Merge branch 'develop' into pt/remove-setNextDt

.github/workflows/ci_tests.yml

@@ -330,7 +330,7 @@ jobs:
             DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors"
             DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"
 
-          - name: Pangea 3 (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
+          - name: Pangea 3 CUDA (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
             BUILD_AND_TEST_CLI_ARGS: "--build-exe-only --no-install-schema"
             CMAKE_BUILD_TYPE: Release
             BUILD_GENERATOR: "--makefile"

src/coreComponents/constitutive/ConstitutiveManager.cpp

@@ -43,6 +43,7 @@ ConstitutiveManager::~ConstitutiveManager()
 
 Group * ConstitutiveManager::createChild( string const & childKey, string const & childName )
 {
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< ConstitutiveBase > material = ConstitutiveBase::CatalogInterface::factory( childKey, childName, this );
   return &registerGroup< ConstitutiveBase >( childName, std::move( material ) );
 }

src/coreComponents/dataRepository/xmlWrapper.cpp

@@ -171,7 +171,7 @@ void xmlDocument::addIncludedXML( xmlNode & targetNode, int const level )
         return isAbsolutePath( fileName ) ? fileName : joinPath( splitPath( currentFilePath ).first, fileName );
       }();
 
-      GEOS_LOG_RANK_0( "Included additionnal XML file: " << getAbsolutePath( includedFilePath ) );
+      GEOS_LOG_RANK_0( "Included additional XML file: " << getAbsolutePath( includedFilePath ) );
 
       xmlDocument includedXmlDocument;
       xmlResult const result = includedXmlDocument.loadFile( includedFilePath, hasNodeFileInfo() );

src/coreComponents/events/EventBase.cpp

@@ -122,7 +122,7 @@ EventBase::CatalogInterface::CatalogType & EventBase::getCatalog()
 
 Group * EventBase::createChild( string const & childKey, string const & childName )
 {
-  GEOS_LOG_RANK_0( "Adding Event: " << childKey << ", " << childName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< EventBase > event = EventBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< EventBase >( childName, std::move( event ) );
 }

src/coreComponents/events/EventManager.cpp

@@ -93,7 +93,7 @@ EventManager::~EventManager()
 
 Group * EventManager::createChild( string const & childKey, string const & childName )
 {
-  GEOS_LOG_RANK_0( "Adding Event: " << childKey << ", " << childName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< EventBase > event = EventBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< EventBase >( childName, std::move( event ) );
 }

src/coreComponents/events/tasks/TasksManager.cpp

@@ -38,6 +38,7 @@ TasksManager::~TasksManager()
 
 Group * TasksManager::createChild( string const & childKey, string const & childName )
 {
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< TaskBase > task = TaskBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< TaskBase >( childName, std::move( task ) );
 }

src/coreComponents/fieldSpecification/FieldSpecificationManager.cpp

@@ -51,6 +51,7 @@ FieldSpecificationManager & FieldSpecificationManager::getInstance()
 
 Group * FieldSpecificationManager::createChild( string const & childKey, string const & childName )
 {
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< FieldSpecificationBase > bc = FieldSpecificationBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup( childName, std::move( bc ) );
 }

src/coreComponents/fileIO/Outputs/OutputManager.cpp

@@ -39,7 +39,7 @@ OutputManager::~OutputManager()
 
 Group * OutputManager::createChild( string const & childKey, string const & childName )
 {
-  GEOS_LOG_RANK_0( "Adding Output: " << childKey << ", " << childName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< OutputBase > output = OutputBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< OutputBase >( childName, std::move( output ) );
 }

src/coreComponents/finiteElement/FiniteElementDiscretizationManager.cpp

@@ -40,6 +40,7 @@ FiniteElementDiscretizationManager::~FiniteElementDiscretizationManager()
 Group * FiniteElementDiscretizationManager::createChild( string const & childKey, string const & childName )
 {
   // These objects should probably not be registered on managed group...
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< Group > fem = Group::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup( childName, std::move( fem ) );
 }

src/coreComponents/finiteVolume/FiniteVolumeManager.cpp

@@ -42,6 +42,7 @@ FiniteVolumeManager::~FiniteVolumeManager()
 
 Group * FiniteVolumeManager::createChild( string const & childKey, string const & childName )
 {
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   if( childKey == HybridMimeticDiscretization::catalogName() )
   {
     std::unique_ptr< HybridMimeticDiscretization > hm = std::make_unique< HybridMimeticDiscretization >( childName, this );

src/coreComponents/functions/FunctionManager.cpp

@@ -53,7 +53,7 @@ FunctionManager & FunctionManager::getInstance()
 Group * FunctionManager::createChild( string const & functionCatalogKey,
                                       string const & functionName )
 {
-  GEOS_LOG_RANK_0( "   " << functionCatalogKey << ": " << functionName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), functionCatalogKey, functionName ) );
   std::unique_ptr< FunctionBase > function = FunctionBase::CatalogInterface::factory( functionCatalogKey, functionName, this );
   return &this->registerGroup< FunctionBase >( functionName, std::move( function ) );
 }

src/coreComponents/mesh/ElementRegionManager.cpp

@@ -75,7 +75,7 @@ Group * ElementRegionManager::createChild( string const & childKey, string const
 {
   GEOS_ERROR_IF( !(CatalogInterface::hasKeyName( childKey )),
                  "KeyName ("<<childKey<<") not found in ObjectManager::Catalog" );
-  GEOS_LOG_RANK_0( "Adding Object " << childKey<<" named "<< childName<<" from ObjectManager::Catalog." );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
 
   Group & elementRegions = this->getGroup( ElementRegionManager::groupKeyStruct::elementRegionsGroup() );
   return &elementRegions.registerGroup( childName,

src/coreComponents/mesh/ExternalDataSourceBase.cpp

@@ -27,7 +27,7 @@ ExternalDataSourceBase::ExternalDataSourceBase( string const & name, Group * con
 
 Group * ExternalDataSourceBase::createChild( string const & childKey, string const & childName )
 {
-  GEOS_LOG_RANK_0( "Adding External Data Source: " << childKey << ", " << childName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< ExternalDataSourceBase > event = ExternalDataSourceBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< ExternalDataSourceBase >( childName, std::move( event ) );
 }

src/coreComponents/mesh/ExternalDataSourceManager.cpp

@@ -35,7 +35,7 @@ ExternalDataSourceManager::~ExternalDataSourceManager()
 
 Group * ExternalDataSourceManager::createChild( string const & childKey, string const & childName )
 {
-  GEOS_LOG_RANK_0( "Adding External Data Source: " << childKey << ", " << childName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< ExternalDataSourceBase > externalDataSource = ExternalDataSourceBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< ExternalDataSourceBase >( childName, std::move( externalDataSource ) );
 }

src/coreComponents/mesh/FieldIdentifiers.hpp

@@ -98,11 +98,11 @@ class FieldIdentifiers
  * @brief Get the Location object
  *
  * @param key key used to store the list of fields in the map.
- * @param location mesh location where fields defined by the key provided were registered.
+ * @return mesh location where fields defined by the key provided were registered.
  */
-  void getLocation( string const & key,
-                    FieldLocation & location ) const
+  FieldLocation getLocation( string const & key ) const
   {
+    FieldLocation location{};
     if( key.find( m_locationKeys.nodesKey() ) != string::npos )
     {
       location = FieldLocation::Node;
@@ -123,6 +123,7 @@ class FieldIdentifiers
     {
       GEOS_ERROR( GEOS_FMT( "Invalid key, {}, was provided. Location cannot be retrieved.", key ) );
     }
+    return location;
   }
 
 private:

src/coreComponents/mesh/MeshManager.cpp

@@ -20,7 +20,6 @@
 
 #include "mesh/mpiCommunications/SpatialPartition.hpp"
 #include "generators/CellBlockManagerABC.hpp"
-#include "generators/MeshGeneratorBase.hpp"
 #include "mesh/mpiCommunications/CommunicationTools.hpp"
 #include "common/TimingMacros.hpp"
 
@@ -43,7 +42,7 @@ MeshManager::~MeshManager()
 
 Group * MeshManager::createChild( string const & childKey, string const & childName )
 {
-  GEOS_LOG_RANK_0( "Adding Mesh: " << childKey << ", " << childName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< MeshGeneratorBase > mesh = MeshGeneratorBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< MeshGeneratorBase >( childName, std::move( mesh ) );
 }
@@ -81,7 +80,7 @@ void MeshManager::generateMeshes( DomainPartition & domain )
 
 void MeshManager::generateMeshLevels( DomainPartition & domain )
 {
-  this->forSubGroups< MeshGeneratorBase >( [&]( MeshGeneratorBase & meshGen )
+  forSubGroups< MeshGeneratorBase >( [&]( MeshGeneratorBase & meshGen )
   {
     string const & meshName = meshGen.getName();
     domain.getMeshBodies().registerGroup< MeshBody >( meshName ).createMeshLevel( MeshBody::groupStructKeys::baseDiscretizationString() );
@@ -126,66 +125,28 @@ void MeshManager::importFields( DomainPartition & domain )
     }
 
     GEOS_LOG_RANK_0( GEOS_FMT( "{}: importing field data from mesh dataset", generator.getName() ) );
-
-    auto const importFields = [&generator]( ElementRegionBase const & region,
-                                            ElementSubRegionBase & subRegion,
-                                            MeshGeneratorBase::Block block,
-                                            std::map< string, string > const & fieldsMapping,
-                                            FieldIdentifiers & fieldsToBeSync )
-    {
-      std::unordered_set< string > const materialWrapperNames = getMaterialWrapperNames( subRegion );
-      // Writing properties
-      for( auto const & pair : fieldsMapping )
-      {
-        string const & meshFieldName = pair.first;
-        string const & geosFieldName = pair.second;
-        // Find destination
-        if( !subRegion.hasWrapper( geosFieldName ) )
-        {
-          // Skip - the user may have not enabled a particular physics model/solver on this destination region.
-          if( generator.getLogLevel() >= 1 )
-          {
-            GEOS_LOG_RANK_0( "Skipping import of " << meshFieldName << " -> " << geosFieldName <<
-                             " on " << region.getName() << "/" << subRegion.getName() << " (field not found)" );
-          }
-
-          continue;
-        }
-
-        // Now that we know that the subRegion has this wrapper,
-        // we can add the geosFieldName to the list of fields to synchronize
-        fieldsToBeSync.addElementFields( { geosFieldName }, { region.getName() } );
-        WrapperBase & wrapper = subRegion.getWrapperBase( geosFieldName );
-        if( generator.getLogLevel() >= 1 )
-        {
-          GEOS_LOG_RANK_0( "Importing field " << meshFieldName << " into " << geosFieldName <<
-                           " on " << region.getName() << "/" << subRegion.getName() );
-        }
-
-        bool const isMaterialField = materialWrapperNames.count( geosFieldName ) > 0 && wrapper.numArrayDims() > 1;
-        generator.importFieldOnArray( block, subRegion.getName(), meshFieldName, isMaterialField, wrapper );
-      }
-    };
-
-    dataRepository::Group & meshLevels = domain.getMeshBody( generator.getName() ).getMeshLevels();
-    meshLevels.forSubGroups< MeshLevel >( [&]( MeshLevel & meshLevel )
+    MeshBody & meshBody = domain.getMeshBody( generator.getName() );
+    meshBody.forMeshLevels( [&]( MeshLevel & meshLevel )
     {
+      GEOS_LOG_RANK_0( GEOS_FMT( "  mesh level = {}", meshLevel.getName() ) );
       FieldIdentifiers fieldsToBeSync;
       meshLevel.getElemManager().forElementSubRegionsComplete< CellElementSubRegion >(
         [&]( localIndex,
              localIndex,
              ElementRegionBase const & region,
              CellElementSubRegion & subRegion )
       {
-        importFields( region, subRegion, MeshGeneratorBase::Block::VOLUMIC, generator.getVolumicFieldsMapping(), fieldsToBeSync );
+        GEOS_LOG_RANK_0( GEOS_FMT( "  volumic fields on {}/{}", region.getName(), subRegion.getName() ) );
+        importFields( generator, region.getName(), subRegion, MeshGeneratorBase::Block::VOLUMIC, generator.getVolumicFieldsMapping(), fieldsToBeSync );
       } );
       meshLevel.getElemManager().forElementSubRegionsComplete< FaceElementSubRegion >(
         [&]( localIndex,
              localIndex,
              ElementRegionBase const & region,
              FaceElementSubRegion & subRegion )
       {
-        importFields( region, subRegion, MeshGeneratorBase::Block::SURFACIC, generator.getSurfacicFieldsMapping(), fieldsToBeSync );
+        GEOS_LOG_RANK_0( GEOS_FMT( "  surfaic fields on {}/{}", region.getName(), subRegion.getName() ) );
+        importFields( generator, region.getName(), subRegion, MeshGeneratorBase::Block::SURFACIC, generator.getSurfacicFieldsMapping(), fieldsToBeSync );
       } );
       CommunicationTools::getInstance().synchronizeFields( fieldsToBeSync, meshLevel, domain.getNeighbors(), false ); // TODO Validate this.
     } );
@@ -197,4 +158,43 @@ void MeshManager::importFields( DomainPartition & domain )
   } );
 }
 
+void MeshManager::importFields( MeshGeneratorBase const & generator,
+                                string const & regionName,
+                                ElementSubRegionBase & subRegion,
+                                MeshGeneratorBase::Block const block,
+                                std::map< string, string > const & fieldsMapping,
+                                FieldIdentifiers & fieldsToBeSync )
+{
+  std::unordered_set< string > const materialWrapperNames = getMaterialWrapperNames( subRegion );
+  // Writing properties
+  for( auto const & pair : fieldsMapping )
+  {
+    string const & meshFieldName = pair.first;
+    string const & geosFieldName = pair.second;
+    // Find destination
+    if( !subRegion.hasWrapper( geosFieldName ) )
+    {
+      // Skip - the user may have not enabled a particular physics model/solver on this destination region.
+      if( generator.getLogLevel() >= 1 )
+      {
+        GEOS_LOG_RANK_0( GEOS_FMT( "    Skipping import of {} -> {} (field not found)", meshFieldName, geosFieldName ) );
+      }
+
+      continue;
+    }
+
+    // Now that we know that the subRegion has this wrapper,
+    // we can add the geosFieldName to the list of fields to synchronize
+    fieldsToBeSync.addElementFields( { geosFieldName }, { regionName } );
+    WrapperBase & wrapper = subRegion.getWrapperBase( geosFieldName );
+    if( generator.getLogLevel() >= 1 )
+    {
+      GEOS_LOG_RANK_0( GEOS_FMT( "    {} -> {}", meshFieldName, geosFieldName ) );
+    }
+
+    bool const isMaterialField = materialWrapperNames.count( geosFieldName ) > 0 && wrapper.numArrayDims() > 1;
+    generator.importFieldOnArray( block, subRegion.getName(), meshFieldName, isMaterialField, wrapper );
+  }
+}
+
 } /* namespace geos */

src/coreComponents/mesh/MeshManager.hpp

@@ -22,6 +22,7 @@
 
 #include "dataRepository/Group.hpp"
 #include "mesh/DomainPartition.hpp"
+#include "generators/MeshGeneratorBase.hpp"
 
 namespace geos
 {
@@ -74,6 +75,22 @@ class MeshManager : public dataRepository::Group
    */
   void importFields( DomainPartition & domain );
 
+  /**
+   * @brief Import fields data
+   * @param[in] generator reference to mesh generator
+   * @param[in] regionName name of the region
+   * @param[in] subRegion reference to the subregion
+   * @param[in] block block type
+   * @param[in] fieldsMapping mapping for fields
+   * @param[out] fieldsToBeSync list of fields to synchronize
+   */
+  static void importFields( MeshGeneratorBase const & generator,
+                            string const & regionName,
+                            ElementSubRegionBase & subRegion,
+                            MeshGeneratorBase::Block block,
+                            std::map< string, string > const & fieldsMapping,
+                            FieldIdentifiers & fieldsToBeSync );
+
 private:
 
   /**

src/coreComponents/mesh/ParticleManager.cpp

@@ -88,7 +88,7 @@ Group * ParticleManager::createChild( string const & childKey, string const & ch
 {
   GEOS_ERROR_IF( !(CatalogInterface::hasKeyName( childKey )),
                  "KeyName ("<<childKey<<") not found in ObjectManager::Catalog" );
-  GEOS_LOG_RANK_0( "Adding Object " << childKey << " named " << childName << " from ObjectManager::Catalog." );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
 
   Group & particleRegions = this->getGroup( ParticleManager::groupKeyStruct::particleRegionsGroup() );
   return &particleRegions.registerGroup( childName,

src/coreComponents/mesh/generators/MeshGeneratorBase.cpp

@@ -29,7 +29,7 @@ MeshGeneratorBase::MeshGeneratorBase( string const & name, Group * const parent
 
 Group * MeshGeneratorBase::createChild( string const & childKey, string const & childName )
 {
-  GEOS_LOG_RANK_0( "Adding Mesh attribute: " << childKey << ", " << childName );
+  GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
   std::unique_ptr< MeshComponentBase > comp = MeshComponentBase::CatalogInterface::factory( childKey, childName, this );
   return &this->registerGroup< MeshComponentBase >( childName, std::move( comp ) );
 }