[svn-r467] Restructuring documentation.

author: Quincey Koziol <koziol@hdfgroup.org> 1998-07-08 14:54:54 (GMT)
committer: Quincey Koziol <koziol@hdfgroup.org> 1998-07-08 14:54:54 (GMT)
commit: bd1e676c521d881b3143829f493a28b5ced1294b (patch)
tree: 69c50f9fe21ce87f293d8617a6bd51b4cc1e0244 /doc/html/Files.html
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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.
+    </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>
+<!-- Created: Tue Jan 27 09:11:27 EST 1998 -->
+<!-- hhmts start -->
+Last modified: Tue Jun  9 15:03:44 EDT 1998
+<!-- hhmts end -->
+  </body>
+</html>
author	Quincey Koziol <koziol@hdfgroup.org>	1998-07-08 14:54:54 (GMT)
committer	Quincey Koziol <koziol@hdfgroup.org>	1998-07-08 14:54:54 (GMT)
commit	bd1e676c521d881b3143829f493a28b5ced1294b (patch)
tree	69c50f9fe21ce87f293d8617a6bd51b4cc1e0244 /doc/html/Files.html
parent	73345095897d9698bb1f2f7df830bf80a56dc65a (diff)
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