Fix compilation error due to check_c_source_runs

.build_adios2_for_ci.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+set -e
+
+if test $BUILD_ADIOS2 ; then
+    if [[ ! -d $HOME/local/adios/include/adios2.h ]] || test $1 ; then
+	echo "****************************************"
+	echo "Building ADIOS2"
+	echo "****************************************"
+
+	branch=${1:-release_29}
+    if [ ! -d adios2 ]; then
+    	git clone -b $branch https://github.com/ornladios/ADIOS2.git adios2 --depth=1
+    fi
+
+	pushd adios2
+    rm -rf build
+    mkdir -p build
+    pushd build
+
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=$HOME/local \
+        -DADIOS2_USE_MPI=ON \
+        -DADIOS2_USE_Fortran=OFF \
+        -DADIOS2_USE_Python=OFF \
+        -DADIOS2_BUILD_EXAMPLES=OFF \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+        -DBUILD_TESTING=OFF \
+        -DADIOS2_USE_SST=OFF \
+        -DADIOS2_USE_MGARD=OFF \
+        -DADIOS2_USE_HDF5=OFF \
+        -DADIOS2_USE_BZip2=OFF \
+        -DADIOS2_USE_Blosc2=OFF \
+        -DADIOS2_USE_SZ=OFF \
+        -DADIOS2_USE_ZFP=OFF \
+        -DADIOS2_USE_DAOS=OFF \
+        -DADIOS2_USE_UCX=OFF \
+        -DADIOS2_USE_LIBPRESSIO=OFF \
+        -DADIOS2_USE_Sodium=OFF \
+        -DADIOS2_USE_ZeroMQ=OFF \
+        -DADIOS2_USE_MHS=OFF \
+        -DADIOS2_USE_DataMan=OFF
+
+	make -j 4 && make install
+	popd
+
+	echo "****************************************"
+	echo " Finished building ADIOS2"
+	echo "****************************************"
+
+    else
+
+	echo "****************************************"
+	echo " ADIOS2 already installed"
+	echo "****************************************"
+    fi
+else
+    echo "****************************************"
+    echo " ADIOS2 not requested"
+    echo "****************************************"
+fi

.ci_fedora.sh

@@ -50,12 +50,13 @@ then
     cp -a /tmp/BOUT-dev /home/test/
     chown -R test /home/test
     chmod u+rwX /home/test -R
-    sudo -u test ${0/\/tmp/\/home\/test} $mpi
+    su - test -c "${0/\/tmp/\/home\/test} $mpi"
 ## If we are called as normal user, run test
 else
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
     export OMPI_MCA_rmaps_base_oversubscribe=yes
+    export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
     export FLEXIBLAS=NETLIB
     cd

.clang-format

@@ -109,6 +109,8 @@ SpacesInParentheses: false
 SpacesInSquareBrackets: false
 StatementMacros:
   - BOUT_OMP
+  - BOUT_OMP_PERF
+  - BOUT_OMP_SAFE
 Standard:        c++14
 TabWidth:        8
 UseTab:          Never

.github/workflows/clang-tidy-review.yml

@@ -32,7 +32,7 @@ jobs:
           # the unit tests until they're fixed or ignored upstream
           exclude: "tests/unit/*cxx"
           cmake_command: |
-            pip install cmake && \
+            pip install --break-system-packages cmake && \
             cmake --version && \
             git config --global --add safe.directory "$GITHUB_WORKSPACE" && \
             cmake . -B build -DBUILD_SHARED_LIBS=ON \

.github/workflows/tests.yml

@@ -28,6 +28,7 @@ jobs:
       OMP_NUM_THREADS: ${{ matrix.config.omp_num_threads }}
       PYTHONPATH: ${{ github.workspace }}/tools/pylib
       OMPI_MCA_rmaps_base_oversubscribe: yes
+      PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
       MPIRUN: mpiexec -np
     strategy:
       fail-fast: true
@@ -38,20 +39,23 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased"
+          - name: "CMake, PETSc unreleased, ADIOS2"
             os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_ADIOS2=ON
                             -DBOUT_ENABLE_PYTHON=ON
+                            -DADIOS2_ROOT=/home/runner/local/adios2
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
             build_petsc: -petsc-main
             build_petsc_branch: main
+            build_adios2: true
             on_cron: true
 
           - name: "Default options, Ubuntu 20.04"
@@ -185,9 +189,8 @@ jobs:
 
       - name: Install pip packages
         run: |
-          ./.pip_install_for_ci.sh 'cython~=0.29' 'netcdf4~=1.5' 'sympy~=1.5' 'gcovr' 'cmake' zoidberg fastcov
-          # Add the pip install location to the runner's PATH
-          echo ~/.local/bin >> $GITHUB_PATH
+          python -m pip install --upgrade pip setuptools
+          python -m pip install -r requirements.txt
 
       - name: Cache SUNDIALS build
         uses: actions/cache@v3
@@ -201,6 +204,9 @@ jobs:
       - name: Build PETSc
         run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
+      - name: Build ADIOS2
+        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
+
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
@@ -234,3 +240,30 @@ jobs:
         shell: bash
         env:
           TRAVIS_BUILD_DIR: ${{ github.workspace }}
+  CUDA:
+    timeout-minutes: 60
+    runs-on: ubuntu-latest
+    container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04
+        run: |
+          . /spack/share/spack/setup-env.sh
+          spack env activate -p /spack-env
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          rm -rf build
+          cmake -S $GITHUB_WORKSPACE -B build \
+            -DCMAKE_C_COMPILER=gcc \
+            -DCMAKE_CXX_COMPILER=g++ \
+            -DBOUT_ENABLE_RAJA=on \
+            -DBOUT_ENABLE_UMPIRE=on \
+            -DBOUT_ENABLE_CUDA=on \
+            -DCMAKE_CUDA_ARCHITECTURES=80 \
+            -DCUDA_ARCH=compute_80,code=sm_80 \
+            -DBOUT_ENABLE_WARNINGS=off \
+            -DBOUT_USE_SYSTEM_FMT=on
+          cd build
+          make -j 4

.gitignore

@@ -85,3 +85,5 @@ coverage/
 /_version.txt
 /BOUT++-v*.tar.gz
 /BOUT++-v*.tar.xz
+/CMakeCache.txt
+/CMakeFiles/cmake.check_cache

CHANGELOG.md

@@ -1,7 +1,16 @@
 # Changelog
 
-## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0
+## [v6.0.0](https://github.com/boutproject/BOUT-dev/tree/next)
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.0...next)
 
+### Breaking changes
+
+- The autotools `./configure` build system has been removed
+- Parsing of booleans has changed [\#2828][https://github.com/boutproject/BOUT-dev/pull/2828] ([bendudson][https://github.com/bendudson]).
+  See the [manual page](https://bout-dev.readthedocs.io/en/stable/user_docs/bout_options.html#boolean-expressions) for details.
+
+
+## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0)
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.0.0...v5.1.0)
 
 - Update RELEASE_HOWTO.md [\#2741][https://github.com/boutproject/BOUT-dev/pull/2741] ([dschwoerer][https://github.com/dschwoerer])
@@ -44,8 +53,8 @@
 - Merge v5 into next - resolve conflicts [\#2658][https://github.com/boutproject/BOUT-dev/pull/2658] ([dschwoerer][https://github.com/dschwoerer])
 - Update bundled boututils and boutdata [\#2657][https://github.com/boutproject/BOUT-dev/pull/2657] ([dschwoerer][https://github.com/dschwoerer])
 
-## [v5.0.0](https://github.com/boutproject/BOUT-dev/tree/next)
-[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.2...next)
+## [v5.0.0](https://github.com/boutproject/BOUT-dev/tree/v5.0.0)
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.2...v5.0.0)
 
 ### Breaking changes
 

CMakeLists.txt

@@ -83,6 +83,7 @@ function(bout_update_submodules)
 endfunction()
 
 set(BOUT_SOURCES
+  ./include/bout/adios_object.hxx
   ./include/bout/array.hxx
   ./include/bout/assert.hxx
   ./include/bout/boundary_factory.hxx
@@ -114,7 +115,6 @@ set(BOUT_SOURCES
   ./include/bout/field_factory.hxx
   ./include/bout/fieldgroup.hxx
   ./include/bout/fieldperp.hxx
-  ./include/bout/format.hxx
   ./include/bout/fv_ops.hxx
   ./include/bout/generic_factory.hxx
   ./include/bout/globalfield.hxx
@@ -146,7 +146,7 @@ set(BOUT_SOURCES
   ./include/bout/openmpwrap.hxx
   ./include/bout/operatorstencil.hxx
   ./include/bout/options.hxx
-  ./include/bout/options_netcdf.hxx
+  ./include/bout/options_io.hxx
   ./include/bout/optionsreader.hxx
   ./include/bout/output.hxx
   ./include/bout/output_bout_types.hxx
@@ -325,6 +325,7 @@ set(BOUT_SOURCES
   ./src/solver/impls/split-rk/split-rk.cxx
   ./src/solver/impls/split-rk/split-rk.hxx
   ./src/solver/solver.cxx
+  ./src/sys/adios_object.cxx
   ./src/sys/bout_types.cxx
   ./src/sys/boutcomm.cxx
   ./src/sys/boutexception.cxx
@@ -338,7 +339,11 @@ set(BOUT_SOURCES
   ./src/sys/options/optionparser.hxx
   ./src/sys/options/options_ini.cxx
   ./src/sys/options/options_ini.hxx
+  ./src/sys/options/options_io.cxx
   ./src/sys/options/options_netcdf.cxx
+  ./src/sys/options/options_netcdf.hxx
+  ./src/sys/options/options_adios.cxx
+  ./src/sys/options/options_adios.hxx
   ./src/sys/optionsreader.cxx
   ./src/sys/output.cxx
   ./src/sys/petsclib.cxx
@@ -361,7 +366,7 @@ else()
   set(BOUT_GENERATE_FIELDOPS_DEFAULT OFF)
 endif()
 
-execute_process(COMMAND ${Python3_EXECUTABLE} -c "import zoidberg"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import importlib.util ; import sys; sys.exit(importlib.util.find_spec(\"zoidberg\") is None)"
   RESULT_VARIABLE zoidberg_FOUND)
 if (zoidberg_FOUND EQUAL 0)
   set(zoidberg_FOUND ON)
@@ -462,9 +467,9 @@ set_target_properties(bout++ PROPERTIES
 # Set some variables for the bout-config script
 set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++")
 set(BOUT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/include")
-set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS}")
+set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++17")
 
-target_compile_features(bout++ PUBLIC cxx_std_14)
+target_compile_features(bout++ PUBLIC cxx_std_17)
 set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF)
 
 # Optional compiler features
@@ -769,7 +774,7 @@ set(BOUT_HAS_PNETCDF OFF)
 # while for static builds we need the dependencies too
 if (BUILD_SHARED_LIBS)
   # Include rpath linker flag so user doesn't need to set LD_LIBRARY_PATH
-  set(CONFIG_LDFLAGS "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt")
+  set(CONFIG_LDFLAGS "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt ${CONFIG_LDFLAGS_SHARED}")
 else()
   set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS}")
 endif()
@@ -930,6 +935,7 @@ message("
    SUNDIALS support         : ${BOUT_HAS_SUNDIALS}
    HYPRE support            : ${BOUT_HAS_HYPRE}
    NetCDF support           : ${BOUT_HAS_NETCDF}
+   ADIOS2 support           : ${BOUT_HAS_ADIOS2}
    FFTW support             : ${BOUT_HAS_FFTW}
    LAPACK support           : ${BOUT_HAS_LAPACK}
    OpenMP support           : ${BOUT_USE_OPENMP}