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HTML
2743 lines
118 KiB
HTML
<html>
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<head><title>
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HDF5/Tools API Specification
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</title>
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<!-- #BeginLibraryItem "/ed_libs/styles_RM.lbi" -->
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
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<link href="ed_styles/RMelect.css" rel="stylesheet" type="text/css">
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<body bgcolor="#FFFFFF">
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<!-- #BeginLibraryItem "/ed_libs/NavBar_RM.lbi" --><hr>
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<center>
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<table border=0 width=98%>
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<tr><td valign=top align=left>
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<a href="index.html">HDF5 documents and links</a> <br>
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<a href="H5.intro.html">Introduction to HDF5</a> <br>
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<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User Guide</a> <br>
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<!--
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<a href="Glossary.html">Glossary</a><br>
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-->
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</td>
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<td valign=top align=right>
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And in this document, the
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<a href="RM_H5Front.html">HDF5 Reference Manual</a>
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<br>
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<a href="RM_H5.html">H5</a>
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<a href="RM_H5A.html">H5A</a>
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<a href="RM_H5D.html">H5D</a>
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<a href="RM_H5E.html">H5E</a>
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<a href="RM_H5F.html">H5F</a>
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<a href="RM_H5G.html">H5G</a>
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<a href="RM_H5I.html">H5I</a>
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<a href="RM_H5P.html">H5P</a>
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<br>
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<a href="RM_H5R.html">H5R</a>
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<a href="RM_H5S.html">H5S</a>
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<a href="RM_H5T.html">H5T</a>
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<a href="RM_H5Z.html">H5Z</a>
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<a href="Tools.html">Tools</a>
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<a href="PredefDTypes.html">Datatypes</a>
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</td></tr>
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</table>
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</center>
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<hr><!-- #EndLibraryItem --><center>
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<h1>HDF5 Tools</h1>
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</center>
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<!-- HEADER RIGHT "HDF5 Tools" -->
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<h2>HDF5 Tool Interfaces</h2>
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<p>
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HDF5-related tools are available to assist the user in a variety of
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activities, including
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examining or managing HDF5 files,
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converting raw data between HDF5 and other special-purpose formats,
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moving data and files between the HDF4 and HDF5 formats,
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measuring HDF5 library performance, and
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managing HDF5 library and application compilation,
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installation and configuration.
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Unless otherwise specified below, these tools are distributed and
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installed with HDF5.
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<!--
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<table border=0>
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<tr><td valign=top>
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-->
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<ul>
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<li>User utilities:
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<ul>
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<li><a href="#Tools-Dump">h5dump</a> --
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Enables a user to examine the contents of an HDF5 file
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and dump those contents to an ASCII file
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<li><a href="#Tools-Ls">h5ls</a> --
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Lists specified features of HDF5 file contents
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<li><a href="#Tools-Diff">h5diff</a> --
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Compares two HDF5 files and reports the differences.
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<li><a href="#Tools-Repack">h5repack</a> -- Copies an HDF5 file to a new
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file with or without compression/chunking.
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<li><a href="#Tools-Perf">h5perf</a> --
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Measures HDF5 performance
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<li><a href="#Tools-Repart">h5repart</a> --
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Repartitions a file, creating a family of files
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<br><br>
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</ul>
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<li>Configuration and library management utilities:
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<ul>
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<li><a href="#Tools-Redeploy">h5redeploy</a> --
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Updates HDF5 compiler tools after an HDF5 software installation
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in a new location
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<li><a href="#Tools-H5CC">h5cc</a> --
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Simplifies the compilation of HDF5 programs written in C
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<li><a href="#Tools-H5FC">h5fc</a> --
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Simplifies the compilation of HDF5 programs written in Fortran90
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<li><a href="#Tools-H5C++">h5c++</a> --
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Simplifies the compilation of HDF5 programs written in C++
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<br><br>
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</ul>
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<li><a href="http://hdf.ncsa.uiuc.edu/hdf-java-html/"
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target="ToolsExt">Java-based tools for HDF5</a>
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for viewing, manipulating, and generating HDF4 and HDF5 files:
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<br>
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<em>(Distributed separately; external link is
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<code>http://hdf.ncsa.uiuc.edu/hdf-java-html/</code>)</em>
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<ul>
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<li><code>HDFview</code> -- a browser that
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works with both HDF4 and HDF5 files and
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can be used to transfer data between the two formats
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<li>Java interfaces for both the HDF4 and HDF5 libraries
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<li>Other HDF4- and HDF5-related products
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<br><br>
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</ul>
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<li>Data conversion utilities:
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<ul>
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<li><a href="#Tools-Import">h5import</a> --
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Imports data into an existing or new HDF5 file
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<li><a href="#Tools-GIF2H5">gif2h5</a> --
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Converts a GIF file to an HDF5 file
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<li><a href="#Tools-H52GIF">h52gif</a> --
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Converts images in an HDF5 file to a GIF file
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<br><br>
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</ul>
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<li><a href="http://hdf.ncsa.uiuc.edu/h4toh5/" target="ToolsExt">
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HDF5/HDF4 conversion tools</a>:
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<br>
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<em>(Distributed separately; external link is
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<code>http://hdf.ncsa.uiuc.edu/h4toh5/</code>)</em>
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<ul>
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<li><a href="http://hdf.ncsa.uiuc.edu/h4toh5/"
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target="ToolsExt">H4toH5 Conversion Library</a> --
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Provides APIs for use in tools that perform customized
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conversions of HDF4 files to HDF5 files
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<li><a href="#Tools-H5toh4">h5toh4</a> --
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Converts an HDF5 file to an HDF4 file
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<li><a href="#Tools-H4toh5">h4toh5</a> --
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Converts an HDF4 file to an HDF5 file
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<br><br>
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</ul>
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<li><a href="http://hdf.ncsa.uiuc.edu/tools5.html"
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target="ToolsExt">Other tools</a>,
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including third-party and commercial utilities and applications
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<br>
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<em>(Distributed separately; external link is
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<code>http://hdf.ncsa.uiuc.edu/tools5.html</code>)</em>
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||
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||
</ul>
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<!--
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||
</td></tr>
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||
</table>
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||
-->
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||
<!-- NEW PAGE -->
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<!-- NEW PAGE -->
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<!-- HEADER RIGHT "h5dump" -->
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<p>
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<hr>
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<dl>
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<dt><strong>Tool Name:</strong> <a name="Tools-Dump">h5dump</a>
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<dt><strong>Syntax:</strong>
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<dd><code>h5dump
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[</code><em>OPTIONS</em><code>]</code> <em>file</em>
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<dt><strong>Purpose:</strong>
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<dd>Displays HDF5 file contents.
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<dt><strong>Description:</strong>
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<dd><code>h5dump</code> enables the user to examine
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the contents of an HDF5 file and dump those contents, in human
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readable form, to an ASCII file.
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<p>
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<code>h5dump</code> dumps HDF5 file content to standard output.
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It can display the contents of the entire HDF5 file or
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selected objects, which can be groups, datasets, a subset of a
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dataset, links, attributes, or datatypes.
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<p>
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The <code>--header</code> option displays object header
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information only.
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<p>
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Names are the absolute names of the objects. <code>h5dump</code>
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displays objects in the order same as the command order. If a
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name does not start with a slash, <code>h5dump</code> begins
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searching for the specified object starting at the root group.
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<p>
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If an object is hard linked with multiple names,
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<code>h5dump</code> displays the content of the object in the
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first occurrence. Only the link information is displayed in later
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occurrences.
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<p>
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<code>h5dump</code> assigns a name for any unnamed datatype in
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the form of
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<code>#</code><em>oid1</em><code>:</code><em>oid2</em>, where
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<em>oid1</em> and <em>oid2</em> are the object identifiers
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assigned by the library. The unnamed types are displayed within
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the root group.
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<p>
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Datatypes are displayed with standard type names. For example,
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if a dataset is created with <code>H5T_NATIVE_INT</code> type
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and the standard type name for integer on that machine is
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<code>H5T_STD_I32BE</code>, <code>h5dump</code> displays
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<code>H5T_STD_I32BE</code> as the type of the dataset.
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<p>
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<code>h5dump</code> can also dump a subset of a dataset.
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This feature operates in much the same way as hyperslabs in HDF5;
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the parameters specified on the command line are passed to the
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function <a href="RM_H5S.html#Dataspace-SelectHyperslab">
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<code>H5Sselect_hyperslab</code></a> and the resulting selection
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is displayed.
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<p>
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The <code>h5dump</code> output is described in detail in the
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<a href="ddl.html"><cite>DDL for HDF5</cite></a>, the
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<cite>Data Description Language</cite> document.
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||
<p>
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<em>Note</em>: It is not permissible to specify multiple
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attributes, datasets, datatypes, groups, or soft links with one
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flag. For example, one may not issue the command
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<br>
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<font size=-1>WRONG:</font>
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<code>h5dump -a /attr1 /attr2 foo.h5</code>
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</br>
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to display both <code>/attr1</code> and <code>/attr2</code>.
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One must issue the following command:
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<br>
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<font size=-1>CORRECT:</font>
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<code>h5dump -a /attr1 -a /attr2 foo.h5</code>
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</br>
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<p>
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It's possible to select the file driver with which to open the
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HDF5 file by using the --filedriver (-f) command-line option.
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Acceptable values for the --filedriver option are: "sec2",
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"family", "split", "multi", and "stream". If the file driver flag
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isn't specified, then the file will be opened with each driver in
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turn and in the order specified above until one driver succeeds
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in opening the file.
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</p>
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<p>
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One byte integer type data is displayed in decimal by default. When
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displayed in ASCII, a non-printable code is displayed in 3 octal
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||
digits preceeded by a back-slash unless there is a C language escape
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sequence for it. For example, CR and LF are printed as \r and \n.
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||
Though the NUL code is represented as \0 in C, it is printed as
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||
\000 to avoid ambiguity as illustrated in the following 1 byte
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||
char data (since this is not a string, embedded NUL is possible).
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<pre>
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141 142 143 000 060 061 062 012
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a b c \0 0 1 2 \n </pre>
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h5dump prints them as "abc\000012\n". But if h5dump prints NUL as \0,
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the output is "abc\0012\n" which is ambiguous.
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</p>
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||
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<!-- NEW PAGE -->
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<dt><strong>XML Output:</strong>
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<dd>With the <code>--xml</code> option, <code>h5dump</code> generates
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XML output. This output contains a complete description of the file,
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marked up in XML. The XML conforms to the HDF5 Document Type
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Definition (DTD) available at
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<a href="http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd">
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<code>http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd</code></a>.
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<p>
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The XML output is suitable for use with other tools, including the
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<a href="http://hdf.ncsa.uiuc.edu/java-hdf5-html">HDF5 Java Tools</a>.
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<dt><strong>Options and Parameters:</strong>
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<ul>
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<table>
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<tr>
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<td valign="top"><code>-h</code> or <code>--help</code></td>
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<td valign="top">Print a usage message and exit.</td>
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</tr>
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<tr>
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<td valign="top"><code>-B</code> or <code>--bootblock</code></td>
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<td valign="top">Print the content of the boot block.<br> <em>(This
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option is not yet implemented.)</em></td>
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</tr>
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<tr>
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<td valign="top"><code>-H</code> or <code>--header</code></td>
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<td valign="top">Print the header only; no data is displayed.</td>
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</tr>
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<tr>
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<td valign="top"><code>-A</code></td>
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<td valign="top">Print the header and value of attributes; data of datasets
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is not displayed.</td>
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</tr>
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<tr>
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<td valign="top"><code>-i</code> or <code>--object-ids</code></td>
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<td valign="top">Print the object ids.</td>
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</tr>
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<tr>
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<td valign="top"><code>-r</code> or <code>--string</code></td>
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<td valign="top">Print 1-bytes integer datasets as ASCII.</td>
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</tr>
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<tr>
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<td valign="top"><code>-V</code> or <code>--version</code></td>
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<td valign="top">Print version number and exit.</td>
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</tr>
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<tr>
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<td valign="top"><code>-a <em>P</em></code> or <code>--attribute=<em>P</em> </code></td>
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<td valign="top">Print the specified attribute.</td>
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</tr>
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<tr>
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<td valign="top"><code>-d <em>P</em></code> or
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<code>--dataset=<em>P</em></code></td>
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<td valign="top">Print the specified dataset.</td>
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</tr>
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<tr>
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<td valign="top"><code>-f<em> D</em></code> or <code>--filedriver=<em>D </em> </code></td>
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<td valign="top">Specify which driver to open the file with.</td>
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</tr>
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<tr>
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<td valign="top"><code>-g <em>P</em></code> or
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<code>--group=<em>P</em></code></td>
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<td valign="top">Print the specified group and all members.</td>
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</tr>
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<tr>
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<td valign="top"><code>-l <em>P</em></code> or <code>--soft-link=<em>P </em></code></td>
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<td valign="top">Print the value(s) of the specified soft link.</td>
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||
</tr>
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<tr>
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<td valign="top"><code>-o <em>F</em></code> or
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<code>--output=<em>F</em></code></td>
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<td valign="top">Output raw data into file F.</td>
|
||
</tr>
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||
<tr>
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||
<td valign="top"><code>-t <em>T</em></code> or
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||
<code>--datatype=<em>T</em></code></td>
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||
<td valign="top">Print the specified named datatype.</td>
|
||
</tr>
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||
<tr>
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||
<td valign="top"><code>-w <em>N</em></code> or
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||
<code>--width=<em>N</em></code></td>
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||
<td valign="top">Set the number of columns of output.</td>
|
||
</tr>
|
||
<tr>
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||
<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
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||
<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>
|
||
<!-- 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</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</td></tr>
|
||
</table>
|
||
|
||
<p>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.
|
||
</ul>
|
||
<dt><strong>Examples:</strong>
|
||
|
||
<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>:<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>:<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>:<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>:<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:<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:
|
||
<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>
|
||
<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>
|
||
<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>
|
||
<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.</td></tr>
|
||
</table></ul>
|
||
<!--
|
||
<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.<2E>
|
||
<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>
|
||
<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">help message.</td></tr>
|
||
<tr>
|
||
<td valign="top"><code>-r</code></td>
|
||
<td valign="top">Report mode. Print the differences.</td></tr>
|
||
<tr>
|
||
<td valign="top"><code>-v</code></td>
|
||
<td valign="top">Verbose mode. Print the differences, list of objects, warnings.</td>
|
||
</tr>
|
||
<tr>
|
||
<td valign="top"><code>-q</code></td>
|
||
<td valign="top">Quiet mode. Do not print output.</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>
|
||
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>
|
||
<!--
|
||
<dt><strong>Current Status:</strong>
|
||
<dd>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</dl>
|
||
|
||
<!-- NEW PAGE -->
|
||
<!-- HEADER RIGHT "h5repart" -->
|
||
<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>
|
||
|
||
<p> </p>
|
||
<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>
|
||
<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>
|
||
<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>
|
||
|
||
<!-- NEW PAGE -->
|
||
|
||
<dt><strong>Options and Parameters:</strong>
|
||
|
||
<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.</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
|
||
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.</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>.</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>.</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></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>
|
||
<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>
|
||
|
||
|
||
<!--
|
||
<dt><strong>Current Status:</strong>
|
||
<dd>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</dl>
|
||
|
||
<!-- NEW PAGE -->
|
||
<!-- HEADER RIGHT "gif2h5" -->
|
||
<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>
|
||
<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>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</dl>
|
||
|
||
<!-- NEW PAGE -->
|
||
<!-- 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>
|
||
<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>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</dl>
|
||
|
||
<!-- NEW PAGE -->
|
||
<!-- 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>
|
||
<dd>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>
|
||
<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>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</dl>
|
||
|
||
<!-- NEW PAGE -->
|
||
<!-- 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>
|
||
<dd>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>
|
||
<ul><table>
|
||
<tr>
|
||
<td valign="top"><code>-h</code></td>
|
||
<td valign="top">Displays a syntax summary.</td></tr>
|
||
<!-- currently no -m option
|
||
<tr>
|
||
<td valign="top"><code>-m</code></td>
|
||
<td valign="top">Converts multiple HDF4 files to multiple HDF5 files.</td></tr>
|
||
-->
|
||
<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>
|
||
<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>
|
||
|
||
<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 -->
|
||
<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 -->
|
||
<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>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</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>
|
||
<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>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</dl>
|
||
|
||
<!-- NEW PAGE -->
|
||
<!-- HEADER RIGHT "h5cc" -->
|
||
<hr>
|
||
<dl>
|
||
<dt><strong>Tool Name:</strong> <a name="Tools-H5CC">h5cc</a>
|
||
<dt><strong>Syntax:</strong>
|
||
<dd><code>h5cc
|
||
[</code><em>OPTIONS</em><code>]</code> <em><compile line></em>
|
||
<dt><strong>Purpose:</strong>
|
||
<dd>Helper script to compile HDF5 applications.
|
||
<dt><strong>Description:</strong>
|
||
<dd><code>h5cc</code> can be used in much the same way 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>h5cc</code> supersedes all other compiler scripts in that
|
||
if you've used them to compile the HDF5 library, then
|
||
<code>h5cc</code> also uses those scripts. For example, when
|
||
compiling an MPIch program, you use the <code>mpicc</code>
|
||
script. If you've 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 isn't necessary
|
||
to use <code>h5cc</code> to compile those modules which don't use
|
||
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>
|
||
|
||
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>
|
||
# h5cc -c prog1.c
|
||
# h5cc -c prog2.c
|
||
# h5cc -shlib -o hdf_prog prog1.o prog2.o</pre>
|
||
|
||
<dt><strong>Options and Parameters:</strong>
|
||
<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.</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.</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>.
|
||
|
||
<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>
|
||
<dt><strong>See Also:</strong>
|
||
<dd>
|
||
-->
|
||
</dl>
|
||
|
||
<!-- NEW PAGE -->
|
||
<!-- HEADER RIGHT "h5fc" -->
|
||
<hr>
|
||
<dl>
|
||
<dt><strong>Tool Name:</strong> <a name="Tools-H5FC">h5fc</a>
|
||
<dt><strong>Syntax:</strong>
|
||
<dd><code>h5fc
|
||
[</code><em>OPTIONS</em><code>]</code> <em><compile line></em>
|
||
<dt><strong>Purpose:</strong>
|
||
<dd>Helper script to compile HDF5 Fortran90 applications.
|
||
<dt><strong>Description:</strong>
|
||
<dd><p>
|
||
<code>h5fc</code> can be used in much the same way 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>h5fc</code> supersedes all other compiler scripts in that
|
||
if you've used them to compile the HDF5 Fortran library, then
|
||
<code>h5fc</code> also uses those scripts. For example, when
|
||
compiling an MPIch program, you use the <code>mpif90</code>
|
||
script. If you've 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 isn't necessary
|
||
to use <code>h5fc</code> to compile those modules which don't use
|
||
HDF5. In fact, since <code>h5fc</code> is only a convenience
|
||
script, you are still able to compile HDF5 Fortran modules in the
|
||
normal way. In that case, you will have to specify the HDF5 libraries
|
||
and include paths yourself.
|
||
<p>
|
||
An example of how to use <code>h5fc</code> to compile the program
|
||
<code>hdf_prog</code>, which consists of modules
|
||
<code>prog1.f90</code> and <code>prog2.f90</code>
|
||
and uses the HDF5 Fortran library, would be as follows:
|
||
<pre>
|
||
# h5fc -c prog1.f90
|
||
# h5fc -c prog2.f90
|
||
# h5fc -o hdf_prog prog1.o prog2.o</pre>
|
||
|
||
<dt><strong>Options and Parameters:</strong>
|
||
<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.</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.</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>.
|
||
<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>
|
||
<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 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> supersedes 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.
|
||
<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>
|
||
<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.</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.</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>.
|
||
<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>
|
||
<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>
|
||
|
||
|
||
-->
|
||
|
||
<!-- HEADER RIGHT " " -->
|
||
|
||
|
||
<!-- #BeginLibraryItem "/ed_libs/NavBar_RM.lbi" --><hr>
|
||
<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>
|
||
</table>
|
||
</center>
|
||
<hr><!-- #EndLibraryItem --><!-- #BeginLibraryItem "/ed_libs/Footer.lbi" --><address>
|
||
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
|
||
<br>
|
||
Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0
|
||
</address><!-- #EndLibraryItem -->
|
||
<dl>
|
||
<dt><dt><SCRIPT LANGUAGE="JAVASCRIPT">
|
||
<!--
|
||
document.writeln("Last modified: 24 November 2004");
|
||
-->
|
||
</SCRIPT>
|
||
|
||
</body>
|
||
</html>
|