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diff --git a/doc/html/Tools.html b/doc/html/Tools.html index 767eab8..2d2007f 100644 --- a/doc/html/Tools.html +++ b/doc/html/Tools.html @@ -64,6 +64,8 @@ And in this document, the <h1>HDF5 Tools</h1> </center> +<!-- HEADER RIGHT "HDF5 Tools" --> + <h2>HDF5 Tool Interfaces</h2> <p> @@ -172,6 +174,7 @@ installed with HDF5. <!-- NEW PAGE --> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5dump" --> <p> <hr> @@ -191,23 +194,19 @@ installed with HDF5. 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 @@ -215,14 +214,12 @@ installed with HDF5. <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; @@ -230,12 +227,10 @@ installed with HDF5. 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 @@ -252,7 +247,6 @@ installed with HDF5. <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. @@ -261,7 +255,6 @@ installed with HDF5. 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> <!-- NEW PAGE --> <dt><strong>XML Output:</strong> @@ -276,115 +269,173 @@ installed with HDF5. <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>-B</code> or - <code>--bootblock</code></dt> - <dd>Print the content of the boot block.<br> - <em>(This option is not yet implemented.)</em></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>-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>-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> - <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> -<!-- NEW PAGE --> - <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>Indicate 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> + <ul> + <table> + <tr> + <td valign="top"><code>-h</code> or <code>--help</code></td> + <td valign="top">Print a usage message and exit.</td> + </tr> + <tr> + <td valign="top"><code>-B</code> or <code>--bootblock</code></td> + <td valign="top">Print the content of the boot block.<br> <em>(This + option is not yet implemented.)</em></td> + </tr> + <tr> + <td valign="top"><code>-H</code> or <code>--header</code></td> + <td valign="top">Print the header only; no data is displayed.</td> + </tr> + <tr> + <td valign="top"><code>-A</code></td> + <td valign="top">Print the header and value of attributes; data of datasets + is not displayed.</td> + </tr> + <tr> + <td valign="top"><code>-i</code> or <code>--object-ids</code></td> + <td valign="top">Print the object ids.</td> + </tr> + <tr> + <td valign="top"><code>-r</code> or <code>--string</code></td> + <td valign="top">Print 1-bytes integer datasets as ASCII.</td> + </tr> + <tr> + <td valign="top"><code>-V</code> or <code>--version</code></td> + <td valign="top">Print version number and exit.</td> + </tr> + <tr> + <td valign="top"><code>-a <em>P</em></code> or <code>--attribute=<em>P</em> </code></td> + <td valign="top">Print the specified attribute.</td> + </tr> + <tr> + <td valign="top"><code>-d <em>P</em></code> or + <code>--dataset=<em>P</em></code></td> + <td valign="top">Print the specified dataset.</td> + </tr> + <tr> + <td valign="top"><code>-f<em> D</em></code> or <code>--filedriver=<em>D </em> </code></td> + <td valign="top">Specify which driver to open the file with.</td> + </tr> + <tr> + <td valign="top"><code>-g <em>P</em></code> or + <code>--group=<em>P</em></code></td> + <td valign="top">Print the specified group and all members.</td> + </tr> + <tr> + <td valign="top"><code>-l <em>P</em></code> or <code>--soft-link=<em>P </em></code></td> + <td valign="top">Print the value(s) of the specified soft link.</td> + </tr> + <tr> + <td valign="top"><code>-o <em>F</em></code> or + <code>--output=<em>F</em></code></td> + <td valign="top">Output raw data into file F.</td> + </tr> + <tr> + <td valign="top"><code>-t <em>T</em></code> or + <code>--datatype=<em>T</em></code></td> + <td valign="top">Print the specified named datatype.</td> + </tr> + <tr> + <td valign="top"><code>-w <em>N</em></code> or + <code>--width=<em>N</em></code></td> + <td valign="top">Set the number of columns of output.</td> + </tr> + <tr> + <td valign="top"><code>-x <em></em></code> or + <code>--xml</code></td> + <td valign="top">Output XML using XML schema (default) instead of DDL.</td> + </tr> + <tr> + <td valign="top"><code>-u <em></em></code> or + <code>--use-dtd</code></td> + <td valign="top">Output XML using XML DTD instead of DDL.</td> + </tr> + <tr> + <td valign="top"><code>-D <em>U</em></code> or + <code>--xml-dtd=<em>U</em></code></td> + <td valign="top">In XML output, refer to the DTD or schema at <em>U</em> + instead of the default schema/DTD.</td> + </tr> + <tr> + <td valign="top"><code>-X <em>S</em></code> or + <code>--xml-dns=<em>S</em></code></td> + <td valign="top">In XML output, (XML Schema) use qualified names in + the XML:<br> ":": no namespace, default: + "hdf5:"</td> + </tr> + <tr> + <td valign="top"><code>-s <em>L</em></code> or + <code>--start=<em>L</em></code></td> + <td valign="top">Offset of start of subsetting selection. <br> + Default: the beginning of the dataset.</td> + </tr> + <tr> + <td valign="top"><code>-S <em>L</em></code> or + <code>--stride=<em>L</em></code></td> + <td valign="top">Hyperslab stride. <br> + Default: 1 in all dimensions.</td> + </tr> + <tr> + <td valign="top"><code>-c <em>L</em></code> or + <code>--count=<em>L</em></code></td> + <td valign="top">Number of blocks to include in the selection.</td> + </tr> + <tr> + <td valign="top"><code>-k <em>L</em></code> or + <code>--block=<em>L</em></code></td> + <td valign="top">Size of block in hyperslab. <br> + Default: 1 in all dimensions.</td> + </tr> + <tr> + <td valign="top"><code>--</code></td> + <td valign="top">Indicate that all following arguments are non-options. + E.g., to dump a file called `-f', use h5dump -- -f.</td> + </tr> + <tr> + <td valign="top"><em>file</em></td> + <td valign="top">The file to be examined.</td> + </tr> + </table> + </ul> <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 +<!-- NEW PAGE --> + <ul> + The option parameters listed above are defined as follows: + <table> + <tr> + <td valign="top"><em>D</em> </td> + <td valign="top">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.</td></tr> + <tr> + <td valign="top"><em>P</em></td> + <td valign="top">The full path from the root group to + the object</td></tr> + <tr> + <td valign="top"><em>T</em></td> + <td valign="top">The name of the datatype</td></tr> + <tr> + <td valign="top"><em>F</em></td> + <td valign="top">A filename</td></tr> + <tr> + <td valign="top"><em>N</em></td> + <td valign="top">An integer greater than 1</td></tr> + <tr> + <td valign="top"><em>L</em></td> + <td valign="top">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 + queried</td></tr> + <tr> + <td valign="top"><em>U</em></td> + <td valign="top">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 + that refers to the DTD to be used to validate the XML</td></tr> + </table> + + <p>Subsetting parameters can also be expressed in a convenient compact form, as follows: <br> @@ -393,50 +444,59 @@ installed with HDF5. 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> - + </ul> <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> + + <table border="0" width="100%"> + <tr><td valign="top"> + <ol> + <li>Dumping the group <code>/GroupFoo/GroupBar</code> in the file + <code>quux.h5</code>:<br> + <code> + h5dump -g /GroupFoo/GroupBar quux.h5</code> + <br> + <br> <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> + <code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:<br> + <code> + h5dump -d /GroupFoo/GroupBar/Fnord quux.h5</code> + <br> + <br> <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> + <code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:<br> + <code> + h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5</code> + <br> + <br> <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 --> + attribute of the root group in the file <code>quux.h5</code>:<br> + <code> + h5dump -a /metadata quux.h5</code> + <br> + <br> + <li>Producing an XML listing of the file <code>bobo.h5</code>:<br> + <code> + h5dump --xml bobo.h5 > bobo.h5.xml</code> + <br> + <br> <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> + in the file <code>quux.h5</code>:<br> + <code> + h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3" + <br> + --count="3,19" --block="1,1" quux.h5</code> + <br> + <br> <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> + subsetting parameters:<br> + <code> + h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5</code> + <br> + <br> + </ol></td></tr> + </table> +<!-- NEW PAGE --> <dt><strong>Current Status:</strong> <dd>The current version of <code>h5dump</code> displays the following information: @@ -497,20 +557,24 @@ installed with HDF5. </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> + <table border="0" width="100%"> + <tr><td valign="top"> + <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> + </td></tr> + </table> + </ul> </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5ls" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-Ls">h5ls</a> @@ -525,60 +589,74 @@ installed with HDF5. <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 + <ul><table> + <tr> + <td valign="top" width="30%"><code>-h</code> or <code>-?</code> or + <code>--help </code></td> + <td valign="top">Print a usage message and exit.</td></tr> + <tr> + <td valign="top"><code>-a</code> or + <code>--address</code></td> + <td valign="top">Print addresses for raw data.</td></tr> + <tr> + <td valign="top"><code>-d</code> or <code>--data</code></td> + <td valign="top">Print the values of datasets.</td></tr> + <tr> + <td valign="top"><code>-e</code> or + <code>--errors</code></td> + <td valign="top">Show all HDF5 error reporting.</td></tr> + <tr> + <td valign="top"><code>-f</code> or + <code>--full</code></td> + <td valign="top">Print full path names instead of base names.</td></tr> + <tr> + <td valign="top"><code>-g</code> or + <code>--group</code></td> + <td valign="top">Show information about a group, not its contents.</td></tr> + <tr> + <td valign="top"><code>-l</code> or + <code>--label</code></td> + <td valign="top">Label members of compound datasets.</td></tr> + <tr> + <td valign="top"><code>-r</code> or <code>--recursive </code></td> + <td valign="top">List all groups recursively, avoiding cycles.</td></tr> + <tr> + <td valign="top"><code>-s</code> or + <code>--string</code></td> + <td valign="top">Print 1-bytes integer datasets as ASCII.</td></tr> + <tr> + <td valign="top"><code>-S</code> or + <code>--simple</code></td> + <td valign="top">Use a machine-readable output format.</td></tr> + <tr> + <td valign="top"><code>-w</code><em>N</em> or + <code>--width=</code><em>N </em></td> + <td valign="top">Set the number of columns of output.</td></tr> + <tr> + <td valign="top"><code>-v</code> or + <code>--verbose</code></td> + <td valign="top">Generate more verbose output.</td></tr> + <tr> + <td valign="top"><code>-V</code> or + <code>--version</code></td> + <td valign="top">Print version number and exit.</td></tr> + <tr> + <td valign="top"><code>-x</code> or + <code>--hexdump</code></td> + <td valign="top">Show raw data in hexadecimal format.</td></tr> + <tr> + <td valign="top"><em>file</em></td> + <td valign="top">The file name may include a printf(3C) integer format + such as <code>%%05d</code> to open a file family.</td></tr> + <tr> + <td valign="top"><em>objects</em></td> + <td valign="top">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> + as "%05d" to open a file family.</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -588,6 +666,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5diff" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-Diff">h5diff</a> <em>(Beta version)</em> @@ -622,47 +701,52 @@ installed with HDF5. <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>Print all differences. - <dt><code>-r</code> - <dd>Print only the names of objects that differ; - do not print the differences. - These objects may be HDF5 datasets, groups, - or named datatypes. - <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> + <ul><table> + <tr> + <td valign="top"><em>file1</em></td> + <td valign="top"> </td></tr> + <tr> + <td valign="top"><em>file2</em></td> + <td valign="top">The HDF5 files to be compared.</td></tr> + <tr> + <td valign="top"><code>-h</code></td> + <td valign="top">Print all differences.</td></tr> + <tr> + <td valign="top"><code>-r</code></td> + <td valign="top">Print only the names of objects that differ; + do not print the differences. These objects may be HDF5 + datasets, groups, or named datatypes.</td></tr> + <tr> + <td valign="top"><code>-n</code> <em>count</em></td> + <td valign="top">Print difference up to <em>count</em> + differences, then stop. <em>count</em> must be a positive integer.</td></tr> + <tr> + <td valign="top"><code>-d</code> <em>delta</em></td> + <td valign="top">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>).</td></tr> + <tr> + <td valign="top"><code>-p</code> <em>relative </em> </td> + <td valign="top">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>).</td></tr> + <tr> + <td valign="top"><em>object1</em></td> + <td valign="top"> </td></tr> + <tr> + <td valign="top"><em>object2</em></td> + <td valign="top">Specific object(s) within the files to be compared.</td></tr> + </table></ul> <dt><strong>Examples:</strong> <dd>The following <code>h5diff</code> call compares the object <code>/a/b</code> in <code>file1</code> @@ -684,6 +768,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5repart" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-Repart">h5repart</a> @@ -711,20 +796,26 @@ installed with HDF5. 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> + <ul><table> + <tr> + <td valign="top"><code>-v</code></td> + <td valign="top">Produce verbose output.</td></tr> + <tr> + <td valign="top"><code>-V</code></td> + <td valign="top">Print a version number and exit.</td></tr> + <tr> + <td valign="top"><code>-b</code><em>N</em></td> + <td valign="top">The I/O block size, defaults to 1kB</td></tr> + <tr> + <td valign="top"><code>-m</code><em>N</em></td> + <td valign="top">The destination member size or 1GB</td></tr> + <tr> + <td valign="top"><em>source_file </em></td> + <td valign="top">The name of the source file</td></tr> + <tr> + <td valign="top"><em>dest_file</em></td> + <td valign="top">The name of the destination files</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -734,6 +825,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5import" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-Import">h5import</a> @@ -1288,50 +1380,40 @@ installed with HDF5. <tr valign=top align=left><td><hr></td><td><hr></td></tr> </table> - + <!-- NEW PAGE --> - <p> - <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. + + <ul><table> + <tr> + <td valign="top"><code>infile(s)</code></td> + <td valign="top">Name of the Input file(s).</td></tr> + <tr> + <td valign="top"><code>in_options</code></td> + <td valign="top">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.</td></tr> + <tr> + <td valign="top"> <code>-d <em>dim_list</em></code></td> + <td valign="top"> </td></tr> + <tr> + <td valign="top"> <code>-dims <em>dim_list</em></code></td> + <td valign="top">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 + this command-line argument is mandatory.</td></tr> + <tr> + <td valign="top"> <code>-p <em>pathname</em></code></td> + <td valign="top"> </td></tr> + <tr> + <td valign="top"> <code>-pathname <em>pathname + <br> + </em></code></td> + <td valign="top"><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 @@ -1347,36 +1429,55 @@ installed with HDF5. 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 + are not processed.</td></tr> + <tr> + <td valign="top"> <code>-t <em>input_class</em></code></td> + <td valign="top"> </td></tr> + <tr> + <td valign="top"> <code>-type <em>input_class </em></code></td> + <td valign="top"><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 + the default value is <code>FP</code>.</td></tr> + <tr> + <td valign="top"> <code>-s <em>input_size</em></code></td> + <td valign="top"> </td></tr> + <tr> + <td valign="top"> <code>-size <em>input_size</em></code></td> + <td valign="top"><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 + the default value is <code>32</code>.</td></tr> + <tr> + <td valign="top"> <code>-c <em>config_file</em></code></td> + <td valign="top"><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> + <code>-o <em>outfile</em></code></td></tr> + <tr> + <td valign="top"> <code>-h</code></td> + <td valign="top"> </td></tr> + <tr> + <td valign="top"> <code>-help</code></td> + <td valign="top"> + Prints the <code>h5import</code> usage summary:<br> + <code>h5import -h[elp], OR<br> + h5import <infile> <options> [<infile> <options>...] -o[utfile] <outfile></code><br> + Then exits. + </td></tr> + <tr> + <td valign="top"><code>outfile</code></td> + <td valign="top">Name of the HDF5 output file.</td></tr> + </table></ul> +<!-- NEW PAGE --> <dt><strong>Examples:</strong> <dd><b>Using command-line arguments:</b> <table width=100% border=0> @@ -1456,6 +1557,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "gif2h5" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-GIF2H5">gif2h5</a> @@ -1469,12 +1571,14 @@ installed with HDF5. 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> + <ul><table> + <tr> + <td valign="top"><em>gif_file </em></td> + <td valign="top">The name of the input GIF file</td></tr> + <tr> + <td valign="top"><em>h5_file</em></td> + <td valign="top">The name of the output HDF5 file</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -1484,6 +1588,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h52gif" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-H52GIF">h52gif</a> @@ -1511,18 +1616,22 @@ installed with HDF5. 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> + <ul><table> + <tr> + <td valign="top"><em>h5_file</em></td> + <td valign="top">The name of the input HDF5 file</td></tr> + <tr> + <td valign="top"><em>gif_file</em></td> + <td valign="top">The name of the output GIF file</td></tr> + <tr> + <td valign="top"><code>-i</code> <em>h5_image</em></td> + <td valign="top">Image option, specifying the name of an HDF5 image or + dataset containing an image to be converted</td></tr> + <tr> + <td valign="top"><code>-p</code> <em>h5_palette </em></td> + <td valign="top">Palette option, specifying the name of an HDF5 dataset + containing a palette to be used in an image conversion</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -1532,6 +1641,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5toh4" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-H5toh4">h5toh4</a> @@ -1628,16 +1738,20 @@ installed with HDF5. </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> + <ul><table> + <tr> + <td valign="top"><code>-h</code></td> + <td valign="top">Displays a syntax summary.</td></tr> + <tr> + <td valign="top"><code>-m</code></td> + <td valign="top">Converts multiple HDF5 files to multiple HDF4 files.</td></tr> + <tr> + <td valign="top"><em>h5file </em></td> + <td valign="top">The HDF5 file to be converted.</td></tr> + <tr> + <td valign="top"><em>h4file</em></td> + <td valign="top">The HDF4 file to be created.</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -1647,6 +1761,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h4toh5" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-H4toh5">h4toh5</a> @@ -1749,18 +1864,22 @@ installed with HDF5. 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. + <ul><table> + <tr> + <td valign="top"><code>-h</code></td> + <td valign="top">Displays a syntax summary.</td></tr> <!-- currently no -m option - <dt><code>-m</code> - <dd>Converts multiple HDF4 files to multiple HDF5 files. + <tr> + <td valign="top"><code>-m</code></td> + <td valign="top">Converts multiple HDF4 files to multiple HDF5 files.</td></tr> --> - <dt><em>h4file</em> - <dd>The HDF4 file to be converted. - <dt><em>h5file</em> - <dd>The HDF5 file to be created. - </dl> + <tr> + <td valign="top"><em>h4file </em></td> + <td valign="top">The HDF4 file to be converted.</td></tr> + <tr> + <td valign="top"><em>h5file</em></td> + <td valign="top">The HDF5 file to be created.</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -1770,6 +1889,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5perf" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-Perf">h5perf</a> @@ -1821,171 +1941,273 @@ installed with HDF5. <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><strong>Options and Parameters:</strong> + + <ul> + <table width="100%"> + <tr> + <td valign="top" colspan="2">These terms are used as follows in this section:</td></tr> + <tr> + <td valign="top"><em>file </em></td> + <td valign="top">A filename</td></tr> + <tr> + <td valign="top"><em>size</em></td> + <td valign="top">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> + <td valign="top"><em>N</em></td> + <td valign="top">An integer greater than or equal to 0 (zero)</td></tr> + </table><br> + + <table width="100%"> + <tr> + <td valign="top" colspan="2"><code>-h</code>, <code>--help</code></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">Prints a usage message and exits.</td> + </tr> + <tr> + <td colspan="2" valign="top"><code>-a</code> <em>size</em>, <code>--align=</code><em>size</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">Specifies the alignment of objects in the HDF5 file. + (Default: 1)</td> + </tr> + <tr> + <td colspan="2" valign="top"><code>-A</code> <em>api_list</em>, <code>--api=</code><em>api_list</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">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.</td> + </tr> <!-- NEW PAGE --> - <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> - 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> + <tr> + <td valign="top" colspan="2"><code>-B</code> <em>size</em>, <code>--block-size=</code><em>size</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">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> + 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></td> + </tr> + <tr> + <td colspan="2" valign="top"><code>-c</code>, <code>--chunk</code></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">Creates HDF5 datasets in chunked layout. (Default: + Off)</td> + </tr> + <tr> + <td valign="top" colspan="2"><code>-C</code>, <code>--collective</code></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">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></td> + </tr> + <tr> + <td colspan="2" valign="top"><code>-d</code> <em>N</em>, <code>--num-dsets</code><em>N</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">Sets the number of datasets per file. (Default: <code>1</code>)</td> + </tr> + <tr> + <td valign="top" colspan="2"><code>-D</code> <em>debug_flags</em>, <code>--debug=</code><em>debug_flags</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">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></td> + </tr> + <tr> + <td colspan="2" valign="top"><code>-e</code> <em>size</em>, <code>--num-bytes=</code><em>size</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">Specifies the number of bytes per process per dataset. + (Default: <code>256K</code>)</td> + </tr> + <tr> + <td colspan="2" valign="top"><code>-F</code> <em>N</em>, <code>--num-files=</code><em>N</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">Specifies the number of files. (Default: <code>1</code>)</td> + </tr> + <tr> + <td colspan="2" valign="top"><code>-i</code> <em>N</em>, <code>--num-iterations=</code><em>N</em></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">Sets the number of iterations to perform. (Default: + <code>1</code>)</td> + </tr> + </table> + <!-- NEW PAGE --> - 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> + <table width="100%"> + <tr> + <td valign="top" colspan="2"><code>-I</code>, <code>--interleaved</code></td> + </tr> + <tr> + <td valign="top"> </td> + <td valign="top">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></td> + </tr> + </table> + <table width="100%"> + <tr> + <td valign="top"><code>-m</code>, <code>--mpi-posix</code></td> + <td valign="top">Sets use of MPI-posix driver for HDF5 I/O. (Default: + MPI-I/O driver)</td> + </tr> + <tr> + <td valign="top"><code>-n</code>, <code>--no-fill</code></td> + <td valign="top">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)</td> + </tr> + <tr> + <td valign="top"><code>-o</code> <em>file</em>, <code> --output=</code><em>file</em></td> + <td valign="top">Sets the output file for raw data to <em>file</em>. + (Default: None)</td> + </tr> + <tr> + <td valign="top"><code>-p</code> <em>N</em>, <code>--min-num-processes=</code><em>N</em></td> + <td valign="top">Sets the minimum number of processes to be used. (Default: + <code>1</code>)</td> + </tr> + <tr> + <td valign="top"><code>-P</code> <em>N</em>, <code>--max-num-processes=</code><em>N</em><br> + <code> + + + </code> + </td> + <td valign="top">Sets the maximum number of processes to be used.<br> + (Default: All <code>MPI_COMM_WORLD</code>processes)</td> + </tr> + <tr> + <td valign="top"><code>-T</code> <em>size</em>, <code>--threshold=</code><em>size</em></td> + <td valign="top">Sets the threshold for alignment of objects in the + HDF5 file. (Default: <code>1</code>)</td> + </tr> + <tr> + <td valign="top"><code>-w</code>, <code>--write-only</code></td> + <td valign="top">Performs only write tests, not read tests. (Default: + Read and write tests)</td> + </tr> + <tr> + <td valign="top"><code>-x</code> <em>size</em>, <code>--min-xfer-size=</code><em>size</em></td> + <td valign="top">Sets the minimum transfer buffer size. (Default: <code>128K</code>)</td> + </tr> + <tr> + <td valign="top"><code>-X</code> <em>size</em>, <code>--max-xfer-size=</code>size <em></em></td> + <td valign="top">Sets the maximum transfer buffer size. (Default: <code>1M</code>)</td> + </tr> + </table> + </ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -1995,6 +2217,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5redeploy" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-Redeploy">h5redeploy</a> @@ -2015,28 +2238,32 @@ installed with HDF5. 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> + <ul><table> + <tr> + <td valign="top"><code>help</code>, <code>-help</code></td> + <td valign="top">Prints a help message.</td></tr> + <tr> + <td valign="top"><code>-echo</code></td> + <td valign="top">Shows all the shell commands executed.</td></tr> + <tr> + <td valign="top"><code>-force</code></td> + <td valign="top">Performs the requested action without offering any prompt + requesting confirmation.</td></tr> + <tr> + <td valign="top"><code>-prefix=</code><em>dir </em></td> + <td valign="top">Specifies a new directory in which to find the + HDF5 subdirectories <code>lib/</code> and <code>include/</code>. + <br> (Default: current working directory)</td></tr> + <tr> + <td valign="top"><code>-tool=</code><em>tool</em></td> + <td valign="top">Specifies the tool to update. <em>tool</em> must + be in the current directory and must be writable. + <br> (Default: <code>h5cc</code>)</td></tr> + <tr> + <td valign="top"><code>-show</code></td> + <td valign="top">Shows all of the shell commands to be executed + without actually executing them.</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -2046,6 +2273,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5cc" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-H5CC">h5cc</a> @@ -2071,53 +2299,63 @@ installed with HDF5. HDF5. In fact, since <code>h5cc</code> is only a convenience script, you are still able to compile HDF5 modules in the normal way. In that case, you will have to specify the HDF5 libraries - and include paths yourself. - <p> + and include paths yourself.</p> + An example of how to use <code>h5cc</code> to compile the program <code>hdf_prog</code>, which consists of modules <code>prog1.c</code> and <code>prog2.c</code> and uses the HDF5 shared library, would be as follows: - <pre> + + <pre> # h5cc -c prog1.c # h5cc -c prog2.c - # h5cc -shlib -o hdf_prog prog1.o prog2.o - </pre> + # h5cc -shlib -o hdf_prog prog1.o prog2.o</pre></dt> + <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><em>DIR</em></code> to find the HDF5 + <ul><table> + <tr> + <td valign="top"><code>-help</code></td> + <td valign="top">Prints a help message.</td></tr> + <tr> + <td valign="top"><code>-echo</code></td> + <td valign="top">Show all the shell commands executed.</td></tr> + <tr> + <td valign="top"><code>-prefix=DIR</code></td> + <td valign="top">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. + Default: prefix specified when configuring HDF5.</td></tr> + <tr> + <td valign="top"><code>-show</code></td> + <td valign="top">Show the commands without executing them.</td></tr> + <tr> + <td valign="top"><code>-shlib</code></td> + <td valign="top">Compile using shared HDF5 libraries.</td></tr> + <tr> + <td valign="top"><code>-noshlib</code></td> + <td valign="top">Compile using static HDF5 libraries [default].</td></tr> + <tr> + <td valign="top"><em><compile line> </em></td> + <td valign="top">The normal compile line options for your compiler. <code>h5cc</code> uses the same compiler you used to compile HDF5. Check your compiler's manual for more information on which - options are needed. - </dl> + options are needed.</td></tr> + </table></ul> <dt><strong>Environment Variables:</strong> <dd>When set, these environment variables override some of the built-in defaults of <code>h5cc</code>. - <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> + <ul><table> + <tr> + <td valign="top"><code>HDF5_CC</code></td> + <td valign="top">Use a different C compiler.</td></tr> + <tr> + <td valign="top"><code>HDF5_CLINKER</code></td> + <td valign="top">Use a different linker.</td></tr> + <tr> + <td valign="top"><code>HDF5_USE_SHLIB=[yes|no] </code></td> + <td valign="top">Use shared version of the HDF5 library [default: no].</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -2126,7 +2364,8 @@ installed with HDF5. --> </dl> - +<!-- NEW PAGE --> +<!-- HEADER RIGHT "h5fc" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-H5FC">h5fc</a> @@ -2162,37 +2401,43 @@ installed with HDF5. <pre> # h5fc -c prog1.f90 # h5fc -c prog2.f90 - # h5fc -o hdf_prog prog1.o prog2.o - </pre> + # h5fc -o hdf_prog prog1.o prog2.o</pre></dt> + <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 + <ul><table> + <tr> + <td valign="top"><code>-help</code></td> + <td valign="top">Prints a help message.</td></tr> + <tr> + <td valign="top"><code>-echo</code></td> + <td valign="top">Show all the shell commands executed.</td></tr> + <tr> + <td valign="top"><code>-prefix=DIR</code></td> + <td valign="top">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. + Default: prefix specified when configuring HDF5.</td></tr> + <tr> + <td valign="top"><code>-show</code></td> + <td valign="top">Show the commands without executing them.</td></tr> + <tr> + <td valign="top"><em><compile line> </em></td> + <td valign="top">The normal compile line options for your compiler. <code>h5fc</code> uses the same compiler you used to compile HDF5. Check your compiler's manual for - more information on which options are needed. - </dl> + more information on which options are needed.</td></tr> + </table></ul> <dt><strong>Environment Variables:</strong> <dd>When set, these environment variables override some of the built-in defaults of <code>h5cc</code>. - <dl> - <dt><code>HDF5_FC</code> - <dd>Use a different Fortran90 compiler. - <dt><code>HDF5_FLINKER</code> - <dd>Use a different linker. - </dl> + <ul><table> + <tr> + <td valign="top"><code>HDF5_FC</code></td> + <td valign="top">Use a different Fortran90 compiler.</td></tr> + <tr> + <td valign="top"><code>HDF5_FLINKER </code></td> + <td valign="top">Use a different linker.</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -2202,6 +2447,7 @@ installed with HDF5. </dl> <!-- NEW PAGE --> +<!-- HEADER RIGHT "h5c++" --> <hr> <dl> <dt><strong>Tool Name:</strong> <a name="Tools-H5C++">h5c++</a> @@ -2237,35 +2483,43 @@ installed with HDF5. # 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 + <ul><table> + <tr> + <td valign="top"><code>-help</code></td> + <td valign="top">Prints a help message.</td></tr> + <tr> + <td valign="top"><code>-echo</code></td> + <td valign="top">Show all the shell commands executed.</td></tr> + <tr> + <td valign="top"><code>-prefix=DIR</code></td> + <td valign="top">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. + Default: prefix specified when configuring HDF5.</td></tr> + <tr> + <td valign="top"><code>-show</code></td> + <td valign="top">Show the commands without executing them.</td></tr> + <tr> + <td valign="top"><em><compile line></em><br> + <code> </code></td> + <td valign="top">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> + more information on which options are needed.</td></tr> + </table></ul> <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> + <ul><table> + <tr> + <td valign="top"><code>HDF5_CXX</code></td> + <td valign="top">Use a different C++ compiler.</td></tr> + <tr> + <td valign="top"><code>HDF5_CXXLINKER </code></td> + <td valign="top">Use a different linker.</td></tr> + </table></ul> <!-- <dt><strong>Current Status:</strong> <dd> @@ -2320,6 +2574,8 @@ installed with HDF5. --> +<!-- HEADER RIGHT " " --> + <!-- #BeginLibraryItem "/ed_libs/NavBar_RM.lbi" --><hr> <center> @@ -2360,7 +2616,7 @@ And in this document, the Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0 </address><!-- #EndLibraryItem --><dt><dt><SCRIPT LANGUAGE="JAVASCRIPT"> <!-- -document.writeln("Last modified: 24 February 2004"); +document.writeln("Last modified: 11 March 2004"); --> </SCRIPT> |