLDIR/python-casacore/python_casacore_setup_patch.patch
ENV PATCH_LOFAR=$INSTALLDIR/lofar/lofar.patch
# Settings relevant to the installed software.
ENV AOFLAGGER_VERSION=v2.15.0
ENV ARMADILLO_VERSION=9.900.3
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 CFITSIO_VERSION=7.3.47
ENV DPPP_VERSION=v4.2
ENV DYSCO_VERSION=v1.2
#export EVERYBEAM_VERSION=0cc64a81
ENV EVERYBEAM_VERSION=master
ENV FFTW_VERSION=3.5.8
ENV HDF5_VERSION=1.10.5
ENV IDG_VERSION=master
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 LSMTOOL_VERSION=v1.4.2
ENV OPENBLAS_VERSION=3.8.0
ENV PYBDSF_VERSION=master
ENV PYTHON_CASACORE_VERSION=v2.2.1
ENV RMEXTRACT_VERSION=4c61232
ENV SUPERLU_VERSION=5.2.1
ENV WSCLEAN_VERSION=latest
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
RUN ln -s /usr/lib64/libboost_numpy37.so /usr/lib64/libboost_numpy3.so
RUN ln -s /usr/lib64/libboost_python27.so /usr/lib64/libboost_python.so
RUN ln -s /usr/lib64/libboost_numpy27.so /usr/lib64/libboost_numpy.so
RUN ln -s /usr/lib64/libnsl.so.2.0.0 /usr/lib64/libnsl.so
#
# Setup the compiliong enviroment
#
#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"
# Use below to optimize for a specific architecture
#export CFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"
#export CXXFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"
ARG CPLUS_INCLUDE_PATH="/usr/include/openmpi-x86_64:/usr/include/c++/9:$CPLUS_INCLUDE_PATH:/usr/include/python2.7:$INSTALLDIR/casacore/include:/usr/include/boost:/usr/include/cfitsio:$INSTALLDIR/EveryBeam/include"
ARG CPATH="/usr/include/openmpi-x86_64/:/opt/intel/mkl/include:${INSTALLDIR}/casacore/include:$INSTALLDIR/LOFARBeam/include:$INSTALLDIR/idg/include:$INSTALLDIR/aoflagger/include:$INSTALLDIR/EveryBeam/include:$CPATH"
ARG CMAKE_PREFIX_PATH="$INSTALLDIR/aoflagger:$INSTALLDIR/casacore:$INSTALLDIR/lofar:$INSTALLDIR/LOFARBeam:/usr/lib64/openmpi:$INSTALLDIR/EveryBeam"
ARG LD_LIBRARY_PATH="$INSTALLDIR/aoflagger/lib:$INSTALLDIR/casacore/lib:$INSTALLDIR/idg/lib:$INSTALLDIR/LOFARBeam/lib:/usr/lib64/openmpi/lib/:$INSTALLDIR/EveryBeam/lib:LD_LIBRARY_PATH"
ARG PATH="/usr/lib64/openmpi/bin:$PATH"
#ARG make=`which make`
ARG OLD_PYTHONPATH=$PYTHONPATH
#
# Setup the Python environment.
#
RUN wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/fedora/requirements.txt -O $INSTALLDIR/requirements.txt
RUN wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/fedora/requirements3.txt -O $INSTALLDIR/requirements3.txt
RUN pip install xmlrunner
RUN pip3 install xmlrunner
RUN echo lofar-h5plot >> $INSTALLDIR/requirements3.txt
RUN pip --no-cache-dir install "virtualenv<20"
RUN virtualenv $INSTALLDIR/pyenv-py3 --python=python3
RUN source $INSTALLDIR/pyenv-py3/bin/activate && export HDF5_VERSION=1.10.5 && pip install numpy && pip install --no-binary h5py h5py && \
pip install -r $INSTALLDIR/requirements3.txt && deactivate
RUN virtualenv $INSTALLDIR/pyenv-py2 --python=python2
RUN source $INSTALLDIR/pyenv-py2/bin/activate && export HDF5_VERSION=1.10.5 && pip install numpy && pip install --no-binary h5py h5py && \
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 ftp://ftp.astro.caltech.edu/pub/difmap/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 && \
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 && 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
# 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
RUN cd ${INSTALLDIR}/casacore/data && wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar
RUN cd ${INSTALLDIR}/casacore/data && tar xf WSRT_Measures.ztar && rm WSRT_Measures.ztar
RUN cd ${INSTALLDIR}/casacore/build && cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/casacore/ -DDATA_DIR=${INSTALLDIR}/casacore/data -DBUILD_PYTHON=True -DUSE_OPENMP=True -DUSE_FFTW3=TRUE -DUSE_HDF5=True -DBUILD_PYTHON3=False ../src/
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 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 $INSTALLDIR/dysco/build && cmake -DCMAKE_INSTALL_PREFIX=$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 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 update --depth=infinity $INSTALLDIR/lofar/src/CMake
RUN cd $INSTALLDIR/lofar/ && wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/master/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/
ARG CMAKE_C_COMPILER=/usr/bin/gcc
ARG CMAKE_CXX_COMPILER=/usr/bin/g++
ARG CC=/usr/bin/gcc
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.
#
RUN mkdir -p $INSTALLDIR/LOFARBeam/build && cd $INSTALLDIR/LOFARBeam && git clone https://github.com/lofar-astron/LOFARBeam.git src
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
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
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
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
RUN cd $INSTALLDIR/losoto/build/src && source $INSTALLDIR/pyenv-py3/bin/activate && \
python setup.py build && \
python setup.py install && deactivate
RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/losoto
# 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
RUN cd ${INSTALLDIR}/wsclean/wsclean && mkdir build && cd build
ARG CC=/usr/lib64/openmpi/bin/mpicc
ARG CXX=/usr/lib64/openmpi/bin/mpic++
RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/wsclean/wsclean/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/wsclean -DPORTABLE=True -DIDGAPI_LIBRARIES=$INSTALLDIR/idg/lib/libidg-api.so -DIDGAPI_INCLUDE_DIRS=$INSTALLDIR/idg/include .. && \
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++
#
#
# Install DS9
#
RUN mkdir -p $INSTALLDIR/ds9/bin && cd $INSTALLDIR/ds9 && \
wget http://ds9.si.edu/download/fedora30/ds9.fedora30.8.2.tar.gz && \
tar xf ds9*.tar.gz -C $INSTALLDIR/ds9/bin && \
rm ds9*.tar.gz
#
# Finaly cleanup of unnecessary stuff
#
ENV PYTHONPATH=$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 >> $INSTALLDIR/init.sh
RUN sed -e 's/\\\$/\$/g' /opt/lofar/init.sh
USER metauser
vlbi/Dockerfile.base 0 → 100644
+ 156
− 0
View file @ 20a8ba84
FROM fedora:31
MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>
ENV CONTAINER_NAME='lovarVLBIbase'
USER root
#
# Set enviroment
#
ENV J=4
ENV INSTALLDIR=/opt/lofar
ENV PYTHON_VERSION=2.7
# Settings relevant to the installed software.
ENV ARMADILLO_VERSION=9.900.3
ENV BLAS_VERSION=3.8.0
ENV BOOST_DOT_VERSION=1.69.0
ENV BOOST_VERSION=1_69_0
ENV CFITSIO_VERSION=7.3.47
ENV FFTW_VERSION=3.5.8
ENV HDF5_VERSION=1.10.5
ENV LAPACK_VERSION=3.8.0
ENV OPENBLAS_VERSION=3.8.0
ENV SUPERLU_VERSION=5.2.1
ENV WCSLIB_VERSION=6.4
ENV DEBIAN_FRONTEND=noninteractive
#
# System installs
#
RUN dnf -y update
RUN dnf -y install dnf-plugins-core
RUN dnf -y install patch sudo yum-utils git svn wget vim nano emacs
RUN dnf -y install automake autoconf cmake cmake3 make gcc gcc-c++ gcc-gfortran
RUN dnf -y install arpack-devel python-devel python3-devel lapack-devel libpng-devel libxml2-devel readline-devel ncurses-devel f2py bzip2-devel libicu-devel python3-scipy python-setuptools gsl gsl-devel gdal gdal-devel libpqxx libpqxx-devel
RUN dnf -y install bison flex ncurses tar bzip2 which gettext hdf5 hdf5-devel
RUN dnf -y install python python3-devel python-pip python2-tkinter python3-tkinter
RUN dnf -y install libsigc++20-devel gtkmm30-devel
RUN dnf -y install lua lua-devel
RUN dnf -y install https://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-$(rpm -E %fedora).noarch.rpm https://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-$(rpm -E %fedora).noarch.rpm
RUN dnf -y install pgplot python3-numpy-f2py perf qt5
#
# 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
#
# Fedora packages to install
#
RUN dnf -y install rsync
RUN dnf -y install openmpi openmpi-devel
RUN dnf -y install htop mariadb-devel
RUN dnf -y install python3-pybind11 pybind11-devel
###################
# Source installs #
###################
RUN mkdir -p $INSTALLDIR
#
# Install Image Domain Gridder (IDG)
#
RUN mkdir -p $INSTALLDIR/idg && cd $INSTALLDIR/idg
# Use these flags instead for an architecture optimized build.
#export CFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"
#export CXXFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"
# Disable AVX512 instructions and build a generic architecture.
#export CFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
#export CXXFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
RUN export CC=`which gcc` && export CXX=`which g++` && export make=`which make` && \
export LD_LIBRARY_PATH=/usr/local/cuda/lib64:/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH && \
export CMAKE_PREFIX_PATH=/usr/local/cuda/lib64:/opt/intel/mkl/lib/intel64:$CMAKE_PREFIX_PATH && \
export CPATH=/usr/local/cuda/include:/opt/intel/mkl/include:$CPATH && \
git clone https://gitlab.com/astron-idg/idg.git src && cd src && git checkout $IDG_VERSION && mkdir build && cd build && \
cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/idg .. && make -j $J && make install
RUN rm -rf $INSTALLDIR/idg/src
#
# Wrap up installation, remove unnecessary stuff.
RUN dnf -y autoremove
RUN dnf -y clean all
#
# init-lofar
#
RUN echo export INSTALLDIR=$INSTALLDIR > $INSTALLDIR/init.sh
RUN echo export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64/:\$LD_LIBRARY_PATH >> $INSTALLDIR/init.sh
#------------------------
# Local User
#------------------------
# Add group. We chose GID 65527 to try avoiding conflicts.
RUN groupadd -g 65527 metagroup
# Add user. We chose UID 65527 to try avoiding conflicts.
RUN useradd metauser -d /home/metauser -u 65527 -g 65527 -m -s /bin/bash
# Add metuaser user to sudoers
RUN usermod -a -G wheel metauser
RUN sed -i 's/^%wheel/#%wheel/' /etc/sudoers
RUN sed -i 's/^# %wheel/%wheel/' /etc/sudoers
# Rename user home folder as a "vanilla" home folder
RUN mv /home/metauser /metauser_home_vanilla
RUN echo "export PATH=/usr/local/cuda/bin:\$PATH" >> $INSTALLDIR/init.sh
RUN echo "export LD_LIBRARY_PATH=/usr/local/cuda/lib64:/opt/intel/mkl/lib/intel64/:\$LD_LIBRARY_PATH" >> $INSTALLDIR/init.sh
# Give write access to anyone to the home folder so the entrypoint will be able
# to copy over the /home/matauser_vanilla into /home/metauser (for Singularity)
RUN chmod 777 /home
#----------------------
# Entrypoint
#----------------------
# Copy entrypoint
COPY entrypoint.sh /
# Give right permissions
RUN chmod 755 /entrypoint.sh
# Set entrypoint
ENTRYPOINT ["/entrypoint.sh"]
# Set user lofar
USER metauser
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#!/bin/bash
if [ 'xxx${VERSION}' == 'xxx' ]; then
VERSION='latest'
fi
docker build -t morgan1971/vlbi-base:${VERSION} -f Dockerfile.base .
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#!/bin/bash
if [ 'xxx${VERSION}' == 'xxx' ]; then
VERSION='latest'
fi
docker build -t morgan1971/skadc-software:${VERSION} -f Dockerfile .
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#!/bin/bash
# Exit on any error. More complex stuff could be done in future
# (see https://stackoverflow.com/questions/4381618/exit-a-script-on-error)
set -e
if [ "x$SAFE_MODE" == "xTrue" ]; then
echo ""
echo "[INFO] Not executing entrypoint as we are in safe mode, just opening a Bash shell."
exec /bin/bash
else
#---------------------
# Setup home
#---------------------
if [ ! -f "/home/metauser/.initialized" ]; then
echo "[INFO] Setting up home"
[ ! -d "/home/metauser" ] && mkdir -p /home/metauser
# Copy over vanilla home contents
for x in /metauser_home_vanilla/* /metauser_home_vanilla/.[!.]* /metauser_home_vanilla/..?*; do
if [ -e "$x" ]; then cp -a "$x" /home/metauser/; fi
done
echo source $INSTALLDIR/init.sh >> $HOME/.bashrc
# Mark as initialized
[ ! -f "/home/metauser/.initialized" ] && touch /home/metauser/.initialized
fi
#---------------------
# Save env
#---------------------
echo "[INFO] Dumping env"
# Save env vars for later usage (e.g. ssh)
env | \
while read env_var; do
if [[ $env_var == HOME\=* ]]; then
: # Skip HOME var
elif [[ $env_var == PWD\=* ]]; then
: # Skip PWD var
else
echo "export $env_var" >> /tmp/env.sh
fi
done
echo ""
echo "[INFO] Executing entrypoint..."
if [ "xxx$@" == "xxx" ]; 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 $CONTAINER_NAME container!"
echo ""
echo "=============================================================="
echo ""
echo "You are now in /home/metauser with write access as user \"$(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 ""
echo "This image acts as a base for the LOFAR installationi."
echo "It has Fedora 31 setup, with the required dependencies installed:"
echo " * Armadillo 9.900.3"
echo " * Boost 1.69.0"
echo " * Armadillo 9.900.3"
echo " * Boost 1.69.0"
echo " * CFITSIO 7.3.47"
echo " * FFTW 3.5.8"
echo " * HDF5 1.10.5"
echo " * LAPACK 3.8.0"
echo " * OpenBLAS 3.8.0"
echo " * SuperLU 5.2.1"
echo " * WCSLIB 6.4"
echo " * Armadillo 9.900.3"
echo " * Boost 1.69.0"
echo " * Armadillo 9.900.3"
echo " * Boost 1.69.0"
echo " * CFITSIO 7.3.47"
echo " * FFTW 3.5.8"
echo " * HDF5 1.10.5"
echo " * LAPACK 3.8.0"
echo " * OpenBLAS 3.8.0"
echo " * SuperLU 5.2.1"
echo " * WCSLIB 6.4"
echo ""
cd /home/metauser
$COMMAND
fi
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export INSTALLDIR=$INSTALLDIR
export HDF5_USE_FILE_LOCKING=FALSE
source $INSTALLDIR/lofar/lofarinit.sh
export PYTHONPATH=$INSTALLDIR/dppp:$INSTALLDIR/lofar/lib64/python2.7/site-packages
export PATH=/opt/montage/Montage-6.0/bin:$PATH
export PATH=$INSTALLDIR/aoflagger/bin:$PATH
export PATH=$INSTALLDIR/casacore/bin:$PATH
export PATH=$INSTALLDIR/ds9/bin:$PATH
export PATH=$INSTALLDIR/DPPP/bin:$PATH
export PATH=$INSTALLDIR/difmap/uvf_difmap:$PATH
export PATH=$INSTALLDIR/dysco/bin:$PATH
export PATH=$INSTALLDIR/lofar/bin:$PATH
export PATH=$INSTALLDIR/wsclean/bin:$PATH
export PATH=/usr/lib64/openmpi/bin:$PATH
export LD_LIBRARY_PATH=$INSTALLDIR/aoflagger/lib:$INSTALLDIR/casacore/lib:$INSTALLDIR/DPPP/lib:$INSTALLDIR/dysco/lib:$INSTALLDIR/EveryBeam/lib:$INSTALLDIR/idg/lib:$INSTALLDIR/lofar/lib:$INSTALLDIR/lofar/lib64:$INSTALLDIR/LOFARBeam/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH
export OPENBLAS_NUM_THREADS=64
export OPENBLAS_MAX_THREADS=64
export OMP_NUM_THREADS=64
export OMP_MAX_THREADS=64
export PYTHONPATH=$INSTALLDIR/dppp:$INSTALLDIR/lofar/lib64/python2.7/site-packages:$PYTHONPATH
source $INSTALLDIR/pyenv-py2/bin/activate
measures.directory: $INSTALLDIR/casacore/data
export CASARCFILES=$INSTALLDIR/.casarc
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#
# 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
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