purify::H5::H5Handler Class Reference

Purify interface class to handle HDF5 input files. More...

#include <h5reader.h>

Public Member Functions
	H5Handler ()=delete
	H5Handler (const std::string &filename)
	Default constructor (serial behaviour) More...
template<typename T = double>
std::vector< T >	read (const std::string &label) const
	Method to read the entire dataset. More...
template<typename T = double>
std::vector< T >	distread (const std::string &label)
template<typename T = double>
std::vector< T >	stochread (const std::string &label, size_t batchsize, bool shuffle=false)

Detailed Description

Purify interface class to handle HDF5 input files.

Definition at line 48 of file h5reader.h.

Constructor & Destructor Documentation

H5Handler() [1/2]

purify::H5::H5Handler::H5Handler ( )

delete

H5Handler() [2/2]

purify::H5::H5Handler::H5Handler ( const std::string &  filename )

inline

Default constructor (serial behaviour)

Definition at line 55 of file h5reader.h.

      : _comm(nullptr),
        _fap(HighFive::FileAccessProps{}),
        _dtp(HighFive::DataTransferProps{}),
        _file(filename, HighFive::File::ReadOnly) {
    _datalen = _slicepos = _slicelen = _batchpos = 0;
  }

Member Function Documentation

distread()

template<typename T = double>

std::vector<T> purify::H5::H5Handler::distread ( const std::string &  label )

inline

Method to read a dataset slice with slices evenly split across MPI ranks

Definition at line 84 of file h5reader.h.

                                                {
    if (!_comm) throw std::runtime_error("No MPI-collective reading enabled!");
    _loadDataSet(label);
    std::vector<T> data;
    data.reserve(_slicelen);
    _ds[label].select({_slicepos}, {_slicelen}).read(data, _dtp);
    return data;
  }

References read().

Referenced by TEST_CASE().

read()

template<typename T = double>

std::vector<T> purify::H5::H5Handler::read ( const std::string &  label ) const

inline

Method to read the entire dataset.

Definition at line 76 of file h5reader.h.

                                                  {
    auto dataset = _file.getDataSet(label);
    return dataset.read<std::vector<T>>();
  }

Referenced by distread(), purify::H5::read_visibility(), stochread(), and TEST_CASE().

stochread()

template<typename T = double>

std::vector<T> purify::H5::H5Handler::stochread ( const std::string &  label, size_t  batchsize, bool  shuffle = false  )

inline

Method to stochastically draw a subset from the distributed dataset slice

Definition at line 96 of file h5reader.h.

                                                                                         {
    if (!_comm) throw std::runtime_error("No MPI-collective reading enabled!");
 
    _loadDataSet(label);
    if (shuffle) _shuffle();
 
    std::vector<T> data;
    data.reserve(batchsize);
    // account for wrap around near
    // the edges of the slice
    size_t pos = _batchpos;
    while (batchsize) {
      std::vector<T> tmp;
      size_t len = std::min(batchsize, _slicepos + _slicelen - pos);
      _ds[label].select({pos}, {len}).read(tmp, _dtp);
      data.insert(data.end(), std::make_move_iterator(std::begin(tmp)),
                  std::make_move_iterator(std::end(tmp)));
      pos = _slicepos;
      batchsize -= len;
    }
    return data;
  }

References read().

Referenced by purify::H5::stochread_visibility(), and TEST_CASE().

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The documentation for this class was generated from the following file:

• /home/runner/work/purify/purify/cpp/purify/h5reader.h