Hdf5DataWriter.hpp

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*/
 
#ifndef HDF5DATAWRITER_HPP_
#define HDF5DATAWRITER_HPP_
 
#include <vector>
 
#include "AbstractHdf5Access.hpp"
#include "DataWriterVariable.hpp"
#include "DistributedVectorFactory.hpp"
 
class Hdf5DataWriter : public AbstractHdf5Access //: public AbstractDataWriter
{
    friend class TestHdf5DataWriter;
private:
 
    DistributedVectorFactory& mrVectorFactory;
 
    const bool mCleanDirectory;                     
    const bool mUseExistingFile;                    
    bool mIsInDefineMode;                           
    bool mIsFixedDimensionSet;                      
    unsigned mEstimatedUnlimitedLength;             
    unsigned mFileFixedDimensionSize;               
    unsigned mDataFixedDimensionSize;               
    unsigned mLo;                                   
    unsigned mHi;                                   
    unsigned mNumberOwned;                          
    unsigned mOffset;                               
    std::vector<unsigned> mIncompletePermIndices;   
    bool mNeedExtend;                               
    std::vector<DataWriterVariable> mVariables;     
    long unsigned mCurrentTimeStep;                 
    Mat mSinglePermutation;                         
    Mat mDoublePermutation;                         
    bool mUseOptimalChunkSizeAlgorithm;             
    hsize_t mChunkSize[DATASET_DIMS];               
    hsize_t mNumberOfChunks;                        
    hsize_t mFixedChunkSize[DATASET_DIMS];          
    hsize_t mChunkTargetSize;                       
    hsize_t mAlignment;                             
    bool mUseCache;                                 
    long unsigned mCacheFirstTimeStep;              
    std::vector<double> mDataCache;                 
    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",
                   bool useCache=false);
 
    virtual ~Hdf5DataWriter();
 
    void DefineFixedDimension(long dimensionSize);
 
    void DefineFixedDimension(const std::vector<unsigned>& rNodesToOuputOriginalIndices, const std::vector<unsigned>& rNodesToOuputPermutedIndices, 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);
 
    bool IsInDefineMode();
 
    virtual void EndDefineMode();
 
    void PossiblyExtend();
 
    void EmptyDataset();
 
    void PutVector(int variableID, Vec petscVector);
 
    void PutStripedVector(std::vector<int> variableIDs, Vec petscVector);
 
    bool GetUsingCache();
 
    void WriteCache();
 
    void PutUnlimitedVariable(double value);
 
    void Close();
 
    int GetVariableByName(const std::string& rVariableName);
 
 
    bool ApplyPermutation(const std::vector<unsigned>& rPermutation, bool unsafeExtendingMode=false);
 
    void SetFixedChunkSize(const unsigned& rTimestepsPerChunk,
                           const unsigned& rNodesPerChunk,
                           const unsigned& rVariablesPerChunk);
 
    /*
     * * NOTES ON CHUNK SIZE AND ALIGNMENT *
     *
     * The default target chunk size is 128 K, which seems to be a good compromise
     * for small problems (e.g. on a desktop PC). For larger problems, I/O
     * performance often improves with increased chunk size. A sweet spot seems to
     * be 1 M chunks.
     *
     * On a striped filesystem, for best performance set the chunk size and
     * alignment (using `H5Pset_alignment` above) to the file stripe size. With
     * `H5Pset_alignment`, every chunk starts at a multiple of the alignment value.
     *
     * To avoid wasting space, the chunk size should be an integer multiple of the
     * alignment value. Note that the algorithm below automatically goes back one
     * step after exceeding the chunk size, which minimises wasted space. To see
     * why, consider the examples below.
     *
     * (Example 1) Say our file system uses 1 M stripes. If we set
     *     target_size_in_bytes = 1024*1024;
     * below and uncomment
     *     H5Pset_alignment(fapl, 0, 1024*1024);
     * above, i.e. aim for (slightly under) 1 M chunks and align them to 1 M
     * boundaries, then the algorithm below will get as close as possible to 1 M
     * chunks but not exceed it, so each chunk will be padded slightly to sit on
     * the 1 M boundaries. Each chunk will therefore have its own stripe on the
     * file system, which should give us the best bandwidth and least contention.
     * Conclusion: this is optimal!
     *
     * Note: In general the algorithm can get very close to the target so the
     * waste isn't bad. Typical utilization is 99.99% (check with "h5ls -v ...").
     *
     * (Example 2) We set
     *     target_size_in_bytes = 128*1024;
     * and uncomment
     *     H5Pset_alignment(fapl, 0, 1024*1024);
     * i.e. 128 K chunks aligned to 1 M boundaries. This would pad every chunk to
     * 1 M boundaries, wasting 7/8 of the space in the file! A file which might be
     * 5 G with an efficient layout would be more like 40 G! Conclusion: setting
     * the chunk size to less than the alignment value is very bad!
     *
     * (Example 3) Say our file system uses 1 M stripes. We set
     *     target_size_in_bytes = 2*1024*1024;
     * and uncomment
     *     H5Pset_alignment(fapl, 0, 1024*1024);
     * i.e. 2 M chunks aligned to 1 M boundaries. This might not be optimal, but
     * it's OK, since the chunk size is (slightly under) twice the alignment, as in
     * Example 1 the amount of padding would be very small. Each read/write would
     * require accessing 2 stripes on the file system. Conclusion: a chunk size of
     * an integer multiple of the alignment value is fine (but not optimal).
     */
 
    void SetTargetChunkSize(hsize_t targetSize);
 
    void SetAlignment(hsize_t alignment);
};
 
#endif /*HDF5DATAWRITER_HPP_*/