Commit 20a8ba84 authored by Giuliano Taffoni's avatar Giuliano Taffoni
Browse files

vlbi pipeline

parent 1a871b00

vlbi/Dockerfile

0 → 100644
+305 −0
Original line number Diff line number Diff line 
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
Original line number Diff line number Diff line 
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

vlbi/build-base.sh

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#!/bin/bash



if [ 'xxx${VERSION}' == 'xxx' ]; then

   VERSION='latest'

fi







docker build -t morgan1971/vlbi-base:${VERSION} -f Dockerfile.base .

vlbi/build-sw.sh

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#!/bin/bash



if [ 'xxx${VERSION}' == 'xxx' ]; then

   VERSION='latest'

fi







docker build -t morgan1971/skadc-software:${VERSION} -f Dockerfile .

vlbi/entrypoint.sh

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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