[Stacked] OGL Version 0.6

.clang-format

@@ -109,4 +109,3 @@ Standard:        Cpp11
 TabWidth:        8
 UseTab:          Never
 ...
-

.cmake-format.py

@@ -1,6 +1,5 @@
+# SPDX-License-Identifier: Unlicense
 # SPDX-FileCopyrightText: 2024 OGL authors
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
 
 # ----------------------------------
 # Options affecting listfile parsing
@@ -29,7 +28,7 @@
   disable = False
 
   # How wide to allow formatted cmake files
-  line_width = 80
+  line_width = 100
 
   # How many spaces to tab for indent
   tab_size = 2
@@ -168,7 +167,7 @@
 with section("lint"):
 
   # a list of lint codes to disable
-  disabled_codes = []
+  disabled_codes = ["C0103"]
 
   # regular expression pattern describing valid function names
   function_pattern = '[0-9a-z_]+'
@@ -242,4 +241,3 @@
   # A dictionary containing any per-command configuration overrides. Currently
   # only `command_case` is supported.
   per_command = {}
-

.github/workflows/build-foam.yml

@@ -11,7 +11,7 @@ defaults:
 
 on:
   push:
-    branches: 
+    branches:
       - dev
       - main
   pull_request:
@@ -41,7 +41,7 @@ jobs:
      - name: Set matrix data
        id: set-matrix
        run: |
-         pwd 
+         pwd
          echo "matrix=$(jq -c . < .github/workflows/test_matrix.json)" >> $GITHUB_OUTPUT
 
   build:
@@ -58,23 +58,22 @@ jobs:
     - name: Get Ginkgo checkout version
       shell: bash
       run: |
-        grep -A1 "set(GINKGO_CHECKOUT_VERSION" CMakeLists.txt|tail -n1|grep -o  "[0-9a-z\-]*" > GINKGO_CHECKOUT_VERSION
+        grep -A1 "set(GINKGO_CHECKOUT_VERSION" CMakeLists.txt|tail -n1|grep -o  "[0-9a-z\-_.]*" > GINKGO_CHECKOUT_VERSION
         export GINKGO_CHECKOUT_VERSION=$(cat GINKGO_CHECKOUT_VERSION)
         echo "GINKGO_CHECKOUT_VERSION=$GINKGO_CHECKOUT_VERSION" >> $GITHUB_ENV
 
     - name: Cache build folder
       uses: actions/cache@v4
+      if: ${{!contains(github.event.pull_request.labels.*.name, 'Skip-cache')}}
       with:
-        key: build-${{ matrix.OF.path }}-${{env.GINKGO_CHECKOUT_VERSION}}
-        path: |
-          ${{github.workspace}}/build
+         key: build_PR_${{ github.event.pull_request.number }}_${{matrix.OF.path}}
+         path: ${{github.workspace}}/build
 
     - name: Cache FOAM_USER_LIBBIN
       uses: actions/cache@v4
       with:
-        key: FOAM_USER_LIBBIN-${{ matrix.OF.version }}-${{ github.sha }}
-        path: |
-          ${{matrix.OF.foam_user_libbin}}
+         key: FOAM_USER_LIBBIN-${{ matrix.OF.path }}-${{ github.sha }}
+         path: ${{matrix.OF.foam_user_libbin}}
 
     - name: Configure CMake
       # Use a bash shell so we can use the same syntax for environment variable
@@ -83,25 +82,19 @@ jobs:
       run: |
         source /root/OpenFOAM/${{matrix.OF.path}}/etc/bashrc
         mkdir -p ${{matrix.OF.foam_user_libbin}}
-        mkdir -p build
-        cd build
-        [ -d "/github/home/$GINKGO_CHECKOUT_VERSION" ] && cp -rp /github/home/$GINKGO_CHECKOUT_VERSION third_party
-        cmake -GNinja -DOGL_ALLOW_REFERENCE_ONLY=On -DOGL_BUILD_UNITTEST=ON -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=${{matrix.OF.foam_user_libbin}} ..
+        cmake --preset develop
 
     - name: Build OGL
-      working-directory: ${{github.workspace}}/build
+      working-directory: ${{github.workspace}}
       run: |
         source /root/OpenFOAM/${{matrix.OF.path}}/etc/bashrc
-        cmake --build . --config $BUILD_TYPE
+        cmake  --build --preset develop
 
     - name: Install OGL
       working-directory: ${{github.workspace}}
       run: |
         source /root/OpenFOAM/${{matrix.OF.path}}/etc/bashrc
-        cmake --install ./build
-        ls $FOAM_USER_LIBBIN
-        ls ${{matrix.OF.foam_user_libbin}}
-
+        cmake --build --preset develop --target install
 
     - name: Check folders
       working-directory: ${{github.workspace}}

.github/workflows/compile_on_aws.yml

@@ -44,9 +44,9 @@ jobs:
             ]
           pre-runner-script: |
                  #!/bin/bash
-                 sudo yum update -y && \ 
+                 sudo yum update -y && \
                  sudo yum install docker git libicu ninja-build libasan10 -y
-                 sudo amazon-linux-extras install epel -y 
+                 sudo amazon-linux-extras install epel -y
                  sudo yum install Lmod -y
                  sudo systemctl enable docker
                  sudo curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash
@@ -84,7 +84,7 @@ jobs:
           module load conda
           conda activate
           python3 -m pip install --upgrade pip
-          pip install setuptools --upgrade 
+          pip install setuptools --upgrade
           git clone https://github.com/exasim-project/OBR
           cd OBR
           pip install .
@@ -123,8 +123,8 @@ jobs:
           module load openmpi
           module load OpenFOAM
           export GINKGO_EXECUTOR=cuda
-          obr init -g --config test/integration.yaml 
-          obr run -o runParallelSolver 
+          obr init -g --config test/integration.yaml
+          obr run -o runParallelSolver
           obr status
 
   stop-runner:

.github/workflows/format-check.yml

@@ -21,5 +21,5 @@ jobs:
     - name: check for todo fixme note
       run: |
         NTODOS="$(grep -r 'TODO DONT MERGE' --exclude-dir=.github | wc -l)"
-        echo "Found $NTODOS TODO DONT MERGE notes" 
-        ! grep -q -r "TODO DONT MERGE" --exclude-dir=.github  
+        echo "Found $NTODOS TODO DONT MERGE notes"
+        ! grep -q -r "TODO DONT MERGE" --exclude-dir=.github

.github/workflows/integration-tests.yml

@@ -19,15 +19,15 @@ env:
   WM_LINK_LANGUAGE: c++
   WM_LABEL_OPTION:  Int32
   WM_MPLIB: SYSTEMOPENMPI
-  MPI_BUFFER_SIZE: 20000000 
+  MPI_BUFFER_SIZE: 20000000
   BUILD_TYPE: Release
   OMPI_ALLOW_RUN_AS_ROOT: 1
   OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
   OMPI_MCA_btl_vader_single_copy_mechanism: none
   OBR_RUN_CMD: "mpirun --oversubscribe -np {np} {solver} -parallel -case {path}/case > {path}/case/{solver}_{timestamp}.log 2>&1"
   GINKGO_EXECUTOR: reference
 
-on: 
+on:
   workflow_call:
     inputs:
       path:
@@ -74,10 +74,10 @@ jobs:
       run: |
          ls
          python3 -m pip install --upgrade pip
-         pip install setuptools --upgrade 
-         pip uninstall obr -y 
-         pip uninstall owls -y 
-         cd /root/OBR 
+         pip install setuptools --upgrade
+         pip uninstall obr -y
+         pip uninstall owls -y
+         cd /root/OBR
          git pull origin dev
          pip install -e .
          obr --version
@@ -89,7 +89,7 @@ jobs:
         export LD_LIBRARY_PATH=$FOAM_USER_LIBBIN:$WM_PROJECT_DIR/platforms/linux64GccDPInt32Opt/lib:$WM_PROJECT_DIR/platforms/linux64GccDPInt32Opt/lib/sys-openmpi/:$WM_PROJECT_DIR/platforms/linux64GccDPInt32Opt/lib/openmpi-system:$WM_PROJECT_DIR/platforms/linux64GccDPInt32Opt/lib/dummy/:$LD_LIBRARY_PATH
         mkdir -p integration && cd integration
         export CYCLIC_CASE=${{inputs.cyclic_case}}
-        obr init -gy --config /__w/OGL/OGL/test/integration.yaml 
+        obr init -g --config /__w/OGL/OGL/test/integration/lidDrivenCavity.yaml
         cat workspace/*/case/*log
 
   setup_integration_matrix:
@@ -108,7 +108,7 @@ jobs:
     name: run-${{matrix.Case}}-${{inputs.version}}
     strategy:
       fail-fast: false
-      matrix: 
+      matrix:
         Case: ${{fromJson(needs.setup_integration_matrix.outputs.matrix)}}
 
     steps:
@@ -128,7 +128,7 @@ jobs:
     - name: Get Ginkgo checkout version
       shell: bash
       run: |
-        grep -A1 "set(GINKGO_CHECKOUT_VERSION" CMakeLists.txt|tail -n1|grep -o  "[0-9a-z\-]*" > GINKGO_CHECKOUT_VERSION
+        grep -A1 "set(GINKGO_CHECKOUT_VERSION" CMakeLists.txt|tail -n1|grep -o  "[0-9a-z\-_.]*" > GINKGO_CHECKOUT_VERSION
         export GINKGO_CHECKOUT_VERSION=$(cat GINKGO_CHECKOUT_VERSION)
         echo "GINKGO_CHECKOUT_VERSION=$GINKGO_CHECKOUT_VERSION" >> $GITHUB_ENV
         echo "Ginkgo_DIR=${{inputs.foam_user_libbin}}/cmake/Ginkgo" >> $GITHUB_ENV
@@ -137,10 +137,10 @@ jobs:
       working-directory: /github/home/
       run: |
          python3 -m pip install --upgrade pip
-         pip install setuptools --upgrade 
-         pip uninstall obr -y 
-         pip uninstall owls -y 
-         cd /root/OBR 
+         pip install setuptools --upgrade
+         pip uninstall obr -y
+         pip uninstall owls -y
+         cd /root/OBR
          git pull origin dev
          pip install -e .
 
@@ -193,7 +193,7 @@ jobs:
     name: validate-${{matrix.Case}}-${{inputs.version}}
     strategy:
       fail-fast: false
-      matrix: 
+      matrix:
         Case: ${{fromJson(needs.setup_integration_matrix.outputs.matrix)}}
 
     steps:
@@ -204,10 +204,10 @@ jobs:
       run: |
          ls
          python3 -m pip install --upgrade pip
-         pip install setuptools --upgrade 
-         pip uninstall obr -y 
-         pip uninstall owls -y 
-         cd /root/OBR 
+         pip install setuptools --upgrade
+         pip uninstall obr -y
+         pip uninstall owls -y
+         cd /root/OBR
          git pull origin dev
          pip install -e .
 
@@ -220,7 +220,7 @@ jobs:
     - name: Validation of exported mtx files
       working-directory: /github/home/${{matrix.Case}}
       run: |
-        python3 /__w/OGL/OGL/test/data_validation.py workspace
+        python3 /__w/OGL/OGL/test/integration/data_validation.py workspace
 
     - name: Run obr status
       working-directory: /github/home/${{matrix.Case}}
@@ -236,14 +236,14 @@ jobs:
           --filter preconditioner==none \
           --filter matrixFormat==Coo \
           --filter global==completed \
-          --validate_against=/__w/OGL/OGL/test/validation.json
+          --validate_against=/__w/OGL/OGL/test/integration/validation.json
 
     - name: Validate preconditioned state
       working-directory: /github/home/${{matrix.Case}}
       run: |
         obr query \
           -q global -q continuityErrors -q CourantNumber \
-          --validate_against=/__w/OGL/OGL/test/validation.json \
+          --validate_against=/__w/OGL/OGL/test/integration/validation.json \
           --filter preconditioner!=none \
           --filter global==completed \
           --filter case==${{matrix.Case}}
@@ -253,7 +253,7 @@ jobs:
       run: |
         obr query \
           -q global -q continuityErrors -q CourantNumber \
-          --validate_against=/__w/OGL/OGL/test/validation.json \
+          --validate_against=/__w/OGL/OGL/test/integration/validation.json \
           --filter matrixFormat!=Coo \
           --filter global==completed \
           --filter case==${{matrix.Case}}

.github/workflows/static_checks.yaml

@@ -5,78 +5,76 @@
 name: Static checks
 run-name: Static checks
 
+defaults:
+ run:
+  shell: bash -o pipefail -i {0}
+
 on:
     pull_request:
       types: [opened, synchronize]
+
+env:
+  USER: user
+  BUILD_TYPE: Release
+  OMPI_ALLOW_RUN_AS_ROOT: 1
+  OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+
+
 jobs:
   build-compilation-db:
     name: Build with IWYU
     runs-on: ubuntu-latest
+    container: greole/ofbase
     steps:
     - uses: actions/checkout@v4
-
-    - name: Add clang repo
-      run: |
-        sudo add-apt-repository 'deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-16 main'
-        wget https://apt.llvm.org/llvm-snapshot.gpg.key
-        sudo apt-key add llvm-snapshot.gpg.key
-
     - name: Install dependencies
       run: |
-        sudo apt update
-        sudo apt install \
+        apt update
+        apt install -y \
            ninja-build \
-           iwyu \
-           clang-16 \
-           libomp-16-dev
-
+           libomp-dev \
+           iwyu
     - name: Create Compilation Database
       run: |
-        cmake --preset ninja-cpuonly-release \
-        -DCMAKE_CXX_COMPILER=clang++-16 \
-        -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
-        cmake --build --preset ninja-cpuonly-release
+        source /root/OpenFOAM/openfoam/etc/bashrc
+        cmake --preset develop \
+          -DCMAKE_CXX_COMPILER=clang++ \
+          -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+        cmake --build --preset develop
     - uses: actions/upload-artifact@v4
       with:
         name: build-artifact
         path: build
   clang-tidy-check:
     name: Clang-tidy Check
     runs-on: ubuntu-latest
+    container: greole/ofbase
     needs: [build-compilation-db]
     steps:
     - uses: actions/checkout@v4
-
-    - name: Add clang repo
-      run: |
-        sudo add-apt-repository 'deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-16 main'
-        wget https://apt.llvm.org/llvm-snapshot.gpg.key
-        sudo apt-key add llvm-snapshot.gpg.key
-
     - name: Install dependencies
       run: |
-        sudo apt update
-        sudo apt install \
-           clang-tidy-16 \
-           libomp-16-dev
-
+        apt update
+        apt install -y \
+           clang-tidy \
+           jq
     - uses: actions/download-artifact@v4
       with:
         name: build-artifact
         path: build
-
     - name: Run clang-tidy
       run: |
-        # Create list of .cpp files belonging to this repository
-        git ls-files | grep -E "\.(cpp)" > pattern
+        git config --global --add safe.directory /__w/OGL/OGL
+        # Create list of all source files belonging to this repository
+        git ls-files | grep -E "\.(C)" > pattern
         # Create list of .cpp files that are in this repository and part of the
         # compilation database
         # also filters out " at the begin and end of the filename
-        jq ".[] | .file" build/ReleaseAll/compile_commands.json \
+        jq ".[] | .file" build/ReleaseCPUOnly/compile_commands.json \
           | sed 's/^"\(.*\)"$/\1/' \
           | grep -F -f pattern - > files
         # run clang-tidy on all specified files
-        clang-tidy-16 --fix --extra-arg=-w -p build/ReleaseAll $(cat files)
+        clang-tidy --fix --extra-arg=-w -p build/ReleaseCPUOnly $(cat files)
 
     - name: Check for fixes
       run: |