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authorFrank Baker <fbaker@hdfgroup.org>2005-07-19 17:28:56 (GMT)
committerFrank Baker <fbaker@hdfgroup.org>2005-07-19 17:28:56 (GMT)
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Description: All HDF5 user documentation has been moved to a separate hdf5doc/ repository, managed under Subversion. With this 'cvs commit', all files are stripped from hdf5/doc/. THIS CHANGE IS APPLIED ONLY TO THE HDF5 DEVELOPMENT BRANCH, post Release 1.6.x; it is not applied to the release branches.
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-<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
-<html>
- <head>
- <title>File Interface (H5F)</title>
-
-<!-- #BeginLibraryItem "/ed_libs/styles_UG.lbi" -->
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-<link href="ed_styles/UGelect.css" rel="stylesheet" type="text/css">
-<!-- #EndLibraryItem --></head>
-
- <body bgcolor="#FFFFFF">
-
-
-<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.lbi" --><hr>
-<center>
-<table border=0 width=98%>
-<tr><td valign=top align=left>
- <a href="index.html">HDF5 documents and links</a>&nbsp;<br>
- <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
- <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
- <a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide for Release 1.6</a>&nbsp;<br>
- <!--
- <a href="Glossary.html">Glossary</a><br>
- -->
-</td>
-<td valign=top align=right>
- And in this document, the
- <a href="H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>&nbsp;&nbsp;&nbsp;&nbsp;
- <br>
- <a href="Files.html">Files</a>&nbsp;&nbsp;
- <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
- <a href="Datatypes.html">Datatypes</a>&nbsp;&nbsp;
- <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
- <a href="Groups.html">Groups</a>&nbsp;&nbsp;
- <br>
- <a href="References.html">References</a>&nbsp;&nbsp;
- <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
- <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
- <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
- <br>
- <a href="Filters.html">Filters</a>&nbsp;&nbsp;
- <a href="Caching.html">Caching</a>&nbsp;&nbsp;
- <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
- <a href="MountingFiles.html">Mounting Files</a>&nbsp;&nbsp;
- <br>
- <a href="Performance.html">Performance</a>&nbsp;&nbsp;
- <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
- <a href="Environment.html">Environment</a>&nbsp;&nbsp;
- <a href="ddl.html">DDL</a>&nbsp;&nbsp;
-</td></tr>
-</table>
-</center>
-<hr>
-<!-- #EndLibraryItem --><h1>The File Interface (H5F)</h1>
-
- <h2>1. Introduction</h2>
-
- <p>HDF5 files are composed of a <em>super block</em> 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 super 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
- property lists 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>,
- H5F_scope_t <em>scope</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. <em>scope</em> specifies whether the flushing
- action is to be global or local.
- </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 super block of the file. The parameters which can be
- modified are:
-
- <dl>
- <dt>User-Block Size <dd>The <em>user-block</em> 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_fapl_sec2()</code>.
-
- <br><br>
- <dt>Buffered I/O
- <dd>Local permanent files can be accessed with the functions declared
- in the standard C header file <code>stdio.h</code>, 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_fapl_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_fapl_mpi()</code> and
- <code>H5Pget_fapl_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 property lists</h2>
-
- <h3>5.1. Example of using file creation property lists</h3>
-
- <p>This following example shows how to create a file with 64-bit object
- offsets and lengths:<br>
- <pre>
- hid_t create_plist;
- hid_t file_id;
-
- create_plist = H5Pcreate(H5P_FILE_CREATE);
- H5Pset_sizes(create_plist, 8, 8);
-
- file_id = H5Fcreate("test.h5", H5F_ACC_TRUNC,
- create_plist, H5P_DEFAULT);
- .
- .
- .
- H5Fclose(file_id);
- </pre>
-
- <h3>5.2. Example of using file creation plist</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_plist;
- hid_t file_id;
-
- access_plist = H5Pcreate(H5P_FILE_ACCESS);
- H5Pset_fapl_mpi(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL);
-
- /* H5Fopen must be called collectively */
- file_id = H5Fopen("test.h5", H5F_ACC_RDWR, access_plist);
- .
- .
- .
- /* 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 <em>HDF5 file</em> 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>hid_t H5Pget_driver (hid_t <em>access_properties</em>)</code>
- <dd>This function returns the constant <code>H5FD_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_fapl_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.
-
- </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>hid_t H5Pget_driver(hid_t <em>access_properties</em>)</code>
- <dd>This function returns the constant <code>H5FD_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_fapl_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.
-
- </dl>
-
- <h3>6.3. Buffered Temporary Files</h3>
-
- <p>The <em>core</em> driver uses <code>malloc()</code> and
- <code>free()</code> to allocate 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>hid_t H5Pget_driver (hid_t <em>access_properties</em>)</code>
- <dd>This function returns the constant <code>H5FD_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_fapl_core (hid_t <em>access_properties</em>,
- size_t <em>block_size</em>,
- hbool_t <em>backing_store</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_fapl_core (hid_t <em>access_properties</em>,
- size_t *<em>block_size</em>),
- hbool_t *<em>backing_store</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_fapl_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>hid_t H5Pget_driver (hid_t <em>access_properties</em>)</code>
- <dd>This function returns the constant <code>H5FD_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_fapl_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_fapl_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_fapl_mpi()</code>.
- </dl>
-
- <a name="Files_Families">
- <h3>6.5. File Families</h3>
- </a>
-
- <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>hid_t H5Pget_driver (hid_t <em>access_properties</em>)</code>
- <dd>This function returns the constant <code>H5FD_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_fapl_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
- inaccessible. Additional parameters may be added to this
- function in the future.
-
- <br><br>
- <dt><code>herr_t H5Pget_fapl_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()</code> 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_fapl_family()</code>.
- </dl>
-
- <h3>6.6. 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 <code>.meta</code> for
- the meta data file and <code>.raw</code> 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>hid_t H5Pget_driver (hid_t <em>access_properties</em>)</code>
- <dd>This function returns the constant <code>H5FD_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_fapl_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 <code>.meta</code>) 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 <code>.raw</code>) 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.
-
- </dl>
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-Describes HDF5 Release 1.4.5, February 2003
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-Last modified: 26 April 2001
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