fix: rewrite part of the build system,so that paths are not linked to…

… build directories.

Signed-off-by: Franz R. Sattler <[email protected]>

DiFfRG/cmake/install_bundled.cmake

@@ -1,17 +1,4 @@
-set(BUNDLE_DIR ${CMAKE_SOURCE_DIR}/../external)
-
-install(DIRECTORY ${BUNDLE_DIR}/autodiff_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/Catch2_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/dealii_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/kokkos_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/rapidcsv DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/rmm_build DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/spdlog_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/sundials_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/eigen_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/boost_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/qmc_install DESTINATION bundled MESSAGE_NEVER)
-install(DIRECTORY ${BUNDLE_DIR}/thread-pool_install DESTINATION bundled MESSAGE_NEVER)
+cmake_policy(SET CMP0177 NEW)
 
 install(DIRECTORY ${CMAKE_SOURCE_DIR}/../python DESTINATION ./ MESSAGE_NEVER)
 install(DIRECTORY ${CMAKE_SOURCE_DIR}/../Mathematica DESTINATION ./ MESSAGE_NEVER)

DiFfRG/cmake/setup_build_system.cmake

@@ -4,7 +4,9 @@
 
 if(${CMAKE_PROJECT_NAME} STREQUAL "DiFfRG")
   set(BASE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
-  set(BUNDLED_DIR ${BASE_DIR}/../external)
+  if (NOT DEFINED BUNDLED_DIR)
+    set(BUNDLED_DIR ${BASE_DIR}/../external)
+  endif()
 else()
   set(BASE_DIR ${DiFfRG_BASE_DIR})
   set(BUNDLED_DIR ${BASE_DIR}/bundled)
@@ -42,10 +44,12 @@ link_libraries(TBB::tbb)
 find_package(OpenMP REQUIRED)
 link_libraries(OpenMP::OpenMP_CXX)
 
-find_package(Boost 1.80 REQUIRED HINTS ${BUNDLED_DIR}/boost_install)
+find_package(Boost 1.80 REQUIRED HINTS ${BUNDLED_DIR}/boost_install COMPONENTS thread random iostreams math serialization system)
 message(STATUS "Boost version: ${Boost_VERSION}")
 message(STATUS "Boost include dir: ${Boost_INCLUDE_DIRS}")
+message(STATUS "Boost libraries: ${Boost_LIBRARIES}")
 include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
+link_libraries(${Boost_LIBRARIES})
 
 find_package(autodiff REQUIRED PATHS ${BUNDLED_DIR}/autodiff_install)
 link_libraries(autodiff::autodiff)
@@ -61,7 +65,7 @@ link_libraries(GSL::gsl)
 message(STATUS "GSL include dir: ${GSL_INCLUDE_DIR}")
 include_directories(SYSTEM ${GSL_INCLUDE_DIR}) 
 
-include_directories(SYSTEM ${BUNDLED_DIR}/rapidcsv/src)
+include_directories(SYSTEM ${BUNDLED_DIR}/rapidcsv_install/include)
 include_directories(SYSTEM ${BUNDLED_DIR}/qmc_install)
 include_directories(SYSTEM ${BUNDLED_DIR}/thread-pool_install/include)
 

Dockerfile

@@ -16,7 +16,8 @@ RUN dnf --enablerepo=devel install -y gcc-toolset-12 cmake git openblas-devel do
 RUN git reset --hard
 RUN cat config_docker >config
 SHELL [ "/usr/bin/scl", "enable", "gcc-toolset-12"]
-RUN bash -i build.sh -j $threads -f $cuda -i /opt/DiFfRG
+RUN bash -i build.sh -j $threads -f $cuda -i DiFfRG_install &> build.log
+RUN ln -s /DiFfRG/DiFfRG_install /opt/DiFfRG
 
 # run the command
 CMD ["scl", "enable", "gcc-toolset-12", "bash"]

build.sh

@@ -47,65 +47,52 @@ source config
 # ##############################################################################
 
 git submodule update --init --recursive --jobs ${threads}
-echo
-echo "Building bundled libraries..."
-cd ${scriptpath}/external
-start=$(date +%s)
-echo "    Building QMC..."
-bash -i ./build_qmc.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build qmc, aborting."
-  exit 1
-}
-echo "    Building autodiff..."
-bash -i ./build_autodiff.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build autodiff, aborting."
-  exit 1
-}
-echo "    Building Boost..."
-bash -i ./build_boost.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build Boost, aborting."
-  exit 1
-}
-echo "    Building Catch2..."
-bash -i ./build_Catch2.sh -j ${threads} &>/dev/null || { echo "    Failed to build Catch2, tests will not work. Continuing setup process."; }
-echo "    Building Eigen3..."
-bash -i ./build_eigen.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build Eigen, aborting."
-  exit 1
-}
-echo "    Building thread-pool..."
-bash -i ./build_thread-pool.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build thread-pool, aborting."
-  exit 1
-}
-echo "    Building spdlog..."
-bash -i ./build_spdlog.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build spdlog, aborting."
-  exit 1
-}
-echo "    Building rmm..."
-bash -i ./build_rmm.sh -j ${threads} &>/dev/null || { echo "    Failed to build rmm, CUDA will not work. Continuing setup process."; }
-echo "    Building kokkos..."
-bash -i ./build_kokkos.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build kokkos, aborting."
-  exit 1
-}
-echo "    Building sundials..."
-bash -i ./build_sundials.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build SUNDIALS, aborting."
-  exit 1
-}
-echo "    Building deal.II..."
-bash -i ./build_dealii.sh -j ${threads} &>/dev/null || {
-  echo "    Failed to build deal.ii, aborting."
-  exit 1
-}
-end=$(date +%s)
-runtime=$((end - start))
-elapsed="Elapsed: $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
-echo "    Done. (${elapsed})"
-cd ${scriptpath}
-echo
+
+if [[ -z ${install_dir+x} ]]; then
+  echo
+  read -p "Install DiFfRG library globally to /opt/DiFfRG? [y/N/path] " install_dir
+  install_dir=${install_dir:-N}
+fi
+
+if [[ -z ${option_setup_library+x} ]]; then
+  read -p "Build DiFfRG library? [Y/n] " option_setup_library
+  option_setup_library=${option_setup_library:-Y}
+fi
+
+if [[ ${install_dir} != "n" ]] && [[ ${install_dir} != "N" ]]; then
+  cd ${SCRIPTPATH}
+
+  # Make sure the install directory is absolute
+  idir=$(expandPath ${install_dir}/)
+  idir=$(readlink --canonicalize ${idir})
+  echo "DiFfRG library will be installed in ${idir}"
+
+  # Check if the install directory is writable
+  mkdir -p ${idir} &>/dev/null && touch ${idir}/_permission_test &>/dev/null || {
+    failed_first=1
+  }
+
+  # Install dependencies
+  start=$(date +%s)
+  cd ${SCRIPTPATH}/external
+  if [[ $failed_first == 0 ]]; then
+    rm ${idir}/_permission_test
+    echo
+    echo "Installing dependencies..."
+    bash -i ./install.sh -i ${idir}/bundled -j ${THREADS} ${cuda_flag} # &>${LOGPATH}/DiFfRG_dependencies_install.log
+  else
+    echo "Elevated permissions required for install path ${idir}."
+    sudo mkdir -p ${idir}
+    echo
+    echo "Installing dependencies..."
+    sudo -E bash -i ./install.sh -i ${idir}/bundled -j ${THREADS} ${cuda_flag} # &>${LOGPATH}/DiFfRG_dependencies_install.log
+  fi
+  end=$(date +%s)
+  runtime=$((end - start))
+  elapsed="Elapsed: $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
+  echo "    Done. (${elapsed})"
+  echo
+fi
 
 # ##############################################################################
 # Setup and build library

config

@@ -11,8 +11,8 @@
 #   export CXX_FLAGS="-march=core-avx2 -fPIC"
 #   export C_FLAGS="-march=core-avx2 -fPIC"
 #   export CUDA_FLAGS="-arch=sm_35"
-export CXX_FLAGS="-march=native -fPIC -flto"
-export C_FLAGS="-march=native -fPIC -flto"
+export CXX_FLAGS="-march=native -fPIC -flto=auto"
+export C_FLAGS="-march=native -fPIC -flto=auto"
 export CUDA_FLAGS=""
 export CUDA_ARCHITECTURES="native"
 
@@ -45,4 +45,4 @@ if command -v dnsdomainname &>/dev/null; then
     echo ${DEAL_II_CMAKE}
     echo
   fi
-fi
+fi

external/.gitignore

@@ -22,5 +22,7 @@ eigen_build/
 eigen_install/
 qmc_install/
 thread-pool_install/
+rapidcsv_build/
+rapidcsv_install/
 logs/
 *.log

external/build.sh

@@ -0,0 +1,94 @@
+#!/bin/bash
+
+# ##############################################################################
+# Script setup
+# ##############################################################################
+
+threads='1'
+while getopts j:c flag; do
+  case "${flag}" in
+  j) threads=${OPTARG} ;;
+  c) cuda="-c" ;;
+  ?)
+    exit 2
+    ;;
+  esac
+done
+
+source ../config
+
+################################################################################
+# This script builds all the dependencies for the project.
+################################################################################
+
+echo "    Building QMC..."
+bash -i ./build_qmc.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build qmc, aborting."
+  exit 1
+}
+
+echo "    Building autodiff..."
+bash -i ./build_autodiff.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build autodiff, aborting."
+  exit 1
+}
+
+echo "    Building rapidcsv..."
+bash -i ./build_rapidcsv.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build rapidcsv, aborting."
+  exit 1
+}
+
+echo "    Building Boost..."
+bash -i ./build_boost.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build Boost, aborting."
+  exit 1
+}
+
+echo "    Building Catch2..."
+bash -i ./build_Catch2.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build Catch2, tests will not work. Continuing setup process."
+}
+
+echo "    Building Eigen3..."
+bash -i ./build_eigen.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build Eigen, aborting."
+  exit 1
+}
+
+echo "    Building thread-pool..."
+bash -i ./build_thread-pool.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build thread-pool, aborting."
+  exit 1
+}
+
+echo "    Building spdlog..."
+bash -i ./build_spdlog.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build spdlog, aborting."
+  exit 1
+}
+
+if [[ "${cuda}" == "-c" ]]; then
+  echo "    Building rmm..."
+  bash -i ./build_rmm.sh -j ${threads} &>/dev/null || {
+    echo "    Failed to build rmm, CUDA will not work. Continuing setup process."
+  }
+fi
+
+echo "    Building kokkos..."
+bash -i ./build_kokkos.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build kokkos, aborting."
+  exit 1
+}
+
+echo "    Building sundials..."
+bash -i ./build_sundials.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build SUNDIALS, aborting."
+  exit 1
+}
+
+echo "    Building deal.II..."
+bash -i ./build_dealii.sh -j ${threads} &>/dev/null || {
+  echo "    Failed to build deal.ii, aborting."
+  exit 1
+}

external/build_Catch2.sh

@@ -6,8 +6,8 @@ SCRIPT_PATH="$(
   pwd -P
 )"
 
-source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/parse_flags.sh
+source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/cleanup_build_if_asked.sh
 source $SCRIPT_PATH/build_scripts/setup_folders.sh
 

external/build_autodiff.sh

@@ -6,26 +6,26 @@ SCRIPT_PATH="$(
   pwd -P
 )"
 
-source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/parse_flags.sh
+source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/cleanup_build_if_asked.sh
 source $SCRIPT_PATH/build_scripts/setup_folders.sh
 
 cd $BUILD_PATH
 
 cmake -DCMAKE_BUILD_TYPE=Release \
-    -DCMAKE_CUDA_FLAGS=${CUDA_FLAGS} \
-    -DCMAKE_CUDA_ARCHITECTURES=${CUDA_ARCHITECTURES} \
-    -DCMAKE_CXX_FLAGS="${CXX_FLAGS} -O3 -DNDEBUG" \
-    -DCMAKE_EXE_LINKER_FLAGS="${EXE_LINKER_FLAGS}" \
-    -DAUTODIFF_BUILD_TESTS=OFF \
-    -DAUTODIFF_BUILD_PYTHON=OFF \
-    -DAUTODIFF_BUILD_EXAMPLES=OFF \
-    -DAUTODIFF_BUILD_DOCS=OFF \
-    -DEigen3_DIR=${SCRIPT_PATH}/eigen_install \
-    -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} \
-    -S ${SOURCE_PATH} \
-    2>&1 | tee $CMAKE_LOG_FILE
+  -DCMAKE_CUDA_FLAGS=${CUDA_FLAGS} \
+  -DCMAKE_CUDA_ARCHITECTURES=${CUDA_ARCHITECTURES} \
+  -DCMAKE_CXX_FLAGS="${CXX_FLAGS} -O3 -DNDEBUG" \
+  -DCMAKE_EXE_LINKER_FLAGS="${EXE_LINKER_FLAGS}" \
+  -DAUTODIFF_BUILD_TESTS=OFF \
+  -DAUTODIFF_BUILD_PYTHON=OFF \
+  -DAUTODIFF_BUILD_EXAMPLES=OFF \
+  -DAUTODIFF_BUILD_DOCS=OFF \
+  -DEigen3_DIR=${SCRIPT_PATH}/eigen_install \
+  -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} \
+  -S ${SOURCE_PATH} \
+  2>&1 | tee $CMAKE_LOG_FILE
 
 make -j $THREADS 2>&1 | tee $MAKE_LOG_FILE
 make -j $THREADS install

external/build_boost.sh

@@ -6,8 +6,8 @@ SCRIPT_PATH="$(
   pwd -P
 )"
 
-source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/parse_flags.sh
+source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/cleanup_build_if_asked.sh
 source $SCRIPT_PATH/build_scripts/setup_folders.sh
 

external/build_dealii.sh

@@ -6,8 +6,8 @@ SCRIPT_PATH="$(
   pwd -P
 )"
 
-source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/parse_flags.sh
+source $SCRIPT_PATH/build_scripts/populate_paths.sh
 source $SCRIPT_PATH/build_scripts/cleanup_build_if_asked.sh
 source $SCRIPT_PATH/build_scripts/setup_folders.sh
 
@@ -17,19 +17,18 @@ cmake -DCMAKE_BUILD_TYPE=DebugRelease \
   -DDEAL_II_COMPONENT_EXAMPLES=OFF \
   -DDEAL_II_COMPONENT_DOCUMENTATION=OFF \
   -DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=ON \
-  -DDEAL_II_WITH_CUDA=OFF \
   -DDEAL_II_WITH_MPI=OFF \
+  -DDEAL_II_USE_LTO=ON \
   -DDEAL_II_WITH_UMFPACK=ON \
   -DDEAL_II_WITH_TASKFLOW=OFF \
   -DDEAL_II_WITH_VTK=OFF \
-  -DDEAL_II_USE_LTO=ON \
   -DCMAKE_CXX_FLAGS="${CXX_FLAGS}" \
   -DCMAKE_EXE_LINKER_FLAGS="${EXE_LINKER_FLAGS}" \
   -DCMAKE_CXX_STANDARD=17 \
-  -DKOKKOS_DIR=${SCRIPT_PATH}/kokkos_install \
-  -DSUNDIALS_DIR=${SCRIPT_PATH}/sundials_install \
+  -DKOKKOS_DIR=${TOP_INSTALL_PATH}/kokkos_install \
+  -DSUNDIALS_DIR=${TOP_INSTALL_PATH}/sundials_install \
   ${DEAL_II_CMAKE} \
-  -DBOOST_DIR=${SCRIPT_PATH}/boost_install \
+  -DBOOST_DIR=${TOP_INSTALL_PATH}/boost_install \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} \
   -S ${SOURCE_PATH} \
   2>&1 | tee $CMAKE_LOG_FILE