until pyBDSF …

8a3ba000 · Orgis, Dr. Thomas · 0652fc93 · 8a3ba000
Commit 8a3ba000 authored Mar 24, 2020 by Orgis, Dr. Thomas
--- a/build_lofar_cepH.sh
+++ b/build_lofar_cepH.sh
+#!/bin/bash
 # General environment settings.
 . /sw/profile/init.sh
 module switch env env/2019Q4-cuda-gcc-openmpi
-export LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS"
+# ThOr: This provides python and python-config pointing
+# to current python3 and python3-config.
+module load pythonversion/3
+echo "TODO: Ensure conistent use of one openblas variant (the one cblas and numpy use)"
+# ThOr: Maybe not even necessary, at least with cmake builds.
+#export LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS"
 export J=64
-export INSTALLDIR=$HOME/opt/lofar_200318
+# ThOr: Use command line argument for the prefix to ease testing.
-export PYTHON_VERSION=3.6
+# Not all variables shall be exported to children!
-export PYTHON_VERSION_NODOT=36
+scriptdir=$(cd $(dirname $0) && pwd)
-export cmake=`which cmake`
+INSTALLDIR=${1:-$HOME/opt/lofar_200318}
-export make=`which make`
+# ThOr: I hate to hardcode things that can be fetched automatically.
+# This takes whatever python is linked to python3.
+PYTHON_VERSION=$(python3 --version | cut -f 2 -d ' ' | cut -f 1,2 -d .)
+PYTHON_VERSION_NODOT=$(echo $PYTHON_VERSION|tr -d .)
+cmake=`which cmake`
+make=`which make`
 export CC=`which gcc`
 export CXX=`which g++`
-export CFLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS -march=native -O3 -fno-math-errno -ftree-vectorize"
+# ThOr: Fortran is at least checked for by some builds.
+export FC=`which gfortran`
+# ThOr: removed C++-specific defines from CFLAGS
+export CFLAGS="-march=native -O3 -fno-math-errno -ftree-vectorize"
+export FCFLAGS="$CFLAGS"
 export CXXFLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS -march=native -O3 -fno-math-errno -ftree-vectorize"
-export LDFLAGS="-lgsl -lcblas"
+# ThOr: Those should not be global, should they? Let's add -Wl,--as-needed,
-export CMAKE_RPATH="-DCMAKE_BUILD_RPATH=$LD_RUN_PATH -DCMAKE_INSTALL_RPATH=$LD_RUN_PATH"
+# so that unnecessary libraries are dropped from the build.
+# Trying to ensure openblas_openmp here, but that needs to be fixed
+# in the packages, recognizing that a dependency is already using
+# openblas and then not trying to use a different one:-/
+export LDFLAGS="-lgsl -lcblas -lopenblas_openmp -Wl,--as-needed"
+# Ensure that we know what include search path variable is really used.
+# Only leave CPATH set.
+unset INCLUDE
+unset C_INCLUDE_PATH
 # Path to where the patch for python-casacore's setup is stored.
 #export PYTHON_CASACORE_PATCH=$HOME/opt/src/patch_python-casacore.patch
 #export PATCH_AOFLAGGER=/net/lofar1/data1/sweijen/software/LOFAR/aoflagger.patch
 # Settings relevant to the installed software.
+# ThOr: I recommend settling on with or without v and add the v on git
+# command instead.
 export AOFLAGGER_VERSION=v2.14.0
 export BOOST_DOT_VERSION=1.67.0
 export BOOST_VERSION=1_67_0
@@ -34,316 +63,435 @@ export PYTHON_CASACORE_VERSION=3.1.1
 export WSCLEAN_VERSION=latest
 export WCSLIB_VERSION=latest
-mkdir -p $INSTALLDIR
+# ThOr: These functions emulare what proper environment modules would do.
-#######################################
+# Add all given paths to LD_RUN_PATH, staring from
-# Build all external libraries first. #
+# the vanilla environment setting.
-#######################################
+# Also sync LIBRARY_PATH, as some seem to pick that up.
+use_prefix()
+{
+  if test -z "$env_run_path"; then
+    env_run_path=$LD_RUN_PATH
+    env_path=$PATH
+    env_cpath=$CPATH
+    #env_ldflags=$LDFLAGS
+  fi
+  LD_RUN_PATH=$env_run_path
+  PATH=$env_path
+  CPATH=$env_cpath
+  #LDFLAGS=$end_ldflags
+  for d in "$@"
+  do
+    LD_RUN_PATH="$d/lib:$LD_RUN_PATH"
+    PATH="$d/bin:$PATH"
+    CPATH="$d/include:$CPATH"
+    #LDFLAGS="-L$d/lib $LDFLAGS"
+  done
+}
-#if [ ! -d $INSTALLDIR/fftw ]; then
+# ThOr: Run cmake, with standard arguments.
-#    #
+run_cmake()
-#    # Install FFTW
+{
-#    #
+  cmake \
-#    echo Installing FFTW...
+  -DCMAKE_C_COMPILER="$CC" \
-#    mkdir -p ${INSTALLDIR}/fftw
+  -DCMAKE_CXX_COMPILER="$CXX" \
-#    cd ${INSTALLDIR}/fftw && wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
+  -DCMAKE_Fortran_COMPILER="$FC" \
-#    cd ${INSTALLDIR}/fftw && tar xzf fftw*.tar.gz
+  -DCMAKE_C_FLAGS="$CFLAGS" \
-#    cd ${INSTALLDIR}/fftw/fftw*/ && ./configure --prefix=${INSTALLDIR}/fftw --enable-threads --enable-shared
+  -DCMAKE_CXX_FLAGS="$CXXFLAGS" \
-#    cd ${INSTALLDIR}/fftw/fftw*/ && $make -j $J
+  -DCMAKE_Fortran_FLAGS="$FCFLAGS" \
-#    cd ${INSTALLDIR}/fftw/fftw*/ && $make install
+  -DCMAKE_SKIP_RPATH=ON \
-#    cd ${INSTALLDIR}/fftw/fftw*/ && ./configure --prefix=${INSTALLDIR}/fftw --enable-threads --enable-shared --enable-float
+  "$@"
-#    cd ${INSTALLDIR}/fftw/fftw*/ && $make -j $J
+}
-#    cd ${INSTALLDIR}/fftw/fftw*/ && $make install
-#    echo Installed FFTW.
+# ThOr: Locate a libray with provided linker
-#else
+# Arguments: name to grep for (libpng), then compiler/linker arguments.
-#    echo FFTW already installed.
+# Example: find_libfile libpng $(pkg-config --libs libpng) to return
-#fi
+# /some/prefix/lib/libpng16.so.16
-#
+find_libfile()
-#if [ ! -d $INSTALLDIR/hdf5 ]; then
+{
-#    #
+  local libname=$1; shift # Grep ldd output for that.
-#    # Install HDF5
+  wrk=$(mktemp -d) &&
-#    #
+  (
-#    echo Installing HDF5...
+    cd $wrk &&
-#    mkdir -p ${INSTALLDIR}/hdf5
+    echo 'int main(){ return 0; }' > test.c &&
-#    cd ${INSTALLDIR}/hdf5 && wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION%.*}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz
+    g++ "$@" -o test.bin test.c &&
-#    cd ${INSTALLDIR}/hdf5 && tar xzf hdf5*.tar.gz
+    ldd test.bin | grep "$libname" | cut -f 3 -d ' '
-#    cd ${INSTALLDIR}/hdf5/hdf5*/ && ./configure --prefix=${INSTALLDIR}/hdf5 --enable-fortran --enable-cxx
+  )
-#    cd ${INSTALLDIR}/hdf5/hdf5*/ && $make -j $J
+  rm -rf "$wrk"
-#    cd ${INSTALLDIR}/hdf5/hdf5*/ && $make install
+}
-#    echo Installed HDF5.
-#else
+mkdir -p $INSTALLDIR
-#    echo HDF5 already installed.
-#fi
+# ThOr: We got the external libs covered vi pkgsrc.
-#
+# Only need to care for the LOFAR code.
-#export CMAKE_PREFIX_PATH=${INSTALLDIR}/hdf5
-#
-#if [ ! -d $INSTALLDIR/boost ]; then
-#    #
-#    # Install Boost.Python
-#    #
-#    echo Installing Boost.Python...
-#    echo "using python : ${PYTHON_VERSION} : /usr/bin/python3 : /usr/include/python${PYTHON_VERSION} : /usr/lib ;" > $HOME/user-config.jam
-#    mkdir -p $INSTALLDIR/boost/src
-#    cd $INSTALLDIR/boost/ && wget https://dl.bintray.com/boostorg/release/${BOOST_DOT_VERSION}/source/boost_${BOOST_VERSION}.tar.gz && tar xzf boost_${BOOST_VERSION}.tar.gz
-#    cd $INSTALLDIR/boost/boost_*/ && ./bootstrap.sh --prefix=$INSTALLDIR/boost --with-python-version=${PYTHON_VERSION} && ./b2 headers && ./b2 install toolset=gcc cxxflags=-std=c++11 --prefix=$INSTALLDIR/boost --with-atomic --with-chrono --with-date_time --with-filesystem --with-program_options --with-python --with-signals --with-test --with-thread -j $J
-#    # CHECK THE PYTHON VERSION HERE
-#    cd $INSTALLDIR/boost/lib/
-#    ln -s libboost_python${PYTHON_VERSION_NODOT}.a         libboost_python.a
-#    ln -s libboost_python${PYTHON_VERSION_NODOT}.so        libboost_python.so
-#    ln -s libboost_python${PYTHON_VERSION_NODOT}.so.1.67.0 libboost_python.so.1.67.0
-#    ln -s libboost_python${PYTHON_VERSION_NODOT}.a         libboost_python3.a
-#    ln -s libboost_python${PYTHON_VERSION_NODOT}.so        libboost_python3.so
-#    ln -s libboost_python${PYTHON_VERSION_NODOT}.so.1.67.0 libboost_python3.so.1.67.0
-#    ln -s libboost_numpy${PYTHON_VERSION_NODOT}.a          libboost_numpy.a
-#    ln -s libboost_numpy${PYTHON_VERSION_NODOT}.so         libboost_numpy.so
-#    ln -s libboost_numpy${PYTHON_VERSION_NODOT}.so.1.67.0  libboost_numpy.so.1.67.0
-#    ln -s libboost_numpy${PYTHON_VERSION_NODOT}.a          libboost_numpy3.a
-#    ln -s libboost_numpy${PYTHON_VERSION_NODOT}.so         libboost_numpy3.so
-#    ln -s libboost_numpy${PYTHON_VERSION_NODOT}.so.1.67.0  libboost_numpy3.so.1.67.0
-#    echo Installed Boost.Python.
-#else
-#    echo Boost.Python already installed.
-#fi
-#
-#if [ ! -d $INSTALLDIR/openblas ]; then
-#    #
-#    # Install OpenBLAS
-#    #
-#    echo Installing OpenBLAS...
-#    mkdir -p $INSTALLDIR/openblas/
-#    cd $INSTALLDIR/openblas/ && git clone https://github.com/xianyi/OpenBLAS.git src && cd src && git checkout $OPENBLAS_VERSION
-#    cd $INSTALLDIR/openblas/src && $make -j $J 
-#    cd $INSTALLDIR/openblas/src && $make install PREFIX=$INSTALLDIR/openblas
-#    echo Installed OpenBLAS.
-#else
-#    echo OpenBlas already installed.
-#fi
-#
-#export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:${INSTALLDIR}/openblas
-#
-#if [ ! -d $INSTALLDIR/superlu ]; then
-#    #
-#    # Install SuperLU
-#    #
-#    echo Installing SuperLU...
-#    mkdir -p $INSTALLDIR/superlu/build
-#    cd $INSTALLDIR/superlu/ && git clone https://github.com/xiaoyeli/superlu.git src && cd src && git checkout $SUPERLU_VERSION
-#    cd $INSTALLDIR/superlu/build && $cmake -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=1 -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/superlu -DUSE_XSDK_DEFAULTS=TRUE -Denable_blaslib=OFF -DBLAS_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so ../src
-#    cd $INSTALLDIR/superlu/build && $make -j $J 
-#    cd $INSTALLDIR/superlu/build && $make install
-#    echo Installed SuperLU.
-#else
-#    echo SuperLu already installed.
-#fi
-#
-#if [ ! -d $INSTALLDIR/armadillo ]; then
-#    #
-#    # Install Armadillo
-#    #
-#    echo Installing Armadillo...
-#    # check if superlu lib is .../lib or .../lib64
-#    mkdir -p $INSTALLDIR/armadillo/
-#    cd $INSTALLDIR/armadillo && wget http://sourceforge.net/projects/arma/files/armadillo-$ARMADILLO_VERSION.tar.xz 
-#    cd $INSTALLDIR/armadillo && tar xf armadillo-$ARMADILLO_VERSION.tar.xz
-#    cd $INSTALLDIR/armadillo/armadillo*/ && ./configure && $cmake -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=1 -DCMAKE_INSTALL_PREFIX:PATH=$INSTALLDIR/armadillo -Dopenblas_LIBRARY:FILEPATH=$INSTALLDIR/openblas/lib/libopenblas.so  -DSuperLU_INCLUDE_DIR:PATH=$INSTALLDIR/superlu/include -DSuperLU_LIBRARY:FILEPATH=$INSTALLDIR/superlu/lib/libsuperlu.so	
-#    cd $INSTALLDIR/armadillo/armadillo*/ && $make -j $J
-#    cd $INSTALLDIR/armadillo/armadillo*/ && $make install
-#    echo Installed Armadillo.
-#else
-#    echo Armadillo already installed.
-#fi
-#
-#if [ ! -d $INSTALLDIR/cfitsio ]; then
-#    #
-#    # Install-cfitsio
-#    #
-#    echo Installing CFITSIO...
-#    mkdir -p ${INSTALLDIR}/cfitsio/build
-#    cd ${INSTALLDIR}/cfitsio && wget http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-${CFITSIO_VERSION}.tar.gz
-#    cd ${INSTALLDIR}/cfitsio && tar xf cfitsio-${CFITSIO_VERSION}.tar.gz
-#    cd ${INSTALLDIR}/cfitsio/build && $cmake -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=1 -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/cfitsio/ ../cfitsio-${CFITSIO_VERSION}
-#    cd ${INSTALLDIR}/cfitsio/build && $make -j $J
-#    cd ${INSTALLDIR}/cfitsio/build && $make install
-#    echo Installed CFITSIO.
-#else
-#    echo CFITSIO already installed.
-#fi
-#
-#if [ ! -d $INSTALLDIR/wcslib ]; then
-#    #
-#    # Install-wcslib
-#    #
-#    echo Installing WCSLIB...
-#    mkdir ${INSTALLDIR}/wcslib
-#    if [ "${WCSLIB_VERSION}" = "latest" ]; then cd ${INSTALLDIR}/wcslib && wget --retry-connrefused ftp://anonymous@ftp.atnf.csiro.au/pub/software/wcslib/wcslib.tar.bz2 -O wcslib-latest.tar.bz2; fi
-#    if [ "${WCSLIB_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/wcslib && wget --retry-connrefused ftp://anonymous@ftp.atnf.csiro.au/pub/software/wcslib/wcslib-${WCSLIB_VERSION}.tar.bz2; fi
-#    cd ${INSTALLDIR}/wcslib && tar xf wcslib-*.tar.bz2
-#    #cd ${INSTALLDIR} && mkdir wcslib && cd wcslib && svn checkout https://github.com/astropy/astropy/trunk/cextern/wcslib
-#    cd ${INSTALLDIR}/wcslib/wcslib* && ./configure --prefix=${INSTALLDIR}/wcslib --with-cfitsiolib=${INSTALLDIR}/cfitsio/lib/ --with-cfitsioinc=${INSTALLDIR}/cfitsio/include/ --without-pgplot
-#    cd ${INSTALLDIR}/wcslib/wcslib* && $make -j $J
-#    cd ${INSTALLDIR}/wcslib/wcslib* && $make install -j $J
-#    echo Installed WCSLIB.
-#else
-#    echo WCSLIB already installed.
-#fi
-#
-#
-## Make library and header directories easily available for future CMakes.
-#export CMAKE_INCLUDE=$INSTALLDIR/cfitsio/include:$INSTALLDIR/wcslib/include
-#export CMAKE_LIBRARY=$INSTALLDIR/cfitsio/lib:$INSTALLDIR/wcslib/lib
-#export CMAKE_PREFIX_PATH=$INSTALLDIR/casacore:$INSTALLDIR/cfitsio:$INSTALLDIR/dysco:$INSTALLDIR/idg:$INSTALLDIR/wcslib:/usr/lib64
-#export CPATH=$INSTALLDIR/cfitsio/lib:$INSTALLDIR/wcslib/lib
 #########################################
 # Install main LOFAR software packages. #
 #########################################
-if [ ! -d $INSTALLDIR/casacore ]; then
+if [ ! -e $INSTALLDIR/casacore/.done ]; then
    #
    # Install CASAcore
    #
-    echo Installing CASAcore...
+    echo Installing CASAcore... &&
-    mkdir -p ${INSTALLDIR}/casacore/build
+    mkdir -p $INSTALLDIR/casacore &&
-    mkdir -p ${INSTALLDIR}/casacore/data
+    cd $INSTALLDIR/casacore &&
-    cd $INSTALLDIR/casacore && git clone https://github.com/casacore/casacore.git src
+    rm -rf bin lib &&
-    if [ "${CASACORE_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/casacore/src && git checkout tags/${CASACORE_VERSION}; fi
+    if test -e src && test -e data; then
-    cd ${INSTALLDIR}/casacore/data && wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar
+        echo "Re-using existing sources."
-    cd ${INSTALLDIR}/casacore/data && tar xf WSRT_Measures.ztar
-    cd ${INSTALLDIR}/casacore/build && $cmake $CMAKE_RPATH -DCMAKE_CXX_FLAGS=${CXX_FLAGS} -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/casacore/ -DCMAKE_C_COMPILER=$CC -DCMAKE_CXX_COMPILER=$CXX -DDATA_DIR:PATH=${INSTALLDIR}/casacore/data -DBoost_LIBRARY_DIR_RELEASE:PATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -DBoost_PYTHON_LIBRARY_RELEASE:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libboost_python36.so -DBOOST_PYTHON3_LIBRARY_NAME:STRING=python -DENABLE_TABLELOCKING=OFF -DUSE_OPENMP=True -DUSE_FFTW3=True -DUSE_HDF5=True -DBUILD_PYTHON:BOOL=False -DBUILD_PYTHON3:BOOL=True ../src/
-    cd ${INSTALLDIR}/casacore/build && $make -j ${J}
-    cd ${INSTALLDIR}/casacore/build && $make install
-    ln -s ${INSTALLDIR}/casacore/lib/libcasa_python3.so ${INSTALLDIR}/casacore/lib/libcasa_python.so
-    echo Installed CASAcore.
    else
-    echo CASAcore already installed.
+        rm -rf src build data &&
+        mkdir -p build data &&
+        git clone https://github.com/casacore/casacore.git src &&
+        if [ "${CASACORE_VERSION}" != "latest" ]; then
+            ( cd src &&
+            git checkout tags/${CASACORE_VERSION} )
        fi
+        ( cd data &&
+          wget --retry-connrefused \
+            ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar &&
+          tar xf WSRT_Measures.ztar )
+    fi &&
+    cd build &&
+    use_prefix $INSTALLDIR/casacore
+    run_cmake \
+      -DCMAKE_BUILD_TYPE=Release \
+      -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/casacore \
+      -DDATA_DIR:PATH=${INSTALLDIR}/casacore/data \
+      -DENABLE_TABLELOCKING=OFF \
+      -DUSE_OPENMP=ON \
+      -DUSE_FFTW3=ON \
+      -DUSE_HDF5=ON \
+      -DBUILD_PYTHON=OFF \
+      -DBUILD_PYTHON3=ON \
+      ../src/ &&
+    make -j $J &&
+    make install &&
+    # ThOr: Let's see if that is really needed ...
+    #ln -s ${INSTALLDIR}/casacore/lib/libcasa_python3.so \
+    #      ${INSTALLDIR}/casacore/lib/libcasa_python.so &&
+    echo Installed CASAcore. &&
+    touch $INSTALLDIR/casacore/.done
+else
+    echo CASAcore already installed.
+fi || exit 1
+prefix=$INSTALLDIR/python-casacore
+pycasacorelib=$prefix/lib/python$PYTHON_VERSION/site-packages
+# ThOr: Subsequent builds might need that, so export it always here.
+export PYTHONPATH=$pycasacorelib:$PYTHONPATH
-if [ ! -d $INSTALLDIR/python-casacore ]; then
+if [ ! -e $prefix/.done ]; then
    #
    # Install-python-casacore
    #
    # Finding libraries is broken, patch the setup to include the previously installed boost and casacore libraries.
    # note the the python executable needs to be the right one
-    mkdir ${INSTALLDIR}/python-casacore
+    mkdir -p $prefix &&
-    mkdir -p ${INSTALLDIR}/python-casacore/lib/python${PYTHON_VERSION}/site-packages/
+    cd $prefix &&
-    export PYTHONPATH=$INSTALLDIR/python-casacore/lib/python${PYTHON_VERSION}/site-packages/:$PYTHONPATH
+    rm -rf lib bin src &&
+    if test -e src.tar.gz; then
-    cd ${INSTALLDIR}/python-casacore && git clone https://github.com/casacore/python-casacore
+        # ThOr: Dunno how to clean, but we can extract archive to avoid re-dowload.
-    if [ "$PYTHON_CASACORE_VERSION" != "latest" ]; then cd ${INSTALLDIR}/python-casacore/python-casacore && git checkout tags/${PYTHON_CASACORE_VERSION}; fi
+        echo "Using archived sources."
-    cd ${INSTALLDIR}/python-casacore/python-casacore && ./setup.py build_ext --swig-opts=-c++ -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/python3.6:${INSTALLDIR}/casacore/include/ -L/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/:${INSTALLDIR}/casacore/lib/ install --prefix ${INSTALLDIR}/python-casacore/
+        tar -xf src.tar.gz
-    echo Installed Python CASAcore.
+    else
+        echo "Fresh download."
+        git clone https://github.com/casacore/python-casacore src &&
+        if [ "$PYTHON_CASACORE_VERSION" != "latest" ]; then
+            ( cd src && git checkout tags/v$PYTHON_CASACORE_VERSION )
+        fi &&
+        tar -czf src.tar.gz src
+    fi &&
+    # ThOr: Note that ${VAR} serves no other purpose than to delimit
+    # the name VAR itself. It does not imply any quoting. "$VAR" is careful,
+    # ${VAR} is't. "${VAR}" would be. You should either do use the braces
+    # where required only (${VAR}_suffix) or apply them alwas as a matter
+    # of style. I myself don't like them where not needed.
+    mkdir -p $pycasacorelib &&
+    cd src &&
+    # ThOr: with the pythonversion/3 module, the plain python does the correct
+    # thing. But an alternative would be to call python3 setup.py instead of
+    # ./setup.py .
+    use_prefix $INSTALLDIR/casacore $prefix &&
+    # This magically picks up some RPATH, not sure how, but does neither
+    # include confgured casacore path or its own install prefix. But it seems
+    # to honour LDFLAGS.
+    LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS" \
+        ./setup.py build_ext --swig-opts=-c++  \
+        -I$INSTALLDIR/casacore/include -L$INSTALLDIR/casacore/lib \
+        install --prefix $prefix &&
+    echo Installed Python CASAcore. &&
+    touch $prefix/.done
 else
    echo Python-CASAcore already installed.
-fi
+fi || exit 1
-if [ ! -d $INSTALLDIR/dysco ]; then
+prefix=$INSTALLDIR/dysco
+if [ ! -e $prefix/.done ]; then
    #
    # Install Dysco
    #
    echo Installing Dysco...
-    mkdir -p $INSTALLDIR/dysco/build
+    mkdir -p $prefix &&
-    cd $INSTALLDIR/dysco && git clone https://github.com/aroffringa/dysco.git src
+    cd       $prefix &&
-    cd $INSTALLDIR/dysco/build && $cmake $CMAKE_RPATH -DCMAKE_CXX_FLAGS="-D_GLIB_USE_CXX_ABI=1 -march=native -O2 -fno-math-errno -ftree-vectorize" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/dysco -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore ../src
+    rm -rf lib bin build  &&
-    cd $INSTALLDIR/dysco/build && $make -j $J 
+    if [ -e src ]; then
-    cd $INSTALLDIR/dysco/build && $make install
+        echo "Using existing source."
-    echo Installed Dysco.
+    else
+        git clone https://github.com/aroffringa/dysco.git src
+    fi &&
+    mkdir build &&
+    cd    build &&
+    use_prefix $INSTALLDIR/casacore $prefix &&
+    run_cmake \
+        -DCMAKE_INSTALL_PREFIX=$prefix \
+        -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore \
+        ../src &&
+    make -j $J &&
+    make install &&
+    echo Installed Dysco. &&
+    touch $prefix/.done
 else
    echo Dysco already installed.
-fi
+fi || exit 1
-if [ ! -d $INSTALLDIR/aoflagger ]; then
+prefix=$INSTALLDIR/aoflagger
+if [ ! -e $prefix/.done ]; then
+    echo "Installing aoflagger..."
    #
    # Install-aoflagger
    #
-    # might have to comment these in CMakeLists.txt
+    mkdir -p $prefix &&
-    # > pkg_check_modules(GTKMM gtkmm-3.0>=3.0.0)
+    cd       $prefix &&
-    # > pkg_check_modules(SIGCXX sigc++-2.0)
+    rm -rf build bin lib presrc&&
-    mkdir -p ${INSTALLDIR}/aoflagger/build
+    if [ -e src ]; then
-    cd ${INSTALLDIR}/aoflagger && git clone git://git.code.sf.net/p/aoflagger/code aoflagger
+        echo "Using existing sources."
-    if [ "${AOFLAGGER_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/aoflagger/aoflagger && git checkout tags/${AOFLAGGER_VERSION}; fi
-    cd ${INSTALLDIR}/aoflagger/build && $cmake $CMAKE_RPATH -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DCMAKE_CXX_FLAGS="-D_GLIB_USE_CXX_ABI=1 -march=native -O2 -fno-math-errno -ftree-vectorize" -DBoost_PYTHON_LIBRARY_RELEASE:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libboost_python36.so -DPNG_LIBRARY_RELEASE:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libpng16.so -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/aoflagger/ -DBUILD_SHARED_LIBS=ON -DPORTABLE=True ../aoflagger
-    cd ${INSTALLDIR}/aoflagger/build && make -j $J
-    cd ${INSTALLDIR}/aoflagger/build && make install
    else
-    echo AOFlagger already installed.
+        git clone git://git.code.sf.net/p/aoflagger/code presrc
+        if [ "${AOFLAGGER_VERSION}" != "latest" ]; then
+            ( cd presrc && git checkout tags/${AOFLAGGER_VERSION} )
        fi
+        if ! [ grep -q Boost::python presrc/src/CMakeLists.txt ]; then
+          echo "Patching aoflagger, mainly for Boost::python" 
+          (cd presrc && patch -Np1 < "$scriptdir/aoflagger-buildfix.patch" )
+        fi &&
+        mv presrc src
+    fi &&
+    mkdir build &&
+    cd    build &&
+    # ThOr: aoflagger build finds system's libpng, but dependencies use
+    # libpng16 from pkgsrc. So that semi-hardcoded fix stays here.
+    # But the Boost+Python stuff got fixed via the patch above.
+    use_prefix $INSTALLDIR/casacore $prefix &&
+    run_cmake \
+        -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore \
+        -DCMAKE_INSTALL_PREFIX=$prefix \
+        -DPNG_LIBRARY_RELEASE:FILEPATH="$(find_libfile libpng $(pkg-config --libs libpng))" \
+        -DBUILD_SHARED_LIBS=ON -DPORTABLE=ON \
+        ../src &&
+    make -j $J &&
+    make install &&
+    echo "Done with aoflagger." &&
+    touch $prefix/.done
+else
+    echo AOFlagger already installed.
+fi || exit 1
+prefix=$INSTALLDIR/LOFARBeam
-if [ ! -d $INSTALLDIR/LOFARBeam ]; then
+if [ ! -e $prefix/.done ]; then
    #
    # Install the standalone StationResponse libraries.
    #
    echo Installing LOFARBeam...
-    mkdir -p $INSTALLDIR/LOFARBeam/build
+    mkdir -p $prefix &&
-    cd $INSTALLDIR/LOFARBeam && git clone https://github.com/lofar-astron/LOFARBeam.git src
+    cd       $prefix &&
-    cd $INSTALLDIR/LOFARBeam/build && $cmake $CMAKE_RPATH -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DBoost_PYTHON3_LIBRARY_RELEASE:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libboost_python36.so -DBoost_NUMPY3_LIBRARY_RELEASE:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libboost_numpy36.so -DDPYTHON_EXECUTABLE=~/opt/bin/python -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/LOFARBeam ../src
+    rm -rf build bin lib presrc &&
-    cd $INSTALLDIR/LOFARBeam/build && $make -j $J
+    if [ -e src ]; then
-    cd $INSTALLDIR/LOFARBeam/build && $make install
+        echo "Using existing sources."
-fi
+    else
+        git clone https://github.com/lofar-astron/LOFARBeam.git presrc
+        if ! [ grep -q Boost:: presrc/CMakeLists.txt ]; then
+          echo "Patching LOFARBeam, mainly for Boost::python" 
+          (cd presrc && patch -Np1 < "$scriptdir/LOFARBeam-buildfix.patch" )
+        fi &&
+        mv presrc src
+    fi &&
+    mkdir build &&
+    cd    build &&
+    use_prefix $INSTALLDIR/casacore $prefix &&
+    run_cmake \
+        -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore \
+        -DCMAKE_INSTALL_PREFIX=$prefix \
+        ../src &&
+    make -j $J &&
+    make install &&
+    echo Done with LOFARBeam. &&
+    touch $prefix/.done
+fi || exit 1
-if [ ! -d $INSTALLDIR/idg ]; then
+prefix=$INSTALLDIR/idg
+if [ ! -e $prefix/.done ]; then
    #
    # Install the Image Domain Gridder (IDG).
    # 
    echo Installing IDG.
-    mkdir -p $INSTALLDIR/idg/build
+    mkdir -p $prefix &&
-    cd $INSTALLDIR/idg && git clone https://gitlab.com/astron-idg/idg.git src
+    cd       $prefix &&
-    cd $INSTALLDIR/idg/build && $cmake $CMAKE_RPATH -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/idg -DBUILD_WITH_MKL=ON -DBUILD_LIB_CPU=ON -DBUILD_LIB_CUDA=ON -DMKL_INCLUDE_DIRS:PATH=/home/fdg/node31/opt/intel/mkl/include ../src
+    rm -rf bin lib presrc build &&    
-    cd $INSTALLDIR/idg/build && $make -j $J
+    if test -d src; then
-    cd $INSTALLDIR/idg/build && $make install
+        echo "Using existing source."
+    else
+        git clone https://gitlab.com/astron-idg/idg.git presrc &&
+        mv presrc src
+    fi &&
+    mkdir build &&
+    cd    build &&
+    use_prefix $prefix &&
+    # ThOr: The FindMKL included (two copies!) tries to locate libmkl_rt and
+    # sets paths from that one. Uses MKL_LIB as environment hint.
+    module load mkl/2020.0.166 &&
+    MKL_LIB=$LD_RUN_PATH run_cmake \
+        -DCMAKE_INSTALL_PREFIX=$prefix \
+        -DBUILD_WITH_MKL=ON \
+        -DBUILD_LIB_CPU=ON \
+        -DBUILD_LIB_CUDA=ON \
+        -DCUDA_INCLUDE_DIR=$CUDA_HOME/include \
+        -DCUDA_FFT_LIBRARY=$(find_libfile libcufft.so -lcufft) \
+        -DCUDA_NVTX_LIBRARY=$(find_libfile libnvToolsExt.so -lnvToolsExt) \
+        ../src &&
+    make -j $J &&
+    make install &&
+    module unload mkl &&
+    echo "Done with IDG." &&
+    touch $prefix/.done
 else
    echo IDG already installed.
-fi
+fi || exit 1
-if [ ! -d $INSTALLDIR/DP3 ]; then
+prefix=$INSTALLDIR/DP3
+if [ ! -e $prefix/.done ]; then
+    echo Installing DP3...
    #
    # Install DP3.
    #
-    echo Installing DP3...
+    mkdir -p $prefix
-    mkdir -p $INSTALLDIR/DP3/build
+    cd       $prefix
-    git clone https://github.com/lofar-astron/DP3.git $INSTALLDIR/DP3/src
+    rm -rf build bin lib presrc &&
-    cd $INSTALLDIR/DP3/build && $cmake $CMAKE_RPATH -DCMAKE_CXX_FLAGS=${CXX_FLAGS} -DCMAKE_INSTALL_PREFIX:PATH=$INSTALLDIR/DP3 -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DBoost_PYTHON3_LIBRARY_RELEASE:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libboost_python36.so  -DIDGAPI_INCLUDE_DIRS:PATH=$INSTALLDIR/idg/include -DIDGAPI_LIBRARIES:PATH=$INSTALLDIR/idg/lib/libidg-api.so -DLOFAR_STATION_RESPONSE_DIR:PATH=$INSTALLDIR/LOFARBeam/include -DLOFAR_STATION_RESPONSE_LIB:FILEPATH=$INSTALLDIR/LOFARBeam/lib/libstationresponse.so -DAOFLAGGER_INCLUDE_DIR:PATH=$INSTALLDIR/aoflagger/include -DAOFLAGGER_LIB:FILEPATH=$INSTALLDIR/aoflagger/lib/libaoflagger.so -DPYTHON_INCLUDE_DIR:PATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/python3.6 -DPYTHON_LIBRARY:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libpython3.6.so ../src
+    if test -e src; then
-    cd $INSTALLDIR/DP3/build && $make -j $J
+        echo "Using existing sources."
-    cd $INSTALLDIR/DP3/build && $make install
+    else
-    echo Installed DP3.
+        git clone https://github.com/lofar-astron/DP3.git presrc &&
+        if ! [ grep -q Boost::python presrc/src/CMakeLists.txt ]; then
+            echo "Patching build, mainly for Boost::python" 
+            (cd presrc && patch -Np1 < "$scriptdir/DP3-buildfix.patch" )
+        fi &&
+        mv presrc src
+    fi &&
+    mkdir build &&
+    cd    build &&
+    use_prefix \
+      $INSTALLDIR/casacore \
+      $INSTALLDIR/idg \
+      $INSTALLDIR/LOFARBeam \
+      $INSTALLDIR/aoflagger \
+      $prefix &&
+    # ThOr: It's braindead that I still have to provide things like
+    # AOFLAGGER_INCLUDE_DIR and AOFLAGGER_LIB! You should consider
+    # just locating the library via LD_RUN_PATH or LIBRARY_PATH, set
+    # by use_prefix. Or install an aoflagger-config script, like NetCDF.
+    # Or a pkg-config file. Anything standard!
+    # Really … having to specify the full path to the .so file?! Why do
+    # you love hurting yourself (or your fellow astrophysicists) that much?
+    run_cmake \
+        -DCMAKE_INSTALL_PREFIX:PATH=$prefix \
+        -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore \
+        -DIDGAPI_INCLUDE_DIRS:PATH=$INSTALLDIR/idg/include \
+        -DIDGAPI_LIBRARIES:PATH=$INSTALLDIR/idg/lib/libidg-api.so \
+        -DLOFAR_STATION_RESPONSE_DIR:PATH=$INSTALLDIR/LOFARBeam/include \
+        -DAOFLAGGER_INCLUDE_DIR=$INSTALLDIR/aoflagger/include \
+        -DAOFLAGGER_LIB=$INSTALLDIR/aoflagger/lib/libaoflagger.so \
+        ../src &&
+    make -j $J &&
+    make install &&
+    echo Installed DP3. &&
+    touch $prefix/.done
 else
    echo DP3 already installed.
 fi
+prefix=$INSTALLDIR/wsclean
-if [ ! -d $INSTALLDIR/wsclean ]; then
+if [ ! -e $prefix/.done ]; then
    #
    # Install WSClean
    #
    # Sometimes there are FFT to update by hand in CMakeCache.txt
+    # ThOr: Please no! ;-)
    echo Installing WSClean.
-    mkdir -p $INSTALLDIR/wsclean/build
+    mkdir -p $prefix &&
-    if [ "$WSCLEAN_VERSION" != "latest" ]; then cd ${INSTALLDIR}/wsclean && wget http://downloads.sourceforge.net/project/wsclean/wsclean-${WSCLEAN_VERSION}/wsclean-${WSCLEAN_VERSION}.tar.bz2 && tar -xjf wsclean-${WSCLEAN_VERSION}.tar.bz2 && cd wsclean-${WSCLEAN_VERSION}; fi
+    cd       $prefix &&
-    if [ "$WSCLEAN_VERSION" = "latest" ]; then cd ${INSTALLDIR}/wsclean && git clone git://git.code.sf.net/p/wsclean/code src && cd src/wsclean; fi
+    rm -rf build bin lib presrc &&
-    cd $INSTALLDIR/wsclean/build && $cmake $CMAKE_RPATH -DCMAKE_CXX_FLAGS=${CXX_FLAGS} -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/wsclean -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DIDGAPI_INCLUDE_DIRS:PATH=$INSTALLDIR/idg/include -DIDGAPI_LIBRARIES:PATH=$INSTALLDIR/idg/lib/libidg-api.so -DLOFAR_STATION_RESPONSE_INCLUDE_DIR:PATH=$INSTALLDIR/LOFARBeam/include -DLOFAR_STATION_RESPONSE_LIB:FILEPATH=$INSTALLDIR/LOFARBeam/lib/libstationresponse.so ../src/wsclean
+    if test -e src; then
-    cd $INSTALLDIR/wsclean/build && $make -j $J
+        echo "Using existing sources."
-    cd $INSTALLDIR/wsclean/build && $make install
+    else
+        if [ "$WSCLEAN_VERSION" != "latest" ]; then
+            # ThOr: Untested ...
+            wget http://downloads.sourceforge.net/project/wsclean/wsclean-${WSCLEAN_VERSION}/wsclean-${WSCLEAN_VERSION}.tar.bz2 &&
+            tar -xf wsclean-${WSCLEAN_VERSION}.tar.bz2 &&
+            mkdir presrc &&
+            mv wsclean-${WSCLEAN_VERSION} presrc/wsclean
+        else
+            git clone git://git.code.sf.net/p/wsclean/code presrc &&
+            mv presrc src
+        fi
+    fi &&
+    mkdir build &&
+    cd    build &&
+    use_prefix $INSTALLDIR/casacore $INSTALLDIR/LOFARBeam $INSTALLDIR/idg &&
+    LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS" cmake \
+        -DCMAKE_INSTALL_PREFIX=$prefix \
+        -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore \
+        -DIDGAPI_INCLUDE_DIRS=$INSTALLDIR/idg/include \
+        -DIDGAPI_LIBRARIES=$INSTALLDIR/idg/lib/libidg-api.so \
+        -DLOFAR_STATION_RESPONSE_INCLUDE_DIR=$INSTALLDIR/LOFARBeam/include \
+        -DLOFAR_STATION_RESPONSE_LIB=$INSTALLDIR/LOFARBeam/lib/libstationresponse.so \
+        ../src/wsclean &&
+    make -j $J &&
+    make install &&
+    echo "Done with WSClean." &&
+    touch $prefix/.done
 else
    echo WSClean already installed.
 fi
+prefix=$INSTALLDIR/pyBDSF &&
-if [ ! -d $INSTALLDIR/pyBDSF ]; then
+pybdsflib=$prefix/lib/python$PYTHON_VERSION/site-packages
+export PYTHONPATH=$pybdsflib:$PYTHONPATH &&
+if [ ! -e $prefix/.done ]; then
    echo Installing pyBDSF.
    #
    # Install pyBDSF.
    #
-    mkdir -p $INSTALLDIR/pyBDSF/lib/python$PYTHON_VERSION/site-packages
+    mkdir -p $prefix &&
-    export PYTHONPATH=$INSTALLDIR/pyBDSF/lib/python$PYTHON_VERSION/site-packages:$PYTHONPATH
+    cd       $prefix &&
-    export export LIBRARY_PATH=$LD_LIBRARY_PATH
+    rm -rf build bin lib presrc &&
-    cd $INSTALLDIR/pyBDSF && git clone https://github.com/lofar-astron/PyBDSF pyBDSF
+    if test -e src; then
-    cd $INSTALLDIR/pyBDSF/pyBDSF && python setup.py install --prefix=$INSTALLDIR/pyBDSF
+        echo "Using existing sources."
+    else
+        git clone https://github.com/lofar-astron/PyBDSF presrc &&
+        mv presrc src
+    fi &&
+    mkdir -p $pybdsflib &&
+    cd src &&
+    LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS" \
+        NPY_DISTUTILS_APPEND_FLAGS=1 \
+        python setup.py install --prefix=$prefix &&
+    echo "Done with pyBDSF." &&
+    touch $prefix/.done
 else
    echo pyBDSF already installed.
 fi
+exit
 if [ ! -d $INSTALLDIR/lsmtool ]; then
    echo Installing LSMTool.