Previously you learned about creating, reading, and writing dataset selections. Here you will learn how to store dataset selections in a file, and how to read them back using references to dataset regions.
A dataset region reference points to the dataset selection by storing the relative file address of the dataset header and the global heap offset of the referenced selection. The selection referenced is located by retrieving the coordinates of the areas in the selection from the global heap. This internal mechanism of storing and retrieving dataset selections is transparent to the user. A reference to a dataset selection (a region) is constant for the life of the dataset.
Creating and Storing References to Dataset Regions
The following steps are involved in creating and storing references to dataset regions:
- Create a dataset in which to store the dataset regions (the selections).
- Create selections in the dataset(s). The dataset(s) should already exist in the file.
- Create references to the selections and store them in a buffer.
- Write the dataset region references to the file.
- Close all objects.
Reading References to Dataset Regions
The following steps are involved in reading references to dataset regions and referenced dataset regions (selections).
- Open and read the dataset containing references to the dataset regions. The datatype
H5T_STD_REF_DSETREGmust be used during the read operation.
h5rdeference_fto obtain the dataset identifier from the read dataset region reference. OR Use
h5rget_region_fto obtain the dataspace identifier for the dataset containing the selection from the read dataset region reference.
- Obtain information about the selection or read selected data from the dataset.
- Close all objects when they are no longer needed.
The examples below create a dataset in a file, and write references to regions in the dataset to a dataset of region references. (The regions in the dataset are selected using H5S_SELECT_HYPERSLAB and H5S_SELECT_ELEMENTS.)
Then it reopens the file, dereferences the references and outputs the referenced regions to the screen.
A dataset region reference dataset can be created by calling H5D_CREATE with a a datatype of
The dataspace selections are stored as references in the dataset of region references, using the H5R_CREATE call, and passing in
hdset_ref_ref_tfor the reference type.
The dataset with the region references is read by calling H5D_READ with a datatype of
The H5R_DEREFERENCE opens the dataset, using its reference, and returns the dataset identifier.
H5R_DATASET_REGIONis passed in as the reference type.
- The H5R_GET_REGION call obtains the spacial information ( dataspace and selection ) for the region reference.
HDF5 allows you to combine two or more HDF5 files in memory in a manner similar to mounting files in UNIX. The group structure and metadata from one file appear as though they exist in another file. The following steps are involved:
- Open the files.
- Choose the mount point in the first file (the parent file). The mount point in HDF5 is a group, which CANNOT be the root group.
- Use the HDF5 routine
h5fmount_fto mount the second file (the child file) in the first file.
- Work with the objects in the second file as if they were members of the mount point group in the first file. The previous contents of the mount point group are temporarily hidden.
- Unmount the second file using
h5funmount_fwhen the work is done.
In the following example, we create one file containing a group and another file containing a dataset. Mounting is used to access the dataset from the second file as a member of a group in the first file. The following figures illustrate this concept.
FILE1 FILE2 -------------------- -------------------- ! ! ! ! ! / ! ! / ! ! | ! ! | ! ! | ! ! | ! ! V ! ! V ! ! -------- ! ! ---------- ! ! ! Group ! ! ! ! Dataset! ! ! --------- ! ! ---------- ! !------------------! !------------------!
FILE2 under the group in
FILE1, the parent file has the following structure:
FILE1 -------------------- ! ! ! / ! ! | ! ! | ! ! V ! ! -------- ! ! ! Group ! ! ! --------- ! ! | ! ! | ! ! V ! ! ----------- ! ! ! Dataset ! ! ! !---------- ! ! ! !------------------!
[ C program ] -
[ FORTRAN program ] -
For details on compiling an HDF5 application: [ Compiling HDF5 Applications ]
- The first part of the program creates a group in one file and creates and writes a dataset to another file.
- Both files are reopened and the second file is mounted in the first using H5F_MOUNT. If no objects will be modified, the files can be opened with
H5F_ACC_RDONLY_Fin FORTRAN). If the data is to be modified, the files should be opened with
- In this example, we only read data from the dataset
D. One can also modify data. If the dataset is modified while the file is mounted, it is modified in the original file after the file is unmounted.
- The file is unmounted with H5F_UNMOUNT.
- Note that H5F_UNMOUNT does not close files. Files are closed with the respective calls to the H5F_CLOSE function.
- Closing the parent file automatically unmounts the child file.
h5dumputility cannot display files in memory. Therefore, no output of
FILE2was mounted is provided.
In HDF5, a file driver is a mapping between the HDF5 format address space and storage. By default, HDF5 simply maps the format address space directly onto a single file.
However, users may want the ability to map the format address space onto different types of storage with various types of maps. With HDF5 we provide a small set of pre-defined file drivers, and we also provide the Virtual File Layer API to enable users to implement their own mappings.
Detailed information on file drivers can be found under VFL Technical Notes in the Documentation.
File Drivers Defined in HDF5
Following are the file drivers that HDF5 provides.
- H5FD_SEC2: This is the default driver which uses Posix file-system functions like
writeto perform I/O to a single file.
- H5FD_STDIO: This driver uses functions from 'stdio.h' to perform buffered I/O to a single file.
- H5FD_CORE: This driver performs I/O directly to memory and can be used to create small temporary files that never exist on permanent storage.
- H5FD_MPIIO: This driver is used with Parallel HDF5, and is only pre-defined if the library is compiled with parallel I/O support. Refer to the Parallel HDF5 Tutorial for more information on using Parallel HDF5.
- H5FD_MULTI: This driver enables different types of HDF5 data and metadata to be written to separate files. The H5FD_SPLIT driver is an example of what the H5FD_MULTI driver can do.
- H5FD_FAMILY: This driver partitions a large format address space into smaller chunks (separate storage of a user's choice).
- H5FD_SPLIT: This driver splits the meta data and raw data into separate storage of a user's choice.
Programming Model for Using a Pre-Defined File Driver
- Create a copy or instance of the File Access property list:
fapl = H5Pcreate (H5P_FILE_ACCESS);
- Initialize the file driver. Each pre-defined file driver has it's own initialization function, whose name is
H5Pset_fapl_followed by the driver name and which takes a file access property list as the first argument, followed by additional driver-dependent arguments. For example:
size_t member_size = 100*1024*1024; /* 100 MB */ status = H5Pset_fapl_family (fapl, member_size, H5P_DEFAULT);An alternative to using the driver initialization function is to set the driver directly using
H5Pset_driver, which is not covered here.
H5Fcreate, passing in the identifier of the property list just modified.
file_id = H5Fcreate (HDF5FILE, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
- Close the File Access Property List:
status = H5Pclose (fapl);
- Perform I/O on the file, if need be. To do so, a Data Access/Transfer property must be copied, modified, and passed in to
For example, the following sets the MPI-IO driver to use independent access for I/O operations:
dxpl = H5Pcreate (H5P_DATA_XFER); status = H5Pset_dxpl_mpio (dxpl, H5FD_MPIO_INDEPENDENT); status = H5Dread (dataset_id, type, mspace, fspace, buffer, dxpl);
User Designed File Drivers
These are out of the scope of this tutorial. Refer to the Technical Notes documentation on the Virtual File Layer.
How Does a General Application Open an HDF5 File ?
A general application does not know what drivers were used to create a file. It would have to try different file drivers until it succeeds. An example of a general application is the h5dump tool that we provide with HDF5.