feat: in sync with PR#2957

src/CMakeLists.txt

@@ -57,25 +57,27 @@ set(componentSources
 # set(dependencyList mesh)
 set(dependencyList FesapiCpp)
 
-# if(GEOSX_BUILD_SHARED_LIBS)
-set(dependencyList ${dependencyList} geosx_core)
-# else()
-#   set(dependencyList ${dependencyList} ${geosx_core_libs})
-# endif()
+if(GEOS_BUILD_SHARED_LIBS)
+  set(dependencyList ${dependencyList} geosx_core)
+else()
+  set(dependencyList ${dependencyList} ${geosx_core_libs})
+endif()
+
+geos_decorate_link_dependencies( LIST decoratedDependencies
+                                 DEPENDENCIES ${dependencyList} )
 
 message("adding RESQML library:")
 
-blt_add_library(NAME resqml
-  SOURCES ${componentSources}
-  HEADERS ${componentHeaders}
-  DEPENDS_ON ${dependencyList}
-  OBJECT ${GEOSX_BUILD_OBJ_LIBS}
-)
+blt_add_library( NAME resqml
+                 SOURCES ${componentSources}
+                 HEADERS ${componentHeaders}
+                 DEPENDS_ON ${decoratedDependencies}
+                 OBJECT ${GEOS_BUILD_OBJ_LIBS}
+                 SHARED ${GEOS_BUILD_SHARED_LIBS}
+               )
 
 target_compile_definitions(resqml PUBLIC "HAS_UNCAUGHT_EXCEPTIONS")
 
-# target_link_libraries(resqml PUBLIC FesapiCpp)
-# target_include_directories(resqml PUBLIC ${FESAPI_DIR}/include)
 target_include_directories(resqml PUBLIC ${CMAKE_CURRENT_LIST_DIR})
 
-geosx_add_code_checks(PREFIX resqml)
+# geosx_add_code_checks(PREFIX resqml)

src/ETPRepository.cpp

@@ -47,4 +47,10 @@ void ETPRepository::postInputInitialization()
   // while (!storeHandlers->isDone()) {}
 }
 
+void ETPRepository::open()
+{}
+
+REGISTER_CATALOG_ENTRY( ExternalDataRepositoryBase, ETPRepository, string const &,
+                        Group * const )
+
 } // end namespace geosx

src/ETPRepository.hpp

@@ -20,6 +20,13 @@ class ETPRepository : public EnergyMLDataObjectRepository
   ETPRepository( const string & name,
                  Group * const parent );
 
+  /**
+   * @brief Return the name of the ETPRepository in object catalog.
+   * @return string that contains the catalog name of the ETPRepository
+   */
+  static string catalogName() { return "ETPRepository"; }
+
+  void open() override;
 
 protected:
 

src/EnergyMLDataObjectRepository.cpp

@@ -23,21 +23,21 @@ EnergyMLDataObjectRepository::EnergyMLDataObjectRepository( string const & name,
   enableLogLevelInput();
 }
 
-Group * EnergyMLDataObjectRepository::createChild( string const & childKey, string const & childName )
-{
-  // RESQML DataObject Repositories generally don't have child XML nodes, must override this method to enable
-  GEOS_THROW( GEOS_FMT( "EnergyMLDataObjectRepository '{}': invalid child XML node '{}' of type {}", getName(), childName, childKey ),
-              InputError );
-  std::unique_ptr< EnergyMLDataObjectRepository > task = EnergyMLDataObjectRepository::CatalogInterface::factory( childKey, childName, this );
-  return &this->getParent().registerGroup< EnergyMLDataObjectRepository >( childName, std::move( task ) );
-
-}
-
-EnergyMLDataObjectRepository::CatalogInterface::CatalogType & EnergyMLDataObjectRepository::getCatalog()
-{
-  static EnergyMLDataObjectRepository::CatalogInterface::CatalogType catalog;
-  return catalog;
-}
+// Group * EnergyMLDataObjectRepository::createChild( string const & childKey, string const & childName )
+// {
+//   // RESQML DataObject Repositories generally don't have child XML nodes, must override this method to enable
+//   // GEOS_THROW( GEOS_FMT( "EnergyMLDataObjectRepository '{}': invalid child XML node '{}' of type {}", getName(), childName, childKey ),
+//   //             InputError );
+//   std::unique_ptr< EnergyMLDataObjectRepository > task = EnergyMLDataObjectRepository::CatalogInterface::factory( childKey, childName, this );
+//   return &this->getParent().registerGroup< EnergyMLDataObjectRepository >( childName, std::move( task ) );
+
+// }
+
+// EnergyMLDataObjectRepository::CatalogInterface::CatalogType & EnergyMLDataObjectRepository::getCatalog()
+// {
+//   static EnergyMLDataObjectRepository::CatalogInterface::CatalogType catalog;
+//   return catalog;
+// }
 
 common::DataObjectRepository * EnergyMLDataObjectRepository::getData()
 {

src/EnergyMLDataObjectRepository.hpp

@@ -27,37 +27,9 @@ class EnergyMLDataObjectRepository : public ExternalDataRepositoryBase
   explicit EnergyMLDataObjectRepository( string const & name,
                                          Group * const parent );
 
-  /**
-   * @brief Return the name of the MeshGenerator in object catalog.
-   * @return string that contains the catalog name of the MeshGenerator
-   */
-  static string catalogName() { return "EnergyMLDataObjectRepository"; }
-
-  /// using alias for templated Catalog meshGenerator type
-  using CatalogInterface = dataRepository::CatalogInterface< EnergyMLDataObjectRepository, string const &, Group * const >;
-
-  /**
-   * @brief Accessor for the singleton Catalog object
-   * @return a static reference to the Catalog object
-   */
-  static CatalogInterface::CatalogType & getCatalog();
-
-  /**
-   * @brief function to return the catalog name of the derived class
-   * @return a string that contains the catalog name of the derived class
-   */
-  virtual string getCatalogName() = 0;
-  // /**
-  //  * @brief Create a new object as a child of this group.
-  //  * @param childKey the catalog key of the new object to create
-  //  * @param childName the name of the new object in the repository
-  //  * @return the group child
-  //  */
-  virtual Group * createChild( string const & childKey, string const & childName ) override;
 
   common::DataObjectRepository * getData();
 
-
   COMMON_NS::AbstractObject * getDataObject( string const & id );
   COMMON_NS::AbstractObject * getDataObjectByTitle( string const & name );
 

src/EpcDocumentRepository.hpp

@@ -27,8 +27,6 @@ class EpcDocumentRepository : public EnergyMLDataObjectRepository
    */
   static string catalogName() { return "EpcDocumentRepository"; }
 
-  string getCatalogName() override { return catalogName(); }
-
   void open() override;
 
 protected:

src/RESQMLMeshGenerator.cpp

@@ -20,6 +20,7 @@
 #include "common/DataLayouts.hpp"
 #include "common/MpiWrapper.hpp"
 #include "common/TypeDispatch.hpp"
+#include "mesh/ExternalDataRepositoryManager.hpp"
 #include "mesh/MeshBody.hpp"
 #include "mesh/MeshManager.hpp"
 #include "mesh/generators/CellBlockManager.hpp"
@@ -56,6 +57,9 @@ RESQMLMeshGenerator::RESQMLMeshGenerator( string const & name,
   : ExternalMeshGeneratorBase( name, parent ),
   m_repository( nullptr )
 {
+  getWrapperBase( ExternalMeshGeneratorBase::viewKeyStruct::filePathString()).
+    setInputFlag( InputFlags::OPTIONAL );
+
   registerWrapper( viewKeyStruct::repositoryString(), &m_objectName ).
     setInputFlag( InputFlags::REQUIRED ).
     setDescription( "Name of the EnergyML Repository" );
@@ -132,14 +136,27 @@ Group * RESQMLMeshGenerator::createChild( string const & childKey, string const
 
 void RESQMLMeshGenerator::postInputInitialization()
 {
-  MeshManager & meshManager = this->getGroupByPath< MeshManager >( "/Problem/Mesh" );
-  // objectRepository.
-  m_repository = meshManager.getGroupPointer< EnergyMLDataObjectRepository >( m_objectName );
+  ExternalDataRepositoryManager & externalDataManager = this->getGroupByPath< ExternalDataRepositoryManager >( "/Problem/ExternalDataRepository" );
+    // objectRepository.
+  m_repository = externalDataManager.getGroupPointer< EnergyMLDataObjectRepository >( m_objectName );
 
   GEOS_THROW_IF( m_repository == nullptr,
                  getName() << ": EnergyML Data Object Repository not found: " << m_objectName,
                  InputError );
 
+  COMMON_NS::AbstractObject * rep{nullptr};
+
+  if( !m_uuid.empty())
+    rep = m_repository->getDataObject( m_uuid );
+  else if( !m_title.empty())
+    rep = m_repository->getDataObjectByTitle( m_title );
+
+  if( rep == nullptr )
+    GEOS_ERROR( GEOS_FMT( "There exists no such data object with uuid {} or title {} in the epc file", m_uuid, m_title ) );
+
+
+  m_title = rep->getTitle();
+  m_uuid = rep->getUuid();
 }
 
 void RESQMLMeshGenerator::fillCellBlockManager( CellBlockManager & cellBlockManager, SpatialPartition & partition )
@@ -400,6 +417,8 @@ RESQMLMeshGenerator::retrieveUnstructuredGrid()
 
   GEOS_LOG_RANK_0( GEOS_FMT( "GetNumberOfCells  {}", loadedMesh->GetNumberOfCells()) );
   GEOS_LOG_RANK_0( GEOS_FMT( "GetNumberOfPoints {}", loadedMesh->GetNumberOfPoints()) );
+  GEOS_LOG_RANK_0( GEOS_FMT( "UUID {}", m_uuid) );
+  GEOS_LOG_RANK_0( GEOS_FMT( "Title {}", m_title) );
 
   return loadedMesh;
 }

src/RESQMLUtilities.cpp

@@ -29,7 +29,7 @@
 #include <vtkIntArray.h>
 
 
-#include "fesapi/resqml2/AbstractLocal3dCrs.h"
+#include "fesapi/eml2/AbstractLocal3dCrs.h"
 #include "fesapi/resqml2/CategoricalProperty.h"
 #include "fesapi/resqml2/ContinuousProperty.h"
 #include "fesapi/resqml2/DiscreteProperty.h"

src/RESQMLWriterInterface.cpp

@@ -33,14 +33,16 @@
 #include "fesapi/eml2_0/HdfProxyMPI.h"
 #include "fesapi/eml2/TimeSeries.h"
 #include "fesapi/resqml2_0_1/PropertyKind.h"
-#include "fesapi/tools/TimeTools.h"
+// #include "fesapi/tools/TimeTools.h"
 #include "fesapi/resqml2_0_1/ContinuousProperty.h"
 #include "fesapi/resqml2_0_1/DiscreteProperty.h"
 
 // System includes
 #include <random>
 #include <sstream>
 
+#include "hdf5.h"
+
 namespace geos
 {
 
@@ -254,7 +256,9 @@ RESQMLWriterInterface::RESQMLWriterInterface( string name )
   : VTKPolyDataWriterInterface( name ),
   m_outputRepository( new COMMON_NS::DataObjectRepository()),
   m_propertyKind( nullptr )
-{ }
+{ 
+  // H5Eset_auto2(H5E_DEFAULT, nullptr, nullptr);
+}
 
 void RESQMLWriterInterface::initializeOutput()
 {
@@ -264,8 +268,9 @@ void RESQMLWriterInterface::initializeOutput()
 
   m_propertyKind = m_outputRepository->createPropertyKind(
     propertyKind, "propType1", "F2I",
-    gsoap_resqml2_0_1::resqml20__ResqmlUom::m,
-    gsoap_resqml2_0_1::resqml20__ResqmlPropertyKind::length );
+    gsoap_resqml2_0_1::resqml20__ResqmlUom::m, 
+    false,
+    gsoap_resqml2_0_1::resqml20__ResqmlPropertyKind::length);
 
   string timeSeries = uuid::generate_uuid_v4();
   MpiWrapper::broadcast( timeSeries, 0 );
@@ -281,8 +286,8 @@ void RESQMLWriterInterface::initializeOutput()
   EML2_NS::AbstractHdfProxy *m_hdfProxy = m_outputRepository->createHdfProxy(
     hdfProxy, "Parallel Hdf Proxy", m_outputDir, m_outputName + ".h5",
     COMMON_NS::DataObjectRepository::openingMode::OVERWRITE );
-  m_hdfProxy->setCompressionLevel( 5 );
-  dynamic_cast< EML2_0_NS::HdfProxyMPI * >(m_hdfProxy)->setCollectiveIO();
+  // m_hdfProxy->setCompressionLevel( 5 );
+  // dynamic_cast< EML2_0_NS::HdfProxyMPI * >(m_hdfProxy)->setCollectiveIO();
   m_outputRepository->setDefaultHdfProxy( m_hdfProxy );
 
 
@@ -315,8 +320,7 @@ void RESQMLWriterInterface::generateOutput() const
 void RESQMLWriterInterface::generateSubRepresentation(
   ElementRegionManager const & elemManager, string const & field )
 {
-
-  std::vector< globalIndex > data;
+  std::vector< uint64_t > data;
 
   elemManager.forElementRegions< CellElementRegion >(
     [&]( CellElementRegion const & region ) {
@@ -360,8 +364,9 @@ void RESQMLWriterInterface::generateSubRepresentation(
 
   // Alternate way
   subrep_allranks->pushBackSubRepresentationPatch( gsoap_eml2_3::eml23__IndexableElement::cells, totalDataSize );
-  int const rankOffset =
+  int const rankOffset =    
     std::accumulate( dataSizes.begin(), std::next( dataSizes.begin(), MpiWrapper::commRank()), 0 );
+
   subrep_allranks->setElementIndices( reinterpret_cast< uint64_t * >(data.data()), data.size(), rankOffset );
 
   //record the object pointer for each field
@@ -478,7 +483,7 @@ void RESQMLWriterInterface::write( real64 const time,
 
         data->SetNumberOfTuples( numElements );
         data->SetName( field.c_str());
-
+       
 
         //RESQML Property same for all ranks
         string property = uuid::generate_uuid_v4();
@@ -516,7 +521,6 @@ void RESQMLWriterInterface::write( real64 const time,
         globalIndex maxCount =
           m_subrepresentations[field]->getElementCountOfPatch( 0 );
 
-
         if( data->GetNumberOfComponents() == 1 ) // scalar data
         {
           if( data->GetDataType() == VTK_DOUBLE )

src/RESQMLWriterInterface.hpp

@@ -90,6 +90,8 @@ class RESQMLWriterInterface : private vtk::VTKPolyDataWriterInterface
    */
   void setParentRepresentation( const std::tuple< string, string > & parent )
   {
+    GEOS_LOG_RANK_0( GEOS_FMT( "UUID {}", std::get< 0 >( parent )) );
+    GEOS_LOG_RANK_0( GEOS_FMT( "Title {}", std::get< 1 >( parent )) );
     m_parent = m_outputRepository->createPartial< RESQML2_0_1_NS::UnstructuredGridRepresentation >( std::get< 0 >( parent ), std::get< 1 >( parent ));
   }