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/*
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
* HDF5Common.cpp
*
* Created on: April 20, 2017
* Author: Junmin
*/
#include <iostream> //needs to go away, this is just for demo purposes
#include "engine/hdf5/HDF5Common.h"
namespace adios
{
#define H5_ERROR std::cout<<"[ADIOS H5 ERROR] "
HDF5Common::HDF5Common()
:_writeMode(false),
_total_timestep(0),
_currentTimeStep(0)
{
DefH5T_COMPLEX_FLOAT = H5Tcreate(H5T_COMPOUND, sizeof(std::complex<float>));
H5Tinsert(DefH5T_COMPLEX_FLOAT, "freal", 0, H5T_NATIVE_FLOAT);
H5Tinsert(DefH5T_COMPLEX_FLOAT, "fimg", H5Tget_size(H5T_NATIVE_FLOAT),
H5T_NATIVE_FLOAT);
DefH5T_COMPLEX_DOUBLE =
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<double>));
H5Tinsert(DefH5T_COMPLEX_DOUBLE, "dreal", 0, H5T_NATIVE_DOUBLE);
H5Tinsert(DefH5T_COMPLEX_DOUBLE, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
H5T_NATIVE_DOUBLE);
DefH5T_COMPLEX_LongDOUBLE =
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<long double>));
H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble real", 0, H5T_NATIVE_LDOUBLE);
H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble img",
H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);
}
void HDF5Common::H5_Init(const std::string name, MPI_Comm m_MPIComm, bool toWrite)
{
_writeMode = toWrite;
//
_plist_id = H5Pcreate(H5P_FILE_ACCESS);
#ifdef ADIOS2_HAVE_MPI
H5Pset_fapl_mpio(_plist_id, m_MPIComm, MPI_INFO_NULL);
#endif
std::string ts0 = "/TimeStep0";
if (toWrite) {
/*
* Create a new file collectively and release property list identifier.
*/
_file_id = H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, _plist_id);
if (_file_id >= 0)
{
_group_id =
H5Gcreate2(_file_id, ts0.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
} else {
// read a file collectively
_file_id = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (_file_id >= 0)
{
_group_id = H5Gopen(_file_id, ts0.c_str(), H5P_DEFAULT);
}
}
H5Pclose(_plist_id);
}
HDF5Common::~HDF5Common() {}
void HDF5Common::WriteTimeSteps()
{
if (_file_id < 0)
{
//std::cerr<<"[ADIOS HDF5Error]: Invalid file to record timestep to."<<std::endl;
H5_ERROR<<"Invalid file to record timestep to."<<std::endl;
return;
}
hid_t s = H5Screate(H5S_SCALAR);
hid_t attr = H5Acreate(_file_id, "NumTimeSteps", H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
uint totalts = _currentTimeStep+1;
H5Awrite(attr,H5T_NATIVE_UINT,&totalts);
H5Sclose(s);
H5Aclose(attr);
}
int HDF5Common::GetNumTimeSteps()
{
if (_file_id < 0)
{
std::cerr<<"[ADIOS HDF5Error]: Invalid file to read timestep attribute."<<std::endl;
return -1;
}
if (_total_timestep <= 0) {
hid_t attr = H5Aopen(_file_id, "NumTimeSteps", H5P_DEFAULT);
H5Aread(attr,H5T_NATIVE_UINT, &_total_timestep);
H5Aclose(attr);
}
return _total_timestep;
}
void HDF5Common::H5_Close() {
WriteTimeSteps();
H5Gclose(_group_id);
H5Fclose(_file_id);
}
void HDF5Common::H5_Advance(int totalts)
{
_currentTimeStep++;
if (_currentTimeStep > 0) {
H5Gclose(_group_id);
}
std::string tsname="/TimeStep";
tsname.append(std::to_string(_currentTimeStep));
if (_writeMode) {
_group_id =
H5Gcreate2(_file_id, tsname.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
} else {
if ((totalts > 0) && (totalts <= _currentTimeStep))
{
return;
}
//std::cout<<" ... current group "<<tsname.c_str()<<std::endl;
_group_id =
H5Gopen(_file_id, tsname.c_str(), H5P_DEFAULT);
}
}
}