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HDF5 Optimized Functions

HDF5 functions described is this section are implemented in the HDF5 High-level Library as optimized functions. These functions generally require careful setup and testing as they enable an application to bypass portions of the HDF5 Library’s I/O pipeline for performance purposes.

These functions are distributed in the standard HDF5 distribution and are available any time the HDF5 High-level Library is available.

The C Interfaces:

Dataset I/O Optimization


/ast modified: 28 February 2013
Name: H5DOwrite_chunk
herr_t H5DOwrite_chunk( hid_t dset_id, hid_t dxpl_id, uint32_t filter_mask, hsize_t *offset, size_t data_size, const void *buf )

Writes a raw data chunk from a buffer directly to a dataset.

H5DOwrite_chunk writes a raw data chunk from the application memory buffer buf directly to its logical destination offset in a dataset dset_id. Typically, the data in buf is preprocessed in memory by a custom transformation, such as compression. The data chunk will bypass the library’s internal data transfer pipeline, including filters, and will be written directly to the file.

dxpl_id is a data transfer property list identifier. (Currently unused.)

filter_mask is a mask providing a record of which filters are used with the chunk. The default value of the mask is zero (0), indicating that all enabled filters are applied. A filter is skipped if the bit corresponding to the filter’s position in the pipeline (0 ≤ position < 32) is turned on. This mask is saved with the data chunk in the file.

offset is an array specifying the logical position of the first element of the data chunk in the dataset’s dataspace. The length of the offset array must equal the number of dimensions, or rank, of the dataspace. The values in offset must not exceed the dimension limits and must specify a point that falls on a data chunk boundary.

data_size is the size in bytes of the raw data chunk, representing the number of bytes to be read from the buffer buf. If the data chunk has been precompressed, data_size should be the size of the compressed data.

buf is the memory buffer for the data chunk.

hid_t dset_id IN: Identifier for the dataset to write to
hid_t dxpl_id IN: Transfer property list identifier for this I/O operation
(Currently unused)
uint32_t filter_mask    IN: Mask for identifying the filters in use
hsize_t *offset IN: Logical position of the chunk’s first element in the dataspace
size_t data_size IN: Size of the actual data to be written in bytes
const void *buf IN: Buffer containing data to be written to the file

Returns a non-negative value if successful; otherwise returns a negative value.

See Also:
Using the Direct Chunk Write Function” in “Advanced Topics in HDF5(PDF only)
Design document for this feature: “RFC: Direct Chunk Write(PDF only)

Example Usage:
The following code illustrates the use of H5DOwrite_chunk to write an entire dataset, chunk by chunk:
#include <zlib.h>
#include <math.h>
#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s))*1.001)+12)
size_t       buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
const Bytef *z_src = (const Bytef*)(direct_buf);
Bytef       *z_dst;             /* Destination buffer            */
uLongf       z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
uLong        z_src_nbytes = (uLong)buf_size;
int          aggression = 9;    /* Compression aggression setting */
uint32_t     filter_mask = 0;
size_t       buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);

/* Create the data space */
if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
            goto error;
/* Create a new file */
if((file = H5Fcreate(FILE_NAME5, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
            goto error;
/* Modify dataset creation properties, i.e. enable chunking and compression */
if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
            goto error;
if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0)
            goto error;
if((status = H5Pset_deflate( cparms, aggression)) < 0)
            goto error;

/* Create a new dataset within the file using cparms creation properties */
if((dset_id = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
                        cparms, H5P_DEFAULT)) < 0)
        goto error;

/* Initialize data for one chunk */
for(i = n = 0; i < CHUNK_NX; i++)
    for(j = 0; j < CHUNK_NY; j++)
        direct_buf[i][j] = n++;

/* Allocate output (compressed) buffer */
outbuf = malloc(z_dst_nbytes);
z_dst = (Bytef *)outbuf;

/* Perform compression from the source to the destination buffer */
ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);

/* Check for various zlib errors */
if(Z_BUF_ERROR == ret) {
        fprintf(stderr, "overflow");
        goto error;
} else if(Z_MEM_ERROR == ret) {
        fprintf(stderr, "deflate memory error");
        goto error;
} else if(Z_OK != ret) {
        fprintf(stderr, "other deflate error");
        goto error;

/* Write the compressed chunk data repeatedly to cover all the 
 * chunks in the dataset, using the direct write function.     */
for(i=0; i<NX/CHUNK_NX; i++) {
    for(j=0; j<NY/CHUNK_NY; j++) {
        status = H5DOwrite_chunk(dset_id, H5P_DEFAULT, filter_mask, 
                                offset, z_dst_nbytes, outbuf);
        offset[1] += CHUNK_NY;
    offset[0] += CHUNK_NX;
    offset[1] = 0;

/* Overwrite the first chunk with uncompressed data.  Set the filter mask to 
 * indicate the compression filter is skipped */
filter_mask = 0x00000001;
offset[0] = offset[1] = 0;
if(H5DOwrite_chunk(dset_id, H5P_DEFAULT, filter_mask, offset, buf_size, 
             direct_buf) < 0)
        goto error;

/* Read the entire dataset back for data verification converting ints to longs */
if(H5Dread(dataset, H5T_NATIVE_LONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, 
             outbuf_long) < 0)
        goto error;

/* Data verification here */

Release     Change
1.8.11 C function introduced in this release.

The HDF Group Help Desk:
Describes HDF5 Release 1.8.18, November 2016.
  Copyright by The HDF Group