Release V5.2.0

.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

@@ -41,6 +41,7 @@ then
     # Ignore weak depencies
     echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
     echo "minrate=10M" >> /etc/dnf/dnf.conf
+    export FORCE_COLUMNS=200
     time dnf -y install dnf5
     time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort python3-boututils
     # Allow to override packages - see #2073

.ci_with_cmake.sh

@@ -17,12 +17,6 @@ ctest --output-on-failure --timeout 300
 
 export LD_LIBRARY_PATH=/home/runner/local/lib:$LD_LIBRARY_PATH
 
-# Test bout-config basic functionallity
-cd ../examples/make-script
-PATH=../../build/bin:$PATH bout-config --all
-PATH=../../build/bin:$PATH make
-./test --help
-cd -
 # Test bout++Config.cmake
 cd ../examples/conduction
 cmake . -B build -DCMAKE_PREFIX_PATH=../../build
@@ -32,13 +26,6 @@ cd -
 
 make install -j 2
 rm -rf build
-# Test installation with plain `make`
-cd ../examples/make-script
-rm test
-PATH=../../installed/bin:$PATH bout-config --all
-PATH=../../installed/bin:$PATH make
-./test --help
-cd -
 # Test installation with CMake
 cd ../examples/conduction
 cmake . -B build -DCMAKE_PREFIX_PATH=../../installed

.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

.clang-tidy

@@ -1,18 +1,10 @@
 ---
-Checks:          'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters'
+Checks:          'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters,-readability-identifier-length'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
 FormatStyle:     file
 CheckOptions:
 
-  # Allow some common short names
-  - key:             readability-identifier-length.IgnoredVariableNames
-    value:           '^[dn]?[xyz]$'
-  - key:             readability-identifier-length.IgnoredParameterNames
-    value:           '^[dfijknxyz][01xyz]?$'
-  - key:             readability-identifier-length.IgnoredLoopCounterNames
-    value:           '^[ijkxyz_]$'
-
   # Don't expand macros when simplifying boolean expressions,
   # otherwise this breaks `ASSERT` macros!
   - key:             readability-simplify-boolean-expr.IgnoreMacros
@@ -27,6 +19,7 @@ These are all basically unavoidable in HPC numeric code:
 -cppcoreguidelines-pro-bounds-pointer-arithmetic
 -readability-function-cognitive-complexity
 -bugprone-easily-swappable-parameters
+-readability-identifier-length
 
 This doesn't work very well:
 -clang-analyzer-optin.mpi*

.github/workflows/clang-format.yml

@@ -8,6 +8,8 @@ on:
 
 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
@@ -22,7 +24,8 @@ jobs:
 
       - name: Run clang-format
         id: format
-        run: git clang-format origin/${{ github.base_ref }}
+        run:
+          while ! git clang-format origin/${{ github.base_ref }} ; do git add . ; done
 
       - name: Commit to the PR branch
         uses: stefanzweifel/git-auto-commit-action@v5

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

@@ -5,16 +5,15 @@ on:
     paths:
       - '**.cxx'
       - '**.hxx'
-    branches-ignore:
-      # Release candidate branches tend to have big PRs which causes all sorts of problems
-      - 'v*rc'
 
 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
@@ -31,6 +30,7 @@ jobs:
           # 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 && \

.github/workflows/tests.yml

@@ -39,20 +39,24 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased"
+          - 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"
@@ -71,18 +75,20 @@ jobs:
                             -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=3
+            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
 
@@ -94,6 +100,7 @@ jobs:
                             -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
@@ -107,6 +114,7 @@ jobs:
                             -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
@@ -120,6 +128,7 @@ jobs:
                             -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
@@ -157,6 +166,7 @@ jobs:
                  slepc-dev
                  liblapack-dev
                  libparpack2-dev
+                 libhypre-dev
 
       - uses: actions/checkout@v5
         with:
@@ -183,13 +193,16 @@ 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 }}
 
   Fedora:
     # This is its own job as it doesn't use most of the steps of the
     # standard_tests
-    timeout-minutes: 60
+    timeout-minutes: 120
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
@@ -200,3 +213,30 @@ 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