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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html>
  <head>
    <title>HDF5 Files</title>
  </head>

  <body>
    <h1>Files</h1>

    <h2>1. Introduction</h2>

    <p>HDF5 files are composed of a "boot block" describing information
        required to portably access files on multiple platforms, followed
        by information about the groups in a file and the datasets in the
        file.  The boot block contains information about the size of offsets
        and lengths of objects, the number of entries in symbol tables
        (used to store groups) and additional version information for the
        file.

    <h2>2. File access modes</h2>

    <p>The HDF5 library assumes that all files are implicitly opened for read
        access at all times.  Passing the <code>H5F_ACC_RDWR</code>
        parameter to <code>H5Fopen()</code> allows write access to a
        file also.  <code>H5Fcreate()</code> assumes write access as
        well as read access, passing <code>H5F_ACC_TRUNC</code> forces
        the truncation of an existing file, otherwise H5Fcreate will
        fail to overwrite an existing file.

    <h2>3. Creating, Opening, and Closing Files</h2>

    <p>Files are created with the <code>H5Fcreate()</code> function,
      and existing files can be accessed with <code>H5Fopen()</code>. Both
      functions return an object ID which should be eventually released by
      calling <code>H5Fclose()</code>.

    <dl>
      <dt><code>hid_t H5Fcreate (const char *<em>name</em>, uintn
	  <em>flags</em>, hid_t <em>create_properties</em>, hid_t
	  <em>access_properties</em>)</code>
      <dd>This function creates a new file with the specified name in
        the current directory.  The file is opened with read and write
        permission, and if the <code>H5F_ACC_TRUNC</code> flag is set,
        any current file is truncated when the new file is created.
        If a file of the same name exists and the
        <code>H5F_ACC_TRUNC</code> flag is not set (or the
        <code>H5F_ACC_EXCL</code> bit is set), this function will
        fail.  Passing <code>H5P_DEFAULT</code> for the creation
        and/or access property lists uses the library's default
        values for those properties.  Creating and changing the
        values of a property list is documented further below.  The
        return value is an ID for the open file and it should be
        closed by calling <code>H5Fclose()</code> when it's no longer
        needed. A negative value is returned for failure.

	<br><br>
      <dt><code>hid_t H5Fopen (const char *<em>name</em>, uintn
	  <em>flags</em>, hid_t <em>access_properties</em>)</code>
      <dd>This function opens an existing file with read permission
	and write permission if the <code>H5F_ACC_RDWR</code> flag is
	set.  The <em>access_properties</em> is a file access property
	list ID or <code>H5P_DEFAULT</code> for the default I/O access
        parameters.  Creating and changing the parameters for access
        templates is documented further below.  Files which are opened
        more than once return a unique identifier for each
        <code>H5Fopen()</code> call and can be accessed through all
        file IDs.  The return value is an ID for the open file and it
        should be closed by calling <code>H5Fclose()</code> when it's
        no longer needed. A negative value is returned for failure.

	<br><br>
      <dt><code>herr_t H5Fclose (hid_t <em>file_id</em>)</code>
      <dd>This function releases resources used by a file which was
        opened by <code>H5Fcreate()</code> or <code>H5Fopen()</code>. After
        closing a file the <em>file_id</em> should not be used again.  This
        function returns zero for success or a negative value for failure.

	<br><br>
      <dt><code>herr_t H5Fflush (hid_t <em>object_id</em>)</code>
      <dd>This function will cause all buffers associated with a file
	to be immediately flushed to the file.  The <em>object_id</em> 
	can be any object which is associated with a file, including
	the file itself.
    </dl>

    <h2>4. File Property Lists</h2>

    <p>Additional parameters to <code>H5Fcreate()</code> or
        <code>H5Fopen()</code> are passed through property list
        objects, which are created with the <code>H5Pcreate()</code>
        function.  These objects allow many parameters of a file's
        creation or access to be changed from the default values.
        Property lists are used as a portable and extensible method of
        modifying multiple parameter values with simple API functions.
        There are two kinds of file-related property lists,
	namely file creation properties and file access properties.

    <h3>4.1. File Creation Properties</h3>

    <P>File creation property lists apply to <code>H5Fcreate()</code> only
      and are used to control the file meta-data which is maintained
      in the boot block of the file.  The parameters which can be
      modified are:

    <dl>
      <dt>User-Block Size <dd>The "user-block" is a fixed length block of
	data located at the beginning of the file which is ignored by the
	HDF5 library and may be used to store any data information found
	to be useful to applications.  This value may be set to any power
	of two equal to 512 or greater (i.e.  512, 1024, 2048, etc).  This
	parameter is set and queried with the
	<code>H5Pset_userblock()</code> and
	<code>H5Pget_userblock()</code> calls.

	<br><br>
      <dt>Offset and Length Sizes
      <dd>The number of bytes used to store the offset and length of
	objects in the HDF5 file can be controlled with this 
	parameter.  Values of 2, 4 and 8 bytes are currently
	supported to allow 16-bit, 32-bit and 64-bit files to
	be addressed.  These parameters are set and queried
	with the <code>H5Pset_sizes()</code> and
	<code>H5Pget_sizes()</code> calls.

	<br><br>
      <dt>Symbol Table Parameters
      <dd>The size of symbol table B-trees can be controlled by setting
	the 1/2 rank and 1/2 node size parameters of the B-tree. These
	parameters are set and queried with the
	<code>H5Pset_sym_k()</code> and <code>H5Pget_sym_k()</code> calls.

	<br><br>
      <dt>Indexed Storage Parameters
      <dd>The size of indexed storage B-trees can be controlled by
	setting the 1/2 rank and 1/2 node size parameters of the B-tree.
	These parameters are set and queried with the
	<code>H5Pset_istore_k()</code> and <code>H5Pget_istore_k()</code>
	calls.
    </dl>

    <h3>4.2. File Access Property Lists</h3>

    <p>File access property lists apply to <code>H5Fcreate()</code> or
      <code>H5Fopen()</code> and are used to control different methods of
      performing I/O on files.

    <dl>
      <dt>Unbuffered I/O
      <dd>Local permanent files can be accessed with the functions described
	in Section 2 of the Posix manual, namely <code>open()</code>,
	<code>lseek()</code>, <code>read()</code>, <code>write()</code>, and
	<code>close()</code>.  The <code>lseek64()</code> function is used
	on operating systems that support it. This driver is enabled and
	configured with <code>H5Pset_sec2()</code>, and queried with
	<code>H5Pget_sec2()</code>.

	<br><br>
      <dt>Buffered I/O
      <dd>Local permanent files can be accessed with the functions declared
	in the <code>stdio.h</code> header file, namely
	<code>fopen()</code>, <code>fseek()</code>, <code>fread()</code>,
	<code>fwrite()</code>, and <code>fclose()</code>.  The
	<code>fseek64()</code> function is used on operating systems that
	support it.  This driver is enabled and configured with
	<code>H5Pset_stdio()</code>, and queried with
	<code>H5Pget_stdio()</code>.
	
	<br><br>
      <dt>Memory I/O
      <dd>Local temporary files can be created and accessed directly from
	memory without ever creating permanent storage.  The library uses
	<code>malloc()</code> and <code>free()</code> to create storage
	space for the file.  The total size of the file must be small enough
	to fit in virtual memory.  The name supplied to
	<code>H5Fcreate()</code> is irrelevant, and <code>H5Fopen()</code>
	will always fail.
	
	<br><br>
      <dt>Parallel Files using MPI I/O
      <dd>This driver allows parallel access to a file through the MPI I/O
	library.  The parameters which can be modified are the MPI
	communicator, the info object, and the access mode.
	The communicator and info object are saved and then
	passed to <code>MPI_File_open()</code> during file creation or open.
	The access_mode controls the kind of parallel access the application
	intends.  (Note that it is likely that the next API revision will
	remove the access_mode parameter and have access control specified
	via the raw data transfer property list of <code>H5Dread()</code>
	and <code>H5Dwrite()</code>.)  These parameters are set and queried
	with the <code>H5Pset_mpi()</code> and <code>H5Pget_mpi()</code>
	calls.

	<br><br>
      <dt>Data Alignment
      <dd>Sometimes file access is faster if certain things are
	aligned on file blocks. This can be controlled by setting
	alignment properties of a file access property list with the
	<code>H5Pset_alignment()</code> function. Any allocation
	request at least as large as some threshold will be aligned on 
	an address which is a multiple of some number.
    </dl> </ul>

    <h2>5. Examples of using file templates</h2>
    
    <h3>5.1. Example of using file creation templates</h3>
    
    <p>This following example shows how to create a file with 64-bit object
      offsets and lengths:<br>
    <pre>
        hid_t create_template;
        hid_t file_id;

        create_template = H5Pcreate(H5P_FILE_CREATE);
        H5Pset_sizes(create_template, 8, 8);

        file_id = H5Fcreate("test.h5", H5F_ACC_TRUNC,
                             create_template, H5P_DEFAULT);
        .
        .
        .
        H5Fclose(file_id);
    </pre>
        
    <h3>5.2. Example of using file creation templates</h3>

    <p>This following example shows how to open an existing file for
      independent datasets access by MPI parallel I/O:<br>
    <pre>
        hid_t access_template;
        hid_t file_id;

        access_template = H5Pcreate(H5P_FILE_ACCESS);
        H5Pset_mpi(access_template, MPI_COMM_WORLD, MPI_INFO_NULL);

	/* H5Fopen must be called collectively */
        file_id = H5Fopen("test.h5", H5F_ACC_RDWR, access_template);
        .
        .
        .
	/* H5Fclose must be called collectively */
        H5Fclose(file_id);
        </pre>
        

    <h2>6. Low-level File Drivers</h2>

    <p>HDF5 is able to access its address space through various types of
      low-level <em>file drivers</em>.  For instance, an address space might
      correspond to a single file on a Unix file system, multiple files on a
      Unix file system, multiple files on a parallel file system, or a block
      of memory within the application. Generally, an HDF5 address space is
      referred to as an "HDF5 file" regardless of how the space is organized
      at the storage level.

    <h3>6.1 Unbuffered Permanent Files</h3>

    <p>The <em>sec2</em> driver uses functions from section 2 of the
      Posix manual to access files stored on a local file system.  These are
      the <code>open()</code>, <code>close()</code>, <code>read()</code>,
      <code>write()</code>, and <code>lseek()</code> functions.  If the
      operating system supports <code>lseek64()</code> then it is used instead
      of <code>lseek()</code>.  The library buffers meta data regardless of
      the low-level driver, but using this driver prevents data from being
      buffered again by the lowest layers of the HDF5 library.

    <dl>
      <dt><code>H5F_driver_t H5Pget_driver (hid_t
	  <em>access_properties</em>)</code>
      <dd>This function returns the constant <code>H5F_LOW_SEC2</code> if the
	<em>sec2</em> driver is defined as the low-level driver for the
	specified access property list.

	<br><br>
      <dt><code>herr_t H5Pset_sec2 (hid_t <em>access_properties</em>)</code>
      <dd>The file access properties are set to use the <em>sec2</em>
	driver. Any previously defined driver properties are erased from the
	property list.  Additional parameters may be added to this function in
	the future.

	<br><br>
      <dt><code>herr_t H5Pget_sec2 (hid_t <em>access_properties</em>)</code>
      <dd>If the file access property list is set to the <em>sec2</em> driver
	then this function returns zero; otherwise it returns a negative
	value. In the future, additional arguments may be added to this
	function to match those added to <code>H5Pset_sec2()</code>.
    </dl>

    <h3>6.2 Buffered Permanent Files</h3>

    <p>The <em>stdio</em> driver uses the functions declared in the
      <code>stdio.h</code> header file to access permanent files in a local
      file system.  These are the <code>fopen()</code>, <code>fclose()</code>,
      <code>fread()</code>, <code>fwrite()</code>, and <code>fseek()</code>
      functions.  If the operating system supports <code>fseek64()</code> then
      it is used instead of <code>fseek()</code>. Use of this driver
      introduces an additional layer of buffering beneath the HDF5 library.

    <dl>
      <dt><code>H5F_driver_t H5Pget_driver(hid_t
	  <em>access_properties</em>)</code>
      <dd>This function returns the constant <code>H5F_LOW_STDIO</code> if the
	<em>stdio</em> driver is defined as the low-level driver for the
	specified access property list.

	<br><br>
      <dt><code>herr_t H5Pset_stdio (hid_t <em>access_properties</em>)</code>
      <dd>The file access properties are set to use the <em>stdio</em>
	driver.  Any previously defined driver properties are erased from the
	property list.  Additional parameters may be added to this function in
	the future.

	<br><br>
      <dt><code>herr_t H5Pget_stdio (hid_t <em>access_properties</em>)</code>
      <dd>If the file access property list is set to the <em>stdio</em> driver
	then this function returns zero; otherwise it returns a negative
	value.  In the future, additional arguments may be added to this
	function to match those added to <code>H5Pset_stdio()</code>.
    </dl>

    <h3>6.3 Buffered Temporary Files</h3>

    <p>The <em>core</em> driver uses <code>malloc()</code> and
      <code>free()</code> to allocated space for a file in the heap. Reading
      and writing to a file of this type results in mem-to-mem copies instead
      of disk I/O and as a result is somewhat faster.  However, the total file
      size must not exceed the amount of available virtual memory, and only
      one HDF5 file handle can access the file (because the name of such a
      file is insignificant and <code>H5Fopen()</code> always fails).

    <dl>
      <dt><code>H5F_driver_t H5Pget_driver (hid_t
	  <em>access_properties</em>)</code>
      <dd>This function returns the constant <code>H5F_LOW_CORE</code> if the
	<em>core</em> driver is defined as the low-level driver for the
	specified access property list.

	<br><br>
      <dt><code>herr_t H5Pset_core (hid_t <em>access_properties</em>, size_t
	  <em>block_size</em>)</code>
      <dd>The file access properties are set to use the <em>core</em>
	driver and any previously defined driver properties are erased from
	the property list.  Memory for the file will always be allocated in
	units of the specified <em>block_size</em>.  Additional parameters may
	be added to this function in the future.

	<br><br>
      <dt><code>herr_t H5Pget_core (hid_t <em>access_properties</em>, size_t
	  *<em>block_size</em>)</code>
      <dd>If the file access property list is set to the <em>core</em> driver
	then this function returns zero and <em>block_size</em> is set to the
	block size used for the file; otherwise it returns a negative
	value. In the future, additional arguments may be added to this
	function to match those added to <code>H5Pset_core()</code>.
    </dl>

    <h3>6.4 Parallel Files</h3>

    <p>This driver uses MPI I/O to provide parallel access to a file.

    <dl>
      <dt><code>H5F_driver_t H5Pget_driver (hid_t
	  <em>access_properties</em>)</code>
      <dd>This function returns the constant <code>H5F_LOW_MPI</code> if the
	<em>mpi</em> driver is defined as the low-level driver for the
	specified access property list.

	<br><br>
      <dt><code>herr_t H5Pset_mpi (hid_t <em>access_properties</em>, MPI_Comm
	  <em>comm</em>, MPI_info <em>info</em>)</code>
      <dd>The file access properties are set to use the <em>mpi</em>
	driver and any previously defined driver properties are erased from
	the property list.  Additional parameters may be added to this
	function in the future.

	<br><br>
      <dt><code>herr_t H5Pget_mpi (hid_t <em>access_properties</em>, MPI_Comm
	  *<em>comm</em>, MPI_info *<em>info</em>)</code>
      <dd>If the file access property list is set to the <em>mpi</em> driver
	then this function returns zero and <em>comm</em>, and <em>info</em>
	are set to the values stored in the property
	list; otherwise the function returns a negative value. In the future,
	additional arguments may be added to this function to match those
	added to <code>H5Pset_mpi()</code>.
    </dl>

    <h3>6.4 File Families</h3>

    <p>A single HDF5 address space may be split into multiple files which,
      together, form a file family.  Each member of the family must be the
      same logical size although the size and disk storage reported by
      <code>ls</code>(1) may be substantially smaller.  The name passed to
      <code>H5Fcreate()</code> or <code>H5Fopen()</code> should include a
      <code>printf(3c)</code> style integer format specifier which will be
      replaced with the family member number (the first family member is
      zero).

    <p>Any HDF5 file can be split into a family of files by running
      the file through <code>split</code>(1) and numbering the output
      files.  However, because HDF5 is lazy about extending the size
      of family members, a valid file cannot generally be created by
      concatenation of the family members.  Additionally,
      <code>split</code> and <code>cat</code> don't attempt to
      generate files with holes.  The <code>h5repart</code> program
      can be used to repartition an HDF5 file or family into another
      file or family and preserves holes in the files.

    <dl>
      <dt><code>h5repart</code> [<code>-v</code>] [<code>-b</code>
	<em>block_size</em>[<em>suffix</em>]] [<code>-m</code>
	<em>member_size</em>[<em>suffix</em>]] <em>source
	destination</em>
      <dd>This program repartitions an HDF5 file by copying the source
	file or family to the destination file or family preserving
	holes in the underlying Unix files.  Families are used for the
	source and/or destination if the name includes a
	<code>printf</code>-style integer format such as "%d".  The
	<code>-v</code> switch prints input and output file names on
	the standard error stream for progress monitoring,
	<code>-b</code> sets the I/O block size (the default is 1kB),
	and <code>-m</code> sets the output member size if the
	destination is a family name (the default is 1GB).  The block
	and member sizes may be suffixed with the letters
	<code>g</code>, <code>m</code>, or <code>k</code> for GB, MB,
	or kB respectively.

	<br><br>
      <dt><code>H5F_driver_t H5Pget_driver (hid_t
	  <em>access_properties</em>)</code>
      <dd>This function returns the constant <code>H5F_LOW_FAMILY</code> if
	the <em>family</em> driver is defined as the low-level driver for the
	specified access property list.

	<br><br>
      <dt><code>herr_t H5Pset_family (hid_t <em>access_properties</em>,
	  hsize_t <em>memb_size</em>, hid_t <em>member_properties</em>)</code>
      <dd>The file access properties are set to use the <em>family</em>
	driver and any previously defined driver properties are erased
	from the property list.  Each member of the file family will
	use <em>member_properties</em> as its file access property
	list. The <em>memb_size</em> argument gives the logical size
	in bytes of each family member but the actual size could be
	smaller depending on whether the file contains holes.  The
	member size is only used when creating a new file or
	truncating an existing file; otherwise the member size comes
	from the size of the first member of the family being
	opened. Note: if the size of the <code>off_t</code> type is
	four bytes then the maximum family member size is usually
	2^31-1 because the byte at offset 2,147,483,647 is generally
	inaccessable.  Additional parameters may be added to this
	function in the future.

	<br><br>
      <dt><code>herr_t H5Pget_family (hid_t <em>access_properties</em>,
	  hsize_t *<em>memb_size</em>, hid_t
	  *<em>member_properties</em>)</code>
      <dd>If the file access property list is set to the <em>family</em>
	driver then this function returns zero; otherwise the function
	returns a negative value.  On successful return,
	<em>access_properties</em> will point to a copy of the member
	access property list which should be closed by calling
	<code>H5Pclose()</em> when the application is finished with
	it.  If <em>memb_size</em> is non-null then it will contain
	the logical size in bytes of each family member.  In the
	future, additional arguments may be added to this function to
	match those added to <code>H5Pset_family()</code>.
    </dl>

    <h3>6.5 Split Meta/Raw Files</h3>

    <p>On occasion, it might be useful to separate meta data from raw
      data. The <em>split</em> driver does this by creating two files: one for
      meta data and another for raw data.  The application provides a base
      file name to <code>H5Fcreate()</code> or <code>H5Fopen()</code> and this
      driver appends a file extension which defaults to ".meta" for the meta
      data file and ".raw" for the raw data file.  Each file can have its own
      file access property list which allows, for instance, a split file with
      meta data stored with the <em>core</em> driver and raw data stored with
      the <em>sec2</em> driver.

    <dl>
      <dt><code>H5F_driver_t H5Pget_driver (hid_t
	  <em>access_properties</em>)</code>
      <dd>This function returns the constant <code>H5F_LOW_SPLIT</code> if
	the <em>split</em> driver is defined as the low-level driver for the
	specified access property list.

	<br><br>
      <dt><code>herr_t H5Pset_split (hid_t <em>access_properties</em>,
	  const char *<em>meta_extension</em>, hid_t
	  <em>meta_properties</em>, const char *<em>raw_extension</em>, hid_t
	  <em>raw_properties</em>)</code>
      <dd>The file access properties are set to use the <em>split</em>
	driver and any previously defined driver properties are erased from
	the property list.  The meta file will have a name which is formed by
	adding <em>meta_extension</em> (or ".meta") to the end of the base
	name and will be accessed according to the
	<em>meta_properties</em>. The raw file will have a name which is
	formed by appending <em>raw_extension</em> (or ".raw") to the base
	name and will be accessed according to the <em>raw_properties</em>.
	Additional parameters may be added to this function in the future.

	<br><br>
      <dt><code>herr_t H5Pget_split (hid_t <em>access_properties</em>,
	  size_t <em>meta_ext_size</em>, const char *<em>meta_extension</em>,
	  hid_t <em>meta_properties</em>, size_t <em>raw_ext_size</em>, const
	  char *<em>raw_extension</em>, hid_t *<em>raw_properties</em>)</code>
      <dd>If the file access property list is set to the <em>split</em>
	driver then this function returns zero; otherwise the function
	returns a negative value. On successful return,
	<em>meta_properties</em> and <em>raw_properties</em> will
	point to copies of the meta and raw access property lists
	which should be closed by calling <code>H5Pclose()</em> when
	the application is finished with them, but if the meta and/or
	raw file has no property list then a negative value is
	returned for that property list handle. Also, if
	<em>meta_extension</em> and/or <em>raw_extension</em> are
	non-null pointers, at most <em>meta_ext_size</em> or
	<em>raw_ext_size</em> characters of the meta or raw file name
	extension will be copied to the specified buffer. If the
	actual name is longer than what was requested then the result
	will not be null terminated (similar to
	<code>strncpy()</code>).  In the future, additional arguments
	may be added to this function to match those added to
	<code>H5Pset_split()</code>.
    </dl>


    <hr>
    <address><a href="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</a></address>
    <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
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Last modified: Thu Aug  6 16:17:08 EDT 1998
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