Merge branch 'upstream-master' into core/improve-master-slave-constra…

…ints
KratosMultiphysics · Jan 18, 2024 · a9a5da1 · a9a5da1
2 parents 72007d1 + fbc4184
commit a9a5da1
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Showing 464 changed files with 490,563 additions and 13,116 deletions.
diff --git a/.github/get_files_changed_in_pr.py b/.github/get_files_changed_in_pr.py
@@ -5,6 +5,9 @@
 
 def get_files_changed_in_pr(pr_number: int) -> list[str]:
     # from: https://stackoverflow.com/questions/25071579/list-all-files-changed-in-a-pull-request-in-git-github
+
+    modified_files: list[str] = []
+
     try:
         process_output: str = subprocess.run(
             [
@@ -19,14 +22,15 @@ def get_files_changed_in_pr(pr_number: int) -> list[str]:
             ],
             check=True,
             capture_output=True,
-            text=True
+            text=True,
         ).stdout
 
-        return process_output.splitlines()
+        modified_files = process_output.splitlines()
 
     except Exception as e:
         print(f"An error occured while getting the modified files: {e}")
-        return []
+
+    return modified_files
 
 
 if __name__ == "__main__":

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -31,6 +31,7 @@ permissions:
 jobs:
   changed-files:
     runs-on: ubuntu-latest
+    # see https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-defining-outputs-for-a-job
     outputs:
       files: ${{ steps.get_files.outputs.changed_files }}
     steps:
@@ -53,6 +54,8 @@ jobs:
         compiler: [gcc, clang]
     env:
       KRATOS_BUILD_TYPE: ${{ matrix.build-type }}
+      KRATOS_CI_CHANGED_FILES: ${{needs.changed-files.outputs.files}}
+      KRATOS_CI_APPLICATIONS: ".github/workflows/ci_apps_linux.json"
       OMPI_MCA_rmaps_base_oversubscribe: 1 # Allow oversubscription for MPI (needed for OpenMPI >= 3.0)
       OMPI_MCA_btl_vader_single_copy_mechanism: none # suppressing some annoying OpenMPI messages
 
@@ -66,8 +69,9 @@ jobs:
     # - name: Installing dependencies
     # => must be added to the docker container to avoid reinstalling it in every CI run
 
-    - name: Print changed files
-      run: echo "${{needs.changed-files.outputs.files}}"
+    - name: CI configuration
+      shell: bash
+      run: python3 kratos/python_scripts/testing/ci_utilities.py
 
     - name: Build
       shell: bash
@@ -88,6 +92,7 @@ jobs:
         fi
         source /opt/intel/oneapi/setvars.sh
         cp .github/workflows/configure.sh configure.sh
+        python3 kratos/python_scripts/testing/ci_utilities.py
         bash configure.sh
 
     - name: Running python tests
@@ -159,18 +164,25 @@ jobs:
 
   windows:
     runs-on: windows-2022
+    needs: changed-files
     env:
       KRATOS_BUILD_TYPE: Custom
+      KRATOS_CI_CHANGED_FILES: ${{needs.changed-files.outputs.files}}
+      KRATOS_CI_APPLICATIONS: ".github/workflows/ci_apps_windows.json"
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.8'
 
+    - name: CI configuration
+      shell: bash
+      run: python3 kratos/python_scripts/testing/ci_utilities.py
+
     - name: Download boost
       run: |
-        $url = "https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.gz"
+        $url = "https://archives.boost.io/release/1.74.0/source/boost_1_74_0.tar.gz"
         (New-Object System.Net.WebClient).DownloadFile($url, "$env:TEMP\boost.tar.gz")
         7z.exe x "$env:TEMP\boost.tar.gz" -o"$env:TEMP\boostArchive" -y | Out-Null
         7z.exe x "$env:TEMP\boostArchive" -o"$env:TEMP\boost" -y | Out-Null
@@ -188,6 +200,7 @@ jobs:
       shell: cmd
       run: |
         copy .\.github\workflows\configure.cmd
+        python kratos/python_scripts/testing/ci_utilities.py
         configure.cmd
 
     - name: Running python tests
@@ -199,8 +212,11 @@ jobs:
 
   centos:
     runs-on: ubuntu-latest
+    needs: changed-files
     env:
       KRATOS_BUILD_TYPE: Custom
+      KRATOS_CI_CHANGED_FILES: ${{needs.changed-files.outputs.files}}
+      KRATOS_CI_APPLICATIONS: ".github/workflows/ci_apps_centos.json"
 
     container:
       image: kratosmultiphysics/kratos-image-ci-centos7:latest
@@ -212,6 +228,10 @@ jobs:
     # - name: Installing dependencies
     # => must be added to the docker container to avoid reinstalling it in every CI run
 
+    - name: CI configuration
+      shell: bash
+      run: python3.8 kratos/python_scripts/testing/ci_utilities.py
+
     - name: Build
       run: |
         export KRATOS_CMAKE_CXX_FLAGS="-Werror -Wno-deprecated-declarations -Wignored-qualifiers"
@@ -227,8 +247,11 @@ jobs:
 
   ubuntu-core-without-unity:
     runs-on: ubuntu-latest
+    needs: changed-files
     env:
       KRATOS_BUILD_TYPE: Custom
+      KRATOS_CI_CHANGED_FILES: ${{needs.changed-files.outputs.files}}
+      KRATOS_CI_APPLICATIONS: "ONLY_CORE"
       OMPI_MCA_rmaps_base_oversubscribe: 1 # Allow oversubscription for MPI (needed for OpenMPI >= 3.0)
 
     container:
@@ -244,6 +267,10 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
+    - name: CI configuration
+      shell: bash
+      run: python3 kratos/python_scripts/testing/ci_utilities.py
+
     - name: Cache Build
       id: cache-build
       uses: actions/cache@v3
@@ -280,8 +307,7 @@ jobs:
         -DTRILINOS_INCLUDE_DIR="/usr/include/trilinos" \
         -DTRILINOS_LIBRARY_DIR="/usr/lib/x86_64-linux-gnu" \
         -DTRILINOS_LIBRARY_PREFIX="trilinos_" \
-        -DKRATOS_USE_PCH=ON \
-        -DINSTALL_RUNKRATOS=OFF
+        -DKRATOS_USE_PCH=ON
 
         # Build
         cmake --build "${KRATOS_BUILD}/${KRATOS_BUILD_TYPE}" --target install -- -j2
@@ -350,18 +376,25 @@ jobs:
 
   windows-core-without-unity:
     runs-on: windows-2022
+    needs: changed-files
     env:
       KRATOS_BUILD_TYPE: Custom
+      KRATOS_CI_CHANGED_FILES: ${{needs.changed-files.outputs.files}}
+      KRATOS_CI_APPLICATIONS: "ONLY_CORE"
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.8'
 
+    - name: CI configuration
+      shell: bash
+      run: python3 kratos/python_scripts/testing/ci_utilities.py
+
     - name: Download boost
       run: |
-        $url = "https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.gz"
+        $url = "https://archives.boost.io/release/1.74.0/source/boost_1_74_0.tar.gz"
         (New-Object System.Net.WebClient).DownloadFile($url, "$env:TEMP\boost.tar.gz")
         7z.exe x "$env:TEMP\boost.tar.gz" -o"$env:TEMP\boostArchive" -y | Out-Null
         7z.exe x "$env:TEMP\boostArchive" -o"$env:TEMP\boost" -y | Out-Null
@@ -396,7 +429,6 @@ jobs:
           -H"%KRATOS_SOURCE%"                                 ^
           -B"%KRATOS_BUILD%\%KRATOS_BUILD_TYPE%"              ^
           -DBOOST_ROOT="%TEMP%\boost"                         ^
-          -DINSTALL_RUNKRATOS=OFF                             ^
           -DCMAKE_CXX_FLAGS="/Od /we4661 /we4804 /WX /wd4996" ^
           -DKRATOS_USE_PCH=ON                                 ^
           -DFORCE_LOCAL_ZLIB_COMPILATION=ON                   || goto :error
@@ -512,8 +544,11 @@ jobs:
 
   ubuntu-intel:
     runs-on: ubuntu-latest
+    needs: changed-files
     env:
       KRATOS_BUILD_TYPE: Custom
+      KRATOS_CI_CHANGED_FILES: ${{needs.changed-files.outputs.files}}
+      KRATOS_CI_APPLICATIONS: ".github/workflows/ci_apps_intel.json"
       OMPI_MCA_rmaps_base_oversubscribe: 1 # Allow oversubscription for MPI (needed for OpenMPI >= 3.0)
       OMPI_MCA_btl_vader_single_copy_mechanism: none # suppressing some annoying OpenMPI messages
 
@@ -527,6 +562,10 @@ jobs:
     # - name: Installing dependencies
     # => must be added to the docker container to avoid reinstalling it in every CI run
 
+    - name: CI configuration
+      shell: bash
+      run: python3 kratos/python_scripts/testing/ci_utilities.py
+
     - name: Build
       shell: bash
       run: |

diff --git a/.github/workflows/ci_apps_centos.json b/.github/workflows/ci_apps_centos.json
@@ -0,0 +1,9 @@
+[
+    "FluidDynamicsApplication",
+    "MappingApplication",
+    "StructuralMechanicsApplication",
+    "MeshingApplication",
+    "LinearSolversApplication",
+    "ConstitutiveLawsApplication",
+    "CoSimulationApplication"
+]
diff --git a/.github/workflows/ci_apps_intel.json b/.github/workflows/ci_apps_intel.json
@@ -0,0 +1 @@
+[]
diff --git a/.github/workflows/ci_apps_linux.json b/.github/workflows/ci_apps_linux.json
@@ -0,0 +1,35 @@
+[
+    "ConvectionDiffusionApplication",
+    "LinearSolversApplication",
+    "StructuralMechanicsApplication",
+    "FluidDynamicsApplication",
+    "FluidDynamicsBiomedicalApplication",
+    "MeshMovingApplication",
+    "DEMApplication",
+    "CSharpWrapperApplication",
+    "MetisApplication",
+    "TrilinosApplication",
+    "ShapeOptimizationApplication",
+    "CoSimulationApplication",
+    "CableNetApplication",
+    "RANSApplication",
+    "MappingApplication",
+    "FSIApplication",
+    "MeshingApplication",
+    "CompressiblePotentialFlowApplication",
+    "HDF5Application",
+    "ContactStructuralMechanicsApplication",
+    "IgaApplication",
+    "ParticleMechanicsApplication",
+    "ChimeraApplication",
+    "StatisticsApplication",
+    "SwimmingDEMApplication",
+    "ConstitutiveLawsApplication",
+    "RomApplication",
+    "ShallowWaterApplication",
+    "GeoMechanicsApplication",
+    "DamApplication",
+    "PoromechanicsApplication",
+    "OptimizationApplication",
+    "MedApplication"
+]
diff --git a/.github/workflows/ci_apps_windows.json b/.github/workflows/ci_apps_windows.json
@@ -0,0 +1,29 @@
+[
+    "CableNetApplication",
+    "ConvectionDiffusionApplication",
+    "FluidDynamicsApplication",
+    "FluidDynamicsBiomedicalApplication",
+    "FSIApplication",
+    "MeshingApplication",
+    "MeshMovingApplication",
+    "LinearSolversApplication",
+    "StructuralMechanicsApplication",
+    "DEMApplication",
+    "ChimeraApplication",
+    "IgaApplication",
+    "ParticleMechanicsApplication",
+    "MappingApplication",
+    "CoSimulationApplication",
+    "StatisticsApplication",
+    "SwimmingDEMApplication",
+    "ShapeOptimizationApplication",
+    "ConstitutiveLawsApplication",
+    "RANSApplication",
+    "CompressiblePotentialFlowApplication",
+    "RomApplication",
+    "ShallowWaterApplication",
+    "GeoMechanicsApplication",
+    "DamApplication",
+    "PoromechanicsApplication",
+    "OptimizationApplication"
+]
diff --git a/.github/workflows/configure.cmd b/.github/workflows/configure.cmd
@@ -12,6 +12,7 @@ set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\CableNetApplicatio
 set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\ConvectionDiffusionApplication;
 set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\FluidDynamicsApplication;
 set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\FluidDynamicsBiomedicalApplication;
+set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\FluidDynamicsHydraulicsApplication;
 set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\FSIApplication;
 set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\MeshingApplication;
 set KRATOS_APPLICATIONS=%KRATOS_APPLICATIONS%%KRATOS_APP_DIR%\MeshMovingApplication;
@@ -45,7 +46,6 @@ cmake                                                 ^
   -H"%KRATOS_SOURCE%"                                 ^
   -B"%KRATOS_BUILD%\%KRATOS_BUILD_TYPE%"              ^
   -DBOOST_ROOT="%TEMP%\boost"                         ^
-  -DINSTALL_RUNKRATOS=OFF                             ^
   -DCMAKE_CXX_FLAGS="/Od /we4661 /we4804 /WX /wd4996" ^
   -DFORCE_LOCAL_ZLIB_COMPILATION=ON                   ^
   -DCMAKE_UNITY_BUILD=ON                                    || goto :error

diff --git a/.github/workflows/configure.sh b/.github/workflows/configure.sh
@@ -25,6 +25,7 @@ add_app ${KRATOS_APP_DIR}/LinearSolversApplication;
 add_app ${KRATOS_APP_DIR}/StructuralMechanicsApplication;
 add_app ${KRATOS_APP_DIR}/FluidDynamicsApplication;
 add_app ${KRATOS_APP_DIR}/FluidDynamicsBiomedicalApplication;
+add_app ${KRATOS_APP_DIR}/FluidDynamicsHydraulicsApplication;
 add_app ${KRATOS_APP_DIR}/MeshMovingApplication;
 add_app ${KRATOS_APP_DIR}/DEMApplication;
 add_app ${KRATOS_APP_DIR}/CSharpWrapperApplication;

diff --git a/.github/workflows/intel_configure.sh b/.github/workflows/intel_configure.sh
@@ -58,7 +58,6 @@ echo "Kratos build type is ${KRATOS_BUILD_TYPE}"
 # Configure
 cmake -H"${KRATOS_SOURCE}" -B"${KRATOS_BUILD}/${KRATOS_BUILD_TYPE}" \
 ${KRATOS_CMAKE_OPTIONS_FLAGS} \
--DINSTALL_RUNKRATOS=OFF \
 -DUSE_MPI=ON \
 -DPYTHON_EXECUTABLE="/usr/bin/python3.10" \
 -DCMAKE_CXX_FLAGS="${KRATOS_CMAKE_CXX_FLAGS} -O3 -Wall -Werror-all -diag-disable 1478 -diag-disable 1786" \

diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml
@@ -41,7 +41,7 @@ jobs:
         shell: bash
         run: cp -r statik_content/Page_files/* main/docs/
       - name: Setup Pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v4
       - name: Create navigation menus
         shell: bash
         run: cd main/docs && python3 process_pages.py -t web
@@ -51,7 +51,7 @@ jobs:
           source: ./main/docs
           destination: ./main/docs/_site
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: ./main/docs/_site
 
@@ -65,4 +65,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/nightly_build.yml b/.github/workflows/nightly_build.yml
@@ -110,13 +110,13 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.8'
 
     - name: Download boost
       run: |
-        $url = "https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.gz"
+        $url = "https://archives.boost.io/release/1.74.0/source/boost_1_74_0.tar.gz"
         (New-Object System.Net.WebClient).DownloadFile($url, "$env:TEMP\boost.tar.gz")
         7z.exe x "$env:TEMP\boost.tar.gz" -o"$env:TEMP\boostArchive" -y | Out-Null
         7z.exe x "$env:TEMP\boostArchive" -o"$env:TEMP\boost" -y | Out-Null