TimeHistHDF.hpp

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/*
 * ------------------------------------------------------------------------------------------------------------
 * SPDX-License-Identifier: LGPL-2.1-only
 *
 * Copyright (c) 2018-2019 Lawrence Livermore National Security LLC
 * Copyright (c) 2018-2019 The Board of Trustees of the Leland Stanford Junior University
 * Copyright (c) 2018-2019 Total, S.A
 * Copyright (c) 2019-     GEOSX Contributors
 * All right reserved
 *
 * See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
 * ------------------------------------------------------------------------------------------------------------
 */

#ifndef GEOSX_HDFFILE_HPP_
#define GEOSX_HDFFILE_HPP_

#include "LvArray/src/Array.hpp"
#include "codingUtilities/traits.hpp"
#include "common/DataTypes.hpp"
#include "mpiCommunications/MpiWrapper.hpp"

#include "managers/TimeHistory/HistoryDataSpec.hpp"
#include "managers/TimeHistory/HistoryIO.hpp"
#include <hdf5.h>

#include <string>

namespace geosx
{

class HDFTarget
{
public:
  virtual operator hid_t() { return 0; }

  virtual bool CheckInTarget( const string & name )
  {
    htri_t exists = 0;
    H5E_BEGIN_TRY {
      exists = H5Gget_objinfo( this->operator hid_t(), name.c_str(), 0, NULL );
    } H5E_END_TRY
    return (exists == 0);
  }
};

class HDFFile : public HDFTarget
{
public:
  HDFFile( string const & fnm, bool deleteExisting, bool parallelAccess, MPI_Comm comm );

  ~HDFFile();

  virtual operator hid_t() final { return m_fileId; }
private:
  string m_filename;
  hid_t m_fileId;
  hid_t m_faplId;
  bool m_mpioFapl;
  MPI_Comm m_comm;
};

class HDFHistIO : public BufferedHistoryIO
{
public:
  HDFHistIO( string const & filename,
             localIndex rank,
             std::vector< localIndex > const & dims,
             string const & name,
             std::type_index typeId,
             localIndex writeHead = 0,
             localIndex initAlloc = 2,
             localIndex overallocMultiple = 2,
             MPI_Comm comm = MPI_COMM_GEOSX );

  HDFHistIO( string const & filename,
             const HistoryMetadata & spec,
             localIndex writeHead = 0,
             localIndex initAlloc = 2,
             localIndex overallocMultiple = 2,
             MPI_Comm comm = MPI_COMM_GEOSX ):
    HDFHistIO( filename,
               spec.getRank(),
               spec.getDims(),
               spec.getName(),
               spec.getType(),
               writeHead,
               initAlloc,
               overallocMultiple,
               comm )
  { }

  virtual ~HDFHistIO() { }

  virtual void init( bool existsOkay ) override;

  virtual void write( ) override;

  virtual void compressInFile( ) override;

  inline void resizeFileIfNeeded( localIndex bufferedCount );

protected:
  virtual void resizeBuffer( ) override;

private:
  // file io params
  string m_filename;
  const localIndex m_overallocMultiple;
  globalIndex m_globalIdxOffset;
  globalIndex m_globalIdxCount;
  localIndex m_writeLimit;
  localIndex m_writeHead;
  // history metadata
  hsize_t m_hdfType;
  size_t m_typeSize;
  hsize_t m_typeCount;   // prod(dims[0:n])
  hsize_t m_rank;
  std::vector< hsize_t > m_dims;
  string m_name;
  MPI_Comm m_comm;
  MPI_Comm m_subcomm;
};


class HDFSerialHistIO : public BufferedHistoryIO
{
public:
  HDFSerialHistIO( string const & filename,
                   localIndex rank,
                   std::vector< localIndex > const & dims,
                   string const & name,
                   std::type_index typeId,
                   localIndex writeHead = 0,
                   localIndex initAlloc = 2,
                   localIndex overallocMultiple = 2,
                   MPI_Comm comm = MPI_COMM_GEOSX );

  HDFSerialHistIO( string const & filename,
                   const HistoryMetadata & spec,
                   localIndex writeHead = 0,
                   localIndex initAlloc = 2,
                   localIndex overallocMultiple = 2,
                   MPI_Comm comm = MPI_COMM_GEOSX ):
    HDFSerialHistIO( filename,
                     spec.getRank(),
                     spec.getDims(),
                     spec.getName(),
                     spec.getType(),
                     writeHead,
                     initAlloc,
                     overallocMultiple,
                     comm )
  { }

  virtual ~HDFSerialHistIO() { }

  virtual void init( bool existsOkay ) override;

  virtual void write( ) override;

  virtual void compressInFile( ) override;

  inline void resizeFileIfNeeded( localIndex bufferedCount );

protected:
  virtual void resizeBuffer( ) override;

private:
  // file io params
  string m_filename;
  const localIndex m_overallocMultiple;
  localIndex m_writeLimit;
  localIndex m_writeHead;
  // history metadata
  hsize_t m_hdfType;
  size_t m_typeSize;
  hsize_t m_typeCount;   // prod(dims[0:n])
  hsize_t m_rank;
  std::vector< hsize_t > m_dims;
  string m_name;
  MPI_Comm m_comm;
};

}

#endif