Merge remote-tracking branch 'origin/next' into field-format

Author: dschwoerer

.clang-tidy

@@ -20,7 +20,7 @@ CheckOptions:
     value: 'MPI_Comm'
 
   - key: misc-include-cleaner.IgnoreHeaders
-    value: 'adios2/.*;bits/.*;cpptrace/.*'
+    value: 'adios2/.*;bits/.*;cpptrace/.*;petsc.*\.h'
 ---
 
 Disabled checks and reasons:

.docker/fedora/Dockerfile

@@ -26,12 +26,13 @@ ENV HOME=/home/boutuser
 WORKDIR /home/boutuser/BOUT-dev
 
 RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
+          -DCMAKE_BUILD_TYPE=RelWithDebInfo \
           -DBOUT_GENERATE_FIELDOPS=OFF \
           -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/usr/local \
           -DBOUT_ENABLE_PYTHON=ON \
           -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=/usr/lib64/$MPI/ -DSUNDIALS_INCLUDE_DIR=/usr/include/$MPI-x86_64/sundials/ \
 	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1); \
-    make -C build -j 2; \
+    make -C build -j 2 VERBOSE=1; \
     sudo make -C build install; \
     rm -rf build
 

.git-blame-ignore-revs

@@ -5,6 +5,12 @@ ed2117e6d6826a98b6988e2f18c0c34e408563b6
 17ac13c28aa3b34a0e46dbe87bb3874f6b25e706
 # Added by the bot
 4b010b7634aee1045743be80c268d4644522cd29
+52301380586fdbf890f620c04f689b08d89a6c34
 a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
+83cf77923a4c72e44303354923021acf932b4fd2
 2c2402ed59c91164eaff46dee0f79386b7347e9e
 05b7c571544c3bcb153fce67d12b9ac48947fc2d
+c8f38049359170a34c915e209276238ea66b9a1e
+8d5cb39e03c2644715a50684f8cd0318b4e82676
+ec69e8838be2dde140a915e50506f8e1ce3cb534
+f2bc0488a298f136294c523bc5ab4086d090059b

.github/workflows/auto-formatting.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0

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

@@ -21,7 +21,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.23.0
+        uses: ZedThree/clang-tidy-review@v0.23.1
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.23.0
+        uses: ZedThree/clang-tidy-review/upload@v0.23.1

.github/workflows/docker.yml

@@ -26,11 +26,11 @@ jobs:
       matrix:
         mpi: [mpich]
         metric3d:
-          - name: "With OpenMP"
+          - name: "With 3D Metrics"
             cmake: ON
-            base_prefix: "openmp-"
+            base_prefix: ""
             tag_prefix: "3d-"
-          - name: "Without OpenMP"
+          - name: "Without 3D Metrics"
             cmake: OFF
             base_prefix: ""
             tag_prefix: ""
@@ -75,7 +75,7 @@ jobs:
           build-args: |
             BASE=${{ matrix.mpi }}-${{ matrix.metric3d.base_prefix }}${{ matrix.config.base_postfix }}-main
             MPI=${{ matrix.mpi }}
-            CMAKE_OPTIONS=${{ matrix.config.options }} -DBOUT_ENABLE_METRIC_3D=${{ matrix.metric3d.cmake }} -DBOUT_ENABLE_OPENMP=${{ matrix.metric3d.cmake }}
+            CMAKE_OPTIONS=${{ matrix.config.options }} -DBOUT_ENABLE_METRIC_3D=${{ matrix.metric3d.cmake }}
             COMMIT=${{ github.sha }}
             URL=${{ github.server_url }}/${{ github.repository }}
           context: .docker/fedora/

.github/workflows/tests.yml

@@ -40,7 +40,7 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased, ADIOS2"
+          - name: "PETSc unreleased, ADIOS2, 3D metrics"
             os: ubuntu-24.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
@@ -121,22 +121,6 @@ jobs:
             omp_num_threads: 2
             on_cron: false
 
-          - name: "CMake, new PETSc"
-            os: ubuntu-latest
-            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_HYPRE=OFF
-                            -DBOUT_ENABLE_PYTHON=ON
-                            -DSUNDIALS_ROOT=/home/runner/local
-                            -DPETSC_DIR=/home/runner/local/petsc
-                            -DSLEPC_DIR=/home/runner/local/slepc"
-            build_petsc: -petsc
-            on_cron: false
-
         exclude:
           - is_cron: true
             config:
@@ -184,7 +168,7 @@ jobs:
           python -m pip install -r requirements.txt
 
       - name: Cache Zenodo test data
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: build/tests/integrated/test-fci-mpi/grid.fci.nc
           # If we update the test, invalidate the cache
@@ -221,7 +205,7 @@ jobs:
           submodules: true
 
       - name: Cache Zenodo test data
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: build/tests/integrated/test-fci-mpi/grid.fci.nc
           # If we update the test, invalidate the cache
@@ -232,39 +216,3 @@ jobs:
         shell: bash
         env:
           TRAVIS_BUILD_DIR: ${{ github.workspace }}
-  CUDA:
-    timeout-minutes: 60
-    runs-on: ubuntu-latest
-    container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
-    env:
-      BOUT_TEST_DOWNLOAD_FLAGS: --retry-on-http-error=502,503,504 --tries 3
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          submodules: true
-
-      - name: Cache Zenodo test data
-        uses: actions/cache@v4
-        with:
-          path: build/tests/integrated/test-fci-mpi/grid.fci.nc
-          # If we update the test, invalidate the cache
-          key: zenodo-data-${{ hashFiles('tests/integrated/test-fci-mpi/CMakeLists.txt') }}
-
-      - 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

CMakeLists.txt

@@ -231,6 +231,8 @@ set(BOUT_SOURCES
     ./src/field/where.cxx
     ./src/invert/fft_fftw.cxx
     ./src/invert/lapack_routines.cxx
+    ./src/invert/laplace/common_transform.cxx
+    ./src/invert/laplace/common_transform.hxx
     ./src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
     ./src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
     ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
@@ -403,6 +405,7 @@ if(zoidberg_FOUND EQUAL 0)
 else()
   set(zoidberg_FOUND OFF)
 endif()
+message(STATUS "Found Zoidberg for FCI tests: ${zoidberg_FOUND}")
 
 option(
   BOUT_GENERATE_FIELDOPS
@@ -523,10 +526,10 @@ set_target_properties(
 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 ${CMAKE_CXX_FLAGS} -std=c++17"
+    "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++20"
 )
 
-target_compile_features(bout++ PUBLIC cxx_std_17)
+target_compile_features(bout++ PUBLIC cxx_std_20)
 set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF)
 
 # Optional compiler features

bout++Config.cmake.in

@@ -8,7 +8,7 @@ set(BOUT_USE_TRACK @BOUT_USE_TRACK@)
 set(BOUT_USE_SIGFPE @BOUT_USE_SIGFPE@)
 set(BOUT_USE_OPENMP @BOUT_USE_OPENMP@)
 set(BOUT_HAS_CUDA @BOUT_HAS_CUDA@)
-set(BOUT_HAS_OUTPUT_DEBUG @BOUT_HAS_OUTPUT_DEBUG@)
+set(BOUT_USE_OUTPUT_DEBUG @BOUT_USE_OUTPUT_DEBUG@)
 set(BOUT_CHECK_LEVEL @BOUT_CHECK_LEVEL@)
 set(BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@)
 
@@ -182,3 +182,30 @@ if (BOUT_HAS_ADIOS2)
 endif()
 
 include("${CMAKE_CURRENT_LIST_DIR}/bout++Targets.cmake")
+
+add_library(bout++ INTERFACE IMPORTED)
+set_target_properties(bout++
+  PROPERTIES BOUT_USE_SIGNAL @BOUT_USE_SIGNAL@
+  BOUT_USE_COLOR @BOUT_USE_COLOR@
+  BOUT_USE_TRACK @BOUT_USE_TRACK@
+  BOUT_USE_SIGFPE @BOUT_USE_SIGFPE@
+  BOUT_USE_OPENMP @BOUT_USE_OPENMP@
+  BOUT_HAS_CUDA @BOUT_HAS_CUDA@
+  BOUT_USE_OUTPUT_DEBUG @BOUT_USE_OUTPUT_DEBUG@
+  BOUT_CHECK_LEVEL @BOUT_CHECK_LEVEL@
+  BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@
+  BOUT_HAS_PVODE @BOUT_HAS_PVODE@
+  BOUT_HAS_NETCDF @BOUT_HAS_NETCDF@
+  BOUT_HAS_ADIOS2 @BOUT_HAS_ADIOS2@
+  BOUT_HAS_FFTW @BOUT_HAS_FFTW@
+  BOUT_HAS_LAPACK @BOUT_HAS_LAPACK@
+  BOUT_HAS_PETSC @BOUT_HAS_PETSC@
+  BOUT_HAS_SLEPC @BOUT_HAS_SLEPC@
+  BOUT_HAS_SCOREP @BOUT_HAS_SCOREP@
+  BOUT_USE_UUID_SYSTEM_GENERATOR @BOUT_USE_UUID_SYSTEM_GENERATOR@
+  BOUT_HAS_SUNDIALS @BOUT_HAS_SUNDIALS@
+  BOUT_HAS_HYPRE @BOUT_HAS_HYPRE@
+  BOUT_HAS_GETTEXT @BOUT_HAS_GETTEXT@
+  BOUT_HAS_UMPIRE @BOUT_HAS_UMPIRE@
+  BOUT_HAS_RAJA @BOUT_HAS_RAJA@
+)

cmake/SetupBOUTThirdParty.cmake

@@ -362,7 +362,7 @@ if(BOUT_USE_SUNDIALS)
         CACHE BOOL "" FORCE
     )
     set(ENABLE_OPENMP
-        OFF
+        ${BOUT_USE_OPENMP}
         CACHE BOOL "" FORCE
     )
     if(BUILD_SHARED_LIBS)