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regref
regref
References to Dataset Regions

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:

  1. Create a dataset in which to store the dataset regions (the selections).

     

  2. Create selections in the dataset(s). The dataset(s) should already exist in the file.

     

  3. Create references to the selections and store them in a buffer.

     

  4. Write the dataset region references to the file.

     

  5. Close all objects.

Reading References to Dataset Regions

The following steps are involved in reading references to dataset regions and referenced dataset regions (selections).

  1. Open and read the dataset containing references to the dataset regions. The datatype H5T_STD_REF_DSETREG must be used during the read operation.

     

  2. Use H5Rdereference / h5rdeference_f to obtain the dataset identifier from the read dataset region reference. OR Use H5Rget_region / h5rget_region_f to obtain the dataspace identifier for the dataset containing the selection from the read dataset region reference.

     

  3. Obtain information about the selection or read selected data from the dataset.

     

  4. Close all objects when they are no longer needed.

Programming Example

Description

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.

Examples:    C    F90

Remarks

  • A dataset region reference dataset can be created by calling H5D_CREATE with a a datatype of H5T_STD_REF_DSETREG.

  • The dataspace selections are stored as references in the dataset of region references, using the H5R_CREATE call, and passing in hdset_ref_ref_t for the reference type.

  • The dataset with the region references is read by calling H5D_READ with a datatype of H5T_STD_REF_DSETREG.

  • The H5R_DEREFERENCE opens the dataset, using its reference, and returns the dataset identifier. H5R_DATASET_REGION is passed in as the reference type.

  • The H5R_GET_REGION call obtains the spacial information ( dataspace and selection ) for the region reference.
     

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mount
mount
 Mounting a file

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:

  1. Open the files.
  2. 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.
  3. Use the HDF5 routine H5Fmount / h5fmount_f to mount the second file (the child file) in the first file.
  4. 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.
  5. Unmount the second file using H5Funmount / h5funmount_f when the work is done.

Programming Example

Description

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!   !
      !     ---------    !                   !     ----------   !
      !------------------!                   !------------------! 

After mounting FILE2 under the group in FILE1, the parent file has the following structure:

 
                                FILE1                                 
  
                         --------------------                   
                         !                  !                  
                         !      /           !               
                         !       |          !            
                         !       |          !         
                         !       V          !    
                         !     --------     !              
                         !     ! Group !    !            
                         !     ---------    !           
                         !         |        !
                         !         |        !
                         !         V        !
                         !    -----------   !
                         !    ! Dataset !   !
                         !    !----------   !
                         !                  !
                         !------------------!                    

[ C program ] - h5_mount.c
[ FORTRAN program ] - mountexample.f90

For details on compiling an HDF5 application: [ Compiling HDF5 Applications ]

Remarks


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driver
driver
What is a File Driver ?

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_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.

     

  • Call 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 H5Dread or H5Dwrite.

    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.