C++ H5Dwrite函数代码示例

/**
 * Write a hyperslab into the dataset.
 * 
 * @param [in] HDF5_Dataset_id - Dataset id
 * @param [in] Position - Position in the dataset
 * @param [in] Size - Size of the hyperslab
 * @param [in] Data
 * @throw ios::failure
 * 
 */
void THDF5_File::WriteHyperSlab(const hid_t HDF5_Dataset_id, const TDimensionSizes & Position , const TDimensionSizes & Size, const float * Data){
    
    
    
     // Select hyperslab
    const int MatrixRank = 3;    
    hsize_t ElementCount[MatrixRank] = {Size.Z, Size.Y, Size.X};    
    hsize_t Offset[MatrixRank] = {Position.Z,Position.Y,Position.X};
    
    herr_t status;
    hid_t  HDF5_Filespace,HDF5_Memspace;
    
    // Select hyperslab in the file.     
    HDF5_Filespace = H5Dget_space(HDF5_Dataset_id);  
    
    
    status = H5Sselect_hyperslab(HDF5_Filespace, H5S_SELECT_SET, Offset, 0, ElementCount, NULL);
    if (status < 0) {
        char ErrorMessage[256];
        sprintf(ErrorMessage,HDF5_ERR_FMT_CouldNotWriteTo,"");        
        throw ios::failure(ErrorMessage);
     } 
    
    
    // assign memspace
    HDF5_Memspace = H5Screate_simple(MatrixRank, ElementCount, NULL);

    
     status = H5Dwrite(HDF5_Dataset_id, H5T_NATIVE_FLOAT, HDF5_Memspace, HDF5_Filespace,  H5P_DEFAULT, Data);
     if (status < 0) {
        char ErrorMessage[256];
        sprintf(ErrorMessage,HDF5_ERR_FMT_CouldNotWriteTo,"");
        
        throw ios::failure(ErrorMessage);
     } 
    
    H5Sclose(HDF5_Memspace);
    H5Sclose(HDF5_Filespace);  
    
    
    
}// end of WriteHyperSlab

bool save_quad_bc(hid_t parent_group_id, JudyArray<Boundary *> &bcs) {
	herr_t status;

	// create main group
	hid_t group_id = H5Gcreate(parent_group_id, "quad", 0);

	// count
	hid_t dataspace_id = H5Screate(H5S_SCALAR);
	hid_t attr_count = H5Acreate(group_id, "count", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
	uint count = bcs.count();
	status = H5Awrite(attr_count, H5T_NATIVE_UINT32, &count);
	H5Aclose(attr_count);

    ///
	hsize_t dims = Quad::NUM_VERTICES;
	hid_t elem_dataspace_id = H5Screate_simple(1, &dims, NULL);

	hid_t merker_dataspace_id = H5Screate(H5S_SCALAR);

    // dump vertices
    for (int i = 0; i < count; i++) {
    	char name[256];
    	sprintf(name, "%d", i);

		// the dataset
		hid_t dataset_id = H5Dcreate(group_id, name, H5T_NATIVE_UINT32, elem_dataspace_id, H5P_DEFAULT);
		status = H5Dwrite(dataset_id, H5T_NATIVE_UINT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, bcs[i]->get_vertices());

		// marker
		hid_t attr_marker = H5Acreate(dataset_id, "marker", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
		uint marker = bcs[i]->get_marker();
		status = H5Awrite(attr_marker, H5T_NATIVE_UINT32, &marker);
		H5Aclose(attr_marker);

		status = H5Dclose(dataset_id);
    }

    H5Sclose(elem_dataspace_id);
    H5Sclose(dataspace_id);

	status = H5Gclose(group_id);		// close the group
}

void seissol::checkpoint::h5::Fault::write(int timestepFault)
{
	EPIK_TRACER("CheckPointFault_write");
	SCOREP_USER_REGION("CheckPointFault_write", SCOREP_USER_REGION_TYPE_FUNCTION);

	if (numSides() == 0)
		return;

	logInfo(rank()) << "Writing fault check point.";

	// Create array with all pointers
	EPIK_USER_REG(r_write_fault, "checkpoint_write_fault");
	SCOREP_USER_REGION_DEFINE(r_write_fault);
	EPIK_USER_START(r_write_fault);
	SCOREP_USER_REGION_BEGIN(r_write_fault, "checkpoint_write_fault", SCOREP_USER_REGION_TYPE_COMMON);

	// Attributes
	checkH5Err(H5Awrite(m_h5timestepFault[odd()], H5T_NATIVE_INT, &timestepFault));

	// Set memory and file space
	hsize_t fStart[2] = {fileOffset(), 0};
	hsize_t count[2] = {numSides(), numBndGP()};
	hid_t h5memSpace = H5Screate_simple(2, count, 0L);
	checkH5Err(h5memSpace);
	checkH5Err(H5Sselect_all(h5memSpace));
	checkH5Err(H5Sselect_hyperslab(m_h5fSpaceData, H5S_SELECT_SET, fStart, 0L, count, 0L));

	for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
		checkH5Err(H5Dwrite(m_h5data[odd()][i], H5T_NATIVE_DOUBLE, h5memSpace, m_h5fSpaceData,
				h5XferList(), data(i)));
	}

	checkH5Err(H5Sclose(h5memSpace));

	EPIK_USER_END(r_write_fault);
	SCOREP_USER_REGION_END(r_write_fault);

	// Finalize the checkpoint
	finalizeCheckpoint();

	logInfo(rank()) << "Writing fault check point. Done.";
}

herr_t H5TBOwrite_elements( hid_t dataset_id,
                            hid_t mem_type_id,
                            hsize_t nrecords,
                            const void *coords,
                            const void *data )
{

 hsize_t  count[1];
 hid_t    space_id;
 hid_t    mem_space_id;

 /* Get the dataspace handle */
 if ( (space_id = H5Dget_space( dataset_id )) < 0 )
  goto out;

 /* Define a selection of points in the dataset */

 if ( H5Sselect_elements(space_id, H5S_SELECT_SET, (size_t)nrecords, (const hsize_t *)coords) < 0 )
  goto out;

 /* Create a memory dataspace handle */
 count[0] = nrecords;
 if ( (mem_space_id = H5Screate_simple( 1, count, NULL )) < 0 )
  goto out;

 if ( H5Dwrite( dataset_id, mem_type_id, mem_space_id, space_id, H5P_DEFAULT, data ) < 0 )
  goto out;

 /* Terminate access to the memory dataspace */
 if ( H5Sclose( mem_space_id ) < 0 )
  goto out;

 /* Terminate access to the dataspace */
 if ( H5Sclose( space_id ) < 0 )
  goto out;

return 0;

out:
 return -1;

}

/* ------- begin --------------------------   writeMPI_p.c ----- */
void writeMPI_p(int task) {
/* Writes output on indata file, MPI group, one task at once */
  const char routineName[] = "writeMPI_p";
  hsize_t  offset[] = {0, 0, 0, 0};
  hsize_t  count[] = {1, 1, 1, 1};
  hsize_t  dims[4];
  hid_t    file_dspace, mem_dspace;

  dims[0] = 1;
  if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0) HERR(routineName);
  offset[0] = mpi.ix;
  offset[1] = mpi.iy;
  if (( file_dspace = H5Dget_space(io.in_mpi_tm) ) < 0) HERR(routineName);
  if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
                            NULL, count, NULL) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_tm, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.rank) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_tn, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &task) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_it, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.niter[0]) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_conv, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.convergence[0]) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_zc, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.zcut_hist[0]) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_dm, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.dpopsmax[0]) ) < 0) HERR(routineName);
  if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
  if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);

  dims[0] = mpi.niter[0];
  if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0) HERR(routineName);
  offset[0] = mpi.ix;
  offset[1] = mpi.iy;
  count[2] = mpi.niter[0];
  if (( file_dspace = H5Dget_space(io.in_mpi_dmh) ) < 0) HERR(routineName);
  if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
                            NULL, count, NULL) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_dmh, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
                 H5P_DEFAULT, mpi.dpopsmax_hist[0]) ) < 0) HERR(routineName);
  if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
  if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
  return;
}

void hdf5_dataset::write(hdf5_datatype const& type, void const* buffer)
{
    herr_t status =
            H5Dwrite(
                get_id(),
                type.get_id(),
                H5S_ALL,
                H5S_ALL,
                H5P_DEFAULT,
                buffer
            );

    if(status < 0) {
        boost::serialization::throw_exception(
            hdf5_archive_exception(
                hdf5_archive_exception::hdf5_archive_dataset_write_error
            )
        );
    }
}

static int Write_hdf5(void *buf, size_t nbytes)
{
    hid_t dsid;
    herr_t n1, n2;
    char dsname[256];
    static int n = 0;
    if (dspc == -1)
    {
        hsize_t dims = nbytes;
        dspc = H5Screate_simple(1, &dims, &dims);
    }

    sprintf(dsname, "data_%07d", n++);
    dsid = H5Dcreate(fid, dsname, H5T_NATIVE_UCHAR, dspc, H5P_DEFAULT);
    if (dsid < 0) return 0;
    n1 = H5Dwrite(dsid, H5T_NATIVE_UCHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
    n2 = H5Dclose(dsid);
    if (n1 < 0 || n2 < 0) return 0;
    return nbytes;
}

int create_new_dataset(H5block *d){
    hid_t file_id, dataset_id, dataspace_id, status, dcpl, datatype;
    file_id = H5Fopen(d->name, H5F_ACC_RDWR, H5P_DEFAULT);
    hsize_t dims[2];
    dims[0] = d->x_index_dim;
    dims[1] = d->y_index_dim;
    dataspace_id = H5Screate_simple(2, dims, NULL);
    datatype = H5Tcopy(H5T_NATIVE_FLOAT);
     status = H5Tset_order(datatype, H5T_ORDER_LE);
    char buffer[50];
    sprintf(buffer, "/dset%ld", d->ticks);

    dataset_id = H5Dcreate(file_id, buffer, datatype, dataspace_id, H5P_DEFAULT);
    status = H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                        d->field);
    status = H5Dclose(dataset_id);
    status = H5Tclose(datatype);
    status = H5Sclose(dataspace_id);
    status = H5Fclose(file_id);
}

void testCreateStringDataset()
{
    const char * data[STR_DSET_LEN] = {"You have to", "live", "life", "to the limit"};
    hid_t file, memtype, dset;
    hsize_t size = STR_DSET_LEN;
    herr_t status;
    HDF5WriterBase writer;
    string h5Filename = moose::random_string( 10 );
    file = H5Fcreate(h5Filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
    dset = writer.createStringDataset(file, STR_DSET_NAME, size, size);
    assert(dset >= 0);
    memtype = H5Tcopy(H5T_C_S1);
    status = H5Tset_size(memtype, H5T_VARIABLE);
    assert(status >= 0);
    status = H5Dwrite(dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
    assert(status >= 0);
    status = H5Dclose(dset);
    H5Tclose(memtype);
    H5Fclose(file);
}

herr_t ASDF_write_quakeml(hid_t loc_id, const char *quakeml_string) {
  hsize_t dims[1] = {strlen(quakeml_string)};
  hsize_t maxdims[1] = {H5S_UNLIMITED};

  hid_t space_id, dcpl_id, array_id;

  CHK_H5(space_id = H5Screate_simple(1, dims, maxdims));
  CHK_H5(dcpl_id = H5Pcreate(H5P_DATASET_CREATE));
  CHK_H5(H5Pset_chunk(dcpl_id, 1, dims));

  CHK_H5(array_id = H5Dcreate(loc_id, "/QuakeML", H5T_STD_I8LE, space_id,
        H5P_DEFAULT, dcpl_id, H5P_DEFAULT));
  CHK_H5(H5Dwrite(array_id, H5T_STD_I8LE, H5S_ALL, H5S_ALL,
        H5P_DEFAULT, quakeml_string));

  CHK_H5(H5Dclose(array_id));
  CHK_H5(H5Sclose(space_id));

  return 0; // Success
}

herr_t writeDouble2d(hid_t file_id,const char *dsName, void * matrix, int DIM_X, int DIM_Y) {
    hid_t  dataset_id,dataspace_id;
    hsize_t     dims[] = {DIM_Y,DIM_X}; /*DIM_Y corresponds to number of rows, DIM_X to columns*/
    herr_t status;
    /* Create the data space for the dataset. */

    dataspace_id = H5Screate_simple(2, dims, NULL);
    /* Create the dataset. */

    dataset_id = H5Dcreate(file_id, dsName,  H5T_IEEE_F64LE, dataspace_id, 
                          H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    status = H5Sclose(dataspace_id);
    /*Write the dataset*/
    status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, 
                     matrix);
    /* End access to the dataset and release resources used by it. */
    status = H5Dclose(dataset_id);
    return status;    
}

asynStatus NDFileHDF5AttributeDataset::writeAttributeDataset(hdf5::When_t whenToSave, hsize_t *offsets, NDAttribute *ndAttr, int flush, int indexed)
{
  asynStatus status = asynSuccess;
  char * stackbuf[MAX_ATTRIBUTE_STRING_SIZE];
  void* pDatavalue = stackbuf;
  int ret;
  //check if the attribute is meant to be saved at this time
  if (whenToSave_ == whenToSave) {
    // Extend the dataset as required to store the data
    if (indexed == -1){
      extendDataSet(offsets);
    } else {
      extendIndexDataSet(offsets[indexed]);
    }
    // find the data based on datatype
    ret = ndAttr->getValue(ndAttr->getDataType(), pDatavalue, MAX_ATTRIBUTE_STRING_SIZE);
    if (ret == ND_ERROR) {
      memset(pDatavalue, 0, MAX_ATTRIBUTE_STRING_SIZE);
    }
    // Work with HDF5 library to select a suitable hyperslab (one element) and write the new data to it
    H5Dset_extent(dataset_, dims_);
    filespace_ = H5Dget_space(dataset_);

    // Select the hyperslab
    H5Sselect_hyperslab(filespace_, H5S_SELECT_SET, offset_, NULL, elementSize_, NULL);

    // Write the data to the hyperslab.
    H5Dwrite(dataset_, datatype_, memspace_, filespace_, H5P_DEFAULT, pDatavalue);


    // Check if we are being asked to flush
    if (flush == 1){
      status = this->flushDataset();
    }

    H5Sclose(filespace_);
    nextRecord_++;
  }

  return status;
}

void saveParticleComp_Int(int *data,char *fileName,char *dataName,int totalCnt,int cnt,int offSet)
{
  int i,j,k;
  int myrank, nTasks;
  MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
  MPI_Comm_size(MPI_COMM_WORLD, &nTasks);

  hid_t file_id,dset_id,plist_id,tic_id;
  herr_t status;
  hid_t total_file_space,subfilespace,filespace,memspace,ticspace;
  hsize_t dimsf[1],count[1],offset[1];

  plist_id=H5Pcreate(H5P_FILE_ACCESS);
  H5Pset_fapl_mpio(plist_id,MPI_COMM_WORLD,MPI_INFO_NULL);
//    H5Pset_fclose_degree(plist_id,H5F_CLOSE_SEMI);
//    MPI_Barrier(MPI_COMM_WORLD);

  file_id=H5Fopen(fileName,H5F_ACC_RDWR,plist_id);
  H5Pclose(plist_id);

  dimsf[0]=totalCnt;
  filespace=H5Screate_simple(1,dimsf,NULL);

  count[0]=cnt;
  offset[0]=offSet;
  memspace=H5Screate_simple(1,count,NULL);

  dset_id=H5Dcreate2(file_id,dataName,H5T_NATIVE_INT,filespace,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
  subfilespace=H5Dget_space(dset_id);
  H5Sselect_hyperslab(subfilespace,H5S_SELECT_SET,offset,NULL,count,NULL);
  plist_id=H5Pcreate(H5P_DATASET_XFER);
  H5Pset_dxpl_mpio(plist_id,H5FD_MPIO_INDEPENDENT);
  status = H5Dwrite(dset_id, H5T_NATIVE_INT,memspace,subfilespace,plist_id,data);
  H5Pclose(plist_id);
  H5Sclose(subfilespace);
  H5Dclose(dset_id);

  H5Sclose(memspace);
  H5Sclose(filespace);
  H5Fclose(file_id);
}

void F77_FUNC_(pwhdf_open_file,PWHDF_OPEN_FILE)(const char* fname, const int* length)
{
  char * hfname = ( char * ) malloc( (*length) + 1 ) ;
  memcpy( hfname , fname , *length ) ;
  hfname[*length] = '\0' ; 

  if(h_file>=0) H5Fclose(h_file);

  h_file = H5Fcreate(hfname,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT);

  /* impelements version 1.00 hdf5 format */
  int version[]={1,10};
  hsize_t dim=2;
  hid_t dataspace= H5Screate_simple(1, &dim, NULL);
  hid_t dataset= H5Dcreate(h_file, "version", H5T_NATIVE_INT, dataspace, H5P_DEFAULT);
  hid_t ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,version);
  H5Sclose(dataspace);
  H5Dclose(dataset);

  free(hfname);
}

void dumpToH5(int Ni, int Nj, int Nk, int is, int js, int ks, int ie, int je, int ke, float ***f, char *format, ...) {
	char filename[1024];
	va_list ap;
	va_start(ap, format);
	vsprintf(filename, format, ap);
	hid_t file, dataset, filespace, memspace;

	hsize_t dimsm[3] = { Ni, Nj, Nk };
	hsize_t start[3] = { is, js, ks };
	hsize_t count[3] = { 1-is+ie, 1-js+je, 1-ks+ke };
	memspace = H5Screate_simple(3, dimsm, 0);
	filespace = H5Screate_simple(3, count, 0);
	file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
	dataset = H5Dcreate(file, "Data", H5T_NATIVE_FLOAT, filespace, H5P_DEFAULT);
	H5Sselect_hyperslab(memspace, H5S_SELECT_SET, start, 0, count, 0);
	H5Dwrite(dataset, H5T_NATIVE_FLOAT, memspace, filespace, H5P_DEFAULT, f[0][0]);
	H5Dclose(dataset);
	H5Sclose(filespace);
	H5Sclose(memspace);
	H5Fclose(file);
}