ReadHDF5.hpp

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/**
 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
 * storing and accessing finite element mesh data.
 *
 * Copyright 2004 Sandia Corporation.  Under the terms of Contract
 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
 * retains certain rights in this software.
 *
 * This library 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; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 */

#ifndef READ_HDF5_HPP
#define READ_HDF5_HPP

#include 
#include 
#include "mhdf.h"
#include "moab/Forward.hpp"
#include "moab/ReadUtilIface.hpp"
#include "moab/Range.hpp"
#include "moab/ReaderIface.hpp"
#include "moab/RangeMap.hpp"
#include "DebugOutput.hpp"
#include "HDF5Common.hpp"

#ifdef MOAB_HAVE_MPI
#include 
#endif

namespace moab
{

class ParallelComm;
class ReadHDF5Dataset;
class CpuTimer;

/**
 * \brief  Read mesh from MOAB HDF5 (.h5m) file.
 * \author Jason Kraftcheck
 * \date   18 April 2004
 */
class ReadHDF5 : public ReaderIface
{
  public:
#ifdef MOAB_HAVE_MPI
    typedef MPI_Comm Comm;
#else
    typedef int Comm;
#endif

    static ReaderIface* factory( Interface* );

    ReadHDF5( Interface* iface );

    virtual ~ReadHDF5();

    /** Export specified meshsets to file
     * \param filename     The filename to export. Must end in .mhdf
     * \param export_sets  Array of handles to sets to export, or NULL to export all.
     * \param export_set_count Length of export_sets array.
     */
    ErrorCode load_file( const char* file_name,
                         const EntityHandle* file_set,
                         const FileOptions& opts,
                         const SubsetList* subset_list = 0,
                         const Tag* file_id_tag        = 0 );

    ErrorCode read_tag_values( const char* file_name,
                               const char* tag_name,
                               const FileOptions& opts,
                               std::vector< int >& tag_values_out,
                               const SubsetList* subset_list = 0 );
    Interface* moab() const
    {
        return iFace;
    }

    //! Store old HDF5 error handling function
    struct HDF5ErrorHandler
    {
        HDF5_Error_Func_Type func;
        void* data;
    };

  protected:
    ErrorCode load_file_impl( const FileOptions& opts );

    ErrorCode load_file_partial( const ReaderIface::IDTag* subset_list,
                                 int subset_list_length,
                                 int num_parts,
                                 int part_number,
                                 const FileOptions& opts );

    ErrorCode read_tag_values_all( int tag_index, std::vector< int >& results );
    ErrorCode read_tag_values_partial( int tag_index, const Range& file_ids, std::vector< int >& results );

    enum ReadTimingValues
    {
        TOTAL_TIME = 0,
        SET_META_TIME,
        SUBSET_IDS_TIME,
        GET_PARTITION_TIME,
        GET_SET_IDS_TIME,
        GET_SET_CONTENTS_TIME,
        GET_POLYHEDRA_TIME,
        GET_ELEMENTS_TIME,
        GET_NODES_TIME,
        GET_NODEADJ_TIME,
        GET_SIDEELEM_TIME,
        UPDATECONN_TIME,
        ADJACENCY_TIME,
        DELETE_NON_SIDEELEM_TIME,
        READ_SET_IDS_RECURS_TIME,
        FIND_SETS_CONTAINING_TIME,
        READ_SETS_TIME,
        READ_TAGS_TIME,
        STORE_FILE_IDS_TIME,
        READ_QA_TIME,
        NUM_TIMES
    };

    void print_times();

  private:
    ErrorCode init();

    inline int is_error( mhdf_Status& status )
    {
        int i;
        if( ( i = mhdf_isError( &status ) ) ) MB_SET_ERR_CONT( mhdf_message( &status ) );
        return i;
    }

    //! The size of the data buffer (dataBuffer).
    int bufferSize;
    //! A memory buffer to use for all I/O operations.
    char* dataBuffer;

    //! Interface pointer passed to constructor
    Interface* iFace;

    //! The file handle from the mhdf library
    mhdf_FileHandle filePtr;

    //! File summary
    mhdf_FileDesc* fileInfo;

    //! Map from File ID to MOAB handle
    typedef RangeMap< long, EntityHandle > IDMap;
    IDMap idMap;

    //! Cache pointer to read util
    ReadUtilIface* readUtil;

    //! The type of an EntityHandle
    hid_t handleType;

    //! List of connectivity arrays for which conversion from file ID
    //! to handle was deferred until later.
    struct IDConnectivity
    {
        EntityHandle handle;  // Start_handle
        size_t count;         // Num entities
        int nodes_per_elem;   // Per-element connectivity length
        EntityHandle* array;  // Connectivity array
    };
    //! List of connectivity arrays for which conversion from file ID
    //! to handle was deferred until later.
    std::vector< IDConnectivity > idConnectivityList;

    //! Read/write property handle
    //! indepIO -> independent IO during true parallel read
    //! collIO  -> collective IO during true parallel read
    //! Both are H5P_DEFAULT for serial IO and collective
    //! when reading the entire file on all processors.
    hid_t indepIO, collIO;

    ParallelComm* myPcomm;

    //! Use IODebugTrack instances to verify reads.
    //! Enable with the DEBUG_OVERLAPS option.
    bool debugTrack;
    //! Debug output. Verbosity controlled with DEBUG_FORMAT option.
    DebugOutput dbgOut;
    //! Doing true parallel read (PARALLEL=READ_PART)
    bool nativeParallel;
    //! MPI_Comm value (unused if \c !nativeParallel)
    Comm* mpiComm;

    //! Flags for some behavior that can be changed through
    //! reader options
    bool blockedCoordinateIO;
    bool bcastSummary;
    bool bcastDuplicateReads;

    //! Store old HDF5 error handling function
    HDF5ErrorHandler errorHandler;

    long ( *setMeta )[4];

    double _times[NUM_TIMES];
    CpuTimer* timer;
    bool cputime;
    ErrorCode read_all_set_meta();

    ErrorCode set_up_read( const char* file_name, const FileOptions& opts );
    ErrorCode clean_up_read( const FileOptions& opts );

    //! Given a list of tags and values, get the file ids for the
    //! corresponding entities in the file.
    ErrorCode get_subset_ids( const ReaderIface::IDTag* subset_list, int subset_list_length, Range& file_ids_out );

    /**\brief Remove all but the specified fraction of sets from the passed range
     *
     * Select a subset of the gathered set of file ids to read in based on
     * communicator size and rank.
     *\param tmp_file_ids As input: sets to be read on all procs.
     *                    As output: sets to read on this proc.
     *\param num_parts    communicator size
     *\param part_number  communicator rank
     */
    ErrorCode get_partition( Range& tmp_file_ids, int num_parts, int part_number );

    ErrorCode read_nodes( const Range& node_file_ids );

    // Read elements in fileInfo->elems[index]
    ErrorCode read_elems( int index );

    // Read subset of elements in fileInfo->elems[index]
    ErrorCode read_elems( int index, const Range& file_ids, Range* node_ids = 0 );

    //! Read element connectivity.
    //!
    //!\param node_ids  If this is non-null, the union of the connectivity list
    //!                 for all elements is passed back as FILE IDS in this
    //!                 range AND the connectivity list is left in the form
    //!                 of file IDs (NOT NODE HANDLES).
    ErrorCode read_elems( const mhdf_ElemDesc& elems, const Range& file_ids, Range* node_ids = 0 );

    //! Update connectivity data for all element groups for which read_elems
    //! was called with a non-null \c node_ids argument.
    ErrorCode update_connectivity();

    // Read connectivity data for a list of element file ids.
    // passing back the file IDs for the element connectivity
    // w/out actually creating any elements in MOAB.
    ErrorCode read_elems( int index, const Range& element_file_ids, Range& node_file_ids );

    // Scan all elements in group. For each element for which all vertices
    // are contained in idMap (class member), read the element. All new
    // elements are added to idMap.
    //
    // NOTE: Collective IO calls in parallel.
    ErrorCode read_node_adj_elems( const mhdf_ElemDesc& group, Range* read_entities = 0 );

    // Scan all elements in specified file table. For each element for
    // which all vertices are contained in idMap (class member), read the
    // element. All new elements are added to idMap.
    //
    // NOTE: Collective IO calls in parallel.
    ErrorCode read_node_adj_elems( const mhdf_ElemDesc& group, hid_t connectivity_handle, Range* read_entities = 0 );

    //! Read poly(gons|hedra)
    ErrorCode read_poly( const mhdf_ElemDesc& elems, const Range& file_ids );

    //! Clean up elements that were a) read because we had read all of the
    //! nodes and b) weren't actually sides of the top-dimension elements
    //! we were trying to read.
    ErrorCode delete_non_side_elements( const Range& side_ents );

    //! Read sets
    ErrorCode read_sets( const Range& set_file_ids );

    ErrorCode read_adjacencies( hid_t adjacency_table, long table_length );

    //! Create tag and read all data.
    ErrorCode read_tag( int index );

    //! Create new tag or verify type matches existing tag
    ErrorCode create_tag( const mhdf_TagDesc& info, Tag& handle, hid_t& type );

    //! Read dense tag for all entities
    ErrorCode read_dense_tag( Tag tag_handle,
                              const char* ent_name,
                              hid_t hdf_read_type,
                              hid_t data_table,
                              long start_id,
                              long count );

    //! Read sparse tag for all entities.
    ErrorCode read_sparse_tag( Tag tag_handle,
                               hid_t hdf_read_type,
                               hid_t ent_table,
                               hid_t val_table,
                               long num_entities );

    //! Read variable-length tag for all entities.
    ErrorCode read_var_len_tag( Tag tag_handle,
                                hid_t hdf_read_type,
                                hid_t ent_table,
                                hid_t val_table,
                                hid_t off_table,
                                long num_entities,
                                long num_values );

    /**\brief Read index table for sparse tag.
     *
     * Read ID table for a sparse or variable-length tag, returning
     * the handles and offsets within the table for each file ID
     * that corresponds to an entity we've read from the file (an
     * entity that is in \c idMap).
     *
     * \param id_table     The MOAB handle for the tag
     * \param start_offset Some non-zero value because ranges (in this case
     *                     the offset_range) cannot contain zeros.
     * \param offset_range Output: The offsets in the id table for which IDs
     *                     that occur in \c idMap were found. All values
     *                     are increased by \c start_offset to avoid
     *                     putting zeros in the range.
     * \param handle_range Output: For each valid ID read from the table,
     *                     the corresponding entity handle. Note: if
     *                     the IDs did not occur in handle order, then
     *                     this will be empty. Use \c handle_vect instead.
     * \param handle_vect  Output: For each valid ID read from the table,
     *                     the corresponding entity handle. Note: if
     *                     the IDs occurred in handle order, then
     *                     this will be empty. Use \c handle_range instead.
     */
    ErrorCode read_sparse_tag_indices( const char* name,
                                       hid_t id_table,
                                       EntityHandle start_offset,
                                       Range& offset_range,
                                       Range& handle_range,
                                       std::vector< EntityHandle >& handle_vect );

    ErrorCode read_qa( EntityHandle file_set );

  public:
    ErrorCode convert_id_to_handle( EntityHandle* in_out_array, size_t array_length );

    void convert_id_to_handle( EntityHandle* in_out_array, size_t array_length, size_t& array_length_out ) const
    {
        return convert_id_to_handle( in_out_array, array_length, array_length_out, idMap );
    }

    ErrorCode convert_range_to_handle( const EntityHandle* ranges, size_t num_ranges, Range& merge );

    static void convert_id_to_handle( EntityHandle* in_out_array,
                                      size_t array_length,
                                      const RangeMap< long, EntityHandle >& id_map );

    static void convert_id_to_handle( EntityHandle* in_out_array,
                                      size_t array_length,
                                      size_t& array_length_out,
                                      const RangeMap< long, EntityHandle >& id_map );

    static void convert_range_to_handle( const EntityHandle* ranges,
                                         size_t num_ranges,
                                         const RangeMap< long, EntityHandle >& id_map,
                                         Range& merge );

    ErrorCode insert_in_id_map( const Range& file_ids, EntityHandle start_id );

    ErrorCode insert_in_id_map( long file_id, EntityHandle handle );

  private:
    /**\brief Search for entities with specified tag values
     *
     *\NOTE For parallel reads, this function does collective IO.
     *
     *\param tag_index  Index into info->tags specifying which tag to search.
     *\param sorted_values  List of tag values to check for, in ascending sorted
     *                  order.
     *\param file_ids_out  File IDs for entities with specified tag values.
     */
    ErrorCode search_tag_values( int tag_index,
                                 const std::vector< int >& sorted_values,
                                 Range& file_ids_out,
                                 bool sets_only = false );

    /**\brief Search for entities with specified tag
     *
     *\NOTE For parallel reads, this function does collective IO.
     *
     *\param tag_index  Index into info->tags specifying which tag to search.
     *\param file_ids_out  File IDs for entities with specified tag values.
     */
    ErrorCode get_tagged_entities( int tag_index, Range& file_ids_out );

    /**\brief Search a table of tag data for a specified set of values.
     *
     * Search a table of tag values, returning the indices into the table
     * at which matches were found.
     *\NOTE For parallel reads, this function does collective IO.
     *
     *\param info       Summary of data contained in file.
     *\param tag_table     HDF5/mhdf handle for tag values
     *\param table_size    Number of values in table
     *\param sorted_values Sorted list of values to search for.
     *\param value_indices Output: Offsets into the table of data at which
     *                       matching values were found.
     */
    ErrorCode search_tag_values( hid_t tag_table,
                                 unsigned long table_size,
                                 const std::vector< int >& sorted_values,
                                 std::vector< EntityHandle >& value_indices );

    /**\brief Get the file IDs for nodes and elements contained in sets.
     *
     * Read the contents for the specified sets and return the file IDs
     * of all nodes and elements contained within those sets.
     *\param sets       Container of file IDs designating entity sets.
     *\param file_ids   Output: File IDs of entities contained in sets.
     */
    ErrorCode get_set_contents( const Range& sets, Range& file_ids );

    /** Given a list of file IDs for entity sets, find all contained
     *  or child sets (at any depth) and append them to the Range
     *  of file IDs.
     */
    ErrorCode read_set_ids_recursive( Range& sets_in_out, bool containted_sets, bool child_sets );

    /** Find all sets containing one or more entities read from the file
     *  and added to idMap
     */
    ErrorCode find_sets_containing( Range& sets_out, bool read_set_containing_parents );

    /**\brief Read sets from file into MOAB for partial read of file.
     *
     * Given the file IDs for entity sets (sets_in) and elements and
     * nodes (id_map), read in all sets containing any of the elements
     * or nodes and all sets that are (recursively) children of any
     * other set to be read (those in sets_in or those containing any
     * already-read element or node.)
     *\param sets_in    File IDs for sets to read (unconditionally)
     */
    ErrorCode read_sets_partial( const Range& sets_in );

    /** Find file IDs of sets containing any entities in the passed id_map */
    ErrorCode find_sets_containing( hid_t content_handle,
                                    hid_t content_type,
                                    long content_len,
                                    bool read_set_containing_parents,
                                    Range& file_ids );

  public:
    enum SetMode
    {
        CONTENT = 0,
        CHILD   = 1,
        PARENT  = 2
    };

  private:
    // Read the set data specified by by which_data.
    // Update set data in MOAB according to which_data,
    // unless file_ids_out is non-null. If file_ids_out is
    // non-null, then return the file IDs in the passed
    // range and do not make any changes to MOAB data
    // structures. If file_ids_out is NULL, then set_start_handle
    // is ignored.
    ErrorCode read_set_data( const Range& set_file_ids,
                             EntityHandle set_start_handle,
                             ReadHDF5Dataset& set_data_set,
                             SetMode which_data,
                             Range* file_ids_out = 0 );

    /**\brief Store file IDS in tag values
     *
     * Copy file ID from IDMap for each entity read from file
     * into a tag value on the entity.
     */
    ErrorCode store_file_ids( Tag tag );

    /**\brief Store sets file IDS in a custom tag
     *
     * Copy sets file ID from IDMap for each set read from file
     *  into a custom tag on the sets
     *  needed now for the VisIt plugin, to identify sets read
     */
    ErrorCode store_sets_file_ids();

    /**\brief Find index in mhdf_FileDesc* fileInfo for specified tag name
     *
     * Given a tag name, find its index in fileInfo and verify that
     * each tag value is a single integer.
     */
    ErrorCode find_int_tag( const char* name, int& index_out );

    void debug_barrier_line( int lineno );
};

}  // namespace moab

#endif