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<head><title>
HDF5/Tools API Specification
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<a href="index.html">HDF5 documents and links</a> <br>
<a href="H5.intro.html">Introduction to HDF5</a> <br>
<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User Guide</a> <br>
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And in this document, the
<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="RM_H5.html">H5</a>
<a href="RM_H5A.html">H5A</a>
<a href="RM_H5D.html">H5D</a>
<a href="RM_H5E.html">H5E</a>
<a href="RM_H5F.html">H5F</a>
<a href="RM_H5G.html">H5G</a>
<a href="RM_H5I.html">H5I</a>
<a href="RM_H5P.html">H5P</a> <br>
<a href="RM_H5R.html">H5R</a>
<a href="RM_H5S.html">H5S</a>
<a href="RM_H5T.html">H5T</a>
<a href="RM_H5Z.html">H5Z</a>
<a href="Tools.html">Tools</a>
<a href="PredefDTypes.html">Datatypes</a>
</td></tr>
<tr><td colspan="2" align="right">
<i><small>(<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/">PDF</a>
of complete manual formatted as print volume) </small></i>
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</table>
</center>
<hr>
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<h1>HDF5 Tools</h1>
</center>
<h2>HDF5 Tool Interfaces</h2>
<p>
HDF5-related tools are available to assist the user in a variety of
activities, including
examining or managing HDF5 files,
converting raw data between HDF5 and other special-purpose formats,
moving data and files between the HDF4 and HDF5 formats,
measuring HDF5 library performance, and
managing HDF5 library and application compilation,
installation and configuration.
Unless otherwise specified below, these tools are distributed and
installed with HDF5.
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<ul>
<li>User utilities:
<ul>
<li><a href="#Tools-Dump">h5dump</a> --
Enables a user to examine the contents of an HDF5 file
and dump those contents to an ASCII file
<li><a href="#Tools-Ls">h5ls</a> --
Lists specified features of HDF5 file contents
<li><a href="#Tools-Diff">h5diff</a> --
Compares two HDF5 files and reports the differences.
<li><a href="#Tools-Repack">h5repack</a> -- Copies an HDF5 file to a new
file with or without compression/chunking.
<li><a href="#Tools-Perf">h5perf</a> --
Measures HDF5 performance
<li><a href="#Tools-Repart">h5repart</a> --
Repartitions a file, creating a family of files
<li><a href="#Tools-Jam">h5jam</a> --
Adds a user block to the front of an HDF5 file
<li><a href="#Tools-Jam">h5unjam</a> --
Splits an existing user block from an HDF5 file,
placing it in a separate file
<br><br>
</ul>
<li>Configuration and library management utilities:
<ul>
<li><a href="#Tools-Redeploy">h5redeploy</a> --
Updates HDF5 compiler tools after an HDF5 software installation
in a new location
<li><a href="#Tools-H5CC">h5cc</a> and
<a href="#Tools-H5CC">h5pcc</a> --
Simplify the compilation of HDF5 programs written in C
<li><a href="#Tools-H5FC">h5fc</a> and
<a href="#Tools-H5FC">h5pfc</a> --
Simplify the compilation of HDF5 programs written in Fortran90
<li><a href="#Tools-H5C++">h5c++</a> --
Simplifies the compilation of HDF5 programs written in C++
<br><br>
</ul>
<li><a href="http://hdf.ncsa.uiuc.edu/hdf-java-html/"
target="ToolsExt">Java-based tools for HDF5</a>
for viewing, manipulating, and generating HDF4 and HDF5 files:
<br>
<em>(Distributed separately; external link is
<code>http://hdf.ncsa.uiuc.edu/hdf-java-html/</code>)</em>
<ul>
<li><code>HDFview</code> -- a browser that
works with both HDF4 and HDF5 files and
can be used to transfer data between the two formats
<li>Java interfaces for both the HDF4 and HDF5 libraries
<li>Other HDF4- and HDF5-related products
<br><br>
</ul>
<li>Data conversion utilities:
<ul>
<li><a href="#Tools-Import">h5import</a> --
Imports data into an existing or new HDF5 file
<li><a href="#Tools-GIF2H5">gif2h5</a> --
Converts a GIF file to an HDF5 file
<li><a href="#Tools-H52GIF">h52gif</a> --
Converts images in an HDF5 file to a GIF file
<br><br>
</ul>
<li><a href="http://hdf.ncsa.uiuc.edu/h4toh5/" target="ToolsExt">
HDF5/HDF4 conversion tools</a>:
<br>
<em>(Distributed separately; external link is
<code>http://hdf.ncsa.uiuc.edu/h4toh5/</code>)</em>
<ul>
<li><a href="http://hdf.ncsa.uiuc.edu/h4toh5/"
target="ToolsExt">H4toH5 Conversion Library</a> --
Provides APIs for use in tools that perform customized
conversions of HDF4 files to HDF5 files
<li><a href="#Tools-H5toh4">h5toh4</a> --
Converts an HDF5 file to an HDF4 file
<li><a href="#Tools-H4toh5">h4toh5</a> --
Converts an HDF4 file to an HDF5 file
<br><br>
</ul>
<li><a href="http://hdf.ncsa.uiuc.edu/tools5.html"
target="ToolsExt">Other tools</a>,
including third-party and commercial utilities and applications
<br>
<em>(Distributed separately; external link is
<code>http://hdf.ncsa.uiuc.edu/tools5.html</code>)</em>
</ul>
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<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Dump">h5dump</a>
<dt><strong>Syntax:</strong>
<dd><code>h5dump
[</code><em>OPTIONS</em><code>]</code> <em>file</em>
<dt><strong>Purpose:</strong>
<dd>Displays HDF5 file contents.
<dt><strong>Description:</strong>
<dd><code>h5dump</code> enables the user to examine
the contents of an HDF5 file and dump those contents, in human
readable form, to an ASCII file.
<p>
<code>h5dump</code> dumps HDF5 file content to standard output.
It can display the contents of the entire HDF5 file or
selected objects, which can be groups, datasets, a subset of a
dataset, links, attributes, or datatypes.
</p>
<p>
The <code>--header</code> option displays object header
information only.
</p>
<p>
Names are the absolute names of the objects. <code>h5dump</code>
displays objects in the order same as the command order. If a
name does not start with a slash, <code>h5dump</code> begins
searching for the specified object starting at the root group.
</p>
<p>
If an object is hard linked with multiple names,
<code>h5dump</code> displays the content of the object in the
first occurrence. Only the link information is displayed in later
occurrences.
</p>
<p>
<code>h5dump</code> assigns a name for any unnamed datatype in
the form of
<code>#</code><em>oid1</em><code>:</code><em>oid2</em>, where
<em>oid1</em> and <em>oid2</em> are the object identifiers
assigned by the library. The unnamed types are displayed within
the root group.
</p>
<p>
Datatypes are displayed with standard type names. For example,
if a dataset is created with <code>H5T_NATIVE_INT</code> type
and the standard type name for integer on that machine is
<code>H5T_STD_I32BE</code>, <code>h5dump</code> displays
<code>H5T_STD_I32BE</code> as the type of the dataset.
</p>
<p>
<code>h5dump</code> can also dump a subset of a dataset.
This feature operates in much the same way as hyperslabs in HDF5;
the parameters specified on the command line are passed to the
function <a href="RM_H5S.html#Dataspace-SelectHyperslab">
<code>H5Sselect_hyperslab</code></a> and the resulting selection
is displayed.
</p>
<p>
The <code>h5dump</code> output is described in detail in the
<a href="ddl.html"><cite>DDL for HDF5</cite></a>, the
<cite>Data Description Language</cite> document.
</p>
<p>
<em>Note</em>: It is not permissible to specify multiple
attributes, datasets, datatypes, groups, or soft links with one
flag. For example, one may not issue the command
<br>
<font size=-1>WRONG:</font>
<code>h5dump -a /attr1 /attr2 foo.h5</code>
</br>
to display both <code>/attr1</code> and <code>/attr2</code>.
One must issue the following command:
<br>
<font size=-1>CORRECT:</font>
<code>h5dump -a /attr1 -a /attr2 foo.h5</code>
</br>
</p>
<p>
It's possible to select the file driver with which to open the
HDF5 file by using the --filedriver (-f) command-line option.
Acceptable values for the --filedriver option are: "sec2",
"family", "split", "multi", and "stream". If the file driver flag
isn't specified, then the file will be opened with each driver in
turn and in the order specified above until one driver succeeds
in opening the file.
</p>
<p>
One byte integer type data is displayed in decimal by default. When
displayed in ASCII, a non-printable code is displayed in 3 octal
digits preceeded by a back-slash unless there is a C language escape
sequence for it. For example, CR and LF are printed as \r and \n.
Though the NUL code is represented as \0 in C, it is printed as
\000 to avoid ambiguity as illustrated in the following 1 byte
char data (since this is not a string, embedded NUL is possible).
<pre>
141 142 143 000 060 061 062 012
a b c \0 0 1 2 \n </pre>
h5dump prints them as "abc\000012\n". But if h5dump prints NUL as \0,
the output is "abc\0012\n" which is ambiguous.
</p>
<!-- NEW PAGE -->
<dt><strong>XML Output:</strong>
<dd>With the <code>--xml</code> option, <code>h5dump</code> generates
XML output. This output contains a complete description of the file,
marked up in XML. The XML conforms to the HDF5 Document Type
Definition (DTD) available at
<a href="http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd">
<code>http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd</code></a>.
<p>
The XML output is suitable for use with other tools, including the
<a href="http://hdf.ncsa.uiuc.edu/java-hdf5-html">HDF5 Java Tools</a>.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code> or
<code>--help</code></dt>
<dd>Print a usage message and exit.</dd>
<dt><code>-n</code> or
<code>--contents</code></dt>
<dd>Print a list of the file contents and exit.</dd>
<dt><code>-B</code> or
<code>--bootblock</code></dt>
<dd>Print the contents of the boot block.</dd>
<dt><code>-H</code> or
<code>--header</code></dt>
<dd>Print the header only; no data is displayed.</dd>
<dt><code>-A</code>
<dd>Print the header and value of attributes;
data of datasets is not displayed.</dd>
<dt><code>-i</code> or
<code>--object-ids</code></dt>
<dd>Print the object ids.</dd>
<dt><code>-r</code> or
<code>--string</code></dt>
<dd>Print 1-bytes integer datasets as ASCII.</dd>
<dt><code>-e</code></dt>
<dd>Escape non-printing characters.</dd>
<dt><code>-V</code> or
<code>--version</code></dt>
<dd>Print version number and exit.</dd>
<dt><code>-a <em>P</em></code> or
<code>--attribute=<em>P</em></code></dt>
<dd>Print the specified attribute.</dd>
<dt><code>-d <em>P</em></code> or
<code>--dataset=<em>P</em></code></dt>
<dd>Print the specified dataset.</dd>
<dt><code>-y</code></dt>
<dd>Do not print array indices with data.</dd>
<dt><code>-p</code> or
<code>--properties</code></dt>
<dd>Print dataset filters, storage layout, and fill value.</dd>
<dt><code>-f <em>D</em></code> or
<code>--filedriver=<em>D</em></code></dt>
<dd>Specify which driver to open the file with.</dd>
<dt><code>-g <em>P</em></code> or
<code>--group=<em>P</em></code></dt>
<dd>Print the specified group and all members.</dd>
<dt><code>-l <em>P</em></code> or
<code>--soft-link=<em>P</em></code></dt>
<dd>Print the value(s) of the specified soft link.</dd>
<dt><code>-o <em>F</em></code> or
<code>--output=<em>F</em></code></dt>
<dd>Output raw data into file F.</dd>
<dt><code>-t <em>T</em></code> or
<code>--datatype=<em>T</em></code></dt>
<dd>Print the specified named datatype.</dd>
<dt><code>-w <em>N</em></code> or
<code>--width=<em>N</em></code></dt>
<dd>Set the number of columns of output.</dd>
<dt><code>-x <em></em></code> or
<code>--xml</code></dt>
<dd>Output XML using XML schema (default) instead of DDL.</dd>
<dt><code>-u <em></em></code> or
<code>--use-dtd</code></dt>
<dd>Output XML using XML DTD instead of DDL.</dd>
<dt><code>-D <em>U</em></code> or
<code>--xml-dtd=<em>U</em></code></dt>
<dd>In XML output, refer to the DTD or schema at <em>U</em>
instead of the default schema/DTD.</dd>
<dt><code>-X <em>S</em></code> or
<code>--xml-dns=<em>S</em></code></dt>
<dd>In XML output, (XML Schema) use qualified names in the XML:<br>
":": no namespace, default: "hdf5:"</dd>
<!-- NEW PAGE -->
<dt>The next four options enable subsetting, which is
accomplished by selecting a hyperslab from a dataset.
These options mirror the techniques used by an HDF5
application when performing hyperslab selection.
The <code>start</code> and <code>count</code> parameters
are mandatory if subsetting is to be performed;
the <code>stride</code> and <code>block</code> parameters
are optional and will default to <code>1</code> (one).
<dt><code>-s <em>L</em></code> or
<code>--start=<em>L</em></code></dt>
<dd>Offset of start of subsetting selection.
<br>
Default: the beginning of the dataset.</dd>
<dt><code>-S <em>L</em></code> or
<code>--stride=<em>L</em></code></dt>
<dd>Hyperslab stride.
<br>
Default: 1 in all dimensions.</dd>
<dt><code>-c <em>L</em></code> or
<code>--count=<em>L</em></code></dt>
<dd>Number of blocks to include in the selection.</dd>
<dt><code>-k <em>L</em></code> or
<code>--block=<em>L</em></code></dt>
<dd>Size of block in hyperslab.
<br>
Default: 1 in all dimensions.</dd>
<dt><code>--</code></dt>
<dd>Indicates that all following arguments are non-options.
E.g., to dump a file called `-f', use h5dump -- -f.</dd>
<dt><em>file</em></dt>
<dd>The file to be examined.</dd>
<br><br>
<dt>The option parameters listed above are defined as follows:
<dd><em>D</em> -- which file driver to use in opening the
file. Acceptable values are "sec2", "family", "split",
"multi", and "stream". Without the file driver flag the
file will be opened with each driver in turn and in the
order specified above until one driver succeeds in
opening the file.</dd>
<dd><em>P</em> -- The full path from the root group to
the object</dd>
<dd><em>T</em> -- The name of the datatype</dd>
<dd><em>F</em> -- A filename</dd>
<dd><em>N</em> -- An integer greater than 1</dd>
<dd><em>L</em> -- A list of integers, the number of which is
equal to the number of dimensions in the dataspace being
queried</dd>
<dd><em>U</em> -- A URI (as defined in
[<a href="http://www.ietf.org/rfc/rfc2396.txt">IETF RFC 2396</a>],
updated by
[<a href="http://www.ietf.org/rfc/rfc2732.txt">IETF RFC 2732</a>])
that refers to the DTD to be used to validate the XML</dd>
<br><br>
<dt>Subsetting parameters can also be expressed in a convenient
compact form, as follows:
<br>
<code>--dataset="/foo/mydataset[START;STRIDE;COUNT;BLOCK]"</code>
<br>
All of the semicolons (<code>;</code>) are required, even when
a parameter value is not specified.
When not specified, default parameter values are used.
</dl>
<p>
<dt><strong>Examples:</strong>
<ol>
<li>Dumping the group <code>/GroupFoo/GroupBar</code> in the file
<code>quux.h5</code>:
<blockquote>
<code>h5dump -g /GroupFoo/GroupBar quux.h5</code>
</blockquote>
<li>Dumping the dataset <code>Fnord</code> in the group
<code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:
<blockquote>
<code>h5dump -d /GroupFoo/GroupBar/Fnord quux.h5</code>
</blockquote>
<li>Dumping the attribute <code>metadata</code> of the dataset
<code>Fnord</code> which is in group
<code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:
<blockquote>
<code>h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5</code>
</blockquote>
<li>Dumping the attribute <code>metadata</code> which is an
attribute of the root group in the file <code>quux.h5</code>:
<blockquote>
<code>h5dump -a /metadata quux.h5</code>
</blockquote>
<li>Producing an XML listing of the file <code>bobo.h5</code>:
<blockquote>
<code>h5dump --xml bobo.h5 > bobo.h5.xml</code>
</blockquote>
<!-- NEW PAGE -->
<li>Dumping a subset of the dataset <code>/GroupFoo/databar/</code>
in the file <code>quux.h5</code>
<blockquote>
<code>h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3"
<br>
--count="3,19" --block="1,1" quux.h5</code>
</blockquote>
<li>The same example using the short form to specify the
subsetting parameters:
<blockquote>
<code>h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5</code>
</blockquote>
</ol>
<dt><strong>Current Status:</strong>
<dd>The current version of <code>h5dump</code> displays the
following information:
<ul>
<li>Group
<ul>
<li>group attribute (see Attribute)
<li>group member
</ul>
<li>Dataset
<ul>
<li>dataset attribute (see Attribute)
<li>dataset type (see Datatype)
<li>dataset space (see Dataspace)
<li>dataset data
</ul>
<li>Attribute
<ul>
<li>attribute type (see Datatype)
<li>attribute space (see Dataspace)
<li>attribute data
</ul>
<li>Datatype
<ul>
<li>integer type
<br>
- H5T_STD_I8BE, H5T_STD_I8LE, H5T_STD_I16BE, ...
<li>floating point type
<br>
- H5T_IEEE_F32BE, H5T_IEEE_F32LE, H5T_IEEE_F64BE, ...
<li>string type
<li>compound type
<br>
- named, unnamed and transient compound type
<br>
- integer, floating or string type member
<li>opaque types
<li>reference type
<br>
- object references
<br>
- data regions
<li>enum type
<li>variable-length datatypes
<br>
- atomic types only
<br>
- scalar or single dimensional array of variable-length
types supported
</ul>
<li>Dataspace
<ul>
<li>scalar and simple space
</ul>
<li>Soft link
<li>Hard link
<li>Loop detection
</ul>
<dt><strong>See Also:</strong>
<ul>
<li>HDF5 Data Description Language syntax at
<a href="ddl.html"><cite>DDL for HDF5</cite></a>
<li>HDF5 XML Schema at
<a href="http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd">http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd</a>
<li>HDF5 XML information at
<a href="http://hdf.ncsa.uiuc.edu/HDF5/XML">http://hdf.ncsa.uiuc.edu/HDF5/XML/</a>
</ul>
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5ls" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Ls">h5ls</a>
<dt><strong>Syntax:</strong>
<dd><code>h5ls
[</code><em>OPTIONS</em><code>]</code><em>
file</em><code>
[</code><em>OBJECTS...</em><code>]</code>
<dt><strong>Purpose:</strong>
<dd>Prints information about a file or dataset.
<dt><strong>Description:</strong>
<dd><code>h5ls</code> prints selected information about file objects
in the specified format.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code> or
<code>-?</code> or
<code>--help</code>
<dd>Print a usage message and exit.
<dt><code>-a</code> or
<code>--address</code>
<dd>Print addresses for raw data.
<dt><code>-d</code> or <code>--data</code>
<dd>Print the values of datasets.
<dt><code>-e</code> or
<code>--errors</code>
<dd>Show all HDF5 error reporting.
<dt><code>-f</code> or
<code>--full</code>
<dd>Print full path names instead of base names.
<dt><code>-g</code> or
<code>--group</code>
<dd>Show information about a group, not its contents.
<dt><code>-l</code> or
<code>--label</code>
<dd>Label members of compound datasets.
<dt><code>-r</code> or
<code>--recursive</code>
<dd>List all groups recursively, avoiding cycles.
<dt><code>-s</code> or
<code>--string</code>
<dd>Print 1-bytes integer datasets as ASCII.
<dt><code>-S</code> or
<code>--simple</code>
<dd>Use a machine-readable output format.
<dt><code>-w</code><em>N</em> or
<code>--width=</code><em>N</em>
<dd>Set the number of columns of output.
<dt><code>-v</code> or
<code>--verbose</code>
<dd>Generate more verbose output.
<dt><code>-V</code> or
<code>--version</code>
<dd>Print version number and exit.
<dt><code>-x</code> or
<code>--hexdump</code>
<dd>Show raw data in hexadecimal format.
<dt><em>file</em>
<dd>The file name may include a printf(3C) integer format
such as <code>%%05d</code> to open a file family.
<dt><em>objects</em>
<dd>Each object consists of an HDF5 file name optionally
followed by a slash and an object name within the file
(if no object is specified within the file then the
contents of the root group are displayed). The file name
may include a <code>printf(3C)</code> integer format such
as "%05d" to open a file family.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5diff" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Diff">h5diff</a>
<dt><strong>Syntax:</strong>
<dd><code>h5diff </code> <em>file1</em> <em>file2</em>
[<em>OPTIONS</em>]
[<em>object1</em> [<em>object2</em> ] ]
<dt><strong>Purpose:</strong>
<dd>Compares two HDF5 files and reports the differences.
<dt><strong>Description:</strong>
<dd><code>h5diff</code> is a command line tool that compares
two HDF5 files, <em>file1</em> and <em>file2</em>, and
reports the differences between them.
<p>
Optionally, <code>h5diff</code> will compare two objects
within these files.
If only one object, <em>object1</em>, is specified,
<code>h5diff</code> will compare
<em>object1</em> in <em>file1</em>
with <em>object1</em> in <em>file2</em>.
In two objects, <em>object1</em> and <em>object2</em>,
are specified, <code>h5diff</code> will compare
<em>object1</em> in <em>file1</em>
with <em>object2</em> in <em>file2</em>.
These objects must be HDF5 datasets.
<dd>
<p>
<em>object1</em> and <em>object2</em> must be expressed
as absolute paths from the respective file's root group.
<dd>
<p>
<code>h5diff</code> has the following four modes of output:<br>
Normal mode: print the number of differences found and where they occurred<br>
Report mode (-r): print the above plus the differences<br>
Verbose mode (-v): print the above plus a list of objects and warnings<br>
Quiet mode (-q): do not print output (h5diff always returns an exit code of
1 when differences are found).
<dd>
<p>
Additional information, with several sample cases,
can be found in the document
<a href="http://hdf.ncsa.uiuc.edu/HDF5/h5diff/h5diff_design.html">
<cite>H5diff Examples</cite></a>.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><em>file1</em>
<dt><em>file2</em>
<dd>The HDF5 files to be compared.
<dt><code>-h</code>
<dd>help message.
<dt><code>-r</code>
<dd>Report mode. Print the differences.<dt><code>-v</code>
<dd>Verbose mode. Print the differences, list of objects, warnings.<dt><code>-q</code>
<dd>Quiet mode. Do not print output.
<dt><code>-n</code> <em>count</em>
<dd>Print difference up to <em>count</em> differences,
then stop.
<em>count</em> must be a positive integer.
<dt><code>-d</code> <em>delta</em>
<dd>Print only differences that are greater than the
limit <em>delta</em>.
<em>delta</em> must be a positive number.
The comparison criterion is whether the
absolute value of the difference of
two corresponding values is greater than
<em>delta</em>
<br>(e.g., <code> |a–b| > <em>delta</em></code>,
where <code>a</code> is a value in <em>file1</em> and
<code>b</code> is a value in <em>file2</em>).
<dt><code>-p</code> <em>relative</em>
<dd>Print only differences that are greater than a
relative error.
<em>relative</em> must be a positive number.
The comparison criterion is whether the
absolute value of the difference <code>1</code>
and the ratio of two corresponding values
is greater than <em>relative</em>
(e.g., <code>|1–(b/a)| > <em>relative</em></code>
where <code>a</code> is a value in <em>file1</em> and
<code>b</code> is a value in <em>file2</em>).
<dt><em>object1</em>
<dt><em>object2</em>
<dd>Specific object(s) within the files to be compared.
</dl>
<!-- NEW PAGE -->
<dt><strong>Examples:</strong>
<dd>The following <code>h5diff</code> call compares
the object <code>/a/b</code> in <code>file1</code>
with the object <code>/a/c</code> in <code>file2</code>:<br>
<code> h5diff file1 file2 /a/b /a/c</code>
<dd>This <code>h5diff</code> call compares
the object <code>/a/b</code> in <code>file1</code>
with the same object in <code>file2</code>:<br>
<code> h5diff file1 file2 /a/b</code>
<dd>And this <code>h5diff</code> call compares
all objects in both files:<br>
<code> h5diff file1 file2</code>
<br>
file1 and file2 can be the same file. Use:<br>
<code> h5diff </code><code> file1 file1 /g1/dset1 /g1/dset2</code> <br>
to compare <code>/g1/dset1</code> and <code>/g1/dset2</code> in the same file<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5repack" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Repack">h5repack</a>
<dt><strong>Syntax:</strong>
<dd><code>h5repack </code> -i <em>file1</em>-o <em>file2</em> [-h] [-v] [-f
'<i>filter</i>'] [-l '<i>layout</i>'][-m number][-e file]
<dt><strong>Purpose:</strong>
<dd>Copies an HDF5 file to a new file with or without compression/chunking.
<dt><strong>Description:</strong>
<dd><code>h5repack</code> is a command line tool that applies HDF5 filters
to a input file <em>file1</em>, saving the output in a new file, <em>file2</em>.<p>'<i>filter</i>'
is a string with the format <br>
<list of objects> : <name of filter> = <filter
parameters>.<br>
<br>
<list of objects> is a comma separated list of object names
meaning apply compression only to those objects. If no object names are
specified, the filter is applied to all objects<br>
<name of filter> can be: <br>
GZIP, to apply the HDF5 GZIP filter (GZIP compression)<br>
SZIP, to apply the HDF5 SZIP filter (SZIP compression)<br>
SHUF, to apply the HDF5 shuffle filter<br>
FLET, to apply the HDF5 checksum filter<br>
NONE, to remove the filter <br>
<filter parameters> is optional compression info <br>
SHUF (no parameter) <br>
FLET (no parameter) <br>
GZIP=<deflation level> from 1-9 <br>
SZIP=<pixels per block,coding> (pixels per block is a even number in
2-32 and coding method is 'EC' or 'NN')
<dt> </dt>
<dd>'<i>layout'</i> is a string with the format<br>
<list of objects> : <layout type> <br>
<br>
<list of objects> is a comma separated list of object names, meaning
that layout information is supplied for those objects. If no object names are
specified, the layout is applied to all objects <br>
<layout type> can be: <br>
CHUNK, to apply chunking layout <br>
COMPA, to apply compact layout <br>
CONTI, to apply continuous layout <br>
<layout parameters> is present for the chunk case only it is the chunk
size of each dimension: <dim_1 x dim_2 x ... dim_n></dd>
<dt> </dt>
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><em>file1</em>
<dt><em>file2</em>
<dd>The input and output HDF5 files
<dt><code>-h</code>
<dd>help message.<dt><code>-f</code> <em>filter</em>
<dd>Filter type<dt><code>-l</code> <em>layout</em>
<dd>Layout type<dt><code>-v</code>
<dd>Verbose mode. Print output (list of objects in the file, filters
and layout applied).<dt><code>-e</code> <em>file</em>
<dd>File with the -f and -l options (only filter and layout flags)
<dt><code>-d</code> <em>delta</em>
<dd>Print only differences that are greater than the
limit <em>delta</em>.
<em>delta</em> must be a positive number.
The comparison criterion is whether the
absolute value of the difference of
two corresponding values is greater than
<em>delta</em>
<br>(e.g., <code> |a–b| > <em>delta</em></code>,
where <code>a</code> is a value in <em>file1</em> and
<code>b</code> is a value in <em>file2</em>).<dt><code>-m</code> <em>number</em>
<dd>Do not apply the filter to objects which size in bytes is
smaller than number. If no size is specified a minimum of 1024
bytes is assumed.
</dl>
<dt><strong>Examples:</strong>
<dd>1) h5repack -i file1 -o file2 -f GZIP=1 -v<br>
Applies GZIP compression to all
objects in file1 and saves the output in file2
<p>2) h5repack -i file1 -o file2 -f dset1:SZIP=8,NN -v<br>
Applies SZIP compression only
to object 'dset1'</p>
<p>3) h5repack -i file1 -o file2 -l dset1,dset2:CHUNK=20x10 -v<br>
Applies chunked layout to
objects 'dset1' and 'dset2'<br>
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5repart" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Repart">h5repart</a>
<dt><strong>Syntax:</strong>
<dd><code>h5repart
[-v]
[-V]
[-[b|m]</code><em>N</em><code>[g|m|k]]</code>
<em>source_file
dest_file</em>
<dt><strong>Purpose:</strong>
<dd>Repartitions a file or family of files.
<dt><strong>Description:</strong>
<dd><code>h5repart</code> splits a single file into a family of
files, joins a family of files into a single file, or copies
one family of files to another while changing the size of the
family members. <code>h5repart</code> can also be used to
copy a single file to a single file with holes.
<p>
Sizes associated with the <code>-b</code> and <code>-m</code>
options may be suffixed with <code>g</code> for gigabytes,
<code>m</code> for megabytes, or <code>k</code> for kilobytes.
<p>
File family names include an integer <code>printf</code>
format such as <code>%d</code>.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-v</code>
<dd>Produce verbose output.
<dt><code>-V</code>
<dd>Print a version number and exit.
<dt><code>-b</code><em>N</em>
<dd>The I/O block size, defaults to 1kB
<dt><code>-m</code><em>N</em>
<dd>The destination member size or 1GB
<dt><em>source_file</em>
<dd>The name of the source file
<dt><em>dest_file</em>
<dd>The name of the destination files
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5import" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Import">h5import</a>
<dt><strong>Syntax:</strong>
<dd><code>h5import
<em>infile</em> <em>in_options</em>
[<em>infile</em> <em>in_options</em> <b>...</b>]
-o <em>outfile</em>
</code>
<dd><code>h5import
<em>infile</em> <em>in_options</em>
[<em>infile</em> <em>in_options</em> <b>...</b>]
-outfile <em>outfile</em>
</code>
<dd><code>h5import -h</code>
<dd><code>h5import -help</code>
<dt><strong>Purpose:</strong>
<dd>Imports data into an existing or new HDF5 file.
<dt><strong>Description:</strong>
<dd><code>h5import</code> converts data
from one or more ASCII or binary files, <code><i>infile</i></code>,
into the same number of HDF5 datasets
in the existing or new HDF5 file, <code><i>outfile</i></code>.
Data conversion is performed in accordance with the
user-specified type and storage properties
specified in <code><em>in_options</em></code>.
<p>
The primary objective of <code>h5import</code> is to
import floating point or integer data.
The utility's design allows for future versions that
accept ASCII text files and store the contents as a
compact array of one-dimensional strings,
but that capability is not implemented in HDF5 Release 1.6.
<p>
<b>Input data and options:</b><br>
Input data can be provided in one of the following forms:
<ul><li>As an ASCII, or plain-text, file containing either
floating point or integer data
<li>As a binary file containing either 32-bit or
64-bit native floating point data
<li>As a binary file containing native integer data,
signed or unsigned and
8-bit, 16-bit, 32-bit, or 64-bit.
<li>As an ASCII, or plain-text, file containing text data.
(This feature is not implemented in HDF5 Release 1.6.)
</ul>
Each input file, <code><i>infile</i></code>,
contains a single <em>n</em>-dimensional
array of values of one of the above types expressed
in the order of fastest-changing dimensions first.
<p>
Floating point data in an ASCII input file must be
expressed in the fixed floating form (e.g., 323.56)
<code>h5import</code> is designed to accept scientific notation
(e.g., 3.23E+02) in an ASCII, but that is not implemented in HDF5 release 1.6.
<p>
Each input file can be associated with options specifying
the datatype and storage properties.
These options can be specified either as
<em>command line arguments</em>
or in a <em>configuration file</em>.
Note that exactly one of these approaches must be used with a
single input file.
<p>
Command line arguments, best used with simple input files,
can be used to specify
the class, size, dimensions of the input data and
a path identifying the output dataset.
<p>
The recommended means of specifying input data options
is in a configuration file; this is also the only means of
specifying advanced storage features.
See further discussion in "The configuration file" below.
<p>
The only required option for input data is dimension sizes;
defaults are available for all others.
<p>
<code>h5import</code> will accept up to 30 input files in a single call.
Other considerations, such as the maximum length of a command line,
may impose a more stringent limitation.
<p>
<b>Output data and options:</b><br>
The name of the output file is specified following
the <code>-o</code> or <code>-output</code> option
in <code><i>outfile</i></code>.
The data from each input file is stored as a separate dataset
in this output file.
<code><i>outfile</i></code> may be an existing file.
If it does not yet exist, <code>h5import</code> will create it.
<p>
Output dataset information and storage properties can be
specified only by means of a configuration file.
<table width=100% border=0>
<tr valign=top align=left><td width=30> </td><td>
Dataset path
</td><td>If the groups in the path leading to the dataset
do not exist, <code>h5import</code> will create them.<br>
If no group is specified, the dataset will be created
as a member of the root group.<br>
If no dataset name is specified, the default name is
<code>dataset1</code> for the first input dataset,
<code>dataset2</code> for the second input dataset,
<code>dataset3</code> for the third input dataset,
etc.<br>
<code>h5import</code> does not overwrite a pre-existing
dataset of the specified or default name.
When an existing dataset of a conflicting name is
encountered, <code>h5import</code> quits with an error;
the current input file and any subsequent input files
are not processed.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Output type
</td><td>Datatype parameters for output data
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Output data class
</td><td>Signed or unsigned integer or floating point
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Output data size
</td><td>8-, 16-, 32-, or 64-bit integer<br>
32- or 64-bit floating point
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Output architecture
</td><td><code>IEEE</code><br>
<code>STD</code><br>
<code>NATIVE</code> (Default)<br>
Other architectures are included in the <code>h5import</code> design
but are not implemented in this release.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Output byte order
</td><td>Little- or big-endian.<br>
Relevant only if output architecture
is <code>IEEE</code>, <code>UNIX</code>, or <code>STD</code>;
fixed for other architectures.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Dataset layout and storage <br>
properties
</td><td>Denote how raw data is to be organized on the disk.
If none of the following are specified,
the default configuration is contiguous layout and with no compression.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Layout
</td><td>Contiguous (Default)<br>
Chunked
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
External storage
</td><td>Allows raw data to be stored in a non-HDF5 file or in an
external HDF5 file.<br>
Requires contiguous layout.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Compressed
</td><td>Sets the type of compression and the
level to which the dataset must be compressed.<br>
Requires chunked layout.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Extendable
</td><td>Allows the dimensions of the dataset increase over time
and/or to be unlimited.<br>
Requires chunked layout.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
Compressed and<br>
extendable
</td><td>Requires chunked layout.
</td></tr>
<tr valign=top align=left><td width=30> </td><td>
</td><td>
</td></tr>
</table>
<p>
<p>
<b>Command-line arguments:</b><br>
The <code>h5import</code> syntax for the command-line arguments,
<code><em>in_options</em></code>, is as follows:
<table width=100% border=0>
<tr><td> </td><td>
<code>h5import <em>infile</em> -d <em>dim_list</em>
[-p <em>pathname</em>]
[-t <em>input_class</em>]
[-s <em>input_size</em>]
[<em>infile</em> ...]
-o <em>outfile</em></code><br>
or<br>
<code>h5import <em>infile</em> -dims <em>dim_list</em>
[-path <em>pathname</em>]
[-type <em>input_class</em>]
[-size <em>input_size</em>]
[<em>infile</em> ...]
-outfile <em>outfile</em></code><br>
or<br>
<code>h5import <em>infile</em> -c <em>config_file</em>
[<em>infile</em> ...]
-outfile <em>outfile</em></code>
</td></tr>
</table>
Note the following:
If the <code>-c <em>config_file</em></code> option is used with
an input file, no other argument can be used with that input file.
If the <code>-c <em>config_file</em></code> option is not used with
an input data file, the <code>-d <em>dim_list</em></code> argument
(or <code>-dims <em>dim_list</em></code>)
must be used and any combination of the remaining options may be used.
Any arguments used must appear in <em>exactly</em> the order used
in the syntax declarations immediately above.
<p>
<b>The configuration file:</b><br>
A configuration file is specified with the
<code>-c <em>config_file</em></code> option:
<table border=0>
<tr><td> </td><td>
<code>h5import <em>infile</em> -c <em>config_file</em>
[<em>infile</em> -c <em>config_file2</em> ...]
-outfile <em>outfile</em></code>
</td></tr>
</table>
<p>
The configuration file is an ASCII file and must be
organized as "Configuration_Keyword Value" pairs,
with one pair on each line.
For example, the line indicating that
the input data class (configuration keyword <code>INPUT-CLASS</code>)
is floating point in a text file (value <code>TEXTFP</code>)
would appear as follows:<br>
<code> INPUT-CLASS TEXTFP</code>
<p>
A configuration file may have the following keywords each
followed by one of the following defined values.
One entry for each of the first two keywords,
<code>RANK</code> and <code>DIMENSION-SIZES</code>,
is required; all other keywords are optional.
<p>
<table width=100% border=0>
<tr align=left><th valign=top align=left>
<hr>Keyword <br><code> </code>Value
</th><th valign=top align=left><hr>Description
</th></tr>
<tr valign=top align=left><td>
<hr><code>RANK </code>
</td><td><hr>The number of dimensions in the dataset. (Required)
</td></tr>
<tr valign=top align=left><td>
<code> <em>rank</em></code>
</td><td>An integer specifying the number of dimensions in the dataset.<br>
Example: <code> 4 </code> for a 4-dimensional dataset.
</td></tr>
<tr valign=top align=left><td>
<hr><code>DIMENSION-SIZES</code>
</td><td><hr>Sizes of the dataset dimensions. (Required)
</td></tr>
<tr valign=top align=left><td>
<code> <em>dim_sizes</em></code>
</td><td>A string of space-separated integers
specifying the sizes of the dimensions in the dataset.
The number of sizes in this entry must match the value in
the <code>RANK</code> entry.
The fastest-changing dimension must be listed first.<br>
Example: <code> 4 3 4 38 </code> for a 38x4x3x4 dataset.
</td></tr>
<!-- NEW PAGE -->
<tr valign=top align=left><td>
<hr><code>PATH</code>
</td><td><hr>Path of the output dataset.
</td></tr>
<tr valign=top align=left><td>
<code> <em>path</em></code>
</td><td>The full HDF5 pathname identifying the output dataset
relative to the root group within the output file.<br>
I.e., <code><em>path</em></code> is a string consisting of
optional group names, each followed by a slash,
and ending with a dataset name.
If the groups in the path do no exist, they will be
created.<br>
If <code>PATH</code> is not specified, the output dataset
is stored as a member of the root group and the
default dataset name is
<code>dataset1</code> for the first input dataset,
<code>dataset2</code> for the second input dataset,
<code>dataset3</code> for the third input dataset, etc.<br>
Note that <code>h5import</code> does not overwrite a
pre-existing dataset of the specified or default name.
When an existing dataset of a conflicting name is
encountered, <code>h5import</code> quits with an error;
the current input file and any subsequent input files
are not processed.<br>
Example: The configuration file entry
<table border=0>
<tr><td> </td><td>
<code>PATH grp1/grp2/dataset1</code>
</td></tr>
</table>
indicates that the output dataset <code>dataset1</code> will
be written in the group <code>grp2/</code> which is in
the group <code>grp1/</code>,
a member of the root group in the output file.
</td></tr>
<tr valign=top align=left><td>
<hr><code>INPUT-CLASS </code>
</td><td><hr>A string denoting the type of input data.
</td></tr>
<tr valign=top align=left><td>
<code> TEXTIN</code>
</td><td>Input is signed integer data in an ASCII file.
</td></tr>
<tr valign=top align=left><td>
<code> TEXTUIN</code>
</td><td>Input is unsigned integer data in an ASCII file.
</td></tr>
<tr valign=top align=left><td>
<code> TEXTFP</code>
</td><td>Input is floating point data in fixed notation (e.g., 325.34)
in an ASCII file.
</td></tr>
<tr valign=top align=left><td>
<code> TEXTFPE</code>
</td><td>Input is floating point data in scientific notation (e.g., 3.2534E+02)
in an ASCII file.<br>
(Not implemented in this release.)
</td></tr>
<tr valign=top align=left><td>
<code> IN</code>
</td><td>Input is signed integer data in a binary file.
</td></tr>
<tr valign=top align=left><td>
<code> UIN</code>
</td><td>Input is unsigned integer data in a binary file.
</td></tr>
<tr valign=top align=left><td>
<code> FP</code>
</td><td>Input is floating point data in a binary file. (Default)
</td></tr>
<tr valign=top align=left><td>
<code> STR</code>
</td><td>Input is character data in an ASCII file.
With this value, the configuration keywords
<code>RANK</code>, <code>DIMENSION-SIZES</code>,
<code>OUTPUT-CLASS</code>, <code>OUTPUT-SIZE</code>,
<code>OUTPUT-ARCHITECTURE</code>, and <code>OUTPUT-BYTE-ORDER</code>
will be ignored.<br>
(Not implemented in this release.)
</td></tr>
<tr valign=top align=left><td>
<hr><code>INPUT-SIZE</code>
</td><td><hr>An integer denoting the size of the input data, in bits.
</td></tr>
<tr valign=top align=left><td>
<code> 8</code><br>
<code> 16</code><br>
<code> 32</code><br>
<code> 64</code>
</td><td>For signed and unsigned integer data:
<code>TEXTIN</code>, <code>TEXTUIN</code>,
<code>IN</code>, or <code>UIN</code>.
(Default: <code> 32</code>)
</td></tr>
<tr valign=top align=left><td>
<code> 32</code><br>
<code> 64</code>
</td><td>For floating point data:
<code>TEXTFP</code>, <code>TEXTFPE</code>,
or <code>FP</code>.
(Default: <code> 32</code>)
</td></tr>
<!-- NEW PAGE -->
<tr valign=top align=left><td>
<hr><code>OUTPUT-CLASS </code>
</td><td><hr>A string denoting the type of output data.
</td></tr>
<tr valign=top align=left><td>
<code> IN</code>
</td><td>Output is signed integer data.<br>
(Default if <code>INPUT-CLASS</code> is
<code>IN</code> or <code>TEXTIN</code>)
</td></tr>
<tr valign=top align=left><td>
<code> UIN</code>
</td><td>Output is unsigned integer data.<br>
(Default if <code>INPUT-CLASS</code> is
<code>UIN</code> or <code>TEXTUIN</code>)
</td></tr>
<tr valign=top align=left><td>
<code> FP</code>
</td><td>Output is floating point data.<br>
(Default if <code>INPUT-CLASS</code> is not specified or is
<code>FP</code>, <code>TEXTFP</code>, or <code>TEXTFPE</code>)
</td></tr>
<tr valign=top align=left><td>
<code> STR</code>
</td><td>Output is character data,
to be written as a 1-dimensional array of strings.<br>
(Default if <code>INPUT-CLASS</code> is <code>STR</code>)<br>
(Not implemented in this release.)
</td></tr>
<tr valign=top align=left><td>
<hr><code>OUTPUT-SIZE</code>
</td><td><hr>An integer denoting the size of the output data, in bits.
</td></tr>
<tr valign=top align=left><td>
<code> 8</code><br>
<code> 16</code><br>
<code> 32</code><br>
<code> 64</code>
</td><td>For signed and unsigned integer data:
<code>IN</code> or <code>UIN</code>.
(Default: Same as <code>INPUT-SIZE</code>, else <code> 32</code>)
</td></tr>
<tr valign=top align=left><td>
<code> 32</code><br>
<code> 64</code>
</td><td>For floating point data:
<code>FP</code>.
(Default: Same as <code>INPUT-SIZE</code>, else <code> 32</code>)
</td></tr>
<tr valign=top align=left><td>
<hr><code>OUTPUT-ARCHITECTURE</code>
</td><td><hr>A string denoting the type of output architecture.
</td></tr>
<tr valign=top align=left><td>
<code> NATIVE</code><br>
<code> STD</code><br>
<code> IEEE</code><br>
<code> INTEL</code> *<br>
<code> CRAY</code> *<br>
<code> MIPS</code> *<br>
<code> ALPHA</code> *<br>
<code> UNIX</code> *
</td><td>See the "Predefined Atomic Types" section
in the "HDF5 Datatypes" chapter
of the <cite>HDF5 User's Guide</cite>
for a discussion of these architectures.<br>
Values marked with an asterisk (*) are not implemented in this release.<br>
(Default: <code>NATIVE</code>)
</td></tr>
<tr valign=top align=left><td>
<hr><code>OUTPUT-BYTE-ORDER</code>
</td><td><hr>A string denoting the output byte order.
This entry is ignored if the <code>OUTPUT-ARCHITECTURE</code>
is not specified or if it is not specified as <code>IEEE</code>,
<code>UNIX</code>, or <code>STD</code>.
</td></tr>
<tr valign=top align=left><td>
<code> BE</code>
</td><td>Big-endian. (Default)
</td></tr>
<tr valign=top align=left><td>
<code> LE</code>
</td><td>Little-endian.
</td></tr>
<!-- NEW PAGE -->
<tr valign=top align=left><td colspan="2">
<hr>The following options are disabled by default, making
the default storage properties no chunking, no compression,
no external storage, and no extensible dimensions.
</td></tr>
<tr valign=top align=left><td>
<hr><code>CHUNKED-DIMENSION-SIZES</code><br>
</td><td><hr>Dimension sizes of the chunk for chunked output data.
</td></tr>
<tr valign=top align=left><td>
<code> <em>chunk_dims</em></code>
</td><td>A string of space-separated integers specifying the
dimension sizes of the chunk for chunked output data.
The number of dimensions must correspond to the value
of <code>RANK</code>.<br>
The presence of this field indicates that the
output dataset is to be stored in chunked layout;
if this configuration field is absent,
the dataset will be stored in contiguous layout.
</td></tr>
<tr valign=top align=left><td>
<hr><code>COMPRESSION-TYPE</code>
</td><td><hr>Type of compression to be used with chunked storage.
Requires that <code>CHUNKED-DIMENSION-SIZES</code>
be specified.
</td></tr>
<tr valign=top align=left><td>
<code> GZIP</code>
</td><td>Gzip compression.<br>
Other compression algorithms are not implemented
in this release of <code>h5import</code>.
</td></tr>
<tr valign=top align=left><td>
<hr><code>COMPRESSION-PARAM</code>
</td><td><hr>Compression level.
Required if <code>COMPRESSION-TYPE</code> is specified.
</td></tr>
<tr valign=top align=left><td>
<code> 1</code> through <code>9</code>
</td><td>Gzip compression levels:
<code>1</code> will result in the fastest compression
while <code>9</code> will result in the
best compression ratio.<br>
(Default: 6. The default gzip compression level is 6;
not all compression methods will have a default level.)
</td></tr>
<tr valign=top align=left><td>
<hr><code>EXTERNAL-STORAGE</code>
</td><td><hr>Name of an external file in which to create the output dataset.
Cannot be used with <code>CHUNKED-DIMENSIONS-SIZES</code>,
<code>COMPRESSION-TYPE</code>, OR <code>MAXIMUM-DIMENSIONS</code>.
</td></tr>
<tr valign=top align=left><td>
<code> <i>external_file</i> </code>
<!-- THE EXTRA NON-BREAKING SPACES AT THE END OF THE PRECEDING LINE -->
<!-- ARE PADDING SPACES TO ENSURE THE PROPER FORMATTING OF THIS TABLE. -->
<!-- DO NOT REMOVE THEM!!!!!!!!!!!!! -->
</td><td>A string specifying the name of an external file.
</td></tr>
<tr valign=top align=left><td>
<hr><code>MAXIMUM-DIMENSIONS</code>
</td><td><hr>Maximum sizes of all dimensions.
Requires that <code>CHUNKED-DIMENSION-SIZES</code> be specified.
</td></tr>
<tr valign=top align=left><td>
<code> <em>max_dims</em></code>
</td><td>A string of space-separated integers specifying the
maximum size of each dimension of the output dataset.
A value of <code>-1</code> for any dimension implies
unlimited size for that particular dimension.<br>
The number of dimensions must correspond to the value
of <code>RANK</code>.<br>
</td></tr>
<tr valign=top align=left><td><hr></td><td><hr></td></tr>
</table>
<p>
<!-- NEW PAGE -->
<b>The <code>help</code> option:</b><br>
The help option, expressed as one of
<table width=100% border=0>
<tr><td> </td><td>
<code>h5import -h</code><br>
or<br>
<code>h5import -help</code><br>
</td></tr>
<tr><td colspan="2">prints the <code>h5import</code> usage summary</td></tr>
<tr><td> </td><td>
<code>
h5import -h[elp], OR<br>
h5import <infile> <options>
[<infile> <options>...]
-o[utfile] <outfile></code>
</td></tr>
<tr><td colspan="2">then exits.</td></tr>
</table>
<p>
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>infile(s)</code>
<dd>Name of the Input file(s).
<dt><code>in_options</code>
<dd>Input options. Note that while only the <code>-dims</code> argument
is required, arguments must used in the order in which they are listed below.
<dl>
<dt><code>-d <em>dim_list</em></code>
<dt><code>-dims <em>dim_list</em></code>
<dd>Input data dimensions.
<code><em>dim_list</em></code> is a string of
comma-separated numbers with no spaces
describing the dimensions of the input data.
For example, a 50 x 100 2-dimensional array would be
specified as <code>-dims 50,100</code>.<br>
Required argument: if no configuration file is used,
this command-line argument is mandatory.
<dt><code>-p <em>pathname</em></code>
<dt><code>-pathname <em>pathname</em></code>
<dd><code><em>pathname</em></code> is a string consisting of
one or more strings separated by slashes (<code>/</code>)
specifying the path of the dataset in the output file.
If the groups in the path do no exist, they will be
created.<br>
Optional argument: if not specified,
the default path is
<code>dataset1</code> for the first input dataset,
<code>dataset2</code> for the second input dataset,
<code>dataset3</code> for the third input dataset,
etc.<br>
<code>h5import</code> does not overwrite a pre-existing
dataset of the specified or default name.
When an existing dataset of a conflicting name is
encountered, <code>h5import</code> quits with an error;
the current input file and any subsequent input files
are not processed.
<dt><code>-t <em>input_class</em></code>
<dt><code>-type <em>input_class</em></code>
<dd><code><em>input_class</em></code> specifies the class of the
input data and determines the class of the output data.<br>
Valid values are as defined in the Keyword/Values table
in the section "The configuration file" above.<br>
Optional argument: if not specified,
the default value is <code>FP</code>.
<dt><code>-s <em>input_size</em></code>
<dt><code>-size <em>input_size</em></code>
<dd><code><em>input_size</em></code> specifies the size in bits
of the input data and determines the size of the output data.<br>
Valid values for signed or unsigned integers are
<code>8</code>, <code>16</code>, <code>32</code>, and <code>64</code>.<br>
Valid values for floating point data are
<code>32</code> and <code>64</code>.<br>
Optional argument: if not specified,
the default value is <code>32</code>.
<dt><code>-c <em>config_file</em></code>
<dd><code><em>config_file</em></code> specifies a
configuration file.<br>
This argument replaces all other arguments except
<code><em>infile</em></code> and
<code>-o <em>outfile</em></code>
</dl>
<dt><code>outfile</code>
<dd>Name of the HDF5 output file.
</dl>
<dt><strong>Examples:</strong>
<dd><b>Using command-line arguments:</b>
<table width=100% border=0>
<tr><td colspan=2>
<code>h5import infile -dims 2,3,4 -type TEXTIN -size 32 -o out1</code>
</td></tr><tr><td> </td><td>
This command creates a file <code>out1</code> containing
a single 2x3x4 32-bit integer dataset.
Since no pathname is specified, the dataset is stored
in <code>out1</code> as <code>/dataset1</code>.
</td></tr><tr><td colspan=2>
<code>h5import infile -dims 20,50 -path bin1/dset1 -type FP -size 64 -o out2</code>
</td></tr><tr><td> </td><td>
This command creates a file <code>out2</code> containing
a single a 20x50 64-bit floating point dataset.
The dataset is stored in <code>out2</code> as <code>/bin1/dset1</code>.
</td></tr>
</table>
<dd><b>Sample configuration files:</b><br>
The following configuration file specifies the following:<br>
– The input data is a 5x2x4 floating point array in
an ASCII file.<br>
– The output dataset will be saved in chunked layout,
with chunk dimension sizes of 2x2x2.<br>
– The output datatype will be 64-bit floating point,
little-endian, IEEE.<br>
– The output dataset will be stored in
<code><em>outfile</em></code>
at <code>/work/h5/pkamat/First-set</code>.<br>
– The maximum dimension sizes of the output dataset
will be 8x8x(unlimited).
<pre>
PATH work/h5/pkamat/First-set
INPUT-CLASS TEXTFP
RANK 3
DIMENSION-SIZES 5 2 4
OUTPUT-CLASS FP
OUTPUT-SIZE 64
OUTPUT-ARCHITECTURE IEEE
OUTPUT-BYTE-ORDER LE
CHUNKED-DIMENSION-SIZES 2 2 2
MAXIMUM-DIMENSIONS 8 8 -1
</pre>
The next configuration file specifies the following:<br>
– The input data is a 6x3x5x2x4 integer array in
a binary file.<br>
– The output dataset will be saved in chunked layout,
with chunk dimension sizes of 2x2x2x2x2.<br>
– The output datatype will be 32-bit integer in
<code>NATIVE</code> format
(as the output architecture is not specified).<br>
– The output dataset will be compressed using Gzip compression
with a compression level of 7.<br>
– The output dataset will be stored in
<code><em>outfile</em></code> at <code>/Second-set</code>.
<pre>
PATH Second-set
INPUT-CLASS IN
RANK 5
DIMENSION-SIZES 6 3 5 2 4
OUTPUT-CLASS IN
OUTPUT-SIZE 32
CHUNKED-DIMENSION-SIZES 2 2 2 2 2
COMPRESSION-TYPE GZIP
COMPRESSION-PARAM 7
</pre>
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<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
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<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-GIF2H5">gif2h5</a>
<dt><strong>Syntax:</strong>
<dd><code>gif2h5</code>
<em>gif_file</em> <em>h5_file</em>
<dt><strong>Purpose:</strong>
<dd>Converts a GIF file to an HDF5 file.
<dt><strong>Description:</strong>
<dd><code>gif2h5</code> accepts as input the GIF file <em>gif_file</em>
and produces the HDF5 file <em>h5_file</em> as output.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><em>gif_file</em>
<dd>The name of the input GIF file
<dt><em>h5_file</em>
<dd>The name of the output HDF5 file
</dl>
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<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
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<!-- HEADER RIGHT "h52gif" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H52GIF">h52gif</a>
<dt><strong>Syntax:</strong>
<dd><code>h52gif</code>
<em>h5_file</em> <em>gif_file</em>
<code>-i</code> <em>h5_image</em>
<code>[-p</code> <em>h5_palette</em><code>]</code>
<dt><strong>Purpose:</strong>
<dd>Converts an HDF5 file to a GIF file.
<dt><strong>Description:</strong>
<dd><code>h52gif</code> accepts as input the HDF5 file <em>h5_file</em>
and the names of images and associated palettes within that file
as input and produces the GIF file <em>gif_file</em>,
containing those images, as output.
<p>
<code>h52gif</code> expects <em>at least</em>
one <em>h5_image</em>.
You may repeat
<br>
<code>-i</code> <em>h5_image</em>
<code>[-p</code> <em>h5_palette</em><code>]</code>
<br>
up to 50 times, for a maximum of 50 images.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><em>h5_file</em>
<dd>The name of the input HDF5 file
<dt><em>gif_file</em>
<dd>The name of the output GIF file
<dt><code>-i</code> <em>h5_image</em>
<dd>Image option, specifying the name of an HDF5 image or
dataset containing an image to be converted
<dt><code>-p</code> <em>h5_palette</em>
<dd>Palette option, specifying the name of an HDF5 dataset
containing a palette to be used in an image conversion
</dl>
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<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
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</dl>
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<!-- HEADER RIGHT "h5toh4" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H5toh4">h5toh4</a>
<dt><strong>Syntax:</strong>
<dd><code>h5toh4 -h</code><br>
<code>h5toh4 </code><em>
h5file
h4file</em><br>
<code>h5toh4 </code><em>
h5file</em><br>
<code>h5toh4 -m </code><em>
h5file1
h5file2
h5file3</em> ...
<dt><strong>Purpose:</strong>
<dd>Converts an HDF5 file into an HDF4 file.
<dt><strong>Description:</strong>
<dd><code>h5toh4</code> is an HDF5 utility which reads
an HDF5 file, <em>h5file</em>, and converts all
supported objects and pathways to produce an HDF4 file,
<em>h4file</em>. If <em>h4file</em> already exists,
it will be replaced.
<p>
If only one file name is given, the name must end in
<code>.h5</code> and is assumed to represent the
HDF5 input file. <code>h5toh4</code> replaces the
<code>.h5</code> suffix with <code>.hdf</code> to form
the name of the resulting HDF4 file and proceeds as above.
If a file with the name of the intended HDF4 file already
exists, <code>h5toh4</code> exits with an error without
changing the contents of any file.
<p>
The <code>-m</code> option allows multiple HDF5 file
arguments. Each file name is treated the same as the
single file name case above.
<p>
The <code>-h</code> option causes the following
syntax summary to be displayed:
<pre> h5toh4 file.h5 file.hdf
h5toh4 file.h5
h5toh4 -m file1.h5 file2.h5 ...</pre>
<p>
The following HDF5 objects occurring in an HDF5 file are
converted to HDF4 objects in the HDF4 file:
<ul>
<li>HDF5 group objects are converted into HDF4 Vgroup
objects. HDF5 hard links and soft links pointing to
objects are converted to HDF4 Vgroup references.
<li>HDF5 dataset objects of integer datatype are
converted into HDF4 SDS objects. These datasets
may have up to 32 fixed dimensions.
The slowest varying dimension may be extendable.
8-bit, 16-bit, and 32-bit integer datatypes are
supported.
<li>HDF5 dataset objects of floating point datatype
are converted into HDF4 SDS objects.
These datasets may have up to 32 fixed dimensions.
The slowest varying dimension may be extendable.
32-bit and 64-bit floating point datatypes are
supported.
<li>HDF5 dataset objects of single dimension and
compound datatype are converted into HDF4 Vdata
objects. The length of that single dimension may
be fixed or extendable. The members of the
compound datatype are constrained to be no more
than rank 4.
<li>HDF5 dataset objects of single dimension and fixed length string
datatype are converted into HDF4 Vdata objects. The HDF4 Vdata
is a single field whose order is the length of the HDF5 string
type. The number of records of the Vdata is the length of the
single dimension which may be fixed or extendable.
</ul>
Other objects are not converted and are not recorded
in the resulting <em>h4file</em>.
<p>
Attributes associated with any of the supported HDF5
objects are carried over to the HDF4 objects.
Attributes may be of integer, floating point, or fixed length
string datatype and they may have up to 32 fixed dimensions.
<p>
All datatypes are converted to big-endian.
Floating point datatypes are converted to IEEE format.
<dt><strong>Note:</strong>
<dl>The <code>h5toh4</code> and <code>h4toh5</code> utilities
are no longer part of the HDF5 product;
they are distributed separately through the page
<a href="http://hdf.ncsa.uiuc.edu/h4toh5/">
Converting between HDF (4.x) and HDF5</a>.
</p>
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code>
<dd>Displays a syntax summary.
<dt><code>-m</code>
<dd>Converts multiple HDF5 files to multiple HDF4 files.
<dt><em>h5file</em>
<dd>The HDF5 file to be converted.
<dt><em>h4file</em>
<dd>The HDF4 file to be created.
</dl>
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<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
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<!-- HEADER RIGHT "h4toh5" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H4toh5">h4toh5</a>
<dt><strong>Syntax:</strong>
<dd><code>h4toh5 -h</code><br>
<code>h4toh5 </code><em>
h4file
h5file</em><br>
<code>h4toh5 </code><em>
h4file</em><br>
<!-- currently no -m option
<code>h4toh5 -m </code><em>
h4file1
h4file2
h4file3</em> ...
-->
<dt><strong>Purpose:</strong>
<dd>Converts an HDF4 file to an HDF5 file.
<dt><strong>Description:</strong>
<dd><code>h4toh5</code> is a file conversion utility that reads
an HDF4 file, <em>h4file</em> (<code>input.hdf</code> for example),
and writes an HDF5 file, <em>h5file</em> (<code>output.h5</code>
for example), containing the same data.
<p>
If no output file <em>h5file</em> is specified,
<code>h4toh5</code> uses the input filename to designate
the output file, replacing the extension <code>.hdf</code>
with <code>.h5</code>.
For example, if the input file <code>scheme3.hdf</code> is
specified with no output filename, <code>h4toh5</code> will
name the output file <code>scheme3.h5</code>.
<p>
<!-- currently no -m option
The <code>-m</code> option allows multiple HDF5 file
arguments. Each file name is treated the same as the
single file name case above.
<p>
-->
The <code>-h</code> option causes a syntax summary
similar to the following to be displayed:
<pre> h4toh5 inputfile.hdf outputfile.h5
h4toh5 inputfile.hdf <!-- currently no -m option
h4toh5 -m inputfile1.hdf inputfile2.hdf ... --> </pre>
<p>
Each object in the HDF4 file is converted to an equivalent
HDF5 object, according to the mapping described in
<a href="ADGuide/H4toH5Mapping.pdf" target=ExternalWinA>
<cite>Mapping HDF4 Objects to HDF5 Objects</cite></a>.
(If this mapping changes between HDF5 Library releases, a more up-to-date
version may be available at
<a href="http://hdf.ncsa.uiuc.edu/HDF5/papers/h4toh5/H4-to-H5MappingGuidelines.pdf" target=ExternalWinB>
<cite>Mapping HDF4 Objects to HDF5 Objects</cite> on the HDF FTP server</a>.)
<p>
In this initial version, <code>h4toh5</code> converts the following
HDF4 objects:
<center>
<table width=75% border=0>
<tr><th width=40% valign=top align=left>
HDF4 Object
</td><th width=60% valign=top align=left>
Resulting HDF5 Object
</td></tr>
<tr><td width=40% valign=top align=left>
SDS
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
<tr><td width=40% valign=top align=left>
GR, RI8, and RI24 image
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
<tr><td width=40% valign=top align=left>
Vdata
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
<tr><td width=40% valign=top align=left>
Vgroup
</td><td width=60% valign=top align=left>
Group
</td></tr>
<tr><td width=40% valign=top align=left>
Annotation
</td><td width=60% valign=top align=left>
Attribute
</td></tr>
<tr><td width=40% valign=top align=left>
Palette
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
</table>
</center>
<dt><strong>Note:</strong>
<dl>The <code>h4toh5</code> and <code>h5toh4</code> utilities
are no longer part of the HDF5 product;
they are distributed separately through the page
<a href="http://hdf.ncsa.uiuc.edu/h4toh5/">
Converting between HDF (4.x) and HDF5</a>.
</p>
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code>
<dd>Displays a syntax summary.
<!-- currently no -m option
<dt><code>-m</code>
<dd>Converts multiple HDF4 files to multiple HDF5 files.
-->
<dt><em>h4file</em>
<dd>The HDF4 file to be converted.
<dt><em>h5file</em>
<dd>The HDF5 file to be created.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5perf" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Perf">h5perf</a>
<dt><strong>Syntax:</strong>
<dd><code>h5perf </code>[<code>-h </code>|<code> --help</code>]
<dd><code>h5perf </code>[<em>options</em>]
<!--
[<code>-a</code> <em>size</em> | <code>--align=</code><em>size</em>]
[<code>-A</code> <em>api_list</em> | <code>--api=</code><em>api_list</em>]
[<code>-B</code> <em>size</em> | <code>--block-size=</code><em>size</em>]
[<code>-c</code> | <code>--chunk</code>]
[<code>-C</code> | <code>--collective</code>]
[<code>-d</code> <em>N</em> | <code>--num-dsets</code><em>N</em>]
[<code>-D</code> <em>debug_flags</em> | <code>--debug=</code><em>debug_flags</em>]
[<code>-e</code> <em>size</em> | <code>--num-bytes=</code><em>size</em>]
[<code>-F</code> <em>N</em> | <code>--num-files=</code><em>N</em>]
[<code>-i</code> <em>N</em> | <code>--num-iterations=</code><em>N</em>]
[<code>-I</code> | <code>--interleaved</code>]
[<code>-m</code> | <code>--mpi-posix</code>]
[<code>-n</code> | <code>--no-fill</code>]
[<code>-o</code> <em>file</em> | <code> --output=</code><em>file</em>]
[<code>-p</code> <em>N</em> | <code>--min-num-processes=</code><em>N</em>]
[<code>-P</code> <em>N</em> | <code>--max-num-processes=</code><em>N</em>]
[<code>-T</code> <em>size</em> | <code>--threshold=</code><em>size</em>]
[<code>-w</code> | <code>--write-only</code>]
[<code>-x</code> <em>size</em> | <code>--min-xfer-size=</code><em>size</em>]
[<code>-X</code> <em>size</em> | <code>--max-xfer-size=</code>size<em></em>]
-->
<dt><strong>Purpose:</strong>
<dd>Tests Parallel HDF5 performance.
<dt><strong>Description:</strong>
<dd><code>h5perf</code> provides tools for testing the performance
of the Parallel HDF5 library.
<p>
The following environment variables have the following
effects on <code>H5perf</code> behavior:
<table border=0>
<tr align="left" valign="top"><td> </td><td>
<code>HDF5_NOCLEANUP</code></td><td>
If set, <code>h5perf</code> does not remove data files.
(Default: Remove)</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>HDF5_MPI_INFO</code></td><td>
Must be set to a string containing a list of semi-colon separated
key=value pairs for the MPI <code>INFO</code> object.<br>
Example:</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>HDF5_PARAPREFIX </code></td><td>
Sets the prefix for parallel output data files.</td></tr>
</table>
<dt><strong>Options and Parameters:</strong>
<dl>
<dt>These terms are used as follows in this section:
<table border="0">
<tr align="left" valign="top"><td> </td><td>
<em>file </em></td><td>
A filename</td></tr>
<tr align="left" valign="top"><td> </td><td>
<em>size</em></td><td>
A size specifier, expressed as an integer greater than or equal
to 0 (zero) followed by a size indicator:<br>
<code>K </code> for kilobytes (1024 bytes)<br>
<code>M </code> for megabytes (1048576 bytes)<br>
<code>G </code> for gigabytes (1073741824 bytes)<br>
Example: <code>37M</code> specifies 37 megabytes or 38797312 bytes.</td></tr>
<tr align="left" valign="top"><td> </td><td>
<em>N</em></td><td>
An integer greater than or equal to 0 (zero)</td></tr>
</table>
<p>
<dt><code>-h</code>, <code>--help</code>
<dd>Prints a usage message and exits.
<dt><code>-a</code> <em>size</em>, <code>--align=</code><em>size</em>
<dd>Specifies the alignment of objects in the HDF5 file.
(Default: 1)
<dt><code>-A</code> <em>api_list</em>, <code>--api=</code><em>api_list</em>
<dd>Specifies which APIs to test.
<em>api_list</em> is a comma-separated list with the
following valid values:
<table border="0">
<tr align="left" valign="top"><td> </td><td>
<code>phdf5 </code></td><td>Parallel HDF5</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>mpiio</code></td><td>MPI-I/O</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>posix</code></td><td>POSIX</td></tr>
</table>
(Default: All APIs)<br><br>
Example, <code>--api=mpiio,phdf5</code> specifies that the
MPI I/O and parallel HDf5 APIs are to be monitored.<br><br>
<dt><code>-B</code> <em>size</em>, <code>--block-size=</code><em>size</em>
<dd>Specifies the block size within the transfer buffer.
(Default: 128K)<br><br>
Block size versus transfer buffer size:
The <em>transfer buffer size</em> is the size of a
buffer in memory. The data in that buffer is broken
into <em>block size</em> pieces and written to the
file.<br><br>
<!-- NEW PAGE -->
Transfer block size is set by the
<code>-x</code> (or <code>--min-xfer-size</code>) and
<code>-X</code> (or <code>--max-xfer-size</code>)
options.<br>
The pattern in which the blocks
are written to the file is described in the discussion
of the <code>-I</code> (or <code>--interleaved</code>)
option.<br><br>
<dt><code>-c</code>, <code>--chunk</code>
<dd>Creates HDF5 datasets in chunked layout.
(Default: Off)
<dt><code>-C</code>, <code>--collective</code>
<dd>Use collective I/O for the MPI I/O and Parallel HDF5 APIs.<br>
(Default: Off, i.e., independent I/O)<br><br>
If this option is set and the MPI-I/O and PHDF5 APIs
are in use, all the blocks in each transfer buffer
will be written at once with an MPI derived type.
<br><br>
<dt><code>-d</code> <em>N</em>, <code>--num-dsets</code><em>N</em>
<dd>Sets the number of datasets per file.
(Default: <code>1</code>)
<dt><code>-D</code> <em>debug_flags</em>, <code>--debug=</code><em>debug_flags</em>
<dd>Sets the debugging level.
<em>debug_flags</em> is a comma-separated list of
debugging flags with the following valid values:
<table border="0">
<tr align="left" valign="top"><td> </td><td>
<code>1 </code></td><td>Minimal debugging</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>2</code></td><td>Moderate debugging (“not quite everything”)</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>3</code></td><td>Extensive debugging (“everything”)</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>4</code></td><td>All possible debugging (“the kitchen sink”)</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>r</code></td><td>Raw data I/O throughput information</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>t</code></td><td>Times, in additions to throughputs</td></tr>
<tr align="left" valign="top"><td> </td><td>
<code>v</code></td><td>Verify data correctness</td></tr>
</table>
(Default: No debugging)<br><br>
Example: <code>--debug=2,r,t</code> specifies to
run a moderate level of debugging
while collecting raw data I/O throughput information
and verifying the correctness of the data.<br><br>
<dt><code>-e</code> <em>size</em>, <code>--num-bytes=</code><em>size</em>
<dd>Specifies the number of bytes per process per dataset.
(Default: <code>256K</code>)
<dt><code>-F</code> <em>N</em>, <code>--num-files=</code><em>N</em>
<dd>Specifies the number of files.
(Default: <code>1</code>)
<dt><code>-i</code> <em>N</em>, <code>--num-iterations=</code><em>N</em>
<dd>Sets the number of iterations to perform.
(Default: <code>1</code>)
<dt><code>-I</code>, <code>--interleaved</code>
<dd>Sets interleaved block I/O.<br>
(Default: Contiguous block I/O)<br><br>
Interleaved vs. Contiguous blocks
in a parallel environment:<br>
When contiguous blocks are written to a dataset,
the dataset is divided into <em>m</em> regions,
where <em>m</em> is the number of processes writing
separate portions of the dataset. Each process
then writes data to its own region.
When interleaved blocks are written to a dataset,
space for the first block of the first process is
allocated in the dataset, then space is allocated
for the first block of the second process, etc.,
until space has been allocated for the first block
of each process. Space is then allocated for
the second block of the first process,
the second block of the second process, etc.<br><br>
For example, in the case of a 4 process run
with 1M bytes-per-process, 256K transfer buffer size,
and 64KB block size, 16 <em>contiguous</em> blocks
per process would be written to the file in the
manner<br>
<code> 1111111111111111222222222222222233333333333333334444444444444444</code><br>
while 16 interleaved blocks per process would be
written to the file as
<code> 1234123412341234123412341234123412341234123412341234123412341234</code><br>
If collective I/O is turned on, all of the four
blocks per transfer buffer will be written in
one collective I/O call.<br><br>
<dt><code>-m</code>, <code>--mpi-posix</code>
<dd>Sets use of MPI-posix driver for HDF5 I/O.
(Default: MPI-I/O driver)
<dt><code>-n</code>, <code>--no-fill</code>
<dd>Specifies to not write fill values to HDF5 datasets.
This option is supported only in HDF5 Release v1.6 or later.<br>
(Default: Off, i.e., write fill values)
<dt><code>-o</code> <em>file</em>, <code> --output=</code><em>file</em>
<dd>Sets the output file for raw data to <em>file</em>.
(Default: None)
<dt><code>-p</code> <em>N</em>, <code>--min-num-processes=</code><em>N</em>
<dd>Sets the minimum number of processes to be used.
(Default: <code>1</code>)
<dt><code>-P</code> <em>N</em>, <code>--max-num-processes=</code><em>N</em>
<dd>Sets the maximum number of processes to be used.<br>
(Default: All <code>MPI_COMM_WORLD</code>processes)
<dt><code>-T</code> <em>size</em>, <code>--threshold=</code><em>size</em>
<dd>Sets the threshold for alignment of objects in the HDF5 file.
(Default: <code>1</code>)
<dt><code>-w</code>, <code>--write-only</code>
<dd>Performs only write tests, not read tests.
(Default: Read and write tests)
<dt><code>-x</code> <em>size</em>, <code>--min-xfer-size=</code><em>size</em>
<dd>Sets the minimum transfer buffer size.
(Default: <code>128K</code>)
<dt><code>-X</code> <em>size</em>, <code>--max-xfer-size=</code>size<em></em>
<dd>Sets the maximum transfer buffer size.
(Default: <code>1M</code>)
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5jam/h5unjam" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Jam">h5jam/h5unjam</a>
<dt><strong>Syntax:</strong>
<dd><code>h5jam -u user_block -i in_file.h5 [-o out_file.h5] [--clobber]</code></dd>
<dd><code>h5jam -h</code></dd>
<dd> </dd>
<dd><code>h5unjam -i in_file.h5 </code><code>[-u user_block | --delete] [</code><code>-o out_file.h5]</code></dd>
<dd><code>h5unjam -h</code></dd>
<dt><strong>Purpose:</strong>
<dd>Add user block to front of an HDF5 file, to create a new concatenated
file.</dd>
<dd>Split user block and HDF5 file into two files, user block data and
HDF5 data.</dd>
<dt><strong>Description:</strong>
<dd><code>h5jam</code> concatenates a <code>user_block</code>
file and an HDF5 file to create an HDF5 file with a user block.
The user block can be either binary or text.
The output file is padded so that the HDF5 header begins on
byte 512, 1024, etc.. (See the HDF5 File Format.)
<p>If <code>out_file.h5</code> is given, a new file is created with the <code>user_block</code> followed by the contents of<code> in_file.h5. </code>In this case,<code><big> </big>infile.h5 </code>is unchanged.
<p>
If <code>out_file.h5</code> is not specified, the <code>user_block</code> is added to<code> in_file.h5</code>. </dd>
<p>
If in_file.h5 already has a user block, the contents of <code>user_block</code> will be added to the end of the existing user block, and hte file shifted to the next boundary. If <code>-clobber</code> is set, any existing user block will be overwritten.
<p><code>h5unjam</code><code></code> splits an HDF5 file, writing the
user block to a file or stdout and the HDF5 file to an HDF5 file with a header at byte
0 (i.e., with no user block).
<p>If <code>out_file.h5</code> is given, a new file is created with the<code></code><code> in_file.h5 </code>without <code></code>the user block.<code> </code>In this case,<code><big> </big>infile.h5 </code>is unchanged.
<p> If <code>out_file.h5</code> is not specified, the <code>user_block</code> is removed and <code>in_file.h5</code> is rewritten, starting at byte 0.
<p>
If <code>user_block</code> is set,the user block will be written to <code>user_block</code>. If <code>user_block</code> is not set, the user block (if any)<code></code> will be written to stdout. If <code>-delete</code> is selected, the user block will not be not written.</dd>
<dt><strong>Example Usage</strong></dt>
<dd>Create new file, <code>newfile.h5</code>, with the text in file <code>mytext.txt</code> as the user block for the HDF5 file <code>file.h5</code>.
<pre> h5jam -u mytext.txt -i file.h5 -o newfile.h5</pre>
Add text in file <code>mytext.txt</code> to front of HDF5 dataset, <code>file.h5</code><code></code>.
<pre> h5jam -u mytext.txt -i file.h5 </pre>
Overwrite the user block (if any) in <code>file.h5</code> with the contents of <code>mytext.txt</code>.
<pre> h5jam -u mytext.txt -i file.h5 --clobber</pre>
For an HDF5 file, <code>with_ub.h5</code>, with a user block, extract the user block to <code>user_block.txt</code> and the HDF5 file to <code>wo_ub.h5</code>.
<pre> h5unjam -i with_ub.h5 -u user_block.txt -i wo_ub.h5</pre>
<dt><strong></strong></dt><dt><strong>Return Value</strong></dt>
<dd><code>h5jam</code> returns the size of the output file, or -1 if an error occurs.
<p>
<code>h5unjam</code> returns the size of the output file, or -1 if an error occurs.
<dt><strong>Caveats</strong></dt><dt><strong></strong> </dt>
<dd>This tool copies all the data (sequentially) in the file(s) to new offsets.
For a large file, this copy will take a long time.
<p>The most efficient way to create a user block is to create the file
with a user block (see <code>H5Pset_user_block</code>), and write
the user block data into that space from a program.
<p>The user block is completely opaque to the HDF5 library and to the h5jam
and h5unjam tools. The user block is simply read or written as a string
of bytes, which could be text or any kind of binary data. It is up
to the user to know what the contents of the user block means and how to
process it.
<p>
When the user block is extracted, all the data is written to the output, including any padding or unwritten data.
<p>
This tool moves the HDF5 file through byte copies, i.e., it does not read or interpret the HDF5 objects.<br>
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5redeploy" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Redeploy">h5redeploy</a>
<dt><strong>Syntax:</strong>
<dd><code>h5redeploy </code>
[<code>help </code> | <code>-help</code>]
<dd><code>h5redeploy </code>
[<code>-echo</code>]
[<code>-force</code>]
[<code>-prefix=</code><em>dir</em>]
[<code>-tool=</code><em>tool</em>]
[<code>-show</code>]
<dt><strong>Purpose:</strong>
<dd>Updates HDF5 compiler tools after an HDF5 software installation
in a new location.
<dt><strong>Description:</strong>
<dd><code>h5redeploy</code> updates the HDF5 compiler tools after
the HDF5 software has been installed in a new location.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>help</code>, <code>-help</code>
<dd>Prints a help message.
<dt><code>-echo</code>
<dd>Shows all the shell commands executed.
<dt><code>-force</code>
<dd>Performs the requested action without offering any prompt
requesting confirmation.
<dt><code>-prefix=</code><em>dir</em>
<dd>Specifies a new directory in which to find the
HDF5 subdirectories <code>lib/</code> and
<code>include/</code>.<br>
(Default: current working directory)
<dt><code>-tool=</code><em>tool</em>
<dd>Specifies the tool to update.
<em>tool</em> must be in the current directory
and must be writable.<br>
(Default: <code>h5cc</code>)
<dt><code>-show</code>
<dd>Shows all of the shell commands to be executed
without actually executing them.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5cc and h5pcc" -->
<hr>
<dl>
<dt><strong>Tool Names:</strong> <a name="Tools-H5CC">h5cc and h5pcc</a>
<dt><strong>Syntax:</strong>
<dd><code>h5cc
[</code><em>OPTIONS</em><code> ]</code> <em>compile_line</em>
<dd><code>h5pcc
[</code><em>OPTIONS</em><code> ]</code> <em>compile_line</em>
<dt><strong>Purpose:</strong>
<dd>Helper scripts to compile HDF5 C applications.
<dt><strong>Description:</strong>
<dd><code>h5cc</code> and <code>h5pcc</code> can be used in much
the same way as <code>mpicc</code> by MPICH is used to compile
an HDF5 program.
These tools take care of specifying on the command line
the locations of the HDF5 header files and libraries.
<code>h5cc</code> is for use in serial computing environments;
<code>h5pcc</code> is for parallel environments.
<p>
<code>h5cc</code> and <code>h5pcc</code> subsume all other
compiler scripts in that if you have used a set of scripts to compile
the HDF5 library, then <code>h5cc</code> and <code>h5pcc</code>
also use those scripts.
For example, when compiling an MPICH program, you use the
<code>mpicc</code> script.
If you have built HDF5 using MPICH, then <code>h5cc</code>
uses the MPICH program for compilation.
<p>
Some programs use HDF5 in only a few modules.
It is not necessary to use <code>h5cc</code> or <code>h5pcc</code>
to compile those modules which do not use HDF5.
In fact, since <code>h5cc</code> and <code>h5pcc</code> are only
convenience scripts, you can still compile HDF5 modules in the
normal manner, though you will have to specify the HDF5 libraries
and include paths yourself.
Use the <code>-show</code> option to see the details.
<p>
An example of how to use <code>h5cc</code> to compile the program
<code>hdf_prog</code>, which consists of the modules
<code>prog1.c</code> and <code>prog2.c</code> and uses the HDF5
shared library, would be as follows.
<code>h5pcc</code> is used in an identical manner.
<pre>
# h5cc -c prog1.c
# h5cc -c prog2.c
# h5cc -shlib -o hdf_prog prog1.o prog2.o </pre>
<dt><strong>Options and Parameters:</strong>
<dd>
<dl>
<dt><code>-help</code>
<dd>Print a help message.
<dt><code>-echo</code>
<dd>Show all the shell commands executed.
<dt><code>-prefix=DIR</code>
<dd>Use the directory <code><em>DIR</em></code> to find the HDF5
<code>lib/</code> and <code>include/</code> subdirectories.
<br>
Default: prefix specified when configuring HDF5.
<dt><code>-show</code>
<dd>Show the commands without executing them.
<dt><code>-shlib</code>
<dd>Compile using shared HDF5 libraries.
<dt><code>-noshlib</code>
<dd>Compile using static HDF5 libraries [default].
<dt><em>compile_line</em>
<dd>The normal compile line options for your compiler.
<code>h5cc</code> and <code>h5pcc</code> use the
same compiler you used to compile HDF5;
check your compiler's manual for more information
on which options are needed.
</dl>
<dt><strong>Environment Variables:</strong>
<dd>When set, these environment variables override some of the built-in
<code>h5cc</code> and <code>h5pcc</code> defaults.
<dl>
<dt><code>HDF5_CC</code>
<dd>Use a different C compiler.
<dt><code>HDF5_CLINKER</code>
<dd>Use a different linker.
<dt><code>HDF5_USE_SHLIB=[yes|no]</code>
<dd>Use shared version of the HDF5 library [default: no].
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5fc and h5pfc" -->
<hr>
<dl>
<dt><strong>Tool Names:</strong> <a name="Tools-H5FC">h5fc and h5pfc</a>
<dt><strong>Syntax:</strong>
<dd><code>h5fc
[</code><em>OPTIONS</em><code> ]</code> <em>compile_line</em>
<dd><code>h5pfc
[</code><em>OPTIONS</em><code> ]</code> <em>compile_line</em>
<dt><strong>Purpose:</strong>
<dd>Helper scripts to compile HDF5 Fortran90 applications.
<dt><strong>Description:</strong>
<dd><code>h5fc</code> and <code>h5pfc</code> can be used in much the
same way <code>mpif90</code> by MPICH is used to compile
an HDF5 program.
These tools take care of specifying on the command line
the locations of the HDF5 header files and libraries.
<code>h5fc</code> is for use in serial computing environments;
<code>h5pfc</code> is for parallel environments.
<p>
<code>h5fc</code> and <code>h5pfc</code> subsume all other
compiler scripts in that if you have used a set of scripts to compile
the HDF5 Fortran library, then <code>h5fc</code> and <code>h5pfc</code>
also use those scripts. For example, when
compiling an MPICH program, you use the <code>mpif90</code>
script. If you have built HDF5 using MPICH, then <code>h5fc</code>
uses the MPICH program for compilation.
<p>
Some programs use HDF5 in only a few modules. It is not necessary
to use <code>h5fc</code> and <code>h5pfc</code> to compile those
modules which do not use HDF5.
In fact, since <code>h5fc</code> and <code>h5pfc</code> are only
convenience scripts, you can still compile HDF5 Fortran modules in
the normal manner, though you will have to specify the
HDF5 libraries and include paths yourself.
Use the <code>-show</code> option to see the details.
<p>
An example of how to use <code>h5fc</code> to compile the program
<code>hdf_prog</code>, which consists of the modules
<code>prog1.f90</code> and <code>prog2.f90</code>
and uses the HDF5 Fortran library, would be as follows.
<code>h5pfc</code> is used in an identical manner.
<pre>
# h5fc -c prog1.f90
# h5fc -c prog2.f90
# h5fc -o hdf_prog prog1.o prog2.o </pre>
<dt><strong>Options and Parameters:</strong>
<dd>
<dl>
<dt><code>-help</code>
<dd>Print a help message.
<dt><code>-echo</code>
<dd>Show all the shell commands executed.
<dt><code>-prefix=DIR</code>
<dd>Use the directory <code>DIR</code> to find HDF5
<code>lib/</code> and <code>include/</code> subdirectories.
<br>
Default: prefix specified when configuring HDF5.
<dt><code>-show</code>
<dd>Show the commands without executing them.
<dt><em>compile_line</em>
<dd>The normal compile line options for your compiler.
<code>h5fc</code> and <code>h5pfc</code> use the
same compiler you used to compile HDF5;
check your compiler's manual for more information
on which options are needed.
</dl>
<dt><strong>Environment Variables:</strong>
<dd>When set, these environment variables override some of the built-in
<code>h5fc</code> and <code>h5pfc</code> defaults.
<dl>
<dt><code>HDF5_FC</code>
<dd>Use a different Fortran90 compiler.
<dt><code>HDF5_FLINKER</code>
<dd>Use a different linker.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- NEW PAGE -->
<!-- HEADER RIGHT "h5c++" -->
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H5C++">h5c++</a>
<dt><strong>Syntax:</strong>
<dd><code>h5c++
[</code><em>OPTIONS</em><code>]</code> <em><compile line></em>
<dt><strong>Purpose:</strong>
<dd>Helper script to compile HDF5 C++ applications.
<dt><strong>Description:</strong>
<dd><p>
<code>h5c++</code> can be used in much the same way
<code>mpiCC</code> by MPICH is used to compile an HDF5 program.
It takes care of specifying where the
HDF5 header files and libraries are on the command line.
<p>
<code>h5c++</code> subsumes all other compiler scripts in that
if you've used one set of compiler scripts to compile the
HDF5 C++ library, then <code>h5c++</code> uses those same scripts.
For example, when compiling an MPICH program,
you use the <code>mpiCC</code> script.
<p>
Some programs use HDF5 in only a few modules. It isn't necessary
to use <code>h5c++</code> to compile those modules which don't use
HDF5. In fact, since <code>h5c++</code> is only a convenience
script, you are still able to compile HDF5 C++ modules in the
normal way. In that case, you will have to specify the HDF5 libraries
and include paths yourself.
Use the <code>-show</code> option to see the details.
<p>
An example of how to use <code>h5c++</code> to compile the program
<code>hdf_prog</code>, which consists of modules
<code>prog1.cpp</code> and <code>prog2.cpp</code>
and uses the HDF5 C++ library, would be as follows:
<pre>
# h5c++ -c prog1.cpp
# h5c++ -c prog2.cpp
# h5c++ -o hdf_prog prog1.o prog2.o</pre>
<dt><strong>Options and Parameters:</strong>
<dd>
<dl>
<dt><code>-help</code>
<dd>Prints a help message.
<dt><code>-echo</code>
<dd>Show all the shell commands executed.
<dt><code>-prefix=DIR</code>
<dd>Use the directory <code>DIR</code> to find HDF5
<code>lib/</code> and <code>include/</code> subdirectories
<br>
Default: prefix specified when configuring HDF5.
<dt><code>-show</code>
<dd>Show the commands without executing them.
<dt><em><compile line></em>
<dd>The normal compile line options for your compiler.
<code>h5c++</code> uses the same compiler you used
to compile HDF5. Check your compiler's manual for
more information on which options are needed.
</dl>
<dt><strong>Environment Variables:</strong>
<dd>When set, these environment variables override some of the built-in
defaults of <code>h5c++</code>.
<dl>
<dt><code>HDF5_CXX</code>
<dd>Use a different C++ compiler.
<dt><code>HDF5_CXXLINKER</code>
<dd>Use a different linker.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- Template, next 40 lines -->
<!-- Template, next 40 lines -->
<!-- Template, next 40 lines
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H5toh4">h5toh4</a>
<dt><strong>Syntax:</strong>
<dd><code>h5toh4 -h</code><br>
<code>h5toh4 </code><em>
h5file
h4file</em><br>
<code>h5toh4 </code><em>
h5file</em><br>
<code>h5toh4 -m </code><em>
h5file1
h5file2
h5file3</em> ...
<dt><strong>Purpose:</strong>
<dd>Purpose...
<dt><strong>Description:</strong>
<dd><code>TOOL</code> is an HDF5 utility which ...
Paragraph
<pre> sample code
sample code
sample code </pre>
<p>
Paragraph
<p>
Paragraph
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-option</code>
<dd>Description
<dt><em>parameter</em>
<dd>Description
</dl>
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
</dl>
-->
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<center>
<table border=0 width=98%>
<tr><td valign=top align=left>
<a href="index.html">HDF5 documents and links</a> <br>
<a href="H5.intro.html">Introduction to HDF5</a> <br>
<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User Guide</a> <br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
And in this document, the
<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="RM_H5.html">H5</a>
<a href="RM_H5A.html">H5A</a>
<a href="RM_H5D.html">H5D</a>
<a href="RM_H5E.html">H5E</a>
<a href="RM_H5F.html">H5F</a>
<a href="RM_H5G.html">H5G</a>
<a href="RM_H5I.html">H5I</a>
<a href="RM_H5P.html">H5P</a> <br>
<a href="RM_H5R.html">H5R</a>
<a href="RM_H5S.html">H5S</a>
<a href="RM_H5T.html">H5T</a>
<a href="RM_H5Z.html">H5Z</a>
<a href="Tools.html">Tools</a>
<a href="PredefDTypes.html">Datatypes</a>
</td></tr>
<tr><td colspan="2" align="right">
<i><small>(<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/">PDF</a>
of complete manual formatted as print volume) </small></i>
</td></tr>
</table>
</center>
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<address>
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
<br>
Describes HDF5 Release 1.6.4, March 2005
</address>
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