boutpp-nightly 5.2.0.dev910__tar.gz → 5.2.1.dev2__tar.gz

boutpp_nightly-v5.2.1.dev2/.github/workflows/black-fix.yml

@@ -0,0 +1,46 @@
+name: black
+
+on:
+  push:
+    paths:
+      - '**.py'
+      - 'bin/**'
+      - '**/runtest'
+      - '**/run'
+      - 'tests/integrated/test_suite'
+      - 'tests/requirements/*'
+      - 'tools/tokamak_grids/**'
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        ref: ${{ github.head_ref }}
+
+    - name: Install black
+      run: |
+        sudo apt update -y
+        sudo apt -y install python3-pip python3-setuptools python3-wheel
+        pip3 install black
+
+    - name: Version
+      run: |
+        python3 --version
+        $HOME/.local/bin/black --version
+
+    - name: Run black
+      run: |
+        pwd
+        ls
+        $HOME/.local/bin/black tests/ tools/ $(grep -EIlr '^#!.*python.*$' bin/ tests/ tools/ src/ | grep -v _boutpp_build)
+
+    - uses: stefanzweifel/git-auto-commit-action@v5
+      with:
+        commit_message: "Apply black changes"

boutpp_nightly-v5.2.1.dev2/.github/workflows/clang-format.yml

@@ -0,0 +1,33 @@
+name: clang-format-command
+
+on:
+  pull_request:
+    paths:
+      - '**.cxx'
+      - '**.hxx'
+
+jobs:
+  clang-format:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the pull request branch, also include all history
+      - uses: actions/checkout@v5
+        with:
+          ref: ${{ github.head_ref }}
+          fetch-depth: 0
+
+      # This also installs git-clang-format
+      - name: Install clang-format
+        run: sudo apt install clang-format
+
+      - name: Run clang-format
+        id: format
+        run:
+          while ! git clang-format origin/${{ github.base_ref }} ; do git add . ; done
+
+      - name: Commit to the PR branch
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "Apply clang-format changes"

boutpp_nightly-v5.2.1.dev2/.github/workflows/clang-tidy-review.yml

@@ -0,0 +1,49 @@
+name: clang-tidy-review
+
+on:
+  pull_request:
+    paths:
+      - '**.cxx'
+      - '**.hxx'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  review:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+
+      - name: Run clang-tidy
+        uses: ZedThree/clang-tidy-review@v0.21.0
+        id: review
+        with:
+          build_dir: build
+          apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev,uuid-dev"
+          config_file: ".clang-tidy"
+          # Googletest triggers a _lot_ of clang-tidy warnings, so ignore all
+          # the unit tests until they're fixed or ignored upstream
+          exclude: "tests/unit/*cxx"
+          lgtm_comment_body: ''
+          cmake_command: |
+            pip install --break-system-packages cmake && \
+            cmake --version && \
+            git config --global --add safe.directory "$GITHUB_WORKSPACE" && \
+            cmake . -B build -DBUILD_SHARED_LIBS=ON \
+                             -DBOUT_USE_PETSC=ON \
+                             -DBOUT_USE_SLEPC=ON \
+                             -DBOUT_USE_SUNDIALS=ON \
+                             -DBOUT_BUILD_EXAMPLES=ON \
+                             -DBOUT_BUILD_DOCS=OFF \
+                             -DBOUT_ENABLE_PYTHON=OFF \
+                             -DCMAKE_EXPORT_COMPILE_COMMANDS=On \
+                             -DBOUT_UPDATE_GIT_SUBMODULE=OFF
+
+      - name: Upload clang-tidy fixes
+        uses: ZedThree/clang-tidy-review/upload@v0.21.0

boutpp_nightly-v5.2.1.dev2/.github/workflows/docker.yml

@@ -0,0 +1,84 @@
+name: Docker
+
+on:
+  push:
+    branches:
+      - master
+      - next
+      # Add your branch here if you want containers for it
+      - db-WIP
+      - docker-ci
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build:
+    name: Build ${{ matrix.config.name }} Container (${{ matrix.metric3d.name }} ; ${{matrix.mpi}})
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        mpi: [mpich]
+        metric3d:
+          - name: "With OpenMP"
+            cmake: ON
+            base_prefix: "openmp-"
+            tag_prefix: "3d-"
+          - name: "Without OpenMP"
+            cmake: OFF
+            base_prefix: ""
+            tag_prefix: ""
+        config:
+          - name: "Debug"
+            tag_postfix: "debug"
+            options: "-DCHECK=3"
+            base_postfix: "mini"
+
+          - name: "Optimised"
+            tag_postfix: "opt"
+            options: "-DCHECK=0"
+            base_postfix: "mini"
+
+          - name: "Full"
+            tag_postfix: "full"
+            options: "-DCHECK=3"
+            base_postfix: "full"
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@master
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@master
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          flavor: |
+            prefix=${{ matrix.mpi }}-${{matrix.metric3d.tag_prefix}}${{ matrix.config.tag_postfix }}-
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@master
+        with:
+          build-args: |
+            BASE=${{ 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 }}
+            COMMIT=${{ github.sha }}
+            URL=${{ github.server_url }}/${{ github.repository }}
+          context: .docker/fedora/
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

boutpp_nightly-v5.2.1.dev2/.github/workflows/python-package.yml

@@ -0,0 +1,149 @@
+name: Python package
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-wheel:
+    name: Build wheel and install
+
+    runs-on: ubuntu-latest
+    if: always()
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v6
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip &&
+           pip install --upgrade build &&
+           sudo apt update &&
+           sudo apt install -y
+                 libfftw3-dev
+                 libnetcdf-dev
+                 libnetcdf-c++4-dev
+                 netcdf-bin
+                 python3
+                 python3-pip
+                 python3-pytest
+                 python3-numpy
+                 python3-scipy
+                 lcov
+                 openmpi-bin
+                 libopenmpi-dev
+                 petsc-dev
+                 slepc-dev
+                 liblapack-dev
+                 libparpack2-dev
+
+    - name: Build
+      run: |
+        python -m build
+        pip install dist/*whl
+
+  pip-install-sdist:
+    name: Build sdist and install
+
+    runs-on: ubuntu-latest
+    if: always()
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v6
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip &&
+           pip install --upgrade build &&
+           sudo apt update &&
+           sudo apt install -y
+                 libfftw3-dev
+                 libnetcdf-dev
+                 libnetcdf-c++4-dev
+                 netcdf-bin
+                 python3
+                 python3-pip
+                 python3-pytest
+                 python3-numpy
+                 python3-scipy
+                 lcov
+                 openmpi-bin
+                 libopenmpi-dev
+                 petsc-dev
+                 slepc-dev
+                 liblapack-dev
+                 libparpack2-dev
+
+    - name: Build
+      run: |
+        python -m build --sdist
+        pip install dist/*tar.gz
+    - name: Upload
+      if: startsWith(github.ref, 'refs/tags/v')
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        pip install twine
+        test -z $TWINE_PASSWORD || twine upload dist/*tar.gz
+
+
+  pip-install-nighly:
+    name: Build boutpp-nightly and install
+
+    runs-on: ubuntu-latest
+    if: always()
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v6
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip &&
+           pip install --upgrade build &&
+           sudo apt update &&
+           sudo apt install -y
+                 libfftw3-dev
+                 libnetcdf-dev
+                 libnetcdf-c++4-dev
+                 netcdf-bin
+                 python3
+                 python3-pip
+                 python3-pytest
+                 python3-numpy
+                 python3-scipy
+                 lcov
+                 openmpi-bin
+                 libopenmpi-dev
+                 petsc-dev
+                 slepc-dev
+                 liblapack-dev
+                 libparpack2-dev
+
+    - name: Build and install
+      run: |
+        python -m build --sdist -Cnightly
+        pip install dist/*tar.gz
+
+    - name: Upload
+      if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/next'
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD_NIGHTLY }}
+      run: |
+        pip install twine
+        test -z $TWINE_PASSWORD || twine upload dist/*.tar.gz

boutpp_nightly-v5.2.1.dev2/.github/workflows/tests.yml

@@ -0,0 +1,242 @@
+name: Tests
+on:
+  push:
+  pull_request:
+  schedule:
+    # run sunday moring
+    - cron: '30 6 * * 0'
+
+defaults:
+  run:
+    shell: bash
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  standard_tests:
+    timeout-minutes: 60
+    name: ${{ matrix.config.name }}
+    runs-on: ${{ matrix.config.os }}
+    env:
+      BOUT_TEST_TIMEOUT: "6m"
+      PETSC_DIR: /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real
+      PETSC_ARCH: ""
+      SLEPC_DIR: /usr/lib/slepcdir/slepc3.12/x86_64-linux-gnu-real/
+      SLEPC_ARCH: ""
+      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
+      matrix:
+        # Need this to be able to exclude the coverage job
+        is_master_or_next:
+          - ${{ github.ref ==  'refs/heads/master' || github.ref == 'refs/heads/next'  || github.base_ref ==  'master' || github.base_ref == 'next' }}
+        is_cron:
+          - ${{ github.event_name == 'cron' }}
+        config:
+          - name: "CMake, PETSc unreleased, ADIOS2"
+            os: ubuntu-24.04
+            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_HYPRE=OFF
+                            -DBOUT_USE_ADIOS2=ON
+                            -DBOUT_ENABLE_PYTHON=ON
+                            -DADIOS2_ROOT=/home/runner/local
+                            -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 22.04"
+            os: ubuntu-22.04
+            cmake_options: ""
+            on_cron: false
+
+          - name: "Optimised, static"
+            os: ubuntu-latest
+            cmake_options: "-DCHECK=0
+                            -DBUILD_SHARED_LIBS=OFF
+                            -DCMAKE_CXX_FLAGS=-Ofast
+                            -DBOUT_ENABLE_SIGNAL=OFF
+                            -DBOUT_ENABLE_TRACK=OFF
+                            -DBOUT_ENABLE_BACKTRACE=OFF
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
+                            -DSUNDIALS_ROOT=/home/runner/local"
+            on_cron: false
+
+          - name: "Debug, shared"
+            os: ubuntu-latest
+            cmake_options: "-DCHECK=4
+                            -DCMAKE_BUILD_TYPE=Debug
+                            -DBOUT_ENABLE_SIGNAL=ON
+                            -DBOUT_ENABLE_TRACK=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
+                            -DSUNDIALS_ROOT=/home/runner/local"
+            on_cron: false
+
+          - name: "Shared, release"
+            os: ubuntu-latest
+            cmake_options: "-DBUILD_SHARED_LIBS=ON
+                            -DBOUT_ENABLE_OPENMP=ON
+                            -DCMAKE_BUILD_TYPE=Release
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
+                            -DBOUT_BUILD_DOCS=OFF
+                            -DSUNDIALS_ROOT=/home/runner/local"
+            omp_num_threads: 2
+            on_cron: false
+
+          - name: "Shared, OpenMP, 3D metrics"
+            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"
+            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:
+              on_cron: false
+
+    steps:
+      - name: Job information
+        run: |
+          echo Build: ${{ matrix.config.name }}, ${{ matrix.config.os }}
+          echo CMake options: ${{ matrix.config.cmake_options }}
+
+      - name: Install dependencies
+        run: sudo apt update &&
+             sudo apt install -y
+                 libfftw3-dev
+                 libnetcdf-dev
+                 libnetcdf-c++4-dev
+                 netcdf-bin
+                 python3
+                 python3-pip
+                 python3-pytest
+                 python3-numpy
+                 python3-scipy
+                 lcov
+                 openmpi-bin
+                 libopenmpi-dev
+                 petsc-dev
+                 slepc-dev
+                 liblapack-dev
+                 libparpack2-dev
+                 libhypre-dev
+
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.x'
+
+      - name: Install pip packages
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install -r requirements.txt
+
+      - name: Cache SUNDIALS build
+        uses: actions/cache@v4
+        with:
+          path: /home/runner/local
+          key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
+
+      - name: Build SUNDIALS
+        run: ./.build_sundials_for_ci.sh
+
+      - name: Build PETSc
+        run: BUILD_PETSC=${{ 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 }}
+
+  Fedora:
+    # This is its own job as it doesn't use most of the steps of the
+    # standard_tests
+    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+      - name: Build Fedora
+        run: ./.ci_fedora.sh setup openmpi latest
+        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@v5
+        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