Hdf5DataWriter.hpp

/*

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*/

#ifndef HDF5DATAWRITER_HPP_
#define HDF5DATAWRITER_HPP_


// Not sure why this seems to need to be included here as well as in AbstractHdf5Access.hpp,
// but it does on some of the build machines.
#ifndef H5_USE_16_API
#define H5_USE_16_API 1
#endif

#include <vector>

#include "AbstractHdf5Access.hpp"
#include "DataWriterVariable.hpp"
#include "DistributedVectorFactory.hpp"

class Hdf5DataWriter : public AbstractHdf5Access //: public AbstractDataWriter
{
private:

    DistributedVectorFactory& mrVectorFactory;

    bool mCleanDirectory;                           
    bool mUseExistingFile;                          
    bool mIsInDefineMode;                           
    bool mIsFixedDimensionSet;                      
    unsigned mEstimatedUnlimitedLength;             
    unsigned mFileFixedDimensionSize;               
    unsigned mDataFixedDimensionSize;               
    unsigned mLo;                                   
    unsigned mHi;                                   
    unsigned mNumberOwned;                          
    unsigned mOffset;                               
    bool mNeedExtend;                               
    bool mUseMatrixForIncompleteData;               
    std::vector<DataWriterVariable> mVariables;     
    long unsigned mCurrentTimeStep;                 
    Mat mSinglePermutation;                         
    Mat mDoublePermutation;                         
    Mat mSingleIncompleteOutputMatrix;              
    Mat mDoubleIncompleteOutputMatrix;              
    bool mUseOptimalChunkSizeAlgorithm;             
    hsize_t mChunkSize[DATASET_DIMS];               
    hsize_t mNumberOfChunks;                  
    hsize_t mFixedChunkSize[DATASET_DIMS];          
    void CheckVariableName(const std::string& rName);

    void CheckUnitsName(const std::string& rName);

    void ComputeIncompleteOffset();

    void OpenFile();

    hsize_t CalculateNumberOfChunks();

    void CalculateChunkDims( unsigned targetSize, unsigned* pChunkSizeInBytes, bool* pAllOneChunk );

    void SetChunkSize();

public:

    Hdf5DataWriter(DistributedVectorFactory& rVectorFactory,
                   const std::string& rDirectory,
                   const std::string& rBaseName,
                   bool cleanDirectory=true,
                   bool extendData=false,
                   std::string datasetName="Data");

    virtual ~Hdf5DataWriter();

    void DefineFixedDimension(long dimensionSize);

    void DefineFixedDimension(const std::vector<unsigned>& rNodesToOuput, long vecSize);

    void DefineUnlimitedDimension(const std::string& rVariableName, const std::string& rVariableUnits, unsigned estimatedLength = 1);

    void AdvanceAlongUnlimitedDimension();

    int DefineVariable(const std::string& rVariableName, const std::string& rVariableUnits);

    virtual void EndDefineMode();

    void PossiblyExtend();

    void PutVector(int variableID, Vec petscVector);

    void PutStripedVector(std::vector<int> variableIDs, Vec petscVector);

    void PutUnlimitedVariable(double value);

    void Close();

    int GetVariableByName(const std::string& rVariableName);


    bool ApplyPermutation(const std::vector<unsigned>& rPermutation, bool unsafeExtendingMode=false);

    void DefineFixedDimensionUsingMatrix(const std::vector<unsigned>& rNodesToOuput, long vecSize);

    void SetFixedChunkSize(const unsigned& rTimestepsPerChunk,
                           const unsigned& rNodesPerChunk,
                           const unsigned& rVariablesPerChunk);

};

#endif /*HDF5DATAWRITER_HPP_*/