ReadHDF5Dataset.hpp

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/** \file   ReadHDF5Dataset.hpp
 *  \author Jason Kraftcheck
 *  \date   2010-07-09
 */

#ifndef moab_READ_HDF5DATASET_HPP
#define moab_READ_HDF5DATASET_HPP

#include "moab/MOABConfig.h"
#ifdef MOAB_HAVE_MPI
#include 
#endif

#include   // for size_t
#include 
#include 

#include "moab/Range.hpp"
#include 

namespace moab
{

/**\brief Utility used for reading portions of an HDF5 dataset
 *
 * Implement iterative read of table where:
 * - subset of rows to be read can be specified usign an Range of offsets
 * - each read fills as much as possible of a passed buffer
 * - each read call reads a subsequent set of rows of the data set in an
 *   iterator-like fashion.
 *
 * NOTE: This class also implements an RAII pattern for the data set handle:
 *       It will close the data set in its destructor unless it is specified
 *       to the constructor that only a single column should be read.
 *
 * NOTE: This class will always do collective IO for parallel reads.
 */
class ReadHDF5Dataset
{
  public:
#ifdef MOAB_HAVE_MPI
    typedef MPI_Comm Comm;
#else
    typedef int Comm;
#endif

    class Exception
    {
      public:
        int line_no;
        Exception( int l ) : line_no( l ) {}
    };

    /**\brief Setup to read entire table
     *\param data_set_handle The HDF5 DataSet to read.
     *\param parallel    Doing true partial-read parallel read (as opposed
     *                   to read and delete where collective IO is done for
     *                   everything because all procs read the same stuff.)
     *\param communictor If \c parallel is \c true and \c io_prop is
     *                   \c H5FD_MPIO_COLLECTIVE, then this
     *                   must be a pointer to the MPI_Communicator value.
     *\param close_data_set_on_destruct Call \c H5Dclose on passed
     *                 \c data_set_handle in desturctor.
     *
     *\NOTE If \c parallel is \c true and \c io_prop is \c H5FD_MPIO_COLLECTIVE,
     *      then not only must \c communicator be non-null, but this call must
     *      be made collectively!

     *\NOTE Class instance will not be usable until one of either
     *      \c set_file_ids or \c set_all_file_ids is called.
     */
    ReadHDF5Dataset( const char* debug_desc,
                     hid_t data_set_handle,
                     bool parallel,
                     const Comm* communicator        = 0,
                     bool close_data_set_on_destruct = true );

    ReadHDF5Dataset( const char* debug_desc, bool parallel, const Comm* communicator = 0 );
    void init( hid_t data_set_handle, bool close_data_set_on_destruct = true );

    bool will_close_data_set() const
    {
        return closeDataSet;
    }
    void close_data_set_on_destruct( bool val )
    {
        closeDataSet = val;
    }

    ~ReadHDF5Dataset();

    /**\brief Change file ids to read from.
     *
     *\param file_ids    List of rows to read from dataset
     *\param start_id    Rows of dataset are enumerating beginning with
     *                   this value.  Thus the offset row to be read from
     *                   dataset will be \c file_ids.begin() - \c start_id .
     *\param row_count   Read buffer size in number of table rows.
     *\param data_type       The data type of the buffer into which table values
     *                       are to be read.
     */
    void set_file_ids( const Range& file_ids, EntityHandle start_id, hsize_t row_cout, hid_t data_type );

    /**\brief Read all values in dataset (undo set_file_ids)
     *
     *\param row_count   Read buffer size in number of table rows.
     *\param data_type       The data type of the buffer into which table values
     *                       are to be read.
     */
    void set_all_file_ids( hsize_t row_count, hid_t data_type );

    /**\brief Return false if more data to read, true otherwise
     *
     * Test if the iterative read has reached the end.
     */
    bool done() const
    {
        return ( currOffset == rangeEnd ) && ( readCount == 0 );
    }

    /**\brief Read rows of table
     *
     * Read up to max_num_rows from data set.
     *\param buffer    Memory in which to store values read from data set
     *\param rows_read The actual number of rows read from the table.  Will
     *                 never exceed \c max_rows .
     */
    void read( void* buffer, size_t& rows_read );

    /**\brief Return position in \c Range of file IDs at which next read will start
     */
    Range::const_iterator next_file_id() const
    {
        return currOffset;
    }

    /**\brief Do null read operation
     *
     * Do a read call requesting no data.  This functionality is provided
     * so as to allow collective IO when not all processes need to make the
     * same number of read calls.  To prevent deadlock in this case, processes
     * that have finished their necessary read calls can call this function
     * so that all processes are calling the read method collectively.
     */
    void null_read();

    unsigned columns() const;
    void set_column( unsigned c );

    unsigned long get_read_count() const
    {
        return readCount;
    }
    const char* get_debug_desc() const
    {
        return mpeDesc.c_str();
    }

    static void set_hyperslab_selection_limit( size_t val )
    {
        hyperslabSelectionLimit = val;
    }
    static void default_hyperslab_selection_limit();

    /** Use non-standard 'APPEND' operation for hyperslab selection */
    static void append_hyperslabs()
    {
        hyperslabSelectOp = H5S_SELECT_APPEND;
    }
    /** Revert to default select behavior for standard HDF5 library */
    static void or_hyperslabs()
    {
        hyperslabSelectOp = H5S_SELECT_OR;
    }

  private:
    Range::const_iterator next_end( Range::const_iterator iter );

    Range internalRange;  //!< used when reading entire dataset

    bool closeDataSet;  //!< close dataset in destructor
    hsize_t dataSetOffset[64], dataSetCount[64];
    hid_t dataSet;        //!< Handle for HDF5 data set
    hid_t dataSpace;      //!< Data space for data set
    hid_t dataType;       //!< Data type client code wants for data
    hid_t fileType;       //!< Data type as stored in data set
    hid_t ioProp;         //!< Used to specify collective IO
    int dataSpaceRank;    //!< Rank of data set
    hsize_t rowsInTable;  //!< Total number of rows in dataset
    bool doConversion;    //!< True if dataType != fileType
    bool nativeParallel;  //!< If true then reading different data on different procs

    hsize_t readCount;   //!< Number of actual reads to do
    hsize_t bufferSize;  //!< size of buffer passed to \c read, in number of rows
    const Comm* mpiComm;

    Range::const_iterator currOffset, rangeEnd;
    EntityHandle startID;

    static bool haveMPEEvents;
    static std::pair< int, int > mpeReadEvent;
    static std::pair< int, int > mpeReduceEvent;
    std::string mpeDesc;

    static size_t hyperslabSelectionLimit;
    static H5S_seloper_t hyperslabSelectOp;
};

}  // namespace moab

#endif  // moab_READ_HDF5DATASET_HPP