Merge branch 'sanitizer-preset' into 'master'

[ci] Add preset and fix sanitizer See merge request ogs/ogs!4978
ufz · Apr 17, 2024 · 1f2a4c5 · 1f2a4c5
2 parents b561871 + d57b3ef
commit 1f2a4c5
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Showing 15 changed files with 159 additions and 103 deletions.
diff --git a/Applications/ApplicationsLib/CMakeLists.txt b/Applications/ApplicationsLib/CMakeLists.txt
@@ -7,8 +7,11 @@ ogs_add_library(ApplicationsLib ${LIB_SOURCES})
 
 target_link_libraries(
     ApplicationsLib
-    PUBLIC BaseLib GeoLib NumLib
-           $<$<TARGET_EXISTS:VTK::ParallelMPI>:VTK::ParallelMPI>
+    PUBLIC
+        BaseLib
+        GeoLib
+        NumLib
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:VTK::ParallelMPI>>:VTK::ParallelMPI>
     PRIVATE CMakeInfoLib
             MathLib
             MeshLib

diff --git a/Applications/CLI/CMakeLists.txt b/Applications/CLI/CMakeLists.txt
@@ -52,17 +52,17 @@ ogs_add_executable(ogs ogs.cpp CommandLineArgumentParser.cpp)
 
 target_link_libraries(
     ogs
-    PRIVATE ApplicationsLib
-            BaseLib
-            CMakeInfoLib
-            GitInfoLib
-            MeshLib
-            ProcessLib
-            $<$<TARGET_EXISTS:MPI::MPI_CXX>:MPI::MPI_CXX>
-            $<$<TARGET_EXISTS:InSituLib>:InSituLib>
-            $<$<TARGET_EXISTS:petsc>:petsc>
-            $<$<TARGET_EXISTS:VTK::ParallelMPI>:VTK::ParallelMPI>
-            tclap
+    PRIVATE
+        ApplicationsLib
+        BaseLib
+        CMakeInfoLib
+        GitInfoLib
+        MeshLib
+        ProcessLib
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:MPI::MPI_CXX>>:MPI::MPI_CXX>
+        $<$<TARGET_EXISTS:InSituLib>:InSituLib>
+        $<$<TARGET_EXISTS:petsc>:petsc>
+        tclap
 )
 
 # ---- Tests ----

diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt b/Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt
@@ -3,8 +3,14 @@ if(OGS_USE_MPI)
         binaryToPVTU BinaryToPVTU.cpp NodeWiseMeshPartitioner.cpp
     )
     target_link_libraries(
-           binaryToPVTU GitInfoLib ProcessLib MeshLib MeshToolsLib tclap
-        $<$<TARGET_EXISTS:MPI::MPI_CXX>:MPI::MPI_CXX> VTK::ParallelMPI
+        binaryToPVTU
+        GitInfoLib
+        ProcessLib
+        MeshLib
+        MeshToolsLib
+        tclap
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:MPI::MPI_CXX>>:MPI::MPI_CXX>
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:VTK::ParallelMPI>>:VTK::ParallelMPI>
     )
     install(TARGETS binaryToPVTU RUNTIME DESTINATION bin)
 endif()

diff --git a/CMakePresets.json b/CMakePresets.json
@@ -215,6 +215,27 @@
         "OGS_USE_MFRONT": "ON",
         "BUILD_SHARED_LIBS": "ON"
       }
+    },
+    {
+      "name": "sanitizer",
+      "inherits": "debug-all",
+      "cacheVariables": {
+        "BUILD_SHARED_LIBS": "ON",
+        "OGS_CXX_FLAGS": "-O3;-fno-var-tracking",
+        "OGS_EIGEN_DYNAMIC_SHAPE_MATRICES": "OFF",
+        "ENABLE_ASAN": "ON",
+        "ENABLE_UBSAN": "ON",
+        "ENABLE_LSAN": "ON",
+        "OGS_BUILD_TFEL": "ON",
+        "OGS_BUILD_VTK": "ON",
+        "OGS_BUILD_HDF5": "ON"
+      },
+      "environment": {
+        "CC": "clang",
+        "CXX": "clang++",
+        "UBSAN_OPTIONS": "print_stacktrace=1",
+        "LSAN_OPTIONS": "suppressions=${sourceDir}/scripts/test/leak_sanitizer.suppressions"
+      }
     }
   ],
   "buildPresets": [
@@ -314,6 +335,10 @@
     {
       "name": "wheel",
       "configurePreset": "wheel"
+    },
+    {
+      "name": "sanitizer",
+      "configurePreset": "sanitizer"
     }
   ],
   "testPresets": [
@@ -326,6 +351,9 @@
       "filter": {
         "include": {
           "label": "default"
+        },
+        "exclude": {
+          "name": "nb-"
         }
       },
       "execution": {
@@ -403,6 +431,13 @@
       "inherits": [
         "release"
       ]
+    },
+    {
+      "name": "sanitizer",
+      "configurePreset": "sanitizer",
+      "inherits": [
+        "release"
+      ]
     }
   ]
 }
diff --git a/MeshLib/CMakeLists.txt b/MeshLib/CMakeLists.txt
@@ -34,18 +34,19 @@ ogs_add_library(MeshLib ${SOURCES})
 
 target_link_libraries(
     MeshLib
-    PUBLIC BaseLib
-           GeoLib
-           GitInfoLib
-           ${HDF5_LIBRARIES}
-           MathLib
-           VTK::IOXML
-           VTK::IOLegacy
-           range-v3
-           $<$<TARGET_EXISTS:VTK::IOParallelXML>:VTK::IOParallelXML>
-           $<$<TARGET_EXISTS:VTK::ParallelMPI>:VTK::ParallelMPI>
-           $<$<TARGET_EXISTS:MPI::MPI_CXX>:MPI::MPI_CXX>
-           $<$<TARGET_EXISTS:petsc>:petsc>
+    PUBLIC
+        BaseLib
+        GeoLib
+        GitInfoLib
+        ${HDF5_LIBRARIES}
+        MathLib
+        VTK::IOXML
+        VTK::IOLegacy
+        range-v3
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:VTK::IOParallelXML>>:VTK::IOParallelXML>
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:VTK::ParallelMPI>>:VTK::ParallelMPI>
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:MPI::MPI_CXX>>:MPI::MPI_CXX>
+        $<$<TARGET_EXISTS:petsc>:petsc>
     PRIVATE nlohmann_json::nlohmann_json
 )
 
@@ -54,7 +55,7 @@ target_include_directories(MeshLib PUBLIC ${HDF5_INCLUDE_DIRS})
 target_compile_definitions(
     MeshLib
     PUBLIC
-        $<$<AND:$<BOOL:$ENV{VTK_USE_64BIT_IDS}>,$<NOT:$<BOOL:VTK_ADDED>>>:VTK_USE_64BIT_IDS>
+        $<$<AND:$<BOOL:$ENV{VTK_USE_64BIT_IDS}>,$<NOT:$<BOOL:${VTK_ADDED}>>>:VTK_USE_64BIT_IDS>
 )
 
 target_precompile_headers(

diff --git a/MeshToolsLib/CMakeLists.txt b/MeshToolsLib/CMakeLists.txt
@@ -9,16 +9,24 @@ append_source_files(SOURCES MeshQuality)
 ogs_add_library(MeshToolsLib ${SOURCES})
 
 target_link_libraries(
-    MeshToolsLib PUBLIC GeoLib
-                        MeshLib
-                        range-v3
-                        VTK::IOXML
-                        VTK::IOLegacy
-                        $<$<TARGET_EXISTS:VTK::IOParallelXML>:VTK::IOParallelXML>
-                        $<$<TARGET_EXISTS:VTK::ParallelMPI>:VTK::ParallelMPI>
-                 PRIVATE BaseLib MathLib NumLib GitInfoLib
+    MeshToolsLib
+    PUBLIC
+        GeoLib
+        MeshLib
+        range-v3
+        VTK::IOXML
+        VTK::IOLegacy
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:VTK::IOParallelXML>>:VTK::IOParallelXML>
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:VTK::ParallelMPI>>:VTK::ParallelMPI>
+    PRIVATE BaseLib MathLib NumLib GitInfoLib
 )
 
-target_precompile_headers(MeshToolsLib PRIVATE [["BaseLib/Error.h"]]
-    [["BaseLib/ConfigTree.h"]] [["BaseLib/Logging.h"]] [["MeshLib/Mesh.h"]]
-    [["MeshLib/Elements/Element.h"]])
+target_precompile_headers(
+    MeshToolsLib
+    PRIVATE
+    [["BaseLib/Error.h"]]
+    [["BaseLib/ConfigTree.h"]]
+    [["BaseLib/Logging.h"]]
+    [["MeshLib/Mesh.h"]]
+    [["MeshLib/Elements/Element.h"]]
+)
diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt
@@ -85,40 +85,39 @@ endif()
 
 ogs_add_executable(testrunner ${TEST_SOURCES})
 
-target_sources(testrunner
-  PRIVATE
-    ProcessLib/Graph/TestGet.cpp
-    ProcessLib/Graph/TestApply.cpp
+target_sources(
+    testrunner PRIVATE ProcessLib/Graph/TestGet.cpp
+                       ProcessLib/Graph/TestApply.cpp
 )
 
 target_link_libraries(
     testrunner
-    PRIVATE $<$<NOT:$<BOOL:${OGS_BUILD_WHEEL}>>:ApplicationsLib>
-            ApplicationsFileIO
-            autocheck
-            gmock
-            gtest
-            MeshToolsLib
-            MeshGeoToolsLib
-            MaterialLib
-            MathLib
-            MeshLib
-            MeshToolsLib
-            NumLib
-            ParameterLib
-            $<$<NOT:$<BOOL:${OGS_BUILD_WHEEL}>>:ProcessLib>
-            $<$<NOT:$<BOOL:${OGS_BUILD_WHEEL}>>:Processes>
-            TestInfoLib
-            VTK::FiltersGeneral
-            VTK::FiltersSources
-            Boost::boost # TODO move OGSMFrontThermodynamicForcesView to
-                         # MathLib?
-            $<$<TARGET_EXISTS:LIE>:LIE>
-            $<$<TARGET_EXISTS:TH2M>:TH2M>
-            $<$<TARGET_EXISTS:MPI::MPI_CXX>:MPI::MPI_CXX>
-            $<$<TARGET_EXISTS:SwmmInterface>:SwmmInterface>
-            $<$<TARGET_EXISTS:InSituLib>:InSituLib>
-            $<$<TARGET_EXISTS:petsc>:petsc>
+    PRIVATE
+        $<$<NOT:$<BOOL:${OGS_BUILD_WHEEL}>>:ApplicationsLib>
+        ApplicationsFileIO
+        autocheck
+        gmock
+        gtest
+        MeshToolsLib
+        MeshGeoToolsLib
+        MaterialLib
+        MathLib
+        MeshLib
+        MeshToolsLib
+        NumLib
+        ParameterLib
+        $<$<NOT:$<BOOL:${OGS_BUILD_WHEEL}>>:ProcessLib>
+        $<$<NOT:$<BOOL:${OGS_BUILD_WHEEL}>>:Processes>
+        TestInfoLib
+        VTK::FiltersGeneral
+        VTK::FiltersSources
+        Boost::boost # TODO move OGSMFrontThermodynamicForcesView to MathLib?
+        $<$<TARGET_EXISTS:LIE>:LIE>
+        $<$<TARGET_EXISTS:TH2M>:TH2M>
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:MPI::MPI_CXX>>:MPI::MPI_CXX>
+        $<$<TARGET_EXISTS:SwmmInterface>:SwmmInterface>
+        $<$<TARGET_EXISTS:InSituLib>:InSituLib>
+        $<$<TARGET_EXISTS:petsc>:petsc>
     PUBLIC $<$<BOOL:${OGS_USE_MFRONT}>:OgsMFrontBehaviourForUnitTests>
 )
 

diff --git a/scripts/ci/jobs/build-docs.yml b/scripts/ci/jobs/build-docs.yml
@@ -1,7 +1,7 @@
 build docs:
   stage: build
   needs: [meta]
-  tags: [shell, envinf23]
+  tags: [shell, envinf]
   timeout: 30 minutes
   variables:
     DOX_WARNINGS_THRESHOLD: 18

diff --git a/scripts/ci/jobs/build-linux-arch.yml b/scripts/ci/jobs/build-linux-arch.yml
@@ -2,7 +2,7 @@ build linux arch:
   extends:
     - .template-build-linux
     - .test-artifacts
-  tags: [shell, envinf23]
+  tags: [shell, envinf]
   needs: [meta]
   timeout: 3h
   variables:

diff --git a/scripts/ci/jobs/build-linux.yml b/scripts/ci/jobs/build-linux.yml
@@ -2,7 +2,7 @@ linux ctest large:
   extends:
     - .template-build-linux
     - .test-artifacts
-  tags: [shell, envinf23]
+  tags: [shell, envinf]
   needs: [meta]
   rules:
     - when: manual
@@ -26,6 +26,7 @@ build linux (no unity):
   needs: [meta]
   timeout: 3h
   variables:
+    BUILD_PACKAGE: "false"
     BUILD_TESTS: "false"
     BUILD_CTEST: "false"
     CHECK_WARNINGS: "true"
@@ -46,27 +47,14 @@ build linux debug with sanitizers:
   extends:
     - .template-build-linux
     - .test-artifacts
-  tags: [envinf23, shell]
+  tags: [envinf, shell]
   needs: [meta]
   variables:
     BUILD_PACKAGE: "false"
-    CMAKE_PRESET: debug
+    CMAKE_PRESET: sanitizer
     CMAKE_ARGS: >-
-      -DCMAKE_C_COMPILER=/usr/bin/clang
-      -DCMAKE_CXX_COMPILER=/usr/bin/clang++
-      -DBUILD_SHARED_LIBS=ON
-      -DOGS_CXX_FLAGS=-O3;-fno-var-tracking
-      -DOGS_EIGEN_DYNAMIC_SHAPE_MATRICES=OFF
-      -DENABLE_ASAN=ON
-      -DENABLE_UBSAN=ON
-      -DENABLE_LSAN=ON
-      -DOGS_CTEST_MAX_RUNTIME=5
-      -DOGS_USE_PIP=ON
-      -DOGS_USE_MFRONT=ON
-      -DOGS_BUILD_TFEL=ON
-    UBSAN_OPTIONS: "print_stacktrace=1"
-    LSAN_OPTIONS: "suppressions=$CI_PROJECT_DIR/scripts/test/leak_sanitizer.suppressions"
-    CTEST_TIMEOUT: 120
+      -DOGS_CTEST_MAX_RUNTIME=60
+      -DOGS_BUILD_PROCESSES=SteadyStateDiffusion
 
 build linux ubuntu perf:
   extends:

diff --git a/scripts/ci/jobs/code-coverage.yml b/scripts/ci/jobs/code-coverage.yml
@@ -1,6 +1,6 @@
 code coverage:
   stage: check
-  tags: [shell, envinf23]
+  tags: [shell, envinf]
   needs: [meta]
   variables:
     CMAKE_PRESET: coverage

diff --git a/scripts/ci/jobs/code-quality.yml b/scripts/ci/jobs/code-quality.yml
@@ -30,7 +30,6 @@ ruff:
 # Disabled, see !3053
 .code_quality:
   stage: check
-  tags: [envinf1]
   needs: []
   rules:
   variables:

diff --git a/scripts/ci/jobs/package.yml b/scripts/ci/jobs/package.yml
@@ -6,12 +6,7 @@ create cpm cache:
     - if: $CI_COMMIT_TITLE == "[versions] Updated cpm cache info."
       when: never
     - if: $CI_PIPELINE_SOURCE == "merge_request_event"
-      changes:
-        - scripts/cmake/CMakeSetup.cmake
-        - scripts/cmake/Dependencies.cmake
-        - scripts/ci/jobs/package.yml
-        - scripts/cmake/ExternalDependencies.cmake
-        - web/data/versions.json
+      when: manual
   variables:
     BUILD_DIR: "$CI_PROJECT_DIR/../build/cpm"
   allow_failure:

diff --git a/scripts/cmake/Dependencies.cmake b/scripts/cmake/Dependencies.cmake
@@ -358,7 +358,7 @@ if((OGS_BUILD_TESTING OR OGS_BUILD_UTILS) AND NOT GUIX_BUILD)
         NAME xdmf
         VERSION 3.0.0
         GIT_REPOSITORY https://gitlab.opengeosys.org/ogs/xdmflib.git
-        GIT_TAG 92a851f1acb87ad5367eb62f9b97785bedb700bb
+        GIT_TAG 374ee63abf605ab4c6639989bebc5096881f4f57
         OPTIONS "XDMF_LIBNAME OgsXdmf" "CMAKE_MACOSX_RPATH ON"
                 "HDF5_C_INCLUDE_DIR ${HDF5_INCLUDE_DIRS}"
         EXCLUDE_FROM_ALL YES SYSTEM TRUE