sidredatacollection.hpp

Go to the documentation of this file.

// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
// reserved. See file COPYRIGHT for details.
//
// This file is part of the MFEM library. For more information and source code
// availability see http://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the GNU Lesser General Public License (as published by the Free
// Software Foundation) version 2.1 dated February 1999.

#ifndef MFEM_SIDREDATACOLLECTION
#define MFEM_SIDREDATACOLLECTION

#include "../config/config.hpp"

#ifdef MFEM_USE_SIDRE

#include "datacollection.hpp"
#include <sidre/sidre.hpp>

namespace mfem
{

/** @brief Data collection with Sidre routines following the Conduit mesh
    blueprint specification. */
/** SidreDataCollection provides an HDF5-based file format for visualization or
    restart capability.  This functionality is aimed primarily at customers of
    LLNL's axom project that run problems at extreme scales.

    For more information, see:
    - Sidre component of LLNL's axom project (to be open-sourced), http://goo.gl/cZyJdn
    - LLNL conduit/blueprint library, https://github.com/LLNL/conduit
    - HDF5 library, https://support.hdfgroup.org/HDF5

    The layout created in the Sidre DataStore is: (`"──"` denote groups,
    `"─•"` denote views, `"─>"` denote links, i.e. shallow-copy view)

        <root>
         ├── <collection-name>_global          (global group)
         │    └── blueprint_index
         │         └── <collection-name>       (bp_index group)
         │              ├── state
         │              │    ├─• cycle
         │              │    ├─• time
         │              │    └─• number_of_domains = <mesh-mpi-comm-size>
         │              ├── coordsets
         │              │    └── coords
         │              │         ├─• path = "<bp-path>/coordsets/coords"
         │              │         ├─• type ─> <bp-grp>/coordsets/coords/type = "explicit"
         │              │         └─• coord_system = "x"|"xy"|"xyz"
         │              ├── topologies
         │              │    ├── mesh
         │              │    │    ├─• path = "<bp-path>/topologies/mesh"
         │              │    │    ├─• type              ─> <bp-grp>/topologies/mesh/type = "unstructured"
         │              │    │    ├─• coordset          ─> <bp-grp>/topologies/mesh/coordset = "coords"
         │              │    │    ├─• grid_function     ─> <bp-grp>/topologies/mesh/grid_function = "<nodes-field-name>"
         │              │    │    └─• boundary_topology ─> <bp-grp>/topologies/mesh/boundary_topology = "boundary"
         │              │    └── boundary
         │              │         ├─• path = "<bp-path>/topologies/mesh"
         │              │         ├─• type     ─> <bp-grp>/topologies/boundary/type = "unstructured"
         │              │         └─• coordset ─> <bp-grp>/topologies/boundary/coordset = "coords"
         │              └── fields
         │                   ├── mesh_material_attribute
         │                   │    ├─• path = "<bp-path>/fields/mesh_material_attribute"
         │                   │    ├─• association ─> <bp-grp>/fields/mesh_material_attribute/association = "element"
         │                   │    ├─• topology    ─> <bp-grp>/fields/mesh_material_attribute/topology = "mesh"
         │                   │    └─• number_of_components = 1
         │                   ├── boundary_material_attribute
         │                   │    ├─• path = "<bp-path>/fields/boundary_material_attribute"
         │                   │    ├─• association ─> <bp-grp>/fields/boundary_material_attribute/association = "element"
         │                   │    ├─• topology    ─> <bp-grp>/fields/boundary_material_attribute/topology = "boundary"
         │                   │    └─• number_of_components = 1
         │                   ├── grid-function-1
         │                   │    ├─• path = "<bp-path>/fields/grid-function-1"
         │                   │    ├─• basis    ─> <bp-grp>/fields/grid-function-1/basis = "<fe-coll-name>"
         │                   │    ├─• topology ─> <bp-grp>/fields/grid-function-1/topology = "mesh"
         │                   │    └─• number_of_components = gf1->VectorDim()
         │                   ├── grid-function-2
         │                   │    ├─• path = "<bp-path>/fields/grid-function-2"
         │                   │    ├─• basis    ─> <bp-grp>/fields/grid-function-2/basis = "<fe-coll-name>"
         │                   │    ├─• topology ─> <bp-grp>/fields/grid-function-2/topology = "mesh"
         │                   │    └─• number_of_components = gf2->VectorDim()
         │                   ├── ...
         │                  ...
         └── <collection-name>                 (domain group)
              ├── blueprint                    (blueprint group)
              │    ├── state
              │    │    ├─• cycle
              │    │    ├─• time
              │    │    ├─• domain = <mesh-mpi-rank>
              │    │    └─• time_step
              │    ├── coordsets
              │    │    └── coords
              │    │         ├─• type = "explicit"
              │    │         └── values
              │    │              ├─• x = view in <vertex-coords-buffer>/<ext-double-data>
              │    │              ├─• y = view in <vertex-coords-buffer>/<ext-double-data>
              │    │              └─• z = view in <vertex-coords-buffer>/<ext-double-data>
              │    ├── topologies
              │    │    ├── mesh
              │    │    │    ├─• type = "unstructured"
              │    │    │    ├── elements
              │    │    │    │    ├─• shape = "points"|"lines"|...
              │    │    │    │    └─• connectivity = <vert-idx-array>
              │    │    │    ├─• coordset = "coords"
              │    │    │    ├─• grid_function = "<nodes-field-name>"
              │    │    │    └─• boundary_topology = "boundary"
              │    │    └── boundary
              │    │         ├─• type = "unstructured"
              │    │         ├── elements
              │    │         │    ├─• shape = "points"|"lines"|...
              │    │         │    └─• connectivity = <vert-idx-array>
              │    │         └─• coordset = "coords"
              │    └── fields
              │         ├── mesh_material_attribute
              │         │    ├─• association = "element"
              │         │    ├─• topology = "mesh"
              │         │    └─• values = <attr-array>
              │         ├── boundary_material_attribute
              │         │    ├─• association = "element"
              │         │    ├─• topology = "boundary"
              │         │    └─• values = <attr-array>
              │         ├── grid-function-1   (name can include path)
              │         │    ├─• basis = "<fe-coll-name>"
              │         │    ├─• topology = "mesh"
              │         │    └─• values = <ext-double-array>/<named-buffer> (vdim == 1)
              │         ├── grid-function-2   (name can include path)
              │         │    ├─• basis = "<fe-coll-name>"
              │         │    ├─• topology = "mesh"
              │         │    └── values   (vdim > 1)
              │         │         ├─• x0 = view into <ext-double-array>/<named-buffer>
              │         │         ├─• x1 = view into <ext-double-array>/<named-buffer>
              │         │         └─• x2 = view into <ext-double-array>/<named-buffer>
              │         ├── ...
              │        ...
              └── named_buffers                (named_buffers group)
                   ├─• vertex_coords = <double-array>
                   ├─• grid-function-1 = <double-array>
                   ├─• grid-function-2 = <double-array>
                  ...

    @note blueprint_index is used both in serial and in parallel. In parallel,
    only rank 0 will add entries to the blueprint index.

    @note QuadratureFunction%s (q-fields) are not supported.

    @note SidreDataCollection does not manage the FiniteElementSpace%s and
    FiniteElementCollection%s associated with registered GridFunction%s.
    Therefore, field registration is left to the user of SidreDataCollection and
    there are no methods that automatically register GridFunction%s using just
    the content of the Sidre DataStore. Such capabilities can be implemented in
    a derived class, adding any desired object management routines.

    @warning This class is still _experimental_, meaning that in future
    releases, it may not be backward compatible, and the output files generated
    by the current version may become unreadable.
*/
class SidreDataCollection : public DataCollection
{
public:
   typedef NamedFieldsMap< Array<int> > AttributeFieldMap;
   AttributeFieldMap attr_map;

public:

   /// Constructor that allocates and initializes a Sidre DataStore.
   /**
       @param[in] collection_name  Name of the collection used as a file name
                                   when saving
       @param[in] the_mesh         Mesh shared by all grid functions in the
                                   collection (can be NULL)
       @param[in] owns_mesh_data   Does the SidreDC own the mesh vertices?

       With this constructor, the SidreDataCollection owns the allocated Sidre
       DataStore.
    */
   SidreDataCollection(const std::string& collection_name,
                       Mesh *the_mesh = NULL,
                       bool owns_mesh_data = false);

   /// Constructor that links to an external Sidre DataStore.
   /** Specifically, the global and domain groups can be at arbitrary paths.

       @param[in] collection_name  Name of the collection used as a file name
                                   when saving
       @param[in] global_grp       Pointer to the global group in the datastore,
                                   see the above schematic
       @param[in] domain_grp       Pointer to the domain group in the datastore,
                                   see the above schematic
       @param[in] owns_mesh_data   Does the SidreDC own the mesh vertices?

       With this constructor, the SidreDataCollection does not own the Sidre
       DataStore.
       @note No mesh or fields are read from the given Groups. The mesh has
       to be set with SetMesh() and fields registered with RegisterField().
    */
   SidreDataCollection(const std::string& collection_name,
                       axom::sidre::Group * global_grp,
                       axom::sidre::Group * domain_grp,
                       bool owns_mesh_data = false);

#ifdef MFEM_USE_MPI
   /// Associate an MPI communicator with the collection.
   /** If no mesh was associated with the collection, this method should be
       called before using any of the Load() methods to read parallel data. */
   void SetComm(MPI_Comm comm);
#endif

   /// Register a GridFunction in the Sidre DataStore.
   /** This method is a shortcut for the call
       `RegisterField(field_name, gf, field_name, 0)`.
    */
   virtual void RegisterField(const std::string &field_name, GridFunction *gf)
   {
      RegisterField(field_name, gf, field_name, 0);
   }

   /// Register a GridFunction in the Sidre DataStore.
   /** The registration procedure is as follows:
       - if (@a gf's data is NULL), allocate named buffer with the name
         @a buffer_name with size _offset + gf->FESpace()->GetVSize()_ and use
         its data (plus the given @a offset) to set @a gf's data;
       - else, if (DataStore has a named buffer @a buffer_name), replace @a gf's
         data array with that named buffer plus the given @a offset;
       - else, use @a gf's data as external data associated with @a field_name
         in the DataStore;
       - register @a field_name in #field_map.

       Both the @a field_name and @a buffer_name can contain a path prefix.
       @note If @a field_name or @a buffer_name is empty, the method does
       nothing.
       @note If the GridFunction pointer @a gf or it's FiniteElementSpace
       pointer are NULL, the method does nothing.
    */
   void RegisterField(const std::string &field_name, GridFunction *gf,
                      const std::string &buffer_name,
                      axom::sidre::SidreLength offset);

   /// Registers an attribute field in the Sidre DataStore
   /** The registration process is similar to that of RegisterField()
       The attribute field is associated with the elements of the mesh
       when @a is_bdry is false, and with the boundary elements, when
       @a is_bdry is true.
       @sa RegisterField()  */
   void RegisterAttributeField(const std::string& name, bool is_bdry);
   void DeregisterAttributeField(const std::string& name);

   /** Returns a pointer to the attribute field associated with
       @a field_name, or NULL when there is no associated field */
   Array<int>* GetAttributeField(const std::string& field_name) const
   { return attr_map.Get(field_name); }

   /** Checks if there is an attribute field associated with @a field_name */
   bool HasAttributeField(const std::string& field_name) const
   { return attr_map.Has(field_name); }

   /** Checks if any rank in the mesh has boundary elements */
   bool HasBoundaryMesh() const;

   /// Set the name of the mesh nodes field.
   /** This name will be used by SetMesh() to register the mesh nodes, if not
       already registered. Also, this method should be called if the mesh nodes
       GridFunction was or will be registered directly by the user. The default
       value for the name is "mesh_nodes". */
   void SetMeshNodesName(const std::string &nodes_name)
   {
      if (!nodes_name.empty()) { m_meshNodesGFName = nodes_name; }
   }

   /// De-register @a field_name from the SidreDataCollection.
   /** The field is removed from the #field_map and the DataStore, including
       deleting it from the named_buffers group, if allocated. */
   virtual void DeregisterField(const std::string& field_name);

   /// Delete all owned data.
   virtual ~SidreDataCollection();

   /// Set/change the mesh associated with the collection
   /** Uses the field name "mesh_nodes" or the value set by SetMeshNodesName()
       to register the mesh nodes GridFunction, if the mesh uses nodes. */
   virtual void SetMesh(Mesh *new_mesh);

#ifdef MFEM_USE_MPI
   /// Set/change the mesh associated with the collection
   /** Uses the field name "mesh_nodes" or the value set by SetMeshNodesName()
       to register the mesh nodes GridFunction, if the mesh uses nodes. */
   virtual void SetMesh(MPI_Comm comm, Mesh *new_mesh);
#endif

   /// Reset the domain and global datastore group pointers.
   /** These are set in the constructor, but if a host code changes the
       datastore contents ( such as wiping out the datastore and loading in new
       contents from a file, i.e. a restart ) these pointers will need to be
       reset to valid groups in the datastore.
       @sa Load(const std::string &path, const std::string &protocol).
    */
   void SetGroupPointers(axom::sidre::Group * global_grp,
                         axom::sidre::Group * domain_grp);

   axom::sidre::Group * GetBPGroup() { return bp_grp; }
   axom::sidre::Group * GetBPIndexGroup() { return bp_index_grp; }

   /// Prepare the DataStore for writing
   virtual void PrepareToSave();

   /// Save the collection to file.
   /** This method calls `Save(collection_name, "sidre_hdf5")`. */
   virtual void Save();

   /// Save the collection to @a filename.
   /** The collection path prefix is prepended to the @a filename and the
       current cycle is appended, if cycle >= 0. */
   void Save(const std::string& filename, const std::string& protocol);

   /// Load the Sidre DataStore from file.
   /** No mesh or fields are read from the loaded DataStore.

       If the data collection created the datastore, it knows the layout of
       where the domain and global groups are, and can restore them after the
       Load().

       If, however, the data collection does not own the datastore (e.g. it did
       not create the datastore), the host code must reset these pointers after
       the load operation, using SetGroupPointers(), and also reset the state
       variables, using UpdateStateFromDS().
    */
   void Load(const std::string& path, const std::string& protocol);

   /// Load SidreDataCollection from file.
   /** The used file path is based on the current prefix path, collection name,
       and the given @a cycle_. The protocol is "sidre_hdf5".
       @sa Load(const std::string &path, const std::string &protocol).
    */
   virtual void Load(int cycle_ = 0)
   {
      SetCycle(cycle_);
      Load(get_file_path(name), "sidre_hdf5");
   }

   /// Load external data after registering externally owned fields.
   void LoadExternalData(const std::string& path);

   /** @brief Updates the DataCollection's cycle, time, and time-step variables
       with the values from the data store. */
   void UpdateStateFromDS();

   /** @brief Updates the data store's cycle, time, and time-step variables with
       the values from the SidreDataCollection. */
   void UpdateStateToDS();

   /** @name Methods for named buffer access and manipulation. */
   ///@{

   /** @brief Get a pointer to the sidre::View holding the named buffer for
       @a buffer_name. */
   /** If such named buffer is not allocated, the method returns NULL.
       @note To access the underlying pointer, use View::getData().
       @note To query the size of the buffer, use View::getNumElements().
    */
   axom::sidre::View *
   GetNamedBuffer(const std::string& buffer_name) const
   {
      return named_buffers_grp()->hasView(buffer_name)
             ? named_buffers_grp()->getView(buffer_name)
             : NULL;
   }

   /// Return newly allocated or existing named buffer for @a buffer_name.
   /** The buffer is stored in the named_buffers group. If the currently
       allocated buffer size is smaller than @a sz, then the buffer is
       reallocated with size @a sz, destroying its contents.
       @note To access the underlying pointer, use View::getData().
    */
   axom::sidre::View *
   AllocNamedBuffer(const std::string& buffer_name,
                    axom::sidre::SidreLength sz,
                    axom::sidre::TypeID type =
                       axom::sidre::DOUBLE_ID);

   /// Deallocate the named buffer @a buffer_name.
   void FreeNamedBuffer(const std::string& buffer_name)
   { named_buffers_grp()->destroyViewAndData(buffer_name); }

   ///@}

private:
   // Used if the Sidre data collection is providing the datastore itself.
   const bool m_owns_datastore;

   // TODO - Need to evaluate if this bool member can be combined with own_data
   // in parent data collection class. m_owns_mesh_data indicates whether the
   // Sidre dc owns the mesh element data and node positions gf. The DC base
   // class own_data indicates if the dc owns the mesh object pointer itself and
   // GF objects. Can we use one flag and just have DC own all objects vs none?
   const bool m_owns_mesh_data;

   // Name to be used for registering the mesh nodes in the SidreDataCollection.
   // This name is used by SetMesh() and can be overwritten by the method
   // SetMeshNodesName().
   // Default value: "mesh_nodes".
   std::string m_meshNodesGFName;

   // If the data collection owns the datastore, it will store a pointer to it.
   // Otherwise, this pointer is NULL.
   axom::sidre::DataStore * m_datastore_ptr;

protected:
   axom::sidre::Group *named_buffers_grp() const;

   axom::sidre::View *
   alloc_view(axom::sidre::Group *grp,
              const std::string &view_name);

   axom::sidre::View *
   alloc_view(axom::sidre::Group *grp,
              const std::string &view_name,
              const axom::sidre::DataType &dtype);

   axom::sidre::Group *
   alloc_group(axom::sidre::Group *grp,
               const std::string &group_name);

   // return the filename based on prefix_path, collection name and cycle.
   std::string get_file_path(const std::string &filename) const;

private:
   // If the data collection does not own the datastore, it will need pointers
   // to the blueprint and blueprint index group to use.
   axom::sidre::Group * bp_grp;
   axom::sidre::Group * bp_index_grp;

   // This is stored for convenience.
   axom::sidre::Group * named_bufs_grp;

   // Private helper functions

   void RegisterFieldInBPIndex(const std::string& field_name,
                               GridFunction *gf);
   void DeregisterFieldInBPIndex(const std::string & field_name);

   void RegisterAttributeFieldInBPIndex(const std::string& attr_name);
   void DeregisterAttributeFieldInBPIndex(const std::string& attr_name);

   /** @brief Return a string with the conduit blueprint name for the given
       Element::Type. */
   std::string getElementName( Element::Type elementEnum );

   /**
    * \brief A private helper function to set up the views associated with the
       data of a scalar valued grid function in the blueprint style.
    * \pre gf is not null
    * \note This function is expected to be called by RegisterField()
    * \note Handles cases where hierarchy is already set up,
    *      where the data was allocated by this data collection
    *      and where the gridfunction data is external to Sidre
    */
   void addScalarBasedGridFunction(const std::string& field_name,
                                   GridFunction* gf,
                                   const std::string &buffer_name,
                                   axom::sidre::SidreLength offset);

   /**
    * \brief A private helper function to set up the views associated with the
       data of a vector valued grid function in the blueprint style.
    * \pre gf is not null
    * \note This function is expected to be called by RegisterField()
    * \note Handles cases where hierarchy is already set up,
    *      where the data was allocated by this data collection
    *      and where the gridfunction data is external to Sidre
    */
   void addVectorBasedGridFunction(const std::string& field_name,
                                   GridFunction* gf,
                                   const std::string &buffer_name,
                                   axom::sidre::SidreLength offset);

   /** @brief A private helper function to set up the Views associated with
       attribute field named @a field_name */
   void addIntegerAttributeField(const std::string& field_name, bool is_bdry);

   /// Sets up the four main mesh blueprint groups.
   /**
    * \param hasBP Indicates whether the blueprint has already been set up.
    */
   void createMeshBlueprintStubs(bool hasBP);

   /// Sets up the mesh blueprint 'state' group.
   /**
    * \param hasBP Indicates whether the blueprint has already been set up.
    */
   void createMeshBlueprintState(bool hasBP);

   /// Sets up the mesh blueprint 'coordsets' group.
   /**
    * \param hasBP Indicates whether the blueprint has already been set up.
    */
   void createMeshBlueprintCoordset(bool hasBP);

   /// Sets up the mesh blueprint 'topologies' group.
   /**
    * This method is called from SetMesh().
    * \param hasBP Indicates whether the blueprint has already been set up.
    * \param mesh_name The name of the topology.
    * \note Valid values for @a mesh_name are "mesh" and "boundary" and the
            former has to be created with this method before the latter.
    */
   void createMeshBlueprintTopologies(bool hasBP, const std::string& mesh_name);

#ifdef MFEM_USE_MPI
   /// Sets up the mesh blueprint 'adjacencies' group.
   /**
    * \param hasBP Indicates whether the blueprint has already been set up.
    * \note Only valid when using parallel meshes
    */
   void createMeshBlueprintAdjacencies(bool hasBP);
#endif

   /// Verifies that the contents of the mesh blueprint data is valid.
   void verifyMeshBlueprint();
};

} // end namespace mfem

#endif

#endif