Merge branch 'bugfix/elasticHOsrcBug' of https://github.com/GEOS-DEV/…

…GEOS into bugfix/elasticHOsrcBug
GEOS-DEV · Aug 22, 2024 · 474f15d · 474f15d
2 parents 064e9e5 + ee0f4e0
commit 474f15d
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Showing 102 changed files with 462 additions and 487 deletions.
diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -5,6 +5,10 @@ on:
       BUILD_AND_TEST_CLI_ARGS:
         required: false
         type: string
+      BUILD_SHARED_LIBS:
+        required: false
+        type: string
+        default: 'ON'
       BUILD_TYPE:
         required: false
         type: string
@@ -184,6 +188,7 @@ jobs:
         docker_args+=(-e ENABLE_HYPRE=${ENABLE_HYPRE:-OFF})
         docker_args+=(-e ENABLE_HYPRE_DEVICE=${ENABLE_HYPRE_DEVICE:-CPU})
         docker_args+=(-e ENABLE_TRILINOS=${ENABLE_TRILINOS:-ON})
+        docker_args+=(-e GEOS_BUILD_SHARED_LIBS=${{ inputs.BUILD_SHARED_LIBS }})
 
         docker_args+=(--cap-add=SYS_PTRACE --rm)
 

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -149,43 +149,49 @@ jobs:
           - name: Ubuntu (20.04, gcc 9.4.0, open-mpi 4.0.3)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu debug (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces
             CMAKE_BUILD_TYPE: Debug
             DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (22.04, gcc 11.4.0, open-mpi 4.1.2)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
             GCP_BUCKET: geosx/ubuntu22.04-gcc11
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (22.04, gcc 12.3.0, open-mpi 4.1.2)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc12
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (22.04, clang 15.0.7, open-mpi 4.1.2)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu22.04-clang15
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
+            BUILD_SHARED_LIBS: ON
 
     uses: ./.github/workflows/build_and_test.yml
     with:
+      BUILD_SHARED_LIBS: ${{ matrix.BUILD_SHARED_LIBS }}
       CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
       DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
       DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }}
       ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }}
       ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }}
       GCP_BUCKET: ${{ matrix.GCP_BUCKET }}
-      HOST_CONFIG: ${{ matrix.HOST_CONFIG }}
       RUNS_ON: ubuntu-22.04
     secrets: inherit
 
@@ -328,8 +334,6 @@ jobs:
       ENABLE_HYPRE_DEVICE: ${{ matrix.ENABLE_HYPRE_DEVICE }}
       ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }}
       ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }}
-      GCP_BUCKET: ${{ matrix.GCP_BUCKET }}
-      HOST_CONFIG: ${{ matrix.HOST_CONFIG }}
       NPROC: ${{ matrix.NPROC }}
       RUNS_ON: ${{ matrix.RUNS_ON }}
       REQUIRED_LABEL: "ci: run CUDA builds"

diff --git a/host-configs/LBL/[email protected] b/host-configs/LBL/[email protected]
@@ -26,10 +26,6 @@ set(MPIEXEC_NUMPROC_FLAG "-n" CACHE STRING "")
 
 set(GEOS_TPL_DIR "/global/project/projectdirs/m1411/GEOSX/tpls/install-cori-gcc\@8.1.0-release-24-07-20" CACHE PATH "" )
 
-
-set(GEOS_LINK_PREPEND_FLAG  "-Wl,--whole-archive"    CACHE STRING "" FORCE)
-set(GEOS_LINK_POSTPEND_FLAG "-Wl,--no-whole-archive" CACHE STRING "" FORCE)
-
 set(ENABLE_SPHINX_EXECUTABLE OFF CACHE BOOL "")
 set(ENABLE_UNCRUSTIFY OFF CACHE BOOL "")
 set(ENABLE_DOXYGEN OFF CACHE BOOL "")

diff --git a/host-configs/LBL/cori-intel.cmake b/host-configs/LBL/cori-intel.cmake
@@ -26,9 +26,6 @@ set(MPIEXEC_NUMPROC_FLAG "-n" CACHE STRING "")
 
 set(GEOS_TPL_DIR "/global/project/projectdirs/m1411/GEOSX/tpls/install-cori-intel-release-22-07-20" CACHE PATH "" )
 
-set(GEOS_LINK_PREPEND_FLAG  "-Wl,--whole-archive"    CACHE STRING "" FORCE)
-set(GEOS_LINK_POSTPEND_FLAG "-Wl,--no-whole-archive" CACHE STRING "" FORCE)
-
 set(ENABLE_SPHINX_EXECUTABLE OFF CACHE BOOL "")
 set(ENABLE_UNCRUSTIFY OFF CACHE BOOL "")
 set(ENABLE_DOXYGEN OFF CACHE BOOL "")

diff --git a/host-configs/LLNL/lassen-base.cmake b/host-configs/LLNL/lassen-base.cmake
@@ -7,7 +7,6 @@
 #
 ###############################################################################
 
-set( GEOS_BUILD_SHARED_LIBS ON CACHE BOOL "" )
 set( GEOS_BUILD_OBJ_LIBS OFF CACHE BOOL "" )
 # Fortran
 set(ENABLE_FORTRAN OFF CACHE BOOL "")

diff --git a/host-configs/ORNL/frontier-base.cmake b/host-configs/ORNL/frontier-base.cmake
@@ -31,7 +31,6 @@ set( ENABLE_DOCS OFF CACHE BOOL "" FORCE )
 set( ENABLE_SCOTCH OFF CACHE BOOL "" FORCE )
 set( ENABLE_SUPERLU_DIST OFF CACHE BOOL "" FORCE )
 
-set( GEOS_BUILD_SHARED_LIBS ON CACHE BOOL "" FORCE )
 set( GEOS_BUILD_OBJ_LIBS OFF CACHE BOOL "" FORCE )
 
 set( CMAKE_CXX_STANDARD 17 CACHE STRING "" )

diff --git a/host-configs/TOTAL/pangea3-gcc8.4.1-openmpi-4.1.2.cmake b/host-configs/TOTAL/pangea3-gcc8.4.1-openmpi-4.1.2.cmake
@@ -77,7 +77,6 @@ set(ENABLE_MATHPRESSO OFF CACHE BOOL "")
 # Silo configure script doesn't recognize systype
 set(SILO_BUILD_TYPE powerpc64-unknown-linux-gnu CACHE STRING "")
 
-set(GEOS_BUILD_SHARED_LIBS OFF CACHE BOOL "")
 set(ENABLE_PVTPackage ON CACHE BOOL "")
 
 set(ENABLE_CALIPER ON CACHE BOOL "")

diff --git a/host-configs/apple/macOS_base.cmake b/host-configs/apple/macOS_base.cmake
@@ -27,7 +27,8 @@ set( LAPACK_LIBRARIES ${HOMEBREW_DIR}/opt/lapack/lib/liblapack.dylib CACHE PATH
 
 set(ENABLE_DOXYGEN OFF CACHE BOOL "" FORCE)
 set(ENABLE_MATHPRESSO OFF CACHE BOOL "" FORCE )
-#set(GEOS_BUILD_OBJ_LIBS ON CACHE BOOL "" FORCE)
+
+set(GEOS_BUILD_SHARED_LIBS ON CACHE BOOL "" FORCE)
 
 
 

diff --git a/host-configs/environment.cmake b/host-configs/environment.cmake
@@ -78,5 +78,9 @@ if(DEFINED ENV{LAPACK_LIBRARIES})
   set(LAPACK_LIBRARIES "$ENV{LAPACK_LIBRARIES}" CACHE PATH "" FORCE)
 endif()
 
+if(DEFINED ENV{GEOS_BUILD_SHARED_LIBS})
+  set(GEOS_BUILD_SHARED_LIBS "$ENV{GEOS_BUILD_SHARED_LIBS}" CACHE BOOL "" FORCE)
+endif()
+
 set(GEOS_TPL_DIR "$ENV{GEOSX_TPL_DIR}" CACHE PATH "" FORCE)
 include(${CMAKE_CURRENT_LIST_DIR}/tpls.cmake)
diff --git a/inputFiles/singlePhaseFlowFractures/fractureFlow_conforming_2d_vtk_input.xml b/inputFiles/singlePhaseFlowFractures/fractureFlow_conforming_2d_vtk_input.xml
@@ -19,7 +19,7 @@
   <Mesh>
     <VTKMesh
       surfacicFieldsToImport="{aperture}"
-      surfacicFieldsInGEOSX="{elementAperture}"
+      surfacicFieldsInGEOS="{elementAperture}"
       name="mesh1"
       useGlobalIds="1"
       faceBlocks="{fracture}"

diff --git a/src/CMakeGraphVizOptions.cmake b/src/CMakeGraphVizOptions.cmake
@@ -1,4 +1,6 @@
-set( GRAPHVIZ_EXECUTABLES FALSE )
+set( GRAPHVIZ_EXECUTABLES TRUE )
 set( GRAPHVIZ_OBJECT_LIBS TRUE )
 set( GRAPHVIZ_EXTERNAL_LIBS FALSE )
-set( GRAPHVIZ_GENERATE_DEPENDERS FALSE )
+set( GRAPHVIZ_GENERATE_DEPENDERS FALSE )
+set( GRAPHVIZ_IGNORE_TARGETS "test*;example*;benchmark*" )
+set( GRAPHVIZ_CUSTOM_TARGETS FALSE )
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -135,33 +135,18 @@ if( ENABLE_HIP )
   list( APPEND extraComponentsLinkList blt::hip )
 endif()
 
-if ( GEOS_BUILD_SHARED_LIBS )
-  list( APPEND extraComponentsLinkList geosx_core )
-else()
-  list( APPEND extraComponentsLinkList ${geosx_core_libs} )
-endif()
-
 blt_add_executable( NAME geosx
                     SOURCES main/main.cpp
-                    DEPENDS_ON ${extraComponentsLinkList}
-                               ${externalComponentsLinkList} fmt::fmt-header-only HDF5::HDF5 )
-
-# blt_print_target_properties(TARGET               geosx
-#                             CHILDREN             TRUE
-#                             PROPERTY_NAME_REGEX  "LINK_LIBRARIES"
-#                             )
-
-# blt_print_target_properties(TARGET               HDF5::HDF5
-#                             CHILDREN             TRUE )
+                    DEPENDS_ON geosx_core 
+                               ${extraComponentsLinkList}
+                               ${externalComponentsLinkList} )
 
 # Seems to be required on some CMake versions (e.g. 3.16) to get enforce device linking
 if( ${ENABLE_HYPRE_DEVICE} STREQUAL "CUDA"  )
   set_target_properties( geosx PROPERTIES CUDA_RESOLVE_DEVICE_SYMBOLS TRUE )
 endif()
 
 
-target_include_directories( geosx PUBLIC ${CMAKE_SOURCE_DIR}/coreComponents )
-
 # To change the runtime path during installation
 set_target_properties( geosx PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib" )
 set_target_properties( geosx PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE )

diff --git a/src/cmake/GeosxMacros.cmake b/src/cmake/GeosxMacros.cmake
@@ -95,3 +95,39 @@ macro( geos_add_test )
                   COMMAND ${arg_COMMAND} ${ARGN} )
 
 endmacro( geos_add_test )
+
+
+macro( geos_decorate_link_dependencies )
+
+    set( options )
+    set( singleValueArgs LIST )
+    set( multiValueArgs DEPENDENCIES )
+
+    # Parse the arguments to the macro
+    cmake_parse_arguments( arg
+         "${options}" "${singleValueArgs}" "${multiValueArgs}" ${ARGN} )
+
+    set( staticLibs "" )
+    set( otherLibs "" )
+    foreach( dep ${arg_DEPENDENCIES} )
+        if( NOT TARGET ${dep} )
+            message( FATAL_ERROR "Dependency ${dep} not found" )
+        endif()
+
+        get_target_property( targetType ${dep} TYPE)
+        # message( "  ${dep} targetType = ${targetType}" )  # debug
+
+        if (targetType STREQUAL STATIC_LIBRARY)
+            list( APPEND staticLibs ${dep} )
+        else()
+            list( APPEND otherLibs ${dep} )
+        endif()
+    endforeach()
+
+    # message( "  staticLibs = ${staticLibs}" )  # debug
+    # message( "  otherLibs = ${otherLibs}" )  # debug
+
+    string (REPLACE ";" "," staticLibsString "${staticLibs}")
+    set( ${arg_LIST} "$<LINK_LIBRARY:WHOLE_ARCHIVE,${staticLibsString}>" ${otherLibs} )
+
+endmacro( geos_decorate_link_dependencies )
diff --git a/src/cmake/GeosxOptions.cmake b/src/cmake/GeosxOptions.cmake
@@ -158,18 +158,6 @@ if( ${CMAKE_MAKE_PROGRAM} STREQUAL "ninja" OR ${CMAKE_MAKE_PROGRAM} MATCHES ".*/
   set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GEOS_NINJA_FLAGS}" )
 endif()
 
-
-if( CMAKE_HOST_APPLE )
-#    set(GEOS_LINK_PREPEND_FLAG "-Wl,-force_load" CACHE STRING "")
-#    set(GEOS_LINK_POSTPEND_FLAG "" CACHE STRING "")
-# elseif( ENABLE_CUDA )
-#     set( GEOS_LINK_PREPEND_FLAG  "-Xcompiler \\\\\"-Wl,--whole-archive\\\\\""    CACHE STRING "" )
-#     set( GEOS_LINK_POSTPEND_FLAG "-Xcompiler \\\\\"-Wl,--no-whole-archive\\\\\"" CACHE STRING "" )
-else()
-    set( GEOS_LINK_PREPEND_FLAG  "-Wl,--whole-archive"    CACHE STRING "" )
-    set( GEOS_LINK_POSTPEND_FLAG "-Wl,--no-whole-archive" CACHE STRING "" )
-endif()
-
 set( GEOS_LOCALINDEX_TYPE "int" CACHE STRING "" )
 if( ENABLE_HYPRE_MIXINT )
   set( GEOS_GLOBALINDEX_TYPE "long long int" CACHE STRING "" )
@@ -216,6 +204,5 @@ message( "GEOS_GLOBALINDEX_TYPE_FLAG = ${GEOS_GLOBALINDEX_TYPE_FLAG}" )
 
 
 message( "CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}" )
-message( "GEOS_LINK_PREPEND_FLAG=${GEOS_LINK_PREPEND_FLAG}" )
-message( "GEOS_LINK_POSTPEND_FLAG=${GEOS_LINK_POSTPEND_FLAG}" )
+
 message( "Leaving GeosxOptions.cmake\n" )
diff --git a/src/coreComponents/CMakeLists.txt b/src/coreComponents/CMakeLists.txt
@@ -3,19 +3,20 @@ set( subdirs
      common
      codingUtilities
      dataRepository
-     schema
+     denseLinearAlgebra
      functions
      constitutive
+     schema
+     finiteElement
      mesh
-     denseLinearAlgebra
      linearAlgebra
      fieldSpecification
-     finiteElement
      finiteVolume
      discretizationMethods
+     events
+     constitutiveDrivers
      fileIO
      physicsSolvers
-     events
      mainInterface )
 
 unset( parallelDeps )
@@ -56,53 +57,15 @@ foreach( lib ${subdirs} )
   endif()
 endforeach()
 
-# if we're building full static libs and not obj_libs
-if( NOT GEOS_BUILD_SHARED_LIBS )
-  set( geosx_core_list "" )
-  foreach( lib ${coreLibs} )
-    list( APPEND geosx_core_list ${GEOS_LINK_PREPEND_FLAG} ${lib} ${GEOS_LINK_POSTPEND_FLAG} )
-  endforeach()
-  set ( geosx_core_libs "${geosx_core_list}" CACHE INTERNAL "" )
-endif( )
-
 foreach( lib ${subdirs} )
   add_subdirectory( ${lib} )
 endforeach()
 
-if( GEOS_BUILD_SHARED_LIBS AND GEOS_BUILD_OBJ_LIBS )
-  message( "Building shared geosx_core library with object coreComponents, executables link to geosx_core" )
-  blt_add_library ( NAME geosx_core
-                    SOURCES dummy.cpp
-                    DEPENDS_ON  mainInterface physicsSolvers HDF5::HDF5
-                    SHARED TRUE )
-
-elseif( GEOS_BUILD_SHARED_LIBS AND NOT GEOS_BUILD_OBJ_LIBS )
-  message( "Building shared geosx_core library with static coreComponents, executables link to geosx_core" )
-  blt_combine_static_libraries( NAME          geosx_core
-                                SOURCE_LIBS   ${coreLibs}
-                                LIB_TYPE      SHARED
-                                LINK_PREPEND  ${GEOS_LINK_PREPEND_FLAG}
-                                LINK_POSTPEND ${GEOS_LINK_POSTPEND_FLAG} )
-
-elseif( NOT GEOS_BUILD_SHARED_LIBS AND GEOS_BUILD_OBJ_LIBS )
-  message( "Building object coreComponents, executables link to coreComponents" )
+add_library(geosx_core INTERFACE)
+if( GEOS_BUILD_SHARED_LIBS)
+  target_link_libraries(geosx_core INTERFACE mainInterface )
 else()
-  message( "Building static coreComponents, executables link to coreComponents" )
-endif()
-
-if ( TARGET geosx_core )
-  # Seems to be required on some CMake versions (e.g. 3.16) to get enforce device linking
-  if( ${ENABLE_HYPRE_DEVICE} STREQUAL "CUDA" )
-    set_target_properties( geosx_core PROPERTIES CUDA_RESOLVE_DEVICE_SYMBOLS TRUE )
-  endif()
-
-  # To install the library with the runtime path used during the building
-  set_target_properties( geosx_core PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE )
-
-  # To install the shared library
-  install( TARGETS geosx_core LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
-
-  target_include_directories( geosx_core PUBLIC ${CMAKE_SOURCE_DIR}/coreComponents )
+  target_link_libraries(geosx_core INTERFACE $<LINK_LIBRARY:WHOLE_ARCHIVE,mainInterface> )
 endif()
 
 geosx_add_code_checks( PREFIX coreComponents

diff --git a/src/coreComponents/codingUtilities/CMakeLists.txt b/src/coreComponents/codingUtilities/CMakeLists.txt
@@ -20,12 +20,15 @@ set( codingUtilities_sources
    )
 
 set( dependencyList ${parallelDeps} common fast_float )
+geos_decorate_link_dependencies( LIST decoratedDependencies
+                                 DEPENDENCIES ${dependencyList} )
 
 blt_add_library( NAME       codingUtilities
                  SOURCES    ${codingUtilities_sources}
                  HEADERS    ${codingUtilities_headers}
-                 DEPENDS_ON ${dependencyList}
+                 DEPENDS_ON ${decoratedDependencies}
                  OBJECT     ${GEOS_BUILD_OBJ_LIBS}
+                 SHARED     ${GEOS_BUILD_SHARED_LIBS}
                )
 
 # Avoid compiling with nvcc which sometimes crashes on fast_float

diff --git a/src/coreComponents/codingUtilities/tests/CMakeLists.txt b/src/coreComponents/codingUtilities/tests/CMakeLists.txt
@@ -4,16 +4,18 @@ set( testSources
      testParsing.cpp
      testUtilities.cpp )
 
-set( dependencyList gtest codingUtilities ${parallelDeps} )
+set( dependencyList codingUtilities ${parallelDeps} )
 
+geos_decorate_link_dependencies( LIST decoratedDependencies
+                                 DEPENDENCIES ${dependencyList} )
 # Add gtest C++ based tests
 foreach( test ${testSources} )
 
   get_filename_component( test_name ${test} NAME_WE )
   blt_add_executable( NAME ${test_name}
                       SOURCES ${test}
                       OUTPUT_DIR ${TEST_OUTPUT_DIRECTORY}
-                      DEPENDS_ON ${dependencyList} )
+                      DEPENDS_ON ${decoratedDependencies} gtest )
 
   geos_add_test( NAME ${test_name}
                  COMMAND ${test_name} )