Merge branch 'development' into popiii

.ci/azure-pipelines-aarch64-debug.yml

@@ -30,7 +30,7 @@ jobs:
   - task: CMake@1
     displayName: 'Run CTest'
     inputs:
-      cmakeArgs: '-E chdir . ctest -j 2 -T Test --output-on-failure'
+      cmakeArgs: '-E chdir . ctest -j 2 -T Test -E "RadhydroPulseMG*" --output-on-failure'
 
   - task: PublishTestResults@2
     inputs:

.ci/azure-pipelines-aarch64-hwasan.yml

@@ -0,0 +1,41 @@
+# Starter pipeline
+# Start with a minimal pipeline that you can customize to build and deploy your code.
+# Add steps that build, run tests, deploy, and more:
+# https://aka.ms/yaml
+
+trigger:
+- development
+
+pr:
+  autoCancel: true
+  branches:
+    include:
+    - development
+
+jobs:
+- job: BuildAndTest
+  timeoutInMinutes: 180 # how long to run the job before automatically cancelling
+  pool: oracle-cloud
+  steps:
+  - task: CMake@1
+    displayName: 'Configure CMake'
+    inputs:
+      cmakeArgs: '.. -DCMAKE_BUILD_TYPE=Release -DENABLE_HWASAN=ON -DCMAKE_CXX_FLAGS="-fPIC" -DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=lld" -DCMAKE_SHARED_LINKER_FLAGS="-fuse-ld=lld" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DAMReX_SPACEDIM=1'
+
+  - task: CMake@1
+    displayName: 'Build Quokka'
+    inputs:
+      cmakeArgs: '--build .'
+
+  - task: CMake@1
+    displayName: 'Run CTest'
+    inputs:
+      cmakeArgs: '-E chdir . ctest -j 2 -T Test --output-on-failure'
+
+  - task: PublishTestResults@2
+    inputs:
+      testResultsFormat: cTest
+      testResultsFiles: build/Testing/*/Test.xml
+      testRunTitle: $(Agent.JobName)
+    condition: succeededOrFailed()
+    displayName: Publish test results

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

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: ZedThree/clang-tidy-review/[email protected].0
+      - uses: ZedThree/clang-tidy-review/[email protected].1
       # lgtm_comment_body, max_comments, and annotations need to be set on the posting workflow in a split setup
         with:
         # adjust options as necessary

.github/workflows/clang-tidy.yml

@@ -17,7 +17,7 @@ jobs:
         submodules: true
         fetch-depth: 0
 
-    - uses: ZedThree/[email protected].0
+    - uses: ZedThree/[email protected].1
       id: review
       with:
         config_file: src/.clang-tidy
@@ -27,7 +27,7 @@ jobs:
         split_workflow: true
 
     # Uploads an artefact containing clang_fixes.json
-    - uses: ZedThree/clang-tidy-review/[email protected].0
+    - uses: ZedThree/clang-tidy-review/[email protected].1
 
     # If there are any comments, fail the check
     - if: steps.review.outputs.total_comments > 0

.github/workflows/cmake-macos.yml

@@ -17,7 +17,7 @@ env:
 
 jobs:
   build:
-    runs-on: macos-13
+    runs-on: macos-14
 
     steps:
     - uses: actions/checkout@v4
@@ -60,8 +60,7 @@ jobs:
       working-directory: ${{runner.workspace}}/build
       shell: bash
       # Execute the build.  You can specify a specific target with "--target <NAME>"
-      # Restrict to 1 build process at a time to avoid OOM kills.
-      run: cmake --build . --config $BUILD_TYPE --parallel 1
+      run: cmake --build . --config $BUILD_TYPE --parallel 2
 
     - name: Create test output directory
       run: cmake -E make_directory $GITHUB_WORKSPACE/tests

.github/workflows/codeql.yml

@@ -0,0 +1,110 @@
+name: CodeQL
+
+on:
+  push:
+    branches: [ "development" ]
+  pull_request:
+    branches: [ "development" ]
+  schedule:
+    - cron: "27 3 * * 0"
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-codeql
+  cancel-in-progress: true
+
+jobs:
+  analyze:
+    if: ${{ github.repository == 'quokka-astro/quokka' || github.event_name != 'schedule' }}
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python, cpp ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - name: Install Packages (C++)
+        if: ${{ matrix.language == 'cpp' }}
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
+          .github/workflows/dependencies/dependencies_ccache.sh
+          sudo ln -s /usr/local/bin/ccache /usr/local/bin/g++
+
+      - name: Set Up Cache
+        if: ${{ matrix.language == 'cpp' }}
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/ccache
+          key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+          restore-keys: |
+               ccache-${{ github.workflow }}-${{ github.job }}-git-
+
+      - name: Configure (C++)
+        if: ${{ matrix.language == 'cpp' }}
+        run: |
+          cmake -S . -B build                            \
+              -DQUOKKA_PYTHON=OFF                        \
+              -DCMAKE_VERBOSE_MAKEFILE=ON                \
+              -DCMAKE_CXX_COMPILER="/usr/local/bin/g++"
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+          config-file: ./.github/workflows/codeql/codeql-config.yml
+
+      - name: Build (py)
+        uses: github/codeql-action/autobuild@v3
+        if: ${{ matrix.language == 'python' }}
+
+      - name: Build (C++)
+        if: ${{ matrix.language == 'cpp' }}
+        run: |
+          export CCACHE_COMPRESS=1
+          export CCACHE_COMPRESSLEVEL=10
+          export CCACHE_MAXSIZE=30M
+          ccache -z
+
+          cmake --build build -j 4
+
+          ccache -s
+          du -hs ~/.cache/ccache
+
+          # Make sure CodeQL has something to do
+          touch src/main.cpp
+          export CCACHE_DISABLE=1
+          cd build
+          make -j 4
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:${{ matrix.language }}"
+
+  save_pr_number:
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Save PR number
+        env:
+          PR_NUMBER: ${{ github.event.number }}
+        run: |
+          echo $PR_NUMBER > pr_number.txt
+      - uses: actions/upload-artifact@v4
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1

.github/workflows/codeql/codeql-config.yml

@@ -0,0 +1,10 @@
+query-filters:
+  - exclude:
+      id:
+        - cpp/commented-out-code
+        - cpp/complex-condition
+        - cpp/equality-on-floats
+        - cpp/fixme-comment
+        - cpp/path-injection
+        - cpp/poorly-documented-function
+        - cpp/use-of-goto

CMakeLists.txt

@@ -30,6 +30,7 @@ set(AMReX_TINY_PROFILE ON CACHE BOOL "" FORCE)
 option(QUOKKA_PYTHON "Compile with Python support (on/off)" ON)
 option(DISABLE_FMAD "Disable fused multiply-add instructions on GPU (on/off)" ON)
 option(ENABLE_ASAN "Enable AddressSanitizer and UndefinedBehaviorSanitizer" OFF)
+option(ENABLE_HWASAN "Enable HWAddressSanitizer" OFF)
 option(WARNINGS_AS_ERRORS "Treat compiler warnings as errors" OFF)
 option(QUOKKA_OPENPMD "Enable OpenPMD output (on/off)" OFF)
 

src/CMakeLists.txt

@@ -60,6 +60,13 @@ if(ENABLE_ASAN)
   add_link_options(-fsanitize=address -fsanitize=undefined)
 endif(ENABLE_ASAN)
 
+if(ENABLE_HWASAN)
+  # enable HWAddressSanitizer for debugging
+  message(STATUS "Compiling with HWAddressSanitizer *enabled*")
+  add_compile_options(-fsanitize=hwaddress)
+  add_link_options(-fsanitize=hwaddress)
+endif(ENABLE_HWASAN)
+
 if(DISABLE_FMAD)
   message(STATUS "Fused multiply-add (FMAD) is disabled for device code.")
   add_compile_options($<$<COMPILE_LANGUAGE:C>:-ffp-contract=off>)
@@ -171,6 +178,7 @@ add_subdirectory(RadhydroShockCGS)
 add_subdirectory(RadhydroShockMultigroup)
 add_subdirectory(RadhydroUniformAdvecting)
 add_subdirectory(RadhydroPulse)
+add_subdirectory(RadhydroPulseMG)
 
 add_subdirectory(ODEIntegration)
 add_subdirectory(Cooling)

src/RadhydroPulse/CMakeLists.txt

@@ -6,4 +6,4 @@ if (AMReX_SPACEDIM EQUAL 1)
   endif(AMReX_GPU_BACKEND MATCHES "CUDA")
 
   add_test(NAME RadhydroPulse COMMAND test_radhydro_pulse RadhydroPulse.in WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/tests)
-endif()
+endif()