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Commit c606e13c authored by guj's avatar guj
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1 merge request!49setting up for hdf5
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include/engine/hdf5/HDF5WriterP.h
+ 80
− 189
View file @ c606e13c
......@@ -16,7 +16,6 @@
#include "core/Engine.h"
// supported capsules
#include "capsule/heap/STLVector.h"
......@@ -24,200 +23,92 @@
#include <hdf5.h>
namespace adios {
/*
typedef struct {
double _re; //real part
double _im; //imaginary part
} ADIOS2_Complex_Double;
typedef struct {
float _re; // real
float _im; // imaginary part
} ADIOS2_Complex_Float;
namespace adios
{
// using ADIOS2_Complex_Float = std::complex<float>;
typedef struct {
long double _re; //real part
long double _im; //imaginary part
} ADIOS2_Complex_LongDouble;
*/
class HDF5Writer : public Engine {
class HDF5Writer : public Engine
{
public:
/**
* Constructor for single BP capsule engine, writes in BP format into a single
* heap capsule
* @param name unique name given to the engine
* @param accessMode
* @param mpiComm
* @param method
* @param debugMode
*/
HDF5Writer(ADIOS &adios, const std::string name, const std::string accessMode,
MPI_Comm mpiComm, const Method &method);
virtual ~HDF5Writer();
void Write(Variable<char> &variable, const char *values);
void Write(Variable<unsigned char> &variable, const unsigned char *values);
void Write(Variable<short> &variable, const short *values);
void Write(Variable<unsigned short> &variable, const unsigned short *values);
void Write(Variable<int> &variable, const int *values);
void Write(Variable<unsigned int> &variable, const unsigned int *values);
void Write(Variable<long int> &variable, const long int *values);
void Write(Variable<unsigned long int> &variable,
const unsigned long int *values);
void Write(Variable<long long int> &variable, const long long int *values);
void Write(Variable<unsigned long long int> &variable,
const unsigned long long int *values);
void Write(Variable<float> &variable, const float *values);
void Write(Variable<double> &variable, const double *values);
void Write(Variable<long double> &variable, const long double *values);
void Write(Variable<std::complex<float>> &variable,
const std::complex<float> *values);
void Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values);
void Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values);
void Write(const std::string variableName, const char *values);
void Write(const std::string variableName, const unsigned char *values);
void Write(const std::string variableName, const short *values);
void Write(const std::string variableName, const unsigned short *values);
void Write(const std::string variableName, const int *values);
void Write(const std::string variableName, const unsigned int *values);
void Write(const std::string variableName, const long int *values);
void Write(const std::string variableName, const unsigned long int *values);
void Write(const std::string variableName, const long long int *values);
void Write(const std::string variableName,
const unsigned long long int *values);
void Write(const std::string variableName, const float *values);
void Write(const std::string variableName, const double *values);
void Write(const std::string variableName, const long double *values);
void Write(const std::string variableName, const std::complex<float> *values);
void Write(const std::string variableName,
const std::complex<double> *values);
void Write(const std::string variableName,
const std::complex<long double> *values);
void Close(const int transportIndex = -1);
/*
{
std::cout<<" ===> CLOSING HDF5 <===== "<<std::endl;
//H5Dclose(_dset_id);
//H5Sclose(_filespace);
//H5Sclose(_memspace);
//H5Pclose(_plist_id);
H5Fclose(_file_id);
}
*/
/**
* Constructor for single BP capsule engine, writes in BP format into a
* single
* heap capsule
* @param name unique name given to the engine
* @param accessMode
* @param mpiComm
* @param method
* @param debugMode
*/
HDF5Writer(ADIOS &adios, const std::string name,
const std::string accessMode, MPI_Comm mpiComm,
const Method &method);
virtual ~HDF5Writer();
void Write(Variable<char> &variable, const char *values);
void Write(Variable<unsigned char> &variable, const unsigned char *values);
void Write(Variable<short> &variable, const short *values);
void Write(Variable<unsigned short> &variable,
const unsigned short *values);
void Write(Variable<int> &variable, const int *values);
void Write(Variable<unsigned int> &variable, const unsigned int *values);
void Write(Variable<long int> &variable, const long int *values);
void Write(Variable<unsigned long int> &variable,
const unsigned long int *values);
void Write(Variable<long long int> &variable, const long long int *values);
void Write(Variable<unsigned long long int> &variable,
const unsigned long long int *values);
void Write(Variable<float> &variable, const float *values);
void Write(Variable<double> &variable, const double *values);
void Write(Variable<long double> &variable, const long double *values);
void Write(Variable<std::complex<float>> &variable,
const std::complex<float> *values);
void Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values);
void Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values);
void Write(const std::string variableName, const char *values);
void Write(const std::string variableName, const unsigned char *values);
void Write(const std::string variableName, const short *values);
void Write(const std::string variableName, const unsigned short *values);
void Write(const std::string variableName, const int *values);
void Write(const std::string variableName, const unsigned int *values);
void Write(const std::string variableName, const long int *values);
void Write(const std::string variableName, const unsigned long int *values);
void Write(const std::string variableName, const long long int *values);
void Write(const std::string variableName,
const unsigned long long int *values);
void Write(const std::string variableName, const float *values);
void Write(const std::string variableName, const double *values);
void Write(const std::string variableName, const long double *values);
void Write(const std::string variableName,
const std::complex<float> *values);
void Write(const std::string variableName,
const std::complex<double> *values);
void Write(const std::string variableName,
const std::complex<long double> *values);
void Close(const int transportIndex = -1);
private:
capsule::STLVector
m_Buffer; ///< heap capsule, contains data and metadata buffers
capsule::STLVector
m_Buffer; ///< heap capsule, contains data and metadata buffers
void Init();
void clean();
hid_t _plist_id, _file_id, _dset_id;
hid_t _memspace, _filespace;
hid_t DefH5T_COMPLEX_DOUBLE;
hid_t DefH5T_COMPLEX_FLOAT;
hid_t DefH5T_COMPLEX_LongDOUBLE;
void Init();
void clean();
hid_t _plist_id, _file_id, _dset_id;
hid_t _memspace, _filespace;
hid_t DefH5T_COMPLEX_DOUBLE;
hid_t DefH5T_COMPLEX_FLOAT;
hid_t DefH5T_COMPLEX_LongDOUBLE;
//hid_t DefH5T_filetype_COMPLEX_DOUBLE;
//hid_t DefH5T_filetype_COMPLEX_FLOAT;
//hid_t DefH5T_filetype_COMPLEX_LongDOUBLE;
template <class T>
void UseHDFWrite(Variable<T> &variable, const T *values, hid_t h5type);
/*
template<class T>
void UseHDFWrite( Variable<T>& variable, const T* values, hid_t h5type )
{
//here comes your magic at Writing now variable.m_UserValues has the data
passed by the user
//set variable
variable.m_AppValues = values;
m_WrittenVariables.insert( variable.m_Name );
std::cout<<"writting : "<<variable.m_Name<<" dim
size:"<<variable.m_GlobalDimensions.size()<<std::endl;
int dimSize = variable.m_GlobalDimensions.size();
//hsize_t dimsf[dimSize], count[dimSize], offset[dimSize];
std::vector<hsize_t> dimsf, count, offset;
for(int i=0; i<dimSize; i++) {
dimsf.push_back(variable.m_GlobalDimensions[i]);
count.push_back(dimsf[i]);
offset.push_back(0);
}
count[0] = dimsf[0]/m_SizeMPI;
offset[0]= m_RankMPI*count[0];
_filespace = H5Screate_simple(dimSize, dimsf.data(), NULL);
_dset_id = H5Dcreate(_file_id, variable.m_Name.c_str(), h5type,
_filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(_filespace);
_memspace = H5Screate_simple(dimSize, count.data(), NULL);
//Select hyperslab
_filespace = H5Dget_space(_dset_id);
H5Sselect_hyperslab(_filespace, H5S_SELECT_SET, offset.data(), NULL,
count.data(), NULL);
// Create property list for collective dataset write.
_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(_plist_id, H5FD_MPIO_COLLECTIVE);
herr_t status;
if (m_SizeMPI == 1) {
status = H5Dwrite(_dset_id, h5type, _memspace, _filespace, _plist_id,
values);
} else {
std::vector<T> val;
for (int i=0; i<100; i++) {
//hsize_t c = count[i];
//hsize_t o = offset[i];
val.push_back(0);
}
status = H5Dwrite(_dset_id, h5type, _memspace, _filespace, _plist_id,
val.data());
}
if (status < 0) {
// error
std::cerr<<" Write failed. "<<std::endl;
}
std::cout <<" ==> User is responsible for freeing the data "<<std::endl;
//free(values);
//Close/release resources.
//H5Dclose(_dset_id);
//H5Sclose(_filespace);
//H5Sclose(_memspace);
//H5Pclose(_plist_id);
//H5Fclose(_file_id);
H5Dclose(_dset_id);
H5Sclose(_filespace);
H5Sclose(_memspace);
H5Pclose(_plist_id);
template <class T>
void UseHDFWrite(Variable<T> &variable, const T *values, hid_t h5type);
}
*/
};
} // end namespace adios
......
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