diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..45ee85bd87be3132b065876aa68c20edcd2458e3
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+*.log
+build_lofar.sh.config
diff --git a/DP3-buildfix.patch b/DP3-buildfix.patch
index 99c39dfb0ec9362f4318fba220a004e79a59551c..290b428b70aecf8b6a16b82a9f8065d70bc441d7 100644
--- a/DP3-buildfix.patch
+++ b/DP3-buildfix.patch
@@ -1,35 +1,135 @@
+diff --git a/CMake/FindCasacore.cmake b/CMake/FindCasacore.cmake
+index e4689f7..9068fdd 100644
+--- a/CMake/FindCasacore.cmake
++++ b/CMake/FindCasacore.cmake
+@@ -17,6 +17,8 @@
+ #
+ # Variables used by this module:
+ # CASACORE_ROOT_DIR - Casacore root directory.
++# BLAS_LIBS - override BLAS library
++# LAPACK_LIBS - override LAPACK library
+ #
+ # Variables defined by this module:
+ # CASACORE_FOUND - System has Casacore, which means that the
+@@ -232,7 +234,21 @@ else(NOT CASACORE_INCLUDE_DIR)
+ elseif(${_comp} STREQUAL fits)
+ casacore_find_package(CFITSIO REQUIRED)
+ elseif(${_comp} STREQUAL scimath_f)
+- casacore_find_package(LAPACK REQUIRED)
++ # If only looking for LAPACK, no library will be added if LAPACK
++ # is part of BLAS, as it is customary nowadays. So look for both
++ # to avoid confusing linker errors on symbols used in headers/templates.
++ if(DEFINED ENV{BLAS_LIBS})
++ set(BLAS_FOUND YES)
++ list(APPEND CASACORE_LIBRARIES $ENV{BLAS_LIBS})
++ else()
++ casacore_find_package(BLAS REQUIRED)
++ endif()
++ if(DEFINED ENV{LAPACK_LIBS})
++ set(LAPACK_FOUND YES)
++ list(APPEND CASACORE_LIBRARIES $ENV{LAPACK_LIBS})
++ else()
++ casacore_find_package(LAPACK REQUIRED)
++ endif()
+ endif(${_comp} STREQUAL casa)
+ endforeach(_comp ${_find_components})
+ endif(NOT CASACORE_INCLUDE_DIR)
+diff --git a/CMake/PythonInstall.cmake b/CMake/PythonInstall.cmake
+index 173f995..c15bbab 100644
+--- a/CMake/PythonInstall.cmake
++++ b/CMake/PythonInstall.cmake
+@@ -24,10 +24,11 @@
+ # $Id: PythonInstall.cmake 32905 2015-11-17 15:31:54Z schaap $
+
+ # Search for the Python interpreter.
+-find_package(PythonInterp)
++# No. We expect the toplevel CMakeLists.txt to have found python already!
++#find_package(PythonInterp)
+
+ # Derive the Python site-packages installation directory and build directory.
+-if(PYTHON_EXECUTABLE)
++if(Python_EXECUTABLE)
+ set(_cmd
+ "from distutils.sysconfig import get_python_lib"
+ "from os.path import join"
+@@ -36,7 +37,7 @@ if(PYTHON_EXECUTABLE)
+ 'site-packages'))"
+ )
+ execute_process(
+- COMMAND "${PYTHON_EXECUTABLE}" "-c" "${_cmd}"
++ COMMAND "${Python_EXECUTABLE}" "-c" "${_cmd}"
+ OUTPUT_VARIABLE _pydir
+ ERROR_VARIABLE _pyerr
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+@@ -57,7 +58,7 @@ if(PYTHON_EXECUTABLE)
+ message(STATUS "Build directory for Python extensions: ${PYTHON_BUILD_DIR}")
+ message(STATUS "Installation directory for Python extensions: ${PYTHON_INSTALL_DIR}")
+ endif()
+-endif(PYTHON_EXECUTABLE)
++endif(Python_EXECUTABLE)
+
+
+ #
+@@ -66,9 +67,9 @@ endif(PYTHON_EXECUTABLE)
+ macro(python_install)
+
+ # Precondition check.
+- if(NOT PYTHON_EXECUTABLE)
++ if(NOT Python_EXECUTABLE)
+ message(FATAL_ERROR "python_install: Python interpreter not available")
+- endif(NOT PYTHON_EXECUTABLE)
++ endif(NOT Python_EXECUTABLE)
+
+ # Parse arguments.
+ # apart from the python files list, there are two additional arguments
diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 515aae1..0dfbcc6 100644
+index 515aae1..671419d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -1,6 +1,8 @@
- # FindHDF5 uses NATIVE_COMMAND in separate_arguments, which requires
- # CMake 3.9.
--cmake_minimum_required(VERSION 3.9)
-+# ThOr: Let's turn it up to 3.12 for proper FindPython, as a helper
-+# to finding the correct Boost python component.
-+cmake_minimum_required(VERSION 3.12)
-
- project(DP3)
-
-@@ -44,10 +46,15 @@ endif(IDGAPI_LIBRARIES AND IDGAPI_INCLUDE_DIRS)
+@@ -44,10 +44,40 @@ endif(IDGAPI_LIBRARIES AND IDGAPI_INCLUDE_DIRS)
find_package(CFITSIO REQUIRED)
-+find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+-#Prevent accidentally finding old BoostConfig.cmake file from casapy
++# An attempt at common logic for Python and Boost:
++# 0. Try CMake 3.12's FindPython, fall back to FindPythonInterp/Libs.
++# 1. Use a default Python being found (environment should provide that).
++# 2. Use that Python's version to look for modern versioned Boost pythonXY
++# component.
++# 3. If that fails, resort to unversioned Boost python.
++# Baseline for this is CMake 3.5, being available in LTS distros.
++# We could require Boost >= 1.67 and CMake >= 3.12 and get rid
++# of the fallbacks.
++
++find_package(Python COMPONENTS Interpreter Development)
++if(NOT Python_FOUND)
++ message(STATUS "Falling back to deprecated Python search.")
++ find_package(PythonInterp REQUIRED)
++ find_package(PythonLibs REQUIRED)
++ set(Python_VERSION ${PYTHON_VERSION_STRING})
++ set(Python_VERSION_MAJOR ${PYTHON_VERSION_MAJOR})
++ set(Python_VERSION_MINOR ${PYTHON_VERSION_MINOR})
++ set(Python_LIBRARIES ${PYTHON_LIBRARIES})
++ set(Python_INCLUDE_DIRS ${PYTHON_INCLUDE_DIRS})
++endif()
+
- #Prevent accidentally finding old BoostConfig.cmake file from casapy
set(Boost_NO_BOOST_CMAKE ON)
-find_package(Boost COMPONENTS date_time filesystem python3 program_options system unit_test_framework REQUIRED)
++set(boostcomp date_time filesystem program_options system unit_test_framework)
++set(boostpy ${Python_VERSION_MAJOR}${Python_VERSION_MINOR})
++find_package(Boost 1.67.0 COMPONENTS ${boostcomp} python${boostpy})
++if(NOT Boost_FOUND)
++ message(STATUS "Falling back to old Boost search.")
++ set(boostpy "")
++ find_package(Boost REQUIRED COMPONENTS ${boostcomp} python${boostpy})
++endif()
+
-+set(PY ${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR})
-+find_package(Boost COMPONENTS date_time filesystem python${PY} program_options system unit_test_framework REQUIRED)
include_directories(${Boost_INCLUDE_DIR})
-+include_directories(${Python3_INCLUDE_DIRS})
++include_directories(${Python_INCLUDE_DIRS})
find_path(LOFAR_STATION_RESPONSE_DIR NAMES StationResponse/Station.h)
find_library(LOFAR_STATION_RESPONSE_LIB stationresponse)
-@@ -165,8 +172,6 @@ set(DPPP_OBJECT $<TARGET_OBJECTS:DPPP_OBJ>)
+@@ -165,8 +195,6 @@ set(DPPP_OBJECT $<TARGET_OBJECTS:DPPP_OBJ>)
#
# Dependencies of AOFlagger
#
@@ -38,26 +138,26 @@ index 515aae1..0dfbcc6 100644
find_package(LibXml2 REQUIRED)
find_package(PNG REQUIRED)
find_library(FFTW3_LIB fftw3 REQUIRED)
-@@ -193,9 +198,9 @@ set(AOFLAGGERSTEP_OBJECT $<TARGET_OBJECTS:AOFlaggerStep_OBJ>)
+@@ -193,9 +221,9 @@ set(AOFLAGGERSTEP_OBJECT $<TARGET_OBJECTS:AOFlaggerStep_OBJ>)
set(EXTRA_LIBRARIES ${EXTRA_LIBRARIES}
${AOFLAGGER_LIB}
${CASACORE_LIBRARIES}
- ${Boost_DATE_TIME_LIBRARY} ${Boost_FILESYSTEM_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${Boost_PYTHON3_LIBRARY}
-+ Boost::date_time Boost::filesystem Boost::system Boost::program_options Boost::python${PY}
++ Boost::date_time Boost::filesystem Boost::system Boost::program_options Boost::python${boostpy}
${EXTRA_LIBRARIES}
- ${PYTHON_LIBRARIES}
-+ Python3::Python
++ ${Python_LIBRARIES}
${IDGAPI_LIBRARIES}
Threads::Threads)
diff --git a/PythonDPPP/CMakeLists.txt b/PythonDPPP/CMakeLists.txt
-index 9194dc7..69f945a 100644
+index 9194dc7..c8284a8 100644
--- a/PythonDPPP/CMakeLists.txt
+++ b/PythonDPPP/CMakeLists.txt
@@ -1,5 +1,5 @@
# If Boost-Python3 found, build this package. Otherwise give a warning.
-if(${Boost_PYTHON3_FOUND})
-+if(${Boost_PYTHON${PY}_FOUND})
++if(${Boost_PYTHON${boostpy}_FOUND})
include(PythonInstall)
diff --git a/LOFARBeam-buildfix.patch b/LOFARBeam-buildfix.patch
index e64ccc0849f8e8f10da777daf43d19ede3b3ad83..6895b940fa4051e2667ae11867b7d16543a40431 100644
--- a/LOFARBeam-buildfix.patch
+++ b/LOFARBeam-buildfix.patch
@@ -1,3 +1,39 @@
+diff --git a/CMake/FindCasacore.cmake b/CMake/FindCasacore.cmake
+index 51d8339..299530f 100644
+--- a/CMake/FindCasacore.cmake
++++ b/CMake/FindCasacore.cmake
+@@ -17,6 +17,8 @@
+ #
+ # Variables used by this module:
+ # CASACORE_ROOT_DIR - Casacore root directory.
++# BLAS_LIBS - override BLAS library
++# LAPACK_LIBS - override LAPACK library
+ #
+ # Variables defined by this module:
+ # CASACORE_FOUND - System has Casacore, which means that the
+@@ -232,7 +234,21 @@ else(NOT CASACORE_INCLUDE_DIR)
+ elseif(${_comp} STREQUAL fits)
+ casacore_find_package(CFITSIO REQUIRED)
+ elseif(${_comp} STREQUAL scimath_f)
+- casacore_find_package(LAPACK REQUIRED)
++ # If only looking for LAPACK, no library will be added if LAPACK
++ # is part of BLAS, as it is customary nowadays. So look for both
++ # to avoid confusing linker errors on symbols used in headers/templates.
++ if(DEFINED ENV{BLAS_LIBS})
++ set(BLAS_FOUND YES)
++ list(APPEND CASACORE_LIBRARIES $ENV{BLAS_LIBS})
++ else()
++ casacore_find_package(BLAS REQUIRED)
++ endif()
++ if(DEFINED ENV{LAPACK_LIBS})
++ set(LAPACK_FOUND YES)
++ list(APPEND CASACORE_LIBRARIES $ENV{LAPACK_LIBS})
++ else()
++ casacore_find_package(LAPACK REQUIRED)
++ endif()
+ endif(${_comp} STREQUAL casa)
+ endforeach(_comp ${_find_components})
+ endif(NOT CASACORE_INCLUDE_DIR)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2867d9c..7d41a23 100644
--- a/CMakeLists.txt
diff --git a/aoflagger-buildfix.patch b/aoflagger-buildfix.patch
index 28d6068a2aa7e1a068f4b8732dc276d693a0f4b7..3ba3cd0c1e1103b65679e93c674b2ef79f2aa00f 100644
--- a/aoflagger-buildfix.patch
+++ b/aoflagger-buildfix.patch
@@ -1,8 +1,56 @@
+diff --git a/CMake/FindCasacore.cmake b/CMake/FindCasacore.cmake
+index e4689f7..9068fdd 100644
+--- a/CMake/FindCasacore.cmake
++++ b/CMake/FindCasacore.cmake
+@@ -17,6 +17,8 @@
+ #
+ # Variables used by this module:
+ # CASACORE_ROOT_DIR - Casacore root directory.
++# BLAS_LIBS - override BLAS library
++# LAPACK_LIBS - override LAPACK library
+ #
+ # Variables defined by this module:
+ # CASACORE_FOUND - System has Casacore, which means that the
+@@ -232,7 +234,21 @@ else(NOT CASACORE_INCLUDE_DIR)
+ elseif(${_comp} STREQUAL fits)
+ casacore_find_package(CFITSIO REQUIRED)
+ elseif(${_comp} STREQUAL scimath_f)
+- casacore_find_package(LAPACK REQUIRED)
++ # If only looking for LAPACK, no library will be added if LAPACK
++ # is part of BLAS, as it is customary nowadays. So look for both
++ # to avoid confusing linker errors on symbols used in headers/templates.
++ if(DEFINED ENV{BLAS_LIBS})
++ set(BLAS_FOUND YES)
++ list(APPEND CASACORE_LIBRARIES $ENV{BLAS_LIBS})
++ else()
++ casacore_find_package(BLAS REQUIRED)
++ endif()
++ if(DEFINED ENV{LAPACK_LIBS})
++ set(LAPACK_FOUND YES)
++ list(APPEND CASACORE_LIBRARIES $ENV{LAPACK_LIBS})
++ else()
++ casacore_find_package(LAPACK REQUIRED)
++ endif()
+ endif(${_comp} STREQUAL casa)
+ endforeach(_comp ${_find_components})
+ endif(NOT CASACORE_INCLUDE_DIR)
diff --git a/CMakeLists.txt b/CMakeLists.txt
-index fd1d7c7..777a05e 100644
+index fd1d7c7..4dd733c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -25,18 +25,35 @@ find_path(GSL_INCLUDE_DIR NAMES gsl/gsl_version.h)
+@@ -19,27 +19,61 @@ find_package(CFITSIO REQUIRED)
+ find_path(FFTW3_INCLUDE_DIR NAMES fftw3.h)
+
+ find_library(GSL_LIB NAMES gsl)
+-find_library(GSL_CBLAS_LIB NAMES gslcblas)
++if(DEFINED ENV{CBLAS_LIBS})
++ message(STATUS "Using CBLAS_LIBS from environment: $ENV{CBLAS_LIBS}")
++ set(GSL_CBLAS_LIB $ENV{CBLAS_LIBS})
++else()
++ find_library(GSL_CBLAS_LIB NAMES gslcblas)
++endif()
+ find_path(GSL_INCLUDE_DIR NAMES gsl/gsl_version.h)
+
find_package(Threads REQUIRED)
find_package(LibXml2 REQUIRED)
find_package(PNG REQUIRED)
@@ -44,9 +92,26 @@ index fd1d7c7..777a05e 100644
+# errors with missing symbols if not explicitly linking to fftw3_threads.
+find_library(FFTW3_THREADS_LIB fftw3_threads OPTIONAL)
enable_language(Fortran OPTIONAL)
- find_package(BLAS REQUIRED)
- find_package(LAPACK REQUIRED)
-@@ -53,7 +70,7 @@ include_directories(${FFTW3_INCLUDE_DIR})
+-find_package(BLAS REQUIRED)
+-find_package(LAPACK REQUIRED)
++if(DEFINED ENV{BLAS_LIBS})
++ message(STATUS "Using BLAS_LIBS from environment: $ENV{BLAS_LIBS}")
++ set(BLAS_FOUND YES)
++ set(BLAS_LIBRARIES $ENV{BLAS_LIBS})
++else()
++ find_package (BLAS REQUIRED)
++endif()
++if(DEFINED ENV{LAPACK_LIBS})
++ message(STATUS "Using LAPACK_LIBS from environment: $ENV{LAPACK_LIBS}")
++ set(LAPACK_FOUND YES)
++ set(LAPACK_LIBRARIES $ENV{LAPACK_LIBS})
++else()
++ find_package (LAPACK REQUIRED)
++endif()
+ if(CMAKE_SYSTEM_NAME MATCHES "Linux")
+ find_library(RT_LIBRARY rt)
+ # list(APPEND LOFAR_EXTRA_LIBRARIES ${RT_LIBRARY})
+@@ -53,7 +87,7 @@ include_directories(${FFTW3_INCLUDE_DIR})
if(GSL_INCLUDE_DIR)
include_directories(${GSL_INCLUDE_DIR})
endif(GSL_INCLUDE_DIR)
diff --git a/build_lofar.sh b/build_lofar.sh
new file mode 100644
index 0000000000000000000000000000000000000000..38388be422e37ee90090f65d506790c20d757c72
--- /dev/null
+++ b/build_lofar.sh
@@ -0,0 +1,695 @@
+#!/bin/bash
+
+mandatory_vars="\
+lofar_prefix Installation prefix to use. Packages are put into sub-directories of that.
+casacore_version Version of CASAcore.
+pycasa_version Version of CASAcore Python bindings.
+dysco_version Version of Dysco.
+pybdsf_version Version of PyBDSF.
+wsclean_version Version of WSClean.
+CC C compiler command to use.
+CXX C++ compiler command to use.
+FC Fortran compiler command to use.
+CFLAGS C compiler flags (maybe empty, but set).
+CXXFLAGS C++ compiler flags (maybe empty, but set).
+FCFLAGS Fortran compiler flags (maybe empty, but set).
+BLAS_LIBS Linker flags to get BLAS (e.g. -lopenblas).
+CBLAS_LIBS Linker flags to get CBLAS (e.g. -lcblas)
+LAPACK_LIBS Linker flags to get LAPACK (e.g. -lopenblas).
+"
+
+optional_vars="\
+MAKE_JOBS Number of parallel make jobs to run.
+LIBRARY_PATH Path list for link-time library search.
+LD_RUN_PATH Path for run-time library search path fixed at build time.
+CPATH Path list for C/C++ include file search.
+idg_mkl Passed on to idg BUILD_WITH_MKL
+"
+
+config=$0.config
+
+if ! test -e "$config"; then
+ cat <<EOT
+
+HALTIS - Hamburg LOFAR Toolbox Installation Script
+
+Please create/link an appropriate config script named
+
+ $config
+
+. It should load the correct environment for the site, possibly
+using environment modules or just setting variables for paths
+and compilers directly. It also has to set up PATH so that the
+desired python interpreter is directly available as the command
+python (symlinks/wrappers to call python3 and python3-config should
+be enough). Furthermore, GNU Make is expected as make command,
+and the various dependencies are expected to be present, either
+in the base OS or in some additional environment you prepared.
+
+Uppercase variables may be exported, lowercase one should not.
+
+Mandatory variables:
+
+$mandatory_vars
+
+Optional variables:
+
+$optional_vars
+
+Essential variables are exportet by the build script. You
+should only export variables in addition to setting them if you
+really want their value to affect the builds via the environment
+(standard variables like PATH are expected to be exported already).
+
+EOT
+ exit 1
+fi
+
+
+echo "Loading $config ..."
+. "$config" || exit 1
+
+while read var help
+do
+ test -n "$var" || continue
+ echo "Checking mandatory variable $var ..."
+ is_set=$(eval printf %s "\${$var+set}")
+ val=$(eval printf %s "\$$var")
+ if test "$is_set" != set; then
+ echo "Mandatory variable $var is not set." >&2
+ exit 1
+ fi
+ if test -z "$val"; then
+ case "$var" in
+ *FLAGS) true ;;
+ *)
+ echo "Variable $var needs to be non-empty." >&2
+ exit 1
+ ;;
+ esac
+ fi
+done <<< "$mandatory_vars"
+
+case "$lofar_prefix" in
+/*)
+ echo "Good. Given prefix could be an absolute path."
+;;
+*)
+ echo "Please specify absolute LOFAR_PATH!" >&2
+ exit 1
+;;
+esac
+
+# ThOr: These functions emulare what proper environment modules would do.
+
+# Add all given paths to LD_RUN_PATH, staring from
+# the vanilla environment setting.
+# Also sync LIBRARY_PATH, as some seem to pick that up.
+use_prefix()
+{
+ if test -z "$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
+}
+
+# Write the command to be executed to a shell script for debugging
+# and run it. Some minimal quoting is attempted.
+store_and_run()
+{
+ local script=$1; shift
+ export > "$script.env"
+ cat <<EOT > "$script"
+#!$SHELL
+#
+# This reconstructs the central configuraton/build command.
+# To debug interactively, consider loading $script.env, too.
+#
+EOT
+ for n in "$@"
+ do
+ case "$n" in
+ *\'*)
+ echo "Really a command/argument with verbatim ' in it? $n" >&2
+ # This might be broken.
+ printf '%s\\\n' "\"$n\""
+ ;;
+ *[^[:alnum:]_-/:+,.]*|'')
+ printf '%s\\\n' "'$n'"
+ ;;
+ *) # hopefully safe
+ printf '%s\\\n' "$n"
+ ;;
+ esac
+ done >> "$script"
+ echo >> "$script"
+ "$@"
+}
+
+# Run cmake, with standard arguments.
+# One of those is PORTABLE=ON to avoid messing
+# with our provided compiler flags.
+run_cmake()
+{
+ store_and_run "$prefix/configure.sh" cmake \
+ -DCMAKE_C_COMPILER="$CC" \
+ -DCMAKE_CXX_COMPILER="$CXX" \
+ -DCMAKE_Fortran_COMPILER="$FC" \
+ -DCMAKE_C_FLAGS="$CFLAGS" \
+ -DCMAKE_CXX_FLAGS="$CXXFLAGS" \
+ -DCMAKE_Fortran_FLAGS="$FCFLAGS" \
+ -DCMAKE_SKIP_RPATH=ON \
+ -DPORTABLE=ON \
+ "$@"
+}
+
+# Take full version, like 1.2.3 and return git tag
+# name. Some have v1.2.3, some use v1.2.3 but v1.2
+# for 1.2.0.
+git_version_tag()
+{
+ local fullvers=$1 # 1.2.3
+ local mmvers=$(cut -f 1,2 -d . <<< "$1") # 1.2
+ local mvers=$(cut -f 1 -d . <<< "$1") # 1
+ for v in "$fullvers" "$mmvers" "$mvers"
+ do
+ if git tag | grep -q "^v$v\$"; then
+ printf "v%s\n" "$v"
+ return
+ fi
+ done
+}
+
+# ThOr: Locate a libray with provided linker
+# Arguments: name to grep for (libpng), then compiler/linker arguments.
+# Example: find_libfile libpng $(pkg-config --libs libpng) to return
+# /some/prefix/lib/libpng16.so.16
+find_libfile()
+{
+ local libname=$1; shift # Grep ldd output for that.
+ wrk=$(mktemp -d) &&
+ (
+ cd $wrk &&
+ echo 'int main(){ return 0; }' > test.c &&
+ g++ "$@" -o test.bin test.c &&
+ ldd test.bin | grep "$libname" | cut -f 3 -d ' '
+ )
+ rm -rf "$wrk"
+}
+
+begin_pkg()
+{
+ pkg=$1
+ echo "$(date) $pkg"
+ prefix="$lofar_prefix/$pkg"
+ mkdir -p "$prefix"
+}
+
+mkdir -p "$lofar_prefix" &&
+env_python_path=$PYTHON_PATH &&
+scriptdir=$(cd $(dirname $0) && pwd) &&
+config="$scriptdir/$(basename $config)" &&
+pyver=$(python --version | cut -f 2 -d ' ' | cut -f 1,2 -d .) &&
+test -n "$pyver" &&
+case "$pyver" in
+ 2.*)
+ build_python=ON
+ build_python3=OFF
+ ;;
+ 3.*)
+ build_python=OFF
+ build_python3=ON
+ ;;
+ *)
+ echo "There's another Python? Please check if I am OK with that."
+ exit 1
+ ;;
+esac
+# Ensure that we know what include search path variable is really used.
+# Only leave CPATH set.
+unset INCLUDE &&
+unset C_INCLUDE_PATH &&
+
+#########################################
+# Install main LOFAR software packages. #
+#########################################
+
+begin_pkg casacore
+if [ ! -e $prefix/.done ]; then
+ #
+ # Install CASAcore
+ #
+ echo Installing CASAcore... &&
+ cd $prefix &&
+ rm -rf bin build include lib presrc &&
+ if test -e src && test -e data; then
+ echo "Re-using existing sources."
+ else
+ rm -rf src data &&
+ git clone https://github.com/casacore/casacore.git presrc &&
+ if [ "${casacore_version}" != "latest" ]; then
+ ( cd presrc &&
+ git checkout tags/v${casacore_version} )
+ fi &&
+ echo "Patching build (for BLAS, Boost, Python, usually) ..." &&
+ (cd presrc && patch -Np1 < "$scriptdir/casacore-buildfix.patch" ) &&
+ mkdir data &&
+ ( cd data &&
+ wget --retry-connrefused \
+ ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar &&
+ tar xf WSRT_Measures.ztar ) &&
+ mv presrc src
+ fi &&
+ mkdir build &&
+ cd build &&
+ use_prefix $prefix &&
+ run_cmake \
+ -DCMAKE_BUILD_TYPE=Release \
+ -DCMAKE_INSTALL_PREFIX=$lofar_prefix/casacore \
+ -DDATA_DIR:PATH=$lofar_prefix/casacore/data \
+ -DENABLE_TABLELOCKING=OFF \
+ -DUSE_OPENMP=ON \
+ -DUSE_FFTW3=ON \
+ -DUSE_HDF5=ON \
+ -DBUILD_PYTHON=$build_python \
+ -DBUILD_PYTHON3=$build_python3 \
+ ../src/ &&
+ make -j $J &&
+ make install &&
+ echo Installed CASAcore. &&
+ touch $prefix/.done
+else
+ echo CASAcore already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg python-casacore
+pycasacorelib="$prefix/lib/python$pyver/site-packages"
+# ThOr: Subsequent builds might need that, so export it always here.
+export PYTHONPATH=$pycasacorelib:$PYTHONPATH
+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
+ cd $prefix &&
+ rm -rf lib bin src pre &&
+ if test -e src.tar.gz; then
+ # ThOr: Dunno how to clean, but we can extract archive to avoid re-dowload.
+ echo "Using archived sources." &&
+ tar -xf src.tar.gz
+ else
+ echo "Fresh download."
+ git clone https://github.com/casacore/python-casacore presrc &&
+ if [ "$pycasa_version" != "latest" ]; then
+ ( cd presrc && git checkout tags/v$pycasa_version )
+ fi &&
+ mv presrc src &&
+ 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 $lofar_prefix/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) $LDFLAGS" \
+ store_and_run "$prefix/install.sh" \
+ python setup.py build_ext --swig-opts=-c++ \
+ -I$lofar_prefix/casacore/include -L$lofar_prefix/casacore/lib \
+ install --prefix $prefix &&
+ echo Installed Python CASAcore. &&
+ touch $prefix/.done
+else
+ echo Python-CASAcore already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg dysco
+if [ ! -e $prefix/.done ]; then
+ #
+ # Install Dysco
+ #
+ echo Installing Dysco...
+ cd $prefix &&
+ rm -rf lib bin build presrc &&
+ if [ -e src ]; then
+ echo "Using existing source."
+ else
+ git clone https://github.com/aroffringa/dysco.git presrc &&
+ if [ "$dysco_version" != "latest" ]; then
+ ( cd presrc &&
+ git checkout tags/"$(git_version_tag "$dysco_version")" )
+ fi &&
+ echo "Patching build (for BLAS, Boost, Python, usually) ..." &&
+ (cd presrc && patch -Np1 < "$scriptdir/dysco-buildfix.patch" ) &&
+ mv presrc src
+ fi &&
+ mkdir build &&
+ cd build &&
+ use_prefix $lofar_prefix/casacore $prefix &&
+ run_cmake \
+ -DCMAKE_INSTALL_PREFIX=$prefix \
+ -DCASACORE_ROOT_DIR=$lofar_prefix/casacore \
+ ../src &&
+ make -j $J &&
+ make install &&
+ echo Installed Dysco. &&
+ touch $prefix/.done
+else
+ echo Dysco already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg aoflagger
+if [ ! -e $prefix/.done ]; then
+ echo "Installing aoflagger..."
+ #
+ # Install-aoflagger
+ #
+ cd $prefix &&
+ rm -rf build bin lib presrc&&
+ if [ -e src ]; then
+ echo "Using existing sources."
+ else
+ git clone git://git.code.sf.net/p/aoflagger/code presrc
+ if [ "$aoflagger_version" != "latest" ]; then
+ ( cd presrc && git checkout tags/v$aoflagger_version )
+ fi &&
+ echo "Patching build (for BLAS, Boost, Python, usually) ..." &&
+ (cd presrc && patch -Np1 < "$scriptdir/aoflagger-buildfix.patch" ) &&
+ 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 $lofar_prefix/casacore $prefix &&
+ run_cmake \
+ -DCASACORE_ROOT_DIR=$lofar_prefix/casacore \
+ -DCMAKE_INSTALL_PREFIX=$prefix \
+ -DPNG_LIBRARY_RELEASE:FILEPATH="$(find_libfile libpng $(pkg-config --libs libpng))" \
+ -DBUILD_SHARED_LIBS=ON \
+ ../src &&
+ make -j $J &&
+ make install &&
+ echo "Done with aoflagger." &&
+ touch $prefix/.done
+else
+ echo AOFlagger already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg LOFARBeam
+if [ ! -e $prefix/.done ]; then
+ #
+ # Install the standalone StationResponse libraries.
+ #
+ echo Installing LOFARBeam...
+ cd $prefix &&
+ rm -rf build bin lib presrc &&
+ if [ -e src ]; then
+ echo "Using existing sources."
+ else
+ git clone https://github.com/lofar-astron/LOFARBeam.git presrc
+ echo "Patching build (for BLAS, Boost, Python, usually) ..." &&
+ (cd presrc && patch -Np1 < "$scriptdir/LOFARBeam-buildfix.patch" ) &&
+ mv presrc src
+ fi &&
+ mkdir build &&
+ cd build &&
+ use_prefix $lofar_prefix/casacore $prefix &&
+ run_cmake \
+ -DCASACORE_ROOT_DIR=$lofar_prefix/casacore \
+ -DCMAKE_INSTALL_PREFIX=$prefix \
+ ../src &&
+ make -j $J &&
+ make install &&
+ echo Done with LOFARBeam. &&
+ touch $prefix/.done
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg idg
+if [ ! -e $prefix/.done ]; then
+ #
+ # Install the Image Domain Gridder (IDG).
+ #
+ echo Installing IDG.
+ mkdir -p $prefix &&
+ cd $prefix &&
+ rm -rf bin lib presrc build &&
+ if test -d src; then
+ echo "Using existing source."
+ else
+ git clone https://gitlab.com/astron-idg/idg.git presrc &&
+ echo "Patching build (for BLAS, Boost, Python, usually) ..." &&
+ (cd presrc && patch -Np1 < "$scriptdir/idg-buildfix.patch" ) &&
+ mv presrc src
+ fi &&
+ mkdir build &&
+ cd build &&
+ use_prefix $prefix &&
+ # ThOr: The FindMKL included (two copies!) tries to locate libmkl_rt and
+ # sets paths from that one. Uses MKL_LIB as environment hint.
+ MKL_LIB=$LD_RUN_PATH run_cmake \
+ -DCMAKE_INSTALL_PREFIX=$prefix \
+ -DBUILD_WITH_MKL=${idg_mkl:-OFF} \
+ -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 &&
+ echo "Done with IDG." &&
+ touch $prefix/.done
+else
+ echo IDG already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg DP3
+export "PYTHONPATH=$prefix/lib/python$pyver:$PYTHONPATH" &&
+if [ ! -e $prefix/.done ]; then
+ echo Installing DP3...
+ #
+ # Install DP3.
+ #
+ cd $prefix &&
+ rm -rf build bin lib presrc &&
+ if test -e src; then
+ echo "Using existing sources."
+ else
+ git clone https://github.com/lofar-astron/DP3.git presrc &&
+ echo "Patching build (for BLAS, Boost, Python, usually) ..." &&
+ (cd presrc && patch -Np1 < "$scriptdir/DP3-buildfix.patch" ) &&
+ mv presrc src
+ fi &&
+ mkdir build &&
+ cd build &&
+ use_prefix \
+ $lofar_prefix/casacore \
+ $lofar_prefix/idg \
+ $lofar_prefix/LOFARBeam \
+ $lofar_prefix/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=$lofar_prefix/casacore \
+ -DIDGAPI_INCLUDE_DIRS:PATH=$lofar_prefix/idg/include \
+ -DIDGAPI_LIBRARIES:PATH=$lofar_prefix/idg/lib/libidg-api.so \
+ -DLOFAR_STATION_RESPONSE_DIR:PATH=$lofar_prefix/LOFARBeam/include \
+ -DLOFAR_STATION_RESPONSE_LIB=$lofar_prefix/LOFARBeam/lib/libstationresponse.so \
+ -DAOFLAGGER_INCLUDE_DIR=$lofar_prefix/aoflagger/include \
+ -DAOFLAGGER_LIB=$lofar_prefix/aoflagger/lib/libaoflagger.so \
+ ../src &&
+ make -j $J &&
+ make install &&
+ echo Installed DP3. &&
+ touch $prefix/.done
+else
+ echo DP3 already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg wsclean
+if [ ! -e $prefix/.done ]; then
+ #
+ # Install WSClean
+ #
+ # Sometimes there are FFT to update by hand in CMakeCache.txt
+ # ThOr: Please no! ;-)
+ echo Installing WSClean.
+ cd $prefix &&
+ rm -rf build bin lib presrc &&
+ if test -e src; then
+ echo "Using existing sources."
+ else
+ if [ "$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 $lofar_prefix/casacore $lofar_prefix/LOFARBeam $lofar_prefix/idg &&
+ LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS" run_cmake \
+ -DCMAKE_INSTALL_PREFIX=$prefix \
+ -DCASACORE_ROOT_DIR=$lofar_prefix/casacore \
+ -DIDGAPI_INCLUDE_DIRS=$lofar_prefix/idg/include \
+ -DIDGAPI_LIBRARIES=$lofar_prefix/idg/lib/libidg-api.so \
+ -DLOFAR_STATION_RESPONSE_INCLUDE_DIR=$lofar_prefix/LOFARBeam/include \
+ -DLOFAR_STATION_RESPONSE_LIB=$lofar_prefix/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/build.log" 2>&1 || exit 1
+
+begin_pkg pyBDSF
+pybdsflib="$prefix/lib/python$pyver/site-packages"
+export PYTHONPATH=$pybdsflib:$PYTHONPATH &&
+if [ ! -e $prefix/.done ]; then
+ echo Installing pyBDSF.
+ #
+ # Install pyBDSF.
+ #
+ cd $prefix &&
+ rm -rf build bin lib presrc &&
+ if test -e src; then
+ echo "Using existing sources."
+ else
+ git clone https://github.com/lofar-astron/PyBDSF presrc &&
+ if [ "$pybdsf_version" != "latest" ]; then
+ ( cd presrc && git checkout "tags/v$pybdsf_version" )
+ fi &&
+ mv presrc src
+ fi &&
+ mkdir -p $pybdsflib &&
+ cd src &&
+ LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS" \
+ NPY_DISTUTILS_APPEND_FLAGS=1 \
+ store_and_run "$prefix/install.sh" \
+ python setup.py install --prefix=$prefix &&
+ echo "Done with pyBDSF." &&
+ touch $prefix/.done
+else
+ echo pyBDSF already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+begin_pkg lsmtool
+lsmlib="$prefix/lib/python$pyver/site-packages" &&
+export PYTHONPATH=$lsmlib:$PYTHONPATH &&
+if [ ! -e $prefix/.done ]; then
+ echo Installing LSMTool.
+ #
+ # Install LSMTool.
+ #
+ cd $prefix &&
+ rm -rf build bin lib presrc &&
+ if test -e src; then
+ echo "Using existing sources."
+ else
+ git clone https://github.com/darafferty/LSMTool.git presrc &&
+ mv presrc src
+ fi &&
+ mkdir -p $lsmlib &&
+ cd src &&
+ store_and_run "$prefix/install.sh" \
+ python setup.py install --prefix=$prefix &&
+ echo "Done with LSMTool." &&
+ touch $prefix/.done
+else
+ echo LSMTool already installed.
+fi >> "$prefix/build.log" 2>&1 || exit 1
+
+echo "$(date) done with packages"
+
+###############################
+# Finish up the installation. #
+###############################
+
+echo
+echo "Installation directory contents:"
+ls ${INSTALLDIR}
+
+# Use the same environment used to building.
+
+print_init()
+{
+ cat <<EOT
+# LOFAR Tools built by $USER\@$(hostname) on $(date)
+#
+# Sourcing this script shall re-create the build environment and
+# add things from the LOFAR prefix to appropriate path variables.
+# It does _not_ set LD_LIBRARY_PATH, as a proper build should use
+# RPATH in the binaries. But there is LD_RUN_PATH / LIBRARY_PATH
+# set for link-time usage. You can set LD_LIBRARY_PATH=\$LD_RUN_PATH
+# as a hack if some binary fails to find its libs. But this would
+# be a bug in the build script that should be fixed properly.
+#
+# Step 1: The build config with all variables used.
+#
+EOT
+ cat $config
+cat <<EOT
+#
+# Step 2: Paths to LOFAR tools in the prefix.
+#
+EOT
+ for p in lsmtool pyBDSF wsclean dysco DP3\
+ idg aoflagger python-casacore casacore
+ do
+ echo "# $p"
+ pp="$lofar_prefix/$p"
+ test -d "$pp/bin" &&
+ echo "export PATH=\"\$lofar_prefix/$p/bin:\$PATH\""
+ test -d "$pp/lib" &&
+ cat <<EOT
+export LD_RUN_PATH=\"\$lofar_prefix/$p/lib:\$LD_RUN_PATH\"
+export LIBRARY_PATH\"\$lofar_prefix/$p/lib:\$LIBRARY_PATH\"
+EOT
+ test -d "$pp/include" &&
+ echo "export CPATH=\"\$lofar_prefix/$p/include:\$CPATH\""
+ pylib="$p/lib/python$pyver/site-packages"
+ test -d "$lofar_prefix/$pylib" &&
+ echo "export PYTHONPATH=\"\$lofar_prefix/$pylib:\$PYTHONPATH\""
+ done
+}
+
+print_init > "$lofar_prefix/init.sh" &&
+echo "Finished installation. You can source $lofar_prefix/init.sh and run."
diff --git a/build_lofar.sh.config.rrz b/build_lofar.sh.config.rrz
new file mode 100644
index 0000000000000000000000000000000000000000..06c92ce091f8adbe3cea546e908c12478b6e5a9b
--- /dev/null
+++ b/build_lofar.sh.config.rrz
@@ -0,0 +1,37 @@
+# The setup on the Hamburg LOFAR GPU Cluster.
+
+lofar_prefix=$1 # Give installation directory as first argument.
+aoflagger_version=2.14.0
+casacore_version=latest
+dysco_version=1.2.0
+pybdsf_version=latest # weird C++ template error with 1.8.12
+pycasa_version=3.1.1
+wsclean_version=latest
+
+# This gives us CUDA, gcc, Open MPI and dependencies
+# from pkgsrc in separate prefixes.
+
+. /sw/profile/init.sh
+module switch env env/2019Q4-cuda-gcc-openmpi
+module load pythonversion/3
+# You could experiment with idg using MKL, but it is recommened
+# to try a consistent environment where everyone agrees on using
+# MKL for BLAS/LAPACK, too.
+#module load mkl/2020.0.166
+#idg_mkl=ON
+
+make_jobs=64
+
+export CC=gcc
+export CXX=g++
+export FC=gfortran
+export CFLAGS="-march=native -O3 -fno-math-errno -ftree-vectorize"
+export FCFLAGS="$CFLAGS"
+export CXXFLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS $CFLAGS"
+# This should match what BLAS is used in the dependencies.
+# If you venture to link statically, you might have to include
+# BLAS_LIBS in LAPACK_LIBS, same for CBLAS, LAPACKE.
+export BLAS_LIBS=$RRZ_BLAS_LIBS # from the env/ module
+export CBLAS_LIBS=$RRZ_CBLAS_LIBS # from the env/ module
+export LAPACK_LIBS=$RRZ_LAPACK_LIBS # from the env/ module
+export LAPACKE_LIBS=$RRZ_LAPACKE_LIBS # from the env/ modules
diff --git a/build_lofar_cepH.sh b/build_lofar_cepH.sh
deleted file mode 100644
index c812e17657dabf6cdbf35ca13d89562c8099621d..0000000000000000000000000000000000000000
--- a/build_lofar_cepH.sh
+++ /dev/null
@@ -1,536 +0,0 @@
-#!/bin/bash
-
-# General environment settings.
-. /sw/profile/init.sh
-module switch env env/2019Q4-cuda-gcc-openmpi
-# ThOr: This provides python and python-config pointing
-# to current python3 and python3-config.
-module load pythonversion/3
-
-echo "TODO: Ensure conistent use of one openblas variant (the one cblas and numpy use)"
-
-# ThOr: Maybe not even necessary, at least with cmake builds.
-#export LDFLAGS="$(rrz-build-linkpath -R) $LDFLAGS"
-
-export J=64
-# ThOr: Use command line argument for the prefix to ease testing.
-# Not all variables shall be exported to children!
-scriptdir=$(cd $(dirname $0) && pwd)
-INSTALLDIR=${1:-$HOME/opt/lofar_200318}
-# ThOr: I hate to hardcode things that can be fetched automatically.
-# This takes whatever python is linked to python3.
-PYTHON_VERSION=$(python3 --version | cut -f 2 -d ' ' | cut -f 1,2 -d .)
-PYTHON_VERSION_NODOT=$(echo $PYTHON_VERSION|tr -d .)
-export CC=`which gcc`
-export CXX=`which g++`
-# ThOr: Fortran is at least checked for by some builds.
-export FC=`which gfortran`
-# ThOr: removed C++-specific defines from CFLAGS
-export CFLAGS="-march=native -O3 -fno-math-errno -ftree-vectorize"
-export FCFLAGS="$CFLAGS"
-export CXXFLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS -march=native -O3 -fno-math-errno -ftree-vectorize"
-# ThOr: Those should not be global, should they? Let's add -Wl,--as-needed,
-# 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=$HOME/opt/src/patch_python-casacore.patch
-#export PATCH_AOFLAGGER=/net/lofar1/data1/sweijen/software/LOFAR/aoflagger.patch
-
-# Settings relevant to the installed software.
-# ThOr: I recommend settling on with or without v and add the v on git
-# command instead.
-export AOFLAGGER_VERSION=v2.14.0
-export BOOST_DOT_VERSION=1.67.0
-export BOOST_VERSION=1_67_0
-export CASACORE_VERSION=latest
-export CFITSIO_VERSION=3.47
-export DYSCO_VERSION=v1.2.0
-export FFTW_VERSION=3.3.8
-export HDF5_VERSION=1.8.21
-export PYBDSF_VERSION=v1.8.12
-export PYTHON_CASACORE_VERSION=3.1.1
-export WSCLEAN_VERSION=latest
-export WCSLIB_VERSION=latest
-
-# ThOr: These functions emulare what proper environment modules would do.
-
-# Add all given paths to LD_RUN_PATH, staring from
-# the vanilla environment setting.
-# Also sync LIBRARY_PATH, as some seem to pick that up.
-use_prefix()
-{
- if test -z "$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 $LDFLAGS"
- done
-}
-
-# ThOr: Run cmake, with standard arguments.
-run_cmake()
-{
- cmake \
- -DCMAKE_C_COMPILER="$CC" \
- -DCMAKE_CXX_COMPILER="$CXX" \
- -DCMAKE_Fortran_COMPILER="$FC" \
- -DCMAKE_C_FLAGS="$CFLAGS" \
- -DCMAKE_CXX_FLAGS="$CXXFLAGS" \
- -DCMAKE_Fortran_FLAGS="$FCFLAGS" \
- -DCMAKE_SKIP_RPATH=ON \
- "$@"
-}
-
-# ThOr: Locate a libray with provided linker
-# Arguments: name to grep for (libpng), then compiler/linker arguments.
-# Example: find_libfile libpng $(pkg-config --libs libpng) to return
-# /some/prefix/lib/libpng16.so.16
-find_libfile()
-{
- local libname=$1; shift # Grep ldd output for that.
- wrk=$(mktemp -d) &&
- (
- cd $wrk &&
- echo 'int main(){ return 0; }' > test.c &&
- g++ "$@" -o test.bin test.c &&
- ldd test.bin | grep "$libname" | cut -f 3 -d ' '
- )
- rm -rf "$wrk"
-}
-
-mkdir -p $INSTALLDIR
-
-# ThOr: We got the external libs covered vi pkgsrc.
-# Only need to care for the LOFAR code.
-
-#########################################
-# Install main LOFAR software packages. #
-#########################################
-
-if [ ! -e $INSTALLDIR/casacore/.done ]; then
- #
- # Install CASAcore
- #
- echo Installing CASAcore... &&
- mkdir -p $INSTALLDIR/casacore &&
- cd $INSTALLDIR/casacore &&
- rm -rf bin lib &&
- if test -e src && test -e data; then
- echo "Re-using existing sources."
- else
- rm -rf src build data &&
- mkdir -p build data &&
- git clone https://github.com/casacore/casacore.git src &&
- if [ "${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 [ ! -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 -p $prefix &&
- cd $prefix &&
- rm -rf lib bin src &&
- if test -e src.tar.gz; then
- # ThOr: Dunno how to clean, but we can extract archive to avoid re-dowload.
- echo "Using archived sources."
- tar -xf src.tar.gz
- else
- echo "Fresh download."
- git clone https://github.com/casacore/python-casacore src &&
- if [ "$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 $prefix/.done
-else
- echo Python-CASAcore already installed.
-fi || exit 1
-
-prefix=$INSTALLDIR/dysco
-if [ ! -e $prefix/.done ]; then
- #
- # Install Dysco
- #
- echo Installing Dysco...
- mkdir -p $prefix &&
- cd $prefix &&
- rm -rf lib bin build &&
- if [ -e src ]; then
- echo "Using existing source."
- 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 $prefix/.done
-else
- echo Dysco already installed.
-fi || exit 1
-
-prefix=$INSTALLDIR/aoflagger
-if [ ! -e $prefix/.done ]; then
- echo "Installing aoflagger..."
- #
- # Install-aoflagger
- #
- mkdir -p $prefix &&
- cd $prefix &&
- rm -rf build bin lib presrc&&
- if [ -e src ]; then
- echo "Using existing sources."
- else
- git clone git://git.code.sf.net/p/aoflagger/code presrc
- if [ "${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 [ ! -e $prefix/.done ]; then
- #
- # Install the standalone StationResponse libraries.
- #
- echo Installing LOFARBeam...
- mkdir -p $prefix &&
- cd $prefix &&
- rm -rf build bin lib presrc &&
- if [ -e src ]; then
- echo "Using existing sources."
- else
- git clone https://github.com/lofar-astron/LOFARBeam.git presrc
- if ! [ grep -q Boost:: presrc/CMakeLists.txt ]; then
- echo "Patching LOFARBeam, mainly for Boost::python"
- (cd presrc && patch -Np1 < "$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 $prefix/.done
-fi || exit 1
-
-prefix=$INSTALLDIR/idg
-if [ ! -e $prefix/.done ]; then
- #
- # Install the Image Domain Gridder (IDG).
- #
- echo Installing IDG.
- mkdir -p $prefix &&
- cd $prefix &&
- rm -rf bin lib presrc build &&
- if test -d src; then
- 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 $prefix/.done
-else
- echo IDG already installed.
-fi || exit 1
-
-prefix=$INSTALLDIR/DP3
-if [ ! -e $prefix/.done ]; then
- echo Installing DP3...
- #
- # Install DP3.
- #
- mkdir -p $prefix
- cd $prefix
- rm -rf build bin lib presrc &&
- if test -e src; then
- echo "Using existing sources."
- else
- git clone https://github.com/lofar-astron/DP3.git presrc &&
- if ! [ grep -q Boost::python presrc/src/CMakeLists.txt ]; then
- echo "Patching build, mainly for Boost::python"
- (cd presrc && patch -Np1 < "$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 \
- -DLOFAR_STATION_RESPONSE_LIB=$INSTALLDIR/LOFARBeam/lib/libstationresponse.so \
- -DAOFLAGGER_INCLUDE_DIR=$INSTALLDIR/aoflagger/include \
- -DAOFLAGGER_LIB=$INSTALLDIR/aoflagger/lib/libaoflagger.so \
- ../src &&
- make -j $J &&
- make install &&
- echo Installed DP3. &&
- touch $prefix/.done
-else
- echo DP3 already installed.
-fi || exit 1
-
-prefix=$INSTALLDIR/wsclean
-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 $prefix &&
- cd $prefix &&
- rm -rf build bin lib presrc &&
- if test -e src; then
- echo "Using existing sources."
- else
- if [ "$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 $prefix/.done
-else
- echo WSClean already installed.
-fi || exit 1
-
-prefix=$INSTALLDIR/pyBDSF &&
-pybdsflib=$prefix/lib/python$PYTHON_VERSION/site-packages
-export PYTHONPATH=$pybdsflib:$PYTHONPATH &&
-if [ ! -e $prefix/.done ]; then
- echo Installing pyBDSF.
- #
- # Install pyBDSF.
- #
- mkdir -p $prefix &&
- cd $prefix &&
- rm -rf build bin lib presrc &&
- if test -e src; then
- 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 $prefix/.done
-else
- echo pyBDSF already installed.
-fi || exit 1
-
-prefix=$INSTALLDIR/lsmtool &&
-lsmlib=$prefix/lib/python$PYTHON_VERSION/site-packages &&
-export PYTHONPATH=$lsmlib:$PYTHONPATH &&
-if [ ! -e $prefix/.done ]; then
- echo Installing LSMTool.
- #
- # Install LSMTool.
- #
- mkdir -p $prefix &&
- cd $prefix &&
- rm -rf build bin lib presrc &&
- if test -e src; then
- echo "Using existing sources."
- else
- git clone https://github.com/darafferty/LSMTool.git presrc &&
- mv presrc src
- fi &&
- mkdir -p $lsmlib &&
- cd src &&
- python setup.py install --prefix=$prefix &&
- echo "Done with LSMTool." &&
- touch $prefix/.done
-else
- echo LSMTool already installed.
-fi || exit 1
-
-###############################
-# Finish up the installation. #
-###############################
-echo "Installation directory contents:"
-ls ${INSTALLDIR}
-#
-# init-lofar
-#
-echo export INSTALLDIR=$INSTALLDIR > $INSTALLDIR/init.sh
-
-echo export PYTHONPATH=\$INSTALLDIR/python-casacore/lib/python${PYTHON_VERSION}/site-packages/:\$INSTALLDIR/DP3/lib/python${PYTHON_VERSION}/site-packages/:\$INSTALLDIR/pyBDSF/lib/python$PYTHON_VERSION/site-packages:\$PYTHONPATH >> $INSTALLDIR/init.sh
-echo export PATH=\$INSTALLDIR/aoflagger/bin:\$PATH >> $INSTALLDIR/init.sh
-echo export PATH=\$INSTALLDIR/casacore/bin:\$PATH >> $INSTALLDIR/init.sh
-echo export PATH=\$INSTALLDIR/DP3/bin:\$PATH >> $INSTALLDIR/init.sh
-echo export PATH=\$INSTALLDIR/dysco/bin:\$PATH >> $INSTALLDIR/init.sh
-echo export PATH=\$INSTALLDIR/wsclean/bin:\$PATH >> $INSTALLDIR/init.sh
-echo export PATH=\$INSTALLDIR/pyBDSF/bin:\$PATH >> $INSTALLDIR/init.sh
-echo export LD_LIBRARY_PATH=\$INSTALLDIR/aoflagger/lib:\$INSTALLDIR/casacore/lib:\$INSTALLDIR/DP3/lib:\$INSTALLDIR/dysco/lib:\$INSTALLDIR/idg/lib:\$INSTALLDIR/LOFARBeam/lib:\$LD_LIBRARY_PATH >> $INSTALLDIR/init.sh
diff --git a/casacore-buildfix.patch b/casacore-buildfix.patch
new file mode 100644
index 0000000000000000000000000000000000000000..63c4e698e45830fecb25d2ee82f8ebdc6f591f7a
--- /dev/null
+++ b/casacore-buildfix.patch
@@ -0,0 +1,25 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0801faacd..96d23e77b 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -344,8 +344,18 @@ if (_usebison STREQUAL YES)
+ find_package (BISON REQUIRED)
+ endif (_usebison STREQUAL YES)
+ if (_uselapack STREQUAL YES)
+- find_package (BLAS REQUIRED)
+- find_package (LAPACK REQUIRED)
++ if(DEFINED ENV{BLAS_LIBS})
++ set(BLAS_FOUND YES)
++ set(BLAS_LIBRARIES $ENV{BLAS_LIBS})
++ else()
++ find_package (BLAS REQUIRED)
++ endif()
++ if(DEFINED ENV{LAPACK_LIBS})
++ set(LAPACK_FOUND YES)
++ set(LAPACK_LIBRARIES $ENV{LAPACK_LIBS})
++ else()
++ find_package (LAPACK REQUIRED)
++ endif()
+ if (USE_FFTW3)
+ if (FFTW3_DISABLE_THREADS)
+ find_package (FFTW3 COMPONENTS single double REQUIRED)
diff --git a/dysco-buildfix.patch b/dysco-buildfix.patch
new file mode 100644
index 0000000000000000000000000000000000000000..ca8cfef69be73c2c82842197e0e518078da72c0e
--- /dev/null
+++ b/dysco-buildfix.patch
@@ -0,0 +1,18 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 35bc9e8..d9bdd1b 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -10,7 +10,12 @@ find_package(Casacore REQUIRED COMPONENTS casa ms tables measures)
+
+ find_library(GSL_LIB NAMES gsl)
+ find_path(GSL_INCLUDE_DIR NAMES gsl/gsl_version.h)
+-find_library(GSL_CBLAS_LIB NAMES gslcblas)
++if(DEFINED ENV{CBLAS_LIBS})
++ message(STATUS "Using CBLAS_LIBS from environment: $ENV{CBLAS_LIBS}")
++ set(GSL_CBLAS_LIB $ENV{CBLAS_LIBS})
++else()
++ find_library(GSL_CBLAS_LIB NAMES gslcblas)
++endif()
+
+ find_package(Threads REQUIRED)
+
diff --git a/idg-buildfix.patch b/idg-buildfix.patch
new file mode 100644
index 0000000000000000000000000000000000000000..4bcc0e8d35a8f9db1de1ffb9948e0b1edc530888
--- /dev/null
+++ b/idg-buildfix.patch
@@ -0,0 +1,20 @@
+diff --git a/idg-api/CMakeLists.txt b/idg-api/CMakeLists.txt
+index 16babb07..6d7f6ac4 100644
+--- a/idg-api/CMakeLists.txt
++++ b/idg-api/CMakeLists.txt
+@@ -72,7 +72,14 @@ if (BUILD_WITH_MKL AND (${MKL_FOUND}))
+ else()
+ # Fallback to LAPACK libraries
+ # Use LAPACK headers
+- find_package(LAPACK REQUIRED)
++ # One could try to also use underlying BLAS explicitly, to be
++ # safe. Usually, LAPACK is included in the same lib anyway, though.
++ if(DEFINED ENV{LAPACK_LIBS})
++ set(LAPACK_FOUND YES)
++ set(LAPACK_LIBRARIES $ENV{LAPACK_LIBS})
++ else()
++ find_package (LAPACK REQUIRED)
++ endif()
+
+ set (${PROJECT_NAME}_link_libraries
+ ${IDG_LIBRARY}