Merge branch 'develop' into myTempSu2Rep

Author: lcheng9

.clang-format

@@ -2,4 +2,4 @@ BasedOnStyle: Google
 PointerAlignment: Left
 DerivePointerAlignment: false
 ColumnLimit: 120
-SortIncludes: Never
+SortIncludes: false

.github/workflows/code-style.yml

@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
          python-version: '3.10'
          check-latest: true

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Packages (cpp)
         if: ${{ matrix.language == 'cpp' }}
@@ -37,20 +37,20 @@ jobs:
         run: ./meson.py build --optimization=1
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
         if: ${{ matrix.language == 'python' }}
 
       - name: Build cpp
         if: ${{ matrix.language == 'cpp' }}
         run: ./ninja -C build
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/regression.yml

@@ -30,7 +30,7 @@ jobs:
           - config_set: ReverseMPI
             flags: '-Denable-autodiff=true -Denable-normal=false -Denable-pywrapper=true -Denable-tests=true --warnlevel=3 --werror'
           - config_set: ForwardMPI
-            flags: '-Denable-directdiff=true -Denable-normal=false -Denable-tests=true --warnlevel=3 --werror'
+            flags: '-Denable-directdiff=true -Denable-normal=false -Denable-tests=true -Denable-mlpcpp=true --warnlevel=3 --werror'
           - config_set: BaseNoMPI
             flags: '-Denable-pywrapper=true -Denable-openblas=true -Dwith-mpi=disabled -Denable-mlpcpp=true -Denable-tests=true --warnlevel=3 --werror'
           - config_set: ReverseNoMPI
@@ -46,29 +46,29 @@ jobs:
     runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
     steps:
       - name: Cache Object Files
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ccache
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
         run: tar -zcvf install_bin.tgz install/*
       - name: Upload Binaries
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -89,29 +89,67 @@ jobs:
     runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
     steps:
       - name: Cache Object Files
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ccache
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:240320-1536
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
         run: tar -zcvf install_bin.tgz install/*
       - name: Upload Binaries
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+  build_asan:
+    name: Build SU2 (asan)
+    strategy:
+      fail-fast: false
+      matrix:
+        config_set: [BaseNoMPI-asan, ReverseNoMPI-asan]
+        include:
+          - config_set: BaseNoMPI-asan
+            flags: '--buildtype=debugoptimized -Denable-openblas=true -Dwith-mpi=disabled -Denable-mlpcpp=true --warnlevel=3 --werror'
+          - config_set: ReverseNoMPI-asan
+            flags: '--buildtype=debugoptimized -Denable-autodiff=true -Denable-normal=false -Dwith-mpi=disabled --warnlevel=3 --werror'
+    runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
+    steps:
+      - name: Cache Object Files
+        uses: actions/cache@v4
+        with:
+          path: ccache
+          key: ${{ matrix.config_set }}-${{ github.sha }}
+          restore-keys: ${{ matrix.config_set }}
+      - name: Pre Cleanup
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+      - name: Build
+        run: docker run --rm --cap-add SYS_PTRACE -v $(pwd):${{ github.workspace }} -w ${{ github.workspace }} ghcr.io/su2code/su2/build-su2-asan:240320-1536 -b ${{github.ref}} -f "${{matrix.flags}}"
+      - name: Compress binaries
+        run: tar -zcvf install_bin.tgz install/*
+      - name: Upload Binaries
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.config_set }}
+          path: install_bin.tgz
+      - name: Post Cleanup
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -142,12 +180,12 @@ jobs:
             tag: OMP
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Download All artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
       - name: Uncompress and Move Binaries
         run: |
           BIN_FOLDER="$PWD/install/bin"
@@ -168,12 +206,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}}
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -188,12 +226,12 @@ jobs:
         testscript: ['hybrid_regression.py', 'hybrid_regression_AD.py']
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Download All artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
       - name: Uncompress and Move Binaries
         run: |
           BIN_FOLDER="$PWD/install/bin"
@@ -214,12 +252,57 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--tsan"
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+  address_sanitizer_tests:
+    runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
+    name: Address Sanitizer Tests
+    needs: build_asan
+    strategy:
+      fail-fast: false
+      matrix:
+        testscript: ['serial_regression.py', 'serial_regression_AD.py']
+    steps:
+      - name: Pre Cleanup
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+      - name: Download All artifacts
+        uses: actions/download-artifact@v4
+      - name: Uncompress and Move Binaries
+        run: |
+          BIN_FOLDER="$PWD/install/bin"
+          mkdir -p $BIN_FOLDER
+          ls -lah $BIN_FOLDER
+          for type in Base Reverse Forward; do
+            TYPE_FOLDER="${type}NoMPI-asan"
+            echo "Processing '$TYPE_FOLDER' ..."
+            if [ -d $TYPE_FOLDER ]; then
+              pushd $TYPE_FOLDER
+              ls -lah
+              tar -zxvf install_bin.tgz
+              ls -lah install/bin/
+              cp -r install/* $BIN_FOLDER/../
+              popd;
+            fi
+          done
+          chmod a+x $BIN_FOLDER/*
+          ls -lahR $BIN_FOLDER
+      - name: Run Tests in Container
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:240320-1536
+        with:
+          # -t <Tutorials-branch> -c <Testcases-branch>
+          args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--asan"
+      - name: Cleanup
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -240,22 +323,22 @@ jobs:
             tag: MPI
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Download Base
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: ${{format('Base{0}', matrix.tag)}}
           path: ${{format('Base{0}', matrix.tag)}}
       - name: Download Reverse
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: ${{format('Reverse{0}', matrix.tag)}}
           path: ${{format('Reverse{0}', matrix.tag)}}
       - name: Download Forward
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: ${{format('Forward{0}', matrix.tag)}}
           path: ${{format('Forward{0}', matrix.tag)}}
@@ -301,11 +384,11 @@ jobs:
           echo $PWD
           ls -lahR
       - name: Run Unit Tests
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: install/bin/${{matrix.testdriver}}
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}

.github/workflows/release-management.yml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cache Object Files
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ccache
           key: ${{ matrix.os_bin }}-${{ github.sha }}
@@ -44,7 +44,7 @@ jobs:
           zip -r ../${{matrix.os_bin}}.zip bin/*
         # Uploads binaries as artifacts (just as a backup)
       - name: Upload Binaries
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{matrix.os_bin}}
           path: ${{matrix.os_bin}}.zip

.github/workflows/require-labels.yml

@@ -6,7 +6,7 @@ jobs:
   label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v3
+      - uses: mheap/github-action-required-labels@v5
         with:
           mode: exactly
           count: 1

.gitmodules

@@ -27,3 +27,6 @@
 [submodule "subprojects/MLPCpp"]
 	path = subprojects/MLPCpp
 	url = https://github.com/EvertBunschoten/MLPCpp.git
+[submodule "externals/FADO"]
+	path = externals/FADO
+	url = https://github.com/pcarruscag/FADO.git

AUTHORS.md

@@ -69,8 +69,10 @@ Daumantas Kavolis
 Dave Taflin
 Eduardo Molina
 Edwin van der Weide
+Eitan Aberman
 Ethan Alan Hereth
 Florian Dittmann
+Filip Hahs
 Francesco Poli
 Francisco D. Palacios
 Gaurav Bansal
@@ -98,6 +100,7 @@ Kedar Naik
 Kürşat Yurt
 LaSerpe
 Lennaert Tol
+Liang Cheng
 Lisa Kusch
 Matteo Pini
 Max Aehle
@@ -106,6 +109,7 @@ Max Sagebaum
 Michele Gaffuri
 Mickael Philit
 Mladen Banovic
+Mor
 Nat-1
 Nicola Fonzi
 Nijso Beishuizen
@@ -132,11 +136,14 @@ Thomas D. Economon
 Tim Albring
 TobiKattmann
 Trent Lukaczyk
+Vikram Bharadwaj
 Vinzenz Götz
 VivaanKhatri
 Wally Maier
+Yair Mor-Yossef
 Y. Chandukrishna
 Zan Xu
+Zcaic
 aaronyicongfu
 aeroamit
 anilvar