HDF5

https://support.hdfgroup.org/documentation/hdf5/latest
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### Run HDF5 Java Examples

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_c_b__maven_artifacts.html

Commands to execute HDF5 Java example classes using the classpath.

```bash
java -cp hdf5-java-examples-2.0.0.jar examples.intro.H5_CreateFile
```

```bash
java -cp "hdf5-java-jni-2.0.0-linux-x86_64.jar:hdf5-java-examples-2.0.0.jar" \
examples.intro.H5_CreateFile
```

--------------------------------

### Include Example Snippet

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_r_m_t.html

Reference a Doxygen snippet for function usage examples.

```Doxygen
\par Example
\snippet H5F_examples.c minimal
```

--------------------------------

### Specify Dataset Start Offset

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_view_tools_view.html

Example of setting the start offset for a 2-dimensional dataset.

```bash
-s "0,0"
```

--------------------------------

### Example API Snippet Output

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_about.html

The rendered output of the H5Fcreate API example snippet.

```c
{
__label__ fail_fapl, fail_fcpl, fail_file;
hid_t fcpl, fapl, file;
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_fcpl;
}
else {
// adjust the file creation properties
}
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_fapl;
}
else {
// adjust the file access properties
}
unsigned mode = H5F_ACC_EXCL;
char name[] = "f1.h5";
if ((file = H5Fcreate(name, mode, fcpl, fapl)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
// do something useful with FILE
H5Fclose(file);
fail_file:
H5Pclose(fapl);
fail_fapl:
H5Pclose(fcpl);
fail_fcpl:;
}
```

--------------------------------

### Add HDF5 Examples Dependency

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_c_b__maven_artifacts.html

Include the artifact containing educational HDF5 examples in your project.

```xml
<dependency>
<groupId>org.hdfgroup</groupId>
<artifactId>hdf5-java-examples</artifactId>
<version>2.0.0</version>
</dependency>
```

--------------------------------

### h5pget_fapl_direct_f

Source: https://support.hdfgroup.org/documentation/hdf5/latest/group___f_h5_p.html

Gets the configuration settings for the direct I/O driver.

```APIDOC
## subroutine h5pget_fapl_direct_f

### Description
Retrieves the configuration settings for the direct I/O driver from a file access property list.

### Parameters
- **fapl_id** (integer(hid_t)) - Required - File access property list identifier.
- **alignment** (integer(size_t)) - Output - Required memory alignment boundary.
- **block_size** (integer(size_t)) - Output - File system block size.
- **cbuf_size** (integer(size_t)) - Output - Copy buffer size.
- **hdferr** (integer) - Output - Returns 0 if successful and -1 if it fails.
```

--------------------------------

### Configure and Start SWMR Writing

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_s_w_m_r_t_n.html

Demonstrates creating a file with the latest library version bounds and enabling SWMR write mode.

```C
fapl = H5Pcreate (H5P_FILE_ACCESS);
status = H5Pset_libver_bounds (fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
fid = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
// Create objects (files, datasets, ...).
// Close any attributes and named datatype objects.
// Groups and datasets may remain open before starting SWMR access to them.
// Start SWMR access to the file:
status = H5Fstart_swmr_write (fid);
// Reopen the datasets and then start writing, periodically flushing data:
status = H5Dwrite (dset_id, ...);
status = H5Dflush (dset_id);
```

--------------------------------

### Define H5VL_NATIVE_FILE_START_MDC_LOGGING

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_v_lnative_8h.html

Macro definition for starting MDC logging.

```c
#define H5VL_NATIVE_FILE_START_MDC_LOGGING 14
```

--------------------------------

### Navigate to Java Examples Directory

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_c_b__maven_artifacts.html

Command to enter the directory containing local testing scripts.

```bash
cd HDF5Examples/JAVA
```

--------------------------------

### getSelectBounds(hsize_t *start, hsize_t *end)

Source: https://support.hdfgroup.org/documentation/hdf5/latest/class_h5_1_1_data_space.html

Gets the bounding box containing the current selection.

```APIDOC
## getSelectBounds

### Description
Gets the bounding box containing the current selection. For information, please refer to the H5Sget_select_bounds API in the HDF5 C Reference Manual.

### Parameters
- **start** (hsize_t *) - IN: Starting coordinates of the bounding box
- **end** (hsize_t *) - IN: Ending coordinates of the bounding box, i.e., the coordinates of the diagonally opposite corner

### Exceptions
- H5::DataSpaceIException
```

--------------------------------

### Register error stack example

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_e__u_g.html

Shows how to preserve an error stack by registering it before it gets cleared by subsequent HDF5 calls.

```C
if (H5Dwrite(dset_id, mem_type_id, mem_space_id, file_space_id, dset_xfer_plist_id, buf) < 0)
{
// Push client error onto error stack
H5Epush2(H5E_DEFAULT,__FILE__,FUNC,__LINE__,cls_id,
CLIENT_ERR_MAJ_IO,CLIENT_ERR_MINOR_HDF5,
“H5Dwrite failed”);
// Preserve the error stack by assigning an object handle to it
error_stack = H5Eget_current_stack();
// Close dataset
H5Dclose(dset_id);
// Replace the current error stack with the preserved one
H5Eset_current_stack(error_stack);
}
return 0;
```

--------------------------------

### Implement Sec2 Driver Get EOA

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_f_l_t_n.html

Example implementation of the get_eoa function for the sec2 driver, returning the cached EOA value.

```C
static haddr_t
H5FD_sec2_get_eoa(H5FD_t *_file)
{
H5FD_sec2_t *file = (H5FD_sec2_t*)_file;
return file->eoa;
}
```

--------------------------------

### open()

Source: https://support.hdfgroup.org/documentation/hdf5/latest/class_h5_1_1_h5_library.html

Initializes the HDF5 library.

```APIDOC
## void open()

### Description
Initializes the HDF5 library.

### Exceptions
- H5::LibraryIException
```

--------------------------------

### Define H5VL_NATIVE_FILE_START_SWMR_WRITE

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_v_lnative_8h.html

Macro definition for starting SWMR write mode.

```c
#define H5VL_NATIVE_FILE_START_SWMR_WRITE 13
```

--------------------------------

### h5dump output for subset selection

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_view_tools_view.html

Example output showing a subset selection with specific start, stride, count, and block parameters.

```text
HDF5 "OMI-Aura.he5" {
DATASET "HDFEOS/GRIDS/OMI Column Amount O3/Data Fields/SolarZenithAngle" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 720, 1440 ) / ( 720, 1440 ) }
SUBSET {
START ( 1, 0 );
STRIDE ( 2, 3 );
COUNT ( 3, 3 );
BLOCK ( 2, 3 );
DATA {
(1,0): 79.071, 79.071, 79.071, 79.071, 79.071, 79.071, 79.071, 79.071, 79.071,
(2,0): 78.867, 78.867, 78.867, 78.867, 78.867, 78.867, 78.867, 78.867, 78.867,
(3,0): 78.632, 78.632, 78.632, 78.632, 78.632, 78.632, 78.632, 78.632, 78.632,
(4,0): 78.429, 78.429, 78.429, 78.429, 78.429, 78.429, 78.429, 78.429, 78.429,
(5,0): 78.225, 78.225, 78.225, 78.225, 78.225, 78.225, 78.225, 78.225, 78.225,
(6,0): 78.021, 78.021, 78.021, 78.021, 78.021, 78.021, 78.021, 78.021, 78.021
}
}
}
}
```

--------------------------------

### Complete H5DOwrite_chunk Example

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_d_o__u_g.html

Demonstrates the process of creating a chunked dataset, compressing data with zlib, and writing chunks directly to the file using H5DOwrite_chunk.

```C
#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
...
```

--------------------------------

### Configure Multi-File Access Property List

Source: https://support.hdfgroup.org/documentation/hdf5/latest/group___f_a_p_l.html

This example demonstrates how to partition HDF5 data into separate meta and raw files, each occupying half of the virtual address space.

```c
H5FD_mem_t mt, memb_map[H5FD_MEM_NTYPES];
hid_t memb_fapl[H5FD_MEM_NTYPES];
const char *memb[H5FD_MEM_NTYPES];
haddr_t memb_addr[H5FD_MEM_NTYPES];
// The mapping...
for (mt=0; mt<H5FD_MEM_NTYPES; mt++) {
memb_map[mt] = H5FD_MEM_SUPER;
}
memb_map[H5FD_MEM_DRAW] = H5FD_MEM_DRAW;
// Member information
memb_fapl[H5FD_MEM_SUPER] = H5P_DEFAULT;
memb_name[H5FD_MEM_SUPER] = "%s.meta";
memb_addr[H5FD_MEM_SUPER] = 0;
memb_fapl[H5FD_MEM_DRAW] = H5P_DEFAULT;
memb_name[H5FD_MEM_DRAW] = "%s.raw";
memb_addr[H5FD_MEM_DRAW] = HADDR_MAX/2;
hid_t fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_multi(fapl, memb_map, memb_fapl,
memb_name, memb_addr, true);
```

--------------------------------

### blob: get

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

Get a blob through the VOL.

```APIDOC
## blob: get

### Description
Get a blob through the VOL.

### Signature
herr_t (*get)(void *obj, const void *blob_id, void *buf, size_t size, void *ctx);

### Parameters
- **obj** (void*) - IN - Pointer to the blob container.
- **blob_id** (void*) - IN - Pointer to the blob's connector-specific ID.
- **buf** (void*) - IN/OUT - Pointer to the blob.
- **size** (size_t) - IN - Size of the blob.
- **ctx** (void*) - IN - Connector-specific blob context.
```

--------------------------------

### H5Fstart_mdc_logging

Source: https://support.hdfgroup.org/documentation/hdf5/latest/group___j_h5_f.html

Starts logging metadata cache events for a specified file.

```APIDOC
## H5Fstart_mdc_logging

### Description
Starts logging metadata cache events if logging was previously enabled.

### Signature
`void H5Fstart_mdc_logging(long file_id)`

### Parameters
- **file_id** (long) - Identifier of the target file.

### Exceptions
- **HDF5LibraryException** - Error from the HDF5 Library.
```

--------------------------------

### Configure File Image Callbacks

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_f_i_m__u_g.html

Setting up the file access property list with custom image callbacks and initial image data.

```C
<allocate fapl_id>
H5Pset_file_image_callbacks(fapl_id, &callbacks);
H5Pset_file_image(fapl_id, udata.image_ptr, udata.image_len);
<open core file using fapl_id>
<discard fapl any time after the open>
<overwrite data in datasets in the file, and then close it>
assert(udata.ref_count == 0);
// udata now contains the base address and length of the final version of the core file
<use the image of the file>
<repeat the above from the end of initialization onwards to write new data to datasets in file image>
```

--------------------------------

### Attribute Get Callback Signature

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

The get callback retrieves information about the attribute.

```c
herr_t (*get)(void *obj, H5VL_attr_get_args_t *args, hid_t dxpl_id, void **req);
```

--------------------------------

### H5Pset_fapl_direct

Source: https://support.hdfgroup.org/documentation/hdf5/latest/rel_spec_18.html

Sets up direct I/O, bypassing the system cache.

```APIDOC
## H5Pset_fapl_direct

### Signature
herr_t H5Pset_fapl_direct(hid_t fapl_id, size_t alignment, size_t block_size, size_t cbuf_size)
```

--------------------------------

### group: get

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

The get callback retrieves information about the group as specified in the get_type parameter.

```APIDOC
## group: get

### Signature
herr_t (*get)(void *obj, H5VL_group_get_args_t *args, hid_t dxpl_id, void **req);

### Arguments
- **obj** (void *) - The group object where information is retrieved from.
- **args** (H5VL_group_get_args_t *) - Pointer to the arguments struct containing operation type and parameters.
- **dxpl_id** (hid_t) - The data transfer property list.
- **req** (void **) - Pointer to the asynchronous request of the operation.

### Operation Types (H5VL_group_get_t)
- **H5VL_GROUP_GET_GCPL** - Retrieve group creation property list.
- **H5VL_GROUP_GET_INFO** - Retrieve group info.
```

--------------------------------

### Create a 4x6 Integer Dataset

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_intro_h_d_f5.html

Examples demonstrating the creation of a 4x6 integer dataset in the root group using Python and C.

```python
dataset = file.create_dataset("dset",(4, 6), h5py.h5t.STD_I32BE)
```

```c
// Create the dataspace for the dataset.
dims[0] = 4; dims[1] = 6;
dataspace_id = H5Screate_simple(2, dims, NULL);
// Create the dataset.
dataset_id = H5Dcreate (file_id, "/dset", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
// Close the dataset and dataspace
status = H5Dclose(dataset_id);
status = H5Sclose(dataspace_id);
```

--------------------------------

### H5VLinitialize

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_v_lconnector__passthru_8h.html

Initializes a VOL connector.

```APIDOC
## H5VLinitialize

### Signature
`herr_t H5VLinitialize(hid_t connector_id, hid_t vipl_id)`
```

--------------------------------

### Using Standard and Native Datatypes

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_l_b_datatypes.html

Demonstrates creating a dataset with a standard file type while using a native type for writing data from a buffer.

```c
#include "hdf5.h"
main() {
hid_t file_id, dataset_id, dataspace_id; 
herr_t status;
hsize_t dims[2]={4,6};
int i, j, dset_data[4][6];
for (i = 0; i < 4; i++)
for (j = 0; j < 6; j++)
dset_data[i][j] = i * 6 + j + 1;
file_id = H5Fcreate ("dtypes.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dataspace_id = H5Screate_simple (2, dims, NULL);
dataset_id = H5Dcreate (file_id, "/dset", H5T_STD_I32BE, dataspace_id, 
H5P_DEFAULT);
status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, 
H5P_DEFAULT, dset_data);
status = H5Dclose (dataset_id);
status = H5Fclose (file_id);
}
```

--------------------------------

### Datatype Get Operation Enumeration

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

Enumeration defining the types of get operations available for datatypes.

```c
/* Values for datatype 'get' operation */
typedef enum H5VL_datatype_get_t {
H5VL_DATATYPE_GET_BINARY_SIZE, /* Get size of serialized form of transient type */
H5VL_DATATYPE_GET_BINARY, /* Get serialized form of transient type */
H5VL_DATATYPE_GET_TCPL /* Datatype creation property list */
} H5VL_datatype_get_t;
```

--------------------------------

### Dataset Get Operation Enumeration

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

Enumeration defining the types of get operations supported for datasets.

```c
/* Values for dataset 'get' operation */
typedef enum H5VL_dataset_get_t {
H5VL_DATASET_GET_DAPL, /* access property list */
H5VL_DATASET_GET_DCPL, /* creation property list */
H5VL_DATASET_GET_SPACE, /* dataspace */
H5VL_DATASET_GET_SPACE_STATUS, /* space status */
H5VL_DATASET_GET_STORAGE_SIZE, /* storage size */
H5VL_DATASET_GET_TYPE /* datatype */
} H5VL_dataset_get_t;
```

--------------------------------

### H5Pset_fapl_direct / H5Pget_fapl_direct

Source: https://support.hdfgroup.org/documentation/hdf5/latest/group___f_a_p_l.html

Sets up the use of the direct I/O driver or retrieves the current direct I/O driver settings.

```APIDOC
## H5Pset_fapl_direct / H5Pget_fapl_direct

### Description
Sets up the use of the direct I/O driver or retrieves the direct I/O driver settings.
```

--------------------------------

### Scale-offset compression for integer data

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_d__u_g.html

Demonstrates how to configure a dataset creation property list with chunking and the scale-offset filter to compress integer data.

```C
#include "hdf5.h"
#include "stdlib.h"
#define H5FILE_NAME "scaleoffset_test_int.h5"
#define DATASET_NAME "scaleoffset_int"
#define NX 200
#define NY 300
#define CH_NX 10
#define CH_NY 15
int main(void)
{
hid_t file, dataspace, dataset, datatype, dset_create_props;
hsize_t dims[2], chunk_size[2];
int orig_data[NX][NY];
int new_data[NX][NY];
int i, j, fill_val;
// Define dataset datatype
datatype = H5Tcopy(H5T_NATIVE_INT);
// Initialize data buffer
for (i=0; i < NX; i++)
for (j=0; j < NY; j++)
orig_data[i][j] = rand() % 10000;
// Describe the size of the array.
dims[0] = NX;
dims[1] = NY;
if((dataspace = H5Screate_simple (2, dims, NULL)) < 0) {
printf("Error: fail to create dataspace\n");
return -1;
}
// Create a new file using read/write access, default file
// creation properties, and default file access properties.
if((file = H5Fcreate (H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
printf("Error: fail to create file\n");
return -1;
}
// Set the dataset creation property list to specify that
// the raw data is to be partitioned into 10 x 15 element
// chunks and that each chunk is to be compressed.
chunk_size[0] = CH_NX;
chunk_size[1] = CH_NY;
if((dset_create_props = H5Pcreate (H5P_DATASET_CREATE)) < 0) {
printf("Error: fail to create dataset property\n");
return -1;
}
if(H5Pset_chunk (dset_create_props, 2, chunk_size) < 0) {
printf("Error: fail to set chunk\n");
return -1;
}
// Set the fill value of dataset
fill_val = 10000;
if (H5Pset_fill_value(dset_create_props, H5T_NATIVE_INT, &fill_val)<0) {
printf("Error: can not set fill value for dataset\n");
return -1;
}
// Set parameters for scale-offset compression. Check the
// description of the H5Pset_scaleoffset function in the
// HDF5 Reference Manual for more information.
if(H5Pset_scaleoffset (dset_create_props, H5Z_SO_INT, H5Z_SO_INT_MINIMUMBITS_DEFAULT) < 0) {
printf("Error: fail to set scaleoffset filter\n");
return -1;
}
// Create a new dataset within the file. The datatype
// and dataspace describe the data on disk, which may
// or may not be different from the format used in the
// application's memory. The link creation and
// dataset access property list parameters are passed
// with default values.
if((dataset = H5Dcreate (file, DATASET_NAME, datatype, dataspace, H5P_DEFAULT,
dset_create_props, H5P_DEFAULT)) < 0) {
printf("Error: fail to create dataset\n");
return -1;
}
// Write the array to the file. The datatype and dataspace
// describe the format of the data in the 'orig_data' buffer.
// We use default raw data transfer properties.
```

--------------------------------

### H5TBwrite_records

Source: https://support.hdfgroup.org/documentation/hdf5/latest/group___h5_t_b.html

Overwrites records starting at the zero index position start of the table named dset_name.

```APIDOC
## H5TBwrite_records

### Description
Overwrites records starting at the zero index position start of the table named dset_name attached to the object specified by the identifier loc_id.

### Parameters
- **loc_id** (hid_t) - Required - Location identifier (file or group).
- **dset_name** (const char *) - Required - The name of the dataset to overwrite.
- **start** (hsize_t) - Required - The zero index record to start writing.
- **nrecords** (hsize_t) - Required - The number of records to write.
- **type_size** (size_t) - Required - The size of the structure type.
- **field_offset** (const size_t *) - Required - An array containing the offsets of the fields.
- **dst_sizes** (const size_t *) - Required - An array containing the sizes of the fields.
- **buf** (const void *) - Required - Buffer with data.

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

--------------------------------

### Create an empty dataset

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_d__u_g.html

Demonstrates the basic workflow for creating a fixed-size dataset with a specific dataspace and datatype.

```C
hid_t dataset, datatype, dataspace;
// Create dataspace: Describe the size of the array and create the dataspace for fixed-size dataset.
dimsf[0] = 7;
dimsf[1] = 8;
dataspace = H5Screate_simple(2, dimsf, NULL);
// Define datatype for the data in the file.
// For this example, store little-endian integer numbers.
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
// Create a new dataset within the file using defined
// dataspace and datatype. No properties are set.
dataset = H5Dcreate(file, "/dset", datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dclose(dataset);
H5Sclose(dataspace);
H5Tclose(datatype);
```

--------------------------------

### Compile and run HDF5 applications with Unix scripts

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_l_b_compiling.html

Examples of compiling Fortran and C applications and executing the resulting binaries.

```bash
h5fc myprog.f90
./a.out
h5cc -o myprog myprog.c
./myprog
```

--------------------------------

### Define file get callback signature

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

Signature for the get callback used to retrieve container information.

```c
herr_t (*get)(void *obj, H5VL_file_get_args_t *args, hid_t dxpl_id, void **req);
```

--------------------------------

### Dataset Get Callback Signature

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

The function signature for the dataset get operation within the VOL connector.

```c
herr_t (*get)(void *dset, H5VL_dataset_get_args_t *args, hid_t dxpl_id, void **req);
```

--------------------------------

### Implement HDF5 File Driver Open Function

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_f_l_t_n.html

Example implementation of a file driver open function, demonstrating argument validation, flag mapping, and file structure initialization.

```c
static H5FD_t *
H5FD_sec2_open(const char *name, unsigned flags, hid_t fapl_id/*unused*/,
haddr_t maxaddr)
{
unsigned o_flags;
int fd;
struct stat sb;
H5FD_sec2_t *file=NULL;
// Check arguments
if (!name || !*name) return NULL;
if (0==maxaddr || HADDR_UNDEF==maxaddr) return NULL;
if (ADDR_OVERFLOW(maxaddr)) return NULL;
// Build the open flags
o_flags = (H5F_ACC_RDWR & flags) ? O_RDWR : O_RDONLY;
if (H5F_ACC_TRUNC & flags) o_flags |= O_TRUNC;
if (H5F_ACC_CREAT & flags) o_flags |= O_CREAT;
if (H5F_ACC_EXCL & flags) o_flags |= O_EXCL;
// Open the file
if ((fd=open(name, o_flags, 0666))<0) return NULL;
if (fstat(fd, &sb)<0) {
close(fd);
return NULL;
}
// Create the new file struct
file = calloc(1, sizeof(H5FD_sec2_t));
file->fd = fd;
file->eof = sb.st_size;
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
file->device = sb.st_dev;
file->inode = sb.st_ino;
return (H5FD_t*)file;
}
```

--------------------------------

### Attribute Get Operation Enumeration and Structures

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

Definitions for attribute get operations and their associated argument structures.

```c
typedef enum H5VL_attr_get_t {
H5VL_ATTR_GET_ACPL, /* creation property list */
H5VL_ATTR_GET_INFO, /* info */
H5VL_ATTR_GET_NAME, /* access property list */
H5VL_ATTR_GET_SPACE, /* dataspace */
H5VL_ATTR_GET_STORAGE_SIZE, /* storage size */
H5VL_ATTR_GET_TYPE /* datatype */
} H5VL_attr_get_t;

typedef struct H5VL_attr_get_name_args_t {
H5VL_loc_params_t loc_params; /* Location parameters for object access */
size_t buf_size; /* Size of attribute name buffer */
char *buf; /* Buffer for attribute name (OUT) */
size_t *attr_name_len; /* Actual length of attribute name (OUT) */
} H5VL_attr_get_name_args_t;

typedef struct H5VL_attr_get_info_args_t {
H5VL_loc_params_t loc_params; /* Location parameters for object access */
const char *attr_name; /* Attribute name (for get_info_by_name) */
H5A_info_t *ainfo; /* Attribute info (OUT) */
} H5VL_attr_get_info_args_t;

typedef struct H5VL_attr_get_args_t {
H5VL_attr_get_t op_type; /* Operation to perform */
/* Parameters for each operation */
union {
/* H5VL_ATTR_GET_ACPL */
struct {
hid_t acpl_id; /* Attribute creation property list ID (OUT) */
} get_acpl;
/* H5VL_ATTR_GET_INFO */
H5VL_attr_get_info_args_t get_info; /* Attribute info */
/* H5VL_ATTR_GET_NAME */
H5VL_attr_get_name_args_t get_name; /* Attribute name */
/* H5VL_ATTR_GET_SPACE */
struct {
hid_t space_id; /* Dataspace ID (OUT) */
} get_space;
/* H5VL_ATTR_GET_STORAGE_SIZE */
struct {
hsize_t *data_size; /* Size of attribute in file (OUT) */
} get_storage_size;
/* H5VL_ATTR_GET_TYPE */
struct {
hid_t type_id; /* Datatype ID (OUT) */
} get_type;
} args;
} H5VL_attr_get_args_t;
```

--------------------------------

### Create HDF5 File with Gzip Compression

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_comp_t_s.html

Demonstrates creating a dataset with gzip compression and specific chunk dimensions. Note that the chosen chunk dimensions are for demonstration and not recommended for production.

```c
#include <stdlib.h>
#define FILE "h5ex_d_gzip.h5"
#define DATASET "DS1"
#define DIM0 32
#define DIM1 64
#define CHUNK0 5
#define CHUNK1 9
int main (void)
{
hid_t file, space, dset, dcpl; // Handles
herr_t status;
htri_t avail;
H5Z_filter_t filter_type;
hsize_t dims[2] = {DIM0, DIM1}, chunk[2] = {CHUNK0, CHUNK1};
size_t nelmts;
unsigned int flags, filter_info;
int wdata[DIM0][DIM1], // Write buffer
rdata[DIM0][DIM1], // Read buffer
max, i, j;
// Initialize data.
for (i=0; i<DIM0; i++)
for (j=0; j<DIM1; j++)
wdata[i][j] = i * j - j;
// Create a new file using the default properties.
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
space = H5Screate_simple (2, dims, NULL);
// Create the dataset creation property list, add the gzip
// compression filter and set the chunk size.
dcpl = H5Pcreate (H5P_DATASET_CREATE);
status = H5Pset_deflate (dcpl, 9);
status = H5Pset_chunk (dcpl, 2, chunk);
// Create the dataset.
dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT, dcpl, H5P_DEFAULT);
// Write the data to the dataset.
status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata[0]);
// Close and release resources.
status = H5Pclose (dcpl);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Fclose (file);
return 0;
}
```

--------------------------------

### Using New API with Legacy References

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5_r__u_g.html

Demonstrates creating a file with deprecated reference types and reading it back using the modern HDF5 reference API.

```c
#include <stdlib.h>
#include "hdf5.h"
#include <assert.h>
#define H5FILE_NAME "refer_deprec.h5"
#define NDIMS 1 // Number of dimensions
#define BUF_SIZE 4 // Size of example buffer
#define NREFS 1 // Number of references
int main(void) {
hid_t file1, dset1, space1;
hsize_t dset1_dims[NDIMS] = { BUF_SIZE };
int dset_buf[BUF_SIZE];
hid_t dset2, space2;
hsize_t dset2_dims[NDIMS] = { NREFS };
hobj_ref_t ref_buf[NREFS] = { 0 };
H5R_ref_t new_ref_buf[NREFS] = { 0 };
H5O_type_t obj_type;
int i;
for (i = 0; i < BUF_SIZE; i++)
dset_buf[i] = i;
// Create file with one dataset and close it
file1 = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
space1 = H5Screate_simple(NDIMS, dset1_dims, NULL);
dset1 = H5Dcreate2(file1, "dataset1", H5T_NATIVE_INT, space1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_buf);
H5Dclose(dset1);
H5Sclose(space1);
// Create reference to dataset1 with deprecated API
// (reminder: there is no destroy call for those references)
H5Rcreate(&ref_buf[0], file1, "dataset1", H5R_OBJECT, H5I_INVALID_HID);
// Store reference in separate dataset using deprecated reference type
space2 = H5Screate_simple(NDIMS, dset2_dims, NULL);
dset2 = H5Dcreate2(file1, "references", H5T_STD_REF_OBJ, space2, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
H5Dwrite(dset2, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref_buf); H5Dclose(dset2);
H5Sclose(space2);
H5Fclose(file1);
// Read reference from file using new reference type
file1 = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
dset2 = H5Dopen2(file1, "references", H5P_DEFAULT);
H5Dread(dset2, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, new_ref_buf);
H5Dclose(dset2);
// Access reference and read dataset data through new API
assert(H5Rget_type((const H5R_ref_t *)&new_ref_buf[0]) == H5R_OBJECT2);
H5Rget_obj_type3((const H5R_ref_t *)&new_ref_buf[0], H5P_DEFAULT, &obj_type);
assert(obj_type == H5O_TYPE_DATASET);
dset1 = H5Ropen_object((const H5R_ref_t *)&new_ref_buf[0], H5P_DEFAULT, H5P_DEFAULT);
H5Dread(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_buf);
H5Dclose(dset1);
H5Rdestroy(&new_ref_buf[0]);
for (i = 0; i < BUF_SIZE; i++)
assert(dset_buf[i] == i);
return 0;
}
```

--------------------------------

### Create an HDF5 Dataset

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5__u_g.html

Illustrates the creation of a dataset by defining its dataspace and datatype, then initializing the dataset object.

```C
hid_t dataset, datatype, dataspace; // declare identifiers
// Create a dataspace: Describe the size of the array and
// create the dataspace for a fixed-size dataset.
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
// Define a datatype for the data in the dataset.
// We will store little endian integers.
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
// Create a new dataset within the file using the defined
// dataspace and datatype and default dataset creation
// properties.
// NOTE: H5T_NATIVE_INT can be used as the datatype if
// conversion to little endian is not needed.
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
```

--------------------------------

### H5VL File Get Arguments Structure

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

The primary structure for defining file get operations and their associated parameters.

```c
H5VL_file_get_t op_type; /* Operation to perform */
/* Parameters for each operation */
union {
/* H5VL_FILE_GET_CONT_INFO */
struct {
H5VL_file_cont_info_t *info; /* Container info (OUT) */
} get_cont_info;
/* H5VL_FILE_GET_FAPL */
struct {
hid_t fapl_id; /* File access property list (OUT) */
} get_fapl;
/* H5VL_FILE_GET_FCPL */
struct {
hid_t fcpl_id; /* File creation property list (OUT) */
} get_fcpl;
/* H5VL_FILE_GET_FILENO */
struct {
unsigned long *fileno; /* File "number" (OUT) */
} get_fileno;
/* H5VL_FILE_GET_INTENT */
struct {
unsigned *flags; /* File open/create intent flags (OUT) */
} get_intent;
/* H5VL_FILE_GET_NAME */
H5VL_file_get_name_args_t get_name;
/* H5VL_FILE_GET_OBJ_COUNT */
struct {
unsigned types; /* Type of objects to count */
size_t *count; /* # of objects (OUT) */
} get_obj_count;
/* H5VL_FILE_GET_OBJ_IDS */
H5VL_file_get_obj_ids_args_t get_obj_ids;
} args;
} H5VL_file_get_args_t;
```

--------------------------------

### Create a dataset with H5Dcreate2

Source: https://support.hdfgroup.org/documentation/hdf5/latest/group___h5_d.html

Demonstrates creating a dataset with a UTF-8 encoded path and intermediate groups using property lists.

```C
{
__label__ fail_lcpl, fail_dset, fail_file;
hid_t file, lcpl, fspace, dset;
unsigned mode = H5F_ACC_TRUNC;
char file_name[] = "d1.h5";
// link names can be arbitrary Unicode strings
char dset_name[] = "σύνολο/δεδομένων";
if ((file = H5Fcreate(file_name, mode, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
if ((lcpl = H5Pcreate(H5P_LINK_CREATE)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_lcpl;
}
// use UTF-8 encoding for link names
if (H5Pset_char_encoding(lcpl, H5T_CSET_UTF8) < 0) {
ret_val = EXIT_FAILURE;
goto fail_fspace;
}
// create intermediate groups as needed
if (H5Pset_create_intermediate_group(lcpl, 1) < 0) {
ret_val = EXIT_FAILURE;
goto fail_fspace;
}
// create a 1D dataspace
if ((fspace = H5Screate_simple(1, (hsize_t[]){10}, NULL)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_fspace;
}
// create a 32-bit integer dataset
if ((dset = H5Dcreate2(file, dset_name, H5T_STD_I32LE, fspace, lcpl, H5P_DEFAULT, H5P_DEFAULT)) ==
H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_dset;
}
H5Dclose(dset);
fail_dset:
H5Sclose(fspace);
fail_fspace:
H5Pclose(lcpl);
fail_lcpl:
H5Fclose(file);
fail_file:;
}
```

--------------------------------

### Datatype Get Callback Signature

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

The function signature for the datatype get callback used in HDF5 VOL connectors.

```c
herr_t (*get) (void *obj, H5VL_datatype_get_args_t *args, hid_t dxpl_id, void **req);
```

--------------------------------

### View h5jam and h5unjam Help

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_view_tools_edit.html

Display the help menu for the h5jam and h5unjam utilities.

```bash
h5jam -h
```

```bash
h5unjam -h
```

--------------------------------

### Dataset Get Arguments Structure

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

Structure containing the operation type and union of parameters for dataset get operations.

```c
/* Parameters for dataset 'get' operations */
typedef struct H5VL_dataset_get_args_t {
H5VL_dataset_get_t op_type; /* Operation to perform */
/* Parameters for each operation */
union {
/* H5VL_DATASET_GET_DAPL */
struct {
hid_t dapl_id; /* Dataset access property list ID (OUT) */
} get_dapl;
/* H5VL_DATASET_GET_DCPL */
struct {
hid_t dcpl_id; /* Dataset creation property list ID (OUT) */
} get_dcpl;
/* H5VL_DATASET_GET_SPACE */
struct {
hid_t space_id; /* Dataspace ID (OUT) */
} get_space;
/* H5VL_DATASET_GET_SPACE_STATUS */
struct {
H5D_space_status_t *status; /* Storage space allocation status (OUT) */
} get_space_status;
/* H5VL_DATASET_GET_STORAGE_SIZE */
struct {
hsize_t *storage_size; /* Size of dataset's storage (OUT) */
} get_storage_size;
/* H5VL_DATASET_GET_TYPE */
struct {
hid_t type_id; /* Datatype ID (OUT) */
} get_type;
} args;
} H5VL_dataset_get_args_t;
```

--------------------------------

### HDF5 VOL Object Get Callback Signature

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

The function signature for the object 'get' callback used in the VOL connector.

```c
herr_t (*get)(void *obj, H5VL_loc_params_t *loc_params, H5VL_object_get_args_t *args, hid_t dxpl_id, void **req)
```

--------------------------------

### H5Library::open

Source: https://support.hdfgroup.org/documentation/hdf5/latest/class_h5_1_1_h5_library.html

Initializes the HDF5 library.

```APIDOC
## static void open()

### Description
Initializes the HDF5 library.
```

--------------------------------

### HDF5 VOL Link Get Operation Structures

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_v_o_l__connector.html

Enumeration and argument structures defining the parameters for link get operations.

```c
/* Values for link 'get' operation */
typedef enum H5VL_link_get_t {
H5VL_LINK_GET_INFO, /* link info */
H5VL_LINK_GET_NAME, /* link name */
H5VL_LINK_GET_VAL /* link value */
} H5VL_link_get_t;
/* Parameters for link 'get' operations */
typedef struct H5VL_link_get_args_t {
H5VL_link_get_t op_type; /* Operation to perform */
/* Parameters for each operation */
union {
/* H5VL_LINK_GET_INFO */
struct {
H5L_info2_t *linfo; /* Pointer to link's info (OUT) */
} get_info;
/* H5VL_LINK_GET_NAME */
struct {
size_t name_size; /* Size of link name buffer (IN) */
char *name; /* Buffer for link name (OUT) */
size_t *name_len; /* Actual length of link name (OUT) */
} get_name;
/* H5VL_LINK_GET_VAL */
struct {
size_t buf_size; /* Size of link value buffer (IN) */
void *buf; /* Buffer for link value (OUT) */
} get_val;
} args;
} H5VL_link_get_args_t;
```

--------------------------------

### Create an HDF5 Table

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_t_b_l_s_p_e_c.html

Demonstrates the sequence of calls to create a new HDF5 file and initialize a table using the H5TBmake_table function.

```C
// Create a new HDF5 file using default properties.
file_id = H5Fcreate("my_table.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// Call the make table function
H5TBmake_table("Table Title", file_id, "Table1", NFIELDS, NRECORDS, dst_size, field_names, dst_offset, field_type, chunk_size, fill_data, compress, p_data);
// Close the file.
status = H5Fclose(file_id);
```

--------------------------------

### Create an extendable dataset

Source: https://support.hdfgroup.org/documentation/hdf5/latest/_h5__u_g.html

Initialize the dataset using the previously configured creation property list.

```C
// Create a new dataset within the file using cparms creation properties.
dataset = H5Dcreate(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms, H5P_DEFAULT);
```
Tokens:
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