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---------------------- ./config/solaris2.5 Hopefully set up now so it honors the CC and CFLAGS variables and understands solaris cc flags. ./test/big.c Checks to see if creating lots of large sparse files exceeds the user disk quota and skips the test. It also checks that we can actually open ~64 files at once. ./doc/html/Files.html ./src/H5A.c ./src/H5Aprivate.h ./src/H5F.c ./src/H5Fpublic.h Added the H5Fflush() function which takes any object as an argument as long as the object is in some way associated with a file. This required an H5A_entof() ./src/H5.c ./src/H5Flow.c The `%a' format of HDfprintf() now allows a field width and justification flag etc, like the other formats. The old H5F_addr_print() was recoded to call HDfprintf() instead of vice versa.
537 lines
24 KiB
HTML
537 lines
24 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
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<html>
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<head>
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<title>HDF5 Files</title>
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</head>
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<body>
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<h1>Files</h1>
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<h2>1. Introduction</h2>
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<p>HDF5 files are composed of a "boot block" describing information
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required to portably access files on multiple platforms, followed
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by information about the groups in a file and the datasets in the
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file. The boot block contains information about the size of offsets
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and lengths of objects, the number of entries in symbol tables
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(used to store groups) and additional version information for the
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file.
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<h2>2. File access modes</h2>
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<p>The HDF5 library assumes that all files are implicitly opened for read
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access at all times. Passing the <code>H5F_ACC_RDWR</code>
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parameter to <code>H5Fopen()</code> allows write access to a
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file also. <code>H5Fcreate()</code> assumes write access as
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well as read access, passing <code>H5F_ACC_TRUNC</code> forces
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the truncation of an existing file, otherwise H5Fcreate will
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fail to overwrite an existing file.
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<h2>3. Creating, Opening, and Closing Files</h2>
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<p>Files are created with the <code>H5Fcreate()</code> function,
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and existing files can be accessed with <code>H5Fopen()</code>. Both
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functions return an object ID which should be eventually released by
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calling <code>H5Fclose()</code>.
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<dl>
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<dt><code>hid_t H5Fcreate (const char *<em>name</em>, uintn
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<em>flags</em>, hid_t <em>create_properties</em>, hid_t
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<em>access_properties</em>)</code>
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<dd>This function creates a new file with the specified name in
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the current directory. The file is opened with read and write
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permission, and if the <code>H5F_ACC_TRUNC</code> flag is set,
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any current file is truncated when the new file is created.
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If a file of the same name exists and the
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<code>H5F_ACC_TRUNC</code> flag is not set (or the
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<code>H5F_ACC_EXCL</code> bit is set), this function will
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fail. Passing <code>H5P_DEFAULT</code> for the creation
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and/or access property lists uses the library's default
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values for those properties. Creating and changing the
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values of a property list is documented further below. The
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return value is an ID for the open file and it should be
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closed by calling <code>H5Fclose()</code> when it's no longer
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needed. A negative value is returned for failure.
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<br><br>
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<dt><code>hid_t H5Fopen (const char *<em>name</em>, uintn
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<em>flags</em>, hid_t <em>access_properties</em>)</code>
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<dd>This function opens an existing file with read permission
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and write permission if the <code>H5F_ACC_RDWR</code> flag is
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set. The <em>access_properties</em> is a file access property
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list ID or <code>H5P_DEFAULT</code> for the default I/O access
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parameters. Creating and changing the parameters for access
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templates is documented further below. Files which are opened
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more than once return a unique identifier for each
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<code>H5Fopen()</code> call and can be accessed through all
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file IDs. The return value is an ID for the open file and it
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should be closed by calling <code>H5Fclose()</code> when it's
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no longer needed. A negative value is returned for failure.
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<br><br>
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<dt><code>herr_t H5Fclose (hid_t <em>file_id</em>)</code>
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<dd>This function releases resources used by a file which was
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opened by <code>H5Fcreate()</code> or <code>H5Fopen()</code>. After
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closing a file the <em>file_id</em> should not be used again. This
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function returns zero for success or a negative value for failure.
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<br><br>
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<dt><code>herr_t H5Fflush (hid_t <em>object_id</em>)</code>
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<dd>This function will cause all buffers associated with a file
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to be immediately flushed to the file. The <em>object_id</em>
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can be any object which is associated with a file, including
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the file itself.
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</dl>
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<h2>4. File Property Lists</h2>
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<p>Additional parameters to <code>H5Fcreate()</code> or
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<code>H5Fopen()</code> are passed through property list
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objects, which are created with the <code>H5Pcreate()</code>
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function. These objects allow many parameters of a file's
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creation or access to be changed from the default values.
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Property lists are used as a portable and extensible method of
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modifying multiple parameter values with simple API functions.
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There are two kinds of file-related property lists,
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namely file creation properties and file access properties.
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<h3>4.1. File Creation Properties</h3>
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<P>File creation property lists apply to <code>H5Fcreate()</code> only
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and are used to control the file meta-data which is maintained
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in the boot block of the file. The parameters which can be
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modified are:
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<dl>
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<dt>User-Block Size <dd>The "user-block" is a fixed length block of
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data located at the beginning of the file which is ignored by the
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HDF5 library and may be used to store any data information found
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to be useful to applications. This value may be set to any power
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of two equal to 512 or greater (i.e. 512, 1024, 2048, etc). This
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parameter is set and queried with the
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<code>H5Pset_userblock()</code> and
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<code>H5Pget_userblock()</code> calls.
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<br><br>
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<dt>Offset and Length Sizes
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<dd>The number of bytes used to store the offset and length of
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objects in the HDF5 file can be controlled with this
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parameter. Values of 2, 4 and 8 bytes are currently
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supported to allow 16-bit, 32-bit and 64-bit files to
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be addressed. These parameters are set and queried
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with the <code>H5Pset_sizes()</code> and
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<code>H5Pget_sizes()</code> calls.
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<br><br>
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<dt>Symbol Table Parameters
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<dd>The size of symbol table B-trees can be controlled by setting
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the 1/2 rank and 1/2 node size parameters of the B-tree. These
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parameters are set and queried with the
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<code>H5Pset_sym_k()</code> and <code>H5Pget_sym_k()</code> calls.
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<br><br>
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<dt>Indexed Storage Parameters
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<dd>The size of indexed storage B-trees can be controlled by
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setting the 1/2 rank and 1/2 node size parameters of the B-tree.
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These parameters are set and queried with the
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<code>H5Pset_istore_k()</code> and <code>H5Pget_istore_k()</code>
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calls.
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</dl>
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<h3>4.2. File Access Property Lists</h3>
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<p>File access property lists apply to <code>H5Fcreate()</code> or
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<code>H5Fopen()</code> and are used to control different methods of
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performing I/O on files.
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<dl>
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<dt>Unbuffered I/O
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<dd>Local permanent files can be accessed with the functions described
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in Section 2 of the Posix manual, namely <code>open()</code>,
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<code>lseek()</code>, <code>read()</code>, <code>write()</code>, and
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<code>close()</code>. The <code>lseek64()</code> function is used
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on operating systems that support it. This driver is enabled and
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configured with <code>H5Pset_sec2()</code>, and queried with
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<code>H5Pget_sec2()</code>.
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<br><br>
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<dt>Buffered I/O
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<dd>Local permanent files can be accessed with the functions declared
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in the <code>stdio.h</code> header file, namely
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<code>fopen()</code>, <code>fseek()</code>, <code>fread()</code>,
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<code>fwrite()</code>, and <code>fclose()</code>. The
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<code>fseek64()</code> function is used on operating systems that
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support it. This driver is enabled and configured with
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<code>H5Pset_stdio()</code>, and queried with
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<code>H5Pget_stdio()</code>.
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<br><br>
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<dt>Memory I/O
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<dd>Local temporary files can be created and accessed directly from
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memory without ever creating permanent storage. The library uses
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<code>malloc()</code> and <code>free()</code> to create storage
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space for the file. The total size of the file must be small enough
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to fit in virtual memory. The name supplied to
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<code>H5Fcreate()</code> is irrelevant, and <code>H5Fopen()</code>
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will always fail.
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<br><br>
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<dt>Parallel Files using MPI I/O
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<dd>This driver allows parallel access to a file through the MPI I/O
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library. The parameters which can be modified are the MPI
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communicator, the info object, and the access mode.
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The communicator and info object are saved and then
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passed to <code>MPI_File_open()</code> during file creation or open.
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The access_mode controls the kind of parallel access the application
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intends. (Note that it is likely that the next API revision will
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remove the access_mode parameter and have access control specified
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via the raw data transfer property list of <code>H5Dread()</code>
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and <code>H5Dwrite()</code>.) These parameters are set and queried
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with the <code>H5Pset_mpi()</code> and <code>H5Pget_mpi()</code>
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calls.
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<br><br>
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<dt>Data Alignment
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<dd>Sometimes file access is faster if certain things are
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aligned on file blocks. This can be controlled by setting
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alignment properties of a file access property list with the
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<code>H5Pset_alignment()</code> function. Any allocation
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request at least as large as some threshold will be aligned on
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an address which is a multiple of some number.
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</dl> </ul>
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<h2>5. Examples of using file templates</h2>
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<h3>5.1. Example of using file creation templates</h3>
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<p>This following example shows how to create a file with 64-bit object
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offsets and lengths:<br>
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<pre>
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hid_t create_template;
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hid_t file_id;
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create_template = H5Pcreate(H5P_FILE_CREATE);
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H5Pset_sizes(create_template, 8, 8);
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file_id = H5Fcreate("test.h5", H5F_ACC_TRUNC,
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create_template, H5P_DEFAULT);
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.
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.
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.
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H5Fclose(file_id);
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</pre>
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<h3>5.2. Example of using file creation templates</h3>
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<p>This following example shows how to open an existing file for
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independent datasets access by MPI parallel I/O:<br>
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<pre>
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hid_t access_template;
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hid_t file_id;
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access_template = H5Pcreate(H5P_FILE_ACCESS);
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H5Pset_mpi(access_template, MPI_COMM_WORLD, MPI_INFO_NULL);
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/* H5Fopen must be called collectively */
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file_id = H5Fopen("test.h5", H5F_ACC_RDWR, access_template);
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.
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.
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.
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/* H5Fclose must be called collectively */
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H5Fclose(file_id);
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</pre>
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<h2>6. Low-level File Drivers</h2>
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<p>HDF5 is able to access its address space through various types of
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low-level <em>file drivers</em>. For instance, an address space might
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correspond to a single file on a Unix file system, multiple files on a
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Unix file system, multiple files on a parallel file system, or a block
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of memory within the application. Generally, an HDF5 address space is
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referred to as an "HDF5 file" regardless of how the space is organized
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at the storage level.
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<h3>6.1 Unbuffered Permanent Files</h3>
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<p>The <em>sec2</em> driver uses functions from section 2 of the
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Posix manual to access files stored on a local file system. These are
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the <code>open()</code>, <code>close()</code>, <code>read()</code>,
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<code>write()</code>, and <code>lseek()</code> functions. If the
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operating system supports <code>lseek64()</code> then it is used instead
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of <code>lseek()</code>. The library buffers meta data regardless of
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the low-level driver, but using this driver prevents data from being
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buffered again by the lowest layers of the HDF5 library.
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<dl>
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<dt><code>H5F_driver_t H5Pget_driver (hid_t
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<em>access_properties</em>)</code>
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<dd>This function returns the constant <code>H5F_LOW_SEC2</code> if the
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<em>sec2</em> driver is defined as the low-level driver for the
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specified access property list.
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<br><br>
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<dt><code>herr_t H5Pset_sec2 (hid_t <em>access_properties</em>)</code>
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<dd>The file access properties are set to use the <em>sec2</em>
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driver. Any previously defined driver properties are erased from the
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property list. Additional parameters may be added to this function in
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the future.
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<br><br>
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<dt><code>herr_t H5Pget_sec2 (hid_t <em>access_properties</em>)</code>
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<dd>If the file access property list is set to the <em>sec2</em> driver
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then this function returns zero; otherwise it returns a negative
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value. In the future, additional arguments may be added to this
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function to match those added to <code>H5Pset_sec2()</code>.
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</dl>
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<h3>6.2 Buffered Permanent Files</h3>
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<p>The <em>stdio</em> driver uses the functions declared in the
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<code>stdio.h</code> header file to access permanent files in a local
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file system. These are the <code>fopen()</code>, <code>fclose()</code>,
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<code>fread()</code>, <code>fwrite()</code>, and <code>fseek()</code>
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functions. If the operating system supports <code>fseek64()</code> then
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it is used instead of <code>fseek()</code>. Use of this driver
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introduces an additional layer of buffering beneath the HDF5 library.
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<dl>
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<dt><code>H5F_driver_t H5Pget_driver(hid_t
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<em>access_properties</em>)</code>
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<dd>This function returns the constant <code>H5F_LOW_STDIO</code> if the
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<em>stdio</em> driver is defined as the low-level driver for the
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specified access property list.
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<br><br>
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<dt><code>herr_t H5Pset_stdio (hid_t <em>access_properties</em>)</code>
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<dd>The file access properties are set to use the <em>stdio</em>
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driver. Any previously defined driver properties are erased from the
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property list. Additional parameters may be added to this function in
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the future.
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<br><br>
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<dt><code>herr_t H5Pget_stdio (hid_t <em>access_properties</em>)</code>
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<dd>If the file access property list is set to the <em>stdio</em> driver
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then this function returns zero; otherwise it returns a negative
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value. In the future, additional arguments may be added to this
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function to match those added to <code>H5Pset_stdio()</code>.
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</dl>
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<h3>6.3 Buffered Temporary Files</h3>
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<p>The <em>core</em> driver uses <code>malloc()</code> and
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<code>free()</code> to allocated space for a file in the heap. Reading
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and writing to a file of this type results in mem-to-mem copies instead
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of disk I/O and as a result is somewhat faster. However, the total file
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size must not exceed the amount of available virtual memory, and only
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one HDF5 file handle can access the file (because the name of such a
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file is insignificant and <code>H5Fopen()</code> always fails).
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<dl>
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<dt><code>H5F_driver_t H5Pget_driver (hid_t
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<em>access_properties</em>)</code>
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<dd>This function returns the constant <code>H5F_LOW_CORE</code> if the
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<em>core</em> driver is defined as the low-level driver for the
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specified access property list.
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<br><br>
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<dt><code>herr_t H5Pset_core (hid_t <em>access_properties</em>, size_t
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<em>block_size</em>)</code>
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<dd>The file access properties are set to use the <em>core</em>
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driver and any previously defined driver properties are erased from
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the property list. Memory for the file will always be allocated in
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units of the specified <em>block_size</em>. Additional parameters may
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be added to this function in the future.
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<br><br>
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<dt><code>herr_t H5Pget_core (hid_t <em>access_properties</em>, size_t
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*<em>block_size</em>)</code>
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<dd>If the file access property list is set to the <em>core</em> driver
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then this function returns zero and <em>block_size</em> is set to the
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block size used for the file; otherwise it returns a negative
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value. In the future, additional arguments may be added to this
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function to match those added to <code>H5Pset_core()</code>.
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</dl>
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<h3>6.4 Parallel Files</h3>
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<p>This driver uses MPI I/O to provide parallel access to a file.
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<dl>
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<dt><code>H5F_driver_t H5Pget_driver (hid_t
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<em>access_properties</em>)</code>
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<dd>This function returns the constant <code>H5F_LOW_MPI</code> if the
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<em>mpi</em> driver is defined as the low-level driver for the
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specified access property list.
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<br><br>
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<dt><code>herr_t H5Pset_mpi (hid_t <em>access_properties</em>, MPI_Comm
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<em>comm</em>, MPI_info <em>info</em>)</code>
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<dd>The file access properties are set to use the <em>mpi</em>
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driver and any previously defined driver properties are erased from
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the property list. Additional parameters may be added to this
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function in the future.
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<br><br>
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<dt><code>herr_t H5Pget_mpi (hid_t <em>access_properties</em>, MPI_Comm
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*<em>comm</em>, MPI_info *<em>info</em>)</code>
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<dd>If the file access property list is set to the <em>mpi</em> driver
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then this function returns zero and <em>comm</em>, and <em>info</em>
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are set to the values stored in the property
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list; otherwise the function returns a negative value. In the future,
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additional arguments may be added to this function to match those
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added to <code>H5Pset_mpi()</code>.
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</dl>
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<h3>6.4 File Families</h3>
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<p>A single HDF5 address space may be split into multiple files which,
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together, form a file family. Each member of the family must be the
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same logical size although the size and disk storage reported by
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<code>ls</code>(1) may be substantially smaller. The name passed to
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<code>H5Fcreate()</code> or <code>H5Fopen()</code> should include a
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<code>printf(3c)</code> style integer format specifier which will be
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replaced with the family member number (the first family member is
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zero).
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<p>Any HDF5 file can be split into a family of files by running
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the file through <code>split</code>(1) and numbering the output
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files. However, because HDF5 is lazy about extending the size
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of family members, a valid file cannot generally be created by
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concatenation of the family members. Additionally,
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<code>split</code> and <code>cat</code> don't attempt to
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generate files with holes. The <code>h5repart</code> program
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can be used to repartition an HDF5 file or family into another
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file or family and preserves holes in the files.
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<dl>
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<dt><code>h5repart</code> [<code>-v</code>] [<code>-b</code>
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|
<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: Thu Aug 6 16:17:08 EDT 1998
|
|
<!-- hhmts end -->
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</body>
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</html>
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