1998-08-20 06:46:31 +08:00
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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
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<html>
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<head>
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<title>Debugging HDF5 Applications</title>
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1998-12-22 06:52:56 +08:00
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2003-07-03 05:28:11 +08:00
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<!-- #BeginLibraryItem "/ed_libs/styles_UG.lbi" -->
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<!--
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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/UGelect.css" rel="stylesheet" type="text/css">
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2003-03-15 03:12:34 +08:00
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<!-- #EndLibraryItem --></head>
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1998-12-22 06:52:56 +08:00
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2003-03-15 03:12:34 +08:00
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<body bgcolor="#FFFFFF">
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<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.lbi" --><hr>
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1998-12-22 06:52:56 +08:00
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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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2003-03-15 03:12:34 +08:00
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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="RM_H5Front.html">HDF5 Reference Manual</a> <br>
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2003-07-04 03:35:53 +08:00
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<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide for Release 1.6</a> <br>
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2003-03-15 03:12:34 +08:00
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<!--
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<a href="Glossary.html">Glossary</a><br>
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-->
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1998-12-22 06:52:56 +08:00
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</td>
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<td valign=top align=right>
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2003-03-15 03:12:34 +08:00
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And in this document, the
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2003-07-04 03:35:53 +08:00
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<a href="H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>
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2003-03-15 03:12:34 +08:00
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<br>
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<a href="Files.html">Files</a>
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<a href="Datasets.html">Datasets</a>
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<a href="Datatypes.html">Datatypes</a>
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<a href="Dataspaces.html">Dataspaces</a>
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<a href="Groups.html">Groups</a>
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<br>
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<a href="References.html">References</a>
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<a href="Attributes.html">Attributes</a>
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<a href="Properties.html">Property Lists</a>
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<a href="Errors.html">Error Handling</a>
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<br>
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<a href="Filters.html">Filters</a>
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<a href="Caching.html">Caching</a>
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<a href="Chunking.html">Chunking</a>
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<a href="MountingFiles.html">Mounting Files</a>
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<br>
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<a href="Performance.html">Performance</a>
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<a href="Debugging.html">Debugging</a>
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<a href="Environment.html">Environment</a>
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<a href="ddl.html">DDL</a>
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1998-12-22 06:52:56 +08:00
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</td></tr>
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</table>
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</center>
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<hr>
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2003-03-15 03:12:34 +08:00
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<!-- #EndLibraryItem --><h1>Debugging HDF5 Applications</h1>
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1998-08-20 06:46:31 +08:00
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<h2>Introduction</h2>
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<p>The HDF5 library contains a number of debugging features to
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1998-08-21 06:57:35 +08:00
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make programmers' lives easier including the ability to print
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1998-08-20 06:46:31 +08:00
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detailed error messages, check invariant conditions, display
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timings and other statistics, and trace API function calls and
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return values.
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<dl>
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<dt><b>Error Messages</b>
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<dd>Error messages are normally displayed automatically on the
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standard error stream and include a stack trace of the library
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including file names, line numbers, and function names. The
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application has complete control over how error messages are
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displayed and can disable the display on a permanent or
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temporary basis. Refer to the documentation for the H5E error
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handling package.
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<br><br>
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<dt><b>Invariant Conditions</b>
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1998-08-21 06:57:35 +08:00
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<dd>Unless <code>NDEBUG</code> is defined during compiling, the
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1998-08-20 06:46:31 +08:00
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library will include code to verify that invariant conditions
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have the expected values. When a problem is detected the
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library will display the file and line number within the
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library and the invariant condition that failed. A core dump
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may be generated for post mortem debugging. The code to
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perform these checks can be included on a per-package bases.
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<br><br>
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<dt><b>Timings and Statistics</b>
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<dd>The library can be configured to accumulate certain
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statistics about things like cache performance, datatype
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1998-08-20 06:46:31 +08:00
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conversion, data space conversion, and data filters. The code
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is included on a per-package basis and enabled at runtime by
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an environment variable.
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<br><br>
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<dt><b>API Tracing</b>
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<dd>All API calls made by an application can be displayed and
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include formal argument names and actual values and the
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function return value. This code is also conditionally
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included at compile time and enabled at runtime.
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</dl>
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<p>The statistics and tracing can be displayed on any output
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stream (including streams opened by the shell) with output from
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different packages even going to different streams.
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<h2>Error Messages</h2>
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<p>By default any API function that fails will print an error
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stack to the standard error stream.
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<p>
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<center>
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<table border align=center width="100%">
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<tr>
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<td>
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<p><code><pre>
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1998-08-20 06:46:31 +08:00
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HDF5-DIAG: Error detected in thread 0. Back trace follows.
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1998-08-21 06:57:35 +08:00
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#000: H5F.c line 1245 in H5Fopen(): unable to open file
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major(04): File interface
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minor(10): Unable to open file
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#001: H5F.c line 846 in H5F_open(): file does not exist
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major(04): File interface
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minor(10): Unable to open file
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1998-08-20 06:46:31 +08:00
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</code></pre>
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</td>
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</tr>
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</table>
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</center>
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<p>The error handling package (H5E) is described
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1998-08-21 06:57:35 +08:00
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<a href="Errors.html">elsewhere</a>.
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1998-08-20 06:46:31 +08:00
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<h2>Invariant Conditions</h2>
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<p>To include checks for invariant conditions the library should
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be configured with <code>--disable-production</code>, the
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default for versions before 1.2. The library designers have made
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every attempt to handle error conditions gracefully but an
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invariant condition assertion may fail in certain cases. The
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output from a failure usually looks something like this:
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<p>
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<center>
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<table border align=center width="100%">
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<tr>
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<td>
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<p><code><pre>
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1998-08-21 06:57:35 +08:00
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1998-08-20 06:46:31 +08:00
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Assertion failed: H5.c:123: i<NELMTS(H5_debug_g)
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IOT Trap, core dumped.
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</code></pre>
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</td>
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</tr>
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</table>
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</center>
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<h2>Timings and Statistics</h2>
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<p>Code to accumulate statistics is included at compile time by
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using the <code>--enable-debug</code> configure switch. The
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switch can be followed by an equal sign and a comma-separated
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list of package names or else a default list is used.
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<p>
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<center>
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<table border align=center width="80%">
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<tr>
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<th>Name</th>
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<th>Default</th>
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<th>Description</th>
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</tr>
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<tr>
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<td align=center>a</td>
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<td align=center>No</td>
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<td>Attributes</td>
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</tr>
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<tr>
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<td align=center>ac</td>
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<td align=center>Yes</td>
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<td>Meta data cache</td>
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</tr>
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<tr>
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<td align=center>b</td>
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<td align=center>Yes</td>
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<td>B-Trees</td>
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</tr>
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<tr>
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<td align=center>d</td>
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<td align=center>Yes</td>
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<td>Datasets</td>
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</tr>
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<tr>
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<td align=center>e</td>
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<td align=center>Yes</td>
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<td>Error handling</td>
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</tr>
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<tr>
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<td align=center>f</td>
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<td align=center>Yes</td>
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<td>Files</td>
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</tr>
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<tr>
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<td align=center>g</td>
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<td align=center>Yes</td>
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<td>Groups</td>
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</tr>
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<tr>
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<td align=center>hg</td>
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<td align=center>Yes</td>
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<td>Global heap</td>
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</tr>
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<tr>
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<td align=center>hl</td>
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<td align=center>No</td>
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<td>Local heaps</td>
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</tr>
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<tr>
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<td align=center>i</td>
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<td align=center>Yes</td>
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<td>Interface abstraction</td>
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</tr>
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<tr>
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<td align=center>mf</td>
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<td align=center>No</td>
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<td>File memory management</td>
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</tr>
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<tr>
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<td align=center>mm</td>
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<td align=center>Yes</td>
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<td>Library memory managment</td>
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</tr>
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<tr>
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<td align=center>o</td>
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<td align=center>No</td>
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<td>Object headers and messages</td>
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</tr>
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<tr>
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<td align=center>p</td>
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<td align=center>Yes</td>
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<td>Property lists</td>
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</tr>
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<tr>
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<td align=center>s</td>
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<td align=center>Yes</td>
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<td>Data spaces</td>
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</tr>
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<tr>
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<td align=center>t</td>
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<td align=center>Yes</td>
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1999-12-14 04:39:48 +08:00
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<td>Datatypes</td>
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1998-08-20 06:46:31 +08:00
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</tr>
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<tr>
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<td align=center>v</td>
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<td align=center>Yes</td>
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<td>Vectors</td>
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</tr>
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<tr>
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<td align=center>z</td>
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<td align=center>Yes</td>
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<td>Raw data filters</td>
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</tr>
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</table>
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</center>
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<p>In addition to including the code at compile time the
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application must enable each package at runtime. This is done
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by listing the package names in the <code>HDF5_DEBUG</code>
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environment variable. That variable may also contain file
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descriptor numbers (the default is `2') which control the output
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for all following packages up to the next file number. The
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word <code>all</code> refers to all packages. Any word my be
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preceded by a minus sign to turn debugging off for the package.
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<p>
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<center>
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<table border align=center width="100%">
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<caption align=top><b>Sample debug specifications</b></caption>
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<tr valign=top>
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<td><code>all</code></td>
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<td>This causes debugging output from all packages to be
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sent to the standard error stream.</td>
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</tr>
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<tr valign=top>
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<td><code>all -t -s</code></td>
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1999-12-14 04:39:48 +08:00
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<td>Debugging output for all packages except datatypes
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1998-08-20 06:46:31 +08:00
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and data spaces will appear on the standard error
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stream.</td>
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</tr>
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<tr valign=top>
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<td><code>-all ac 255 t,s</code></td>
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<td>This disables all debugging even if the default was to
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debug something, then output from the meta data cache is
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send to the standard error stream and output from data
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types and spaces is sent to file descriptor 255 which
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should be redirected by the shell.</td>
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</tr>
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</table>
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</center>
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<p>The components of the <code>HDF5_DEBUG</code> value may be
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separated by any non-lowercase letter.
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<h2>API Tracing</h2>
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<p>The HDF5 library can trace API calls by printing the
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function name, the argument names and their values, and the
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return value. Some people like to see lots of output during
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program execution instead of using a good symbolic debugger, and
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this feature is intended for their consumption. For example,
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the output from <code>h5ls foo</code> after turning on tracing,
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includes:
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<p>
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<center>
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<table border align=center width="100%">
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<tr>
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<td>
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<code><pre>
|
1998-08-21 06:57:35 +08:00
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1998-08-20 06:46:31 +08:00
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H5Tcopy(type=184549388) = 184549419 (type);
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H5Tcopy(type=184549392) = 184549424 (type);
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H5Tlock(type=184549424) = SUCCEED;
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H5Tcopy(type=184549393) = 184549425 (type);
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H5Tlock(type=184549425) = SUCCEED;
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|
H5Fopen(filename="foo", flags=0, access=H5P_DEFAULT) = FAIL;
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|
|
HDF5-DIAG: Error detected in thread 0. Back trace follows.
|
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|
#000: H5F.c line 1245 in H5Fopen(): unable to open file
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major(04): File interface
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minor(10): Unable to open file
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#001: H5F.c line 846 in H5F_open(): file does not exist
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|
major(04): File interface
|
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minor(10): Unable to open file
|
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|
|
</pre></code>
|
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</td>
|
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|
</tr>
|
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|
</table>
|
|
|
|
|
</center>
|
|
|
|
|
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|
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|
|
<p>The code that performs the tracing must be included in the
|
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|
|
library by specifying the <code>--enable-trace</code>
|
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|
|
|
configuration switch (the default for versions before 1.2). Then
|
|
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|
|
the word <code>trace</code> must appear in the value of the
|
|
|
|
|
<code>HDF5_DEBUG</code> variable. The output will appear on the
|
|
|
|
|
last file descriptor before the word <code>trace</code> or two
|
|
|
|
|
(standard error) by default.
|
|
|
|
|
|
|
|
|
|
<p>
|
|
|
|
|
<center>
|
|
|
|
|
<table border align=center width="100%">
|
|
|
|
|
<tr>
|
|
|
|
|
<td>To display the trace on the standard error stream:
|
|
|
|
|
<code><pre>
|
|
|
|
|
$ env HDF5_DEBUG=trace a.out
|
|
|
|
|
</pre></code>
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td>To send the trace to a file:
|
|
|
|
|
<code><pre>
|
|
|
|
|
$ env HDF5_DEBUG="55 trace" a.out 55>trace-output
|
|
|
|
|
</pre></code>
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
</table>
|
|
|
|
|
</center>
|
|
|
|
|
|
|
|
|
|
<h3>Performance</h3>
|
|
|
|
|
|
|
|
|
|
<p>If the library was not configured for tracing then there is no
|
|
|
|
|
unnecessary overhead since all tracing code is excluded.
|
|
|
|
|
However, if tracing is enabled but not used there is a small
|
|
|
|
|
penalty. First, code size is larger because of extra
|
|
|
|
|
statically-declared character strings used to store argument
|
|
|
|
|
types and names and extra auto variable pointer in each
|
|
|
|
|
function. Also, execution is slower because each function sets
|
|
|
|
|
and tests a local variable and each API function calls the
|
|
|
|
|
<code>H5_trace()</code> function.
|
|
|
|
|
|
|
|
|
|
<p>If tracing is enabled and turned on then the penalties from the
|
|
|
|
|
previous paragraph apply plus the time required to format each
|
|
|
|
|
line of tracing information. There is also an extra call to
|
|
|
|
|
H5_trace() for each API function to print the return value.
|
|
|
|
|
|
|
|
|
|
<h3>Safety</h3>
|
|
|
|
|
|
|
|
|
|
<p>The tracing mechanism is invoked for each API function before
|
|
|
|
|
arguments are checked for validity. If bad arguments are passed
|
|
|
|
|
to an API function it could result in a segmentation fault.
|
|
|
|
|
However, the tracing output is line-buffered so all previous
|
|
|
|
|
output will appear.
|
|
|
|
|
|
|
|
|
|
<h3>Completeness</h3>
|
|
|
|
|
|
|
|
|
|
<p>There are two API functions that don't participate in
|
|
|
|
|
tracing. They are <code>H5Eprint()</code> and
|
|
|
|
|
<code>H5Eprint_cb()</code> because their participation would
|
|
|
|
|
mess up output during automatic error reporting.
|
|
|
|
|
|
|
|
|
|
<p>On the other hand, a number of API functions are called during
|
|
|
|
|
library initialization and they print tracing information.
|
|
|
|
|
|
|
|
|
|
<h3>Implementation</h3>
|
|
|
|
|
|
|
|
|
|
<p>For those interested in the implementation here is a
|
|
|
|
|
description. Each API function should have a call to one of the
|
|
|
|
|
<code>H5TRACE()</code> macros immediately after the
|
|
|
|
|
<code>FUNC_ENTER()</code> macro. The first argument is the
|
|
|
|
|
return type encoded as a string. The second argument is the
|
|
|
|
|
types of all the function arguments encoded as a string. The
|
|
|
|
|
remaining arguments are the function arguments. This macro was
|
|
|
|
|
designed to be as terse and unobtrousive as possible.
|
|
|
|
|
|
|
|
|
|
<p>In order to keep the <code>H5TRACE()</code> calls synchronized
|
|
|
|
|
with the source code we've written a perl script which gets
|
|
|
|
|
called automatically just before Makefile dependencies are
|
|
|
|
|
calculated for the file. However, this only works when one is
|
|
|
|
|
using GNU make. To reinstrument the tracing explicitly, invoke
|
|
|
|
|
the <code>trace</code> program from the hdf5 bin directory with
|
|
|
|
|
the names of the source files that need to be updated. If any
|
|
|
|
|
file needs to be modified then a backup is created by appending
|
|
|
|
|
a tilde to the file name.
|
|
|
|
|
|
|
|
|
|
<p>
|
|
|
|
|
<center>
|
|
|
|
|
<table border align=center width="100%">
|
|
|
|
|
<caption align=top><b>Explicit Instrumentation</b></caption>
|
|
|
|
|
<tr>
|
|
|
|
|
<td>
|
|
|
|
|
<code><pre>
|
1998-08-21 06:57:35 +08:00
|
|
|
|
1998-08-20 06:46:31 +08:00
|
|
|
$ ../bin/trace *.c
|
|
|
|
|
H5E.c: in function `H5Ewalk_cb':
|
|
|
|
|
H5E.c:336: warning: trace info was not inserted
|
|
|
|
|
</pre></code>
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
</table>
|
|
|
|
|
</center>
|
|
|
|
|
|
|
|
|
|
<p>Note: The warning message is the result of a comment of the
|
|
|
|
|
form <code>/*NO TRACE*/</code> somewhere in the function
|
|
|
|
|
body. Tracing information will not be updated or inserted if
|
|
|
|
|
such a comment exists.
|
|
|
|
|
|
|
|
|
|
<p>Error messages have the same format as a compiler so that they
|
|
|
|
|
can be parsed from program development environments like
|
|
|
|
|
Emacs. Any function which generates an error will not be
|
2003-03-15 03:12:34 +08:00
|
|
|
modified.</p>
|
1998-08-20 06:46:31 +08:00
|
|
|
|
|
|
|
|
|
2003-03-15 03:12:34 +08:00
|
|
|
<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.lbi" --><hr>
|
1998-12-22 06:52:56 +08:00
|
|
|
<center>
|
|
|
|
|
<table border=0 width=98%>
|
|
|
|
|
<tr><td valign=top align=left>
|
2003-03-15 03:12:34 +08:00
|
|
|
<a href="index.html">HDF5 documents and links</a> <br>
|
|
|
|
|
<a href="H5.intro.html">Introduction to HDF5</a> <br>
|
|
|
|
|
<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
|
2003-07-04 03:35:53 +08:00
|
|
|
<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide for Release 1.6</a> <br>
|
2003-03-15 03:12:34 +08:00
|
|
|
<!--
|
|
|
|
|
<a href="Glossary.html">Glossary</a><br>
|
|
|
|
|
-->
|
1998-12-22 06:52:56 +08:00
|
|
|
</td>
|
|
|
|
|
<td valign=top align=right>
|
2003-03-15 03:12:34 +08:00
|
|
|
And in this document, the
|
2003-07-04 03:35:53 +08:00
|
|
|
<a href="H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>
|
2003-03-15 03:12:34 +08:00
|
|
|
<br>
|
|
|
|
|
<a href="Files.html">Files</a>
|
|
|
|
|
<a href="Datasets.html">Datasets</a>
|
|
|
|
|
<a href="Datatypes.html">Datatypes</a>
|
|
|
|
|
<a href="Dataspaces.html">Dataspaces</a>
|
|
|
|
|
<a href="Groups.html">Groups</a>
|
|
|
|
|
<br>
|
|
|
|
|
<a href="References.html">References</a>
|
|
|
|
|
<a href="Attributes.html">Attributes</a>
|
|
|
|
|
<a href="Properties.html">Property Lists</a>
|
|
|
|
|
<a href="Errors.html">Error Handling</a>
|
|
|
|
|
<br>
|
|
|
|
|
<a href="Filters.html">Filters</a>
|
|
|
|
|
<a href="Caching.html">Caching</a>
|
|
|
|
|
<a href="Chunking.html">Chunking</a>
|
|
|
|
|
<a href="MountingFiles.html">Mounting Files</a>
|
|
|
|
|
<br>
|
|
|
|
|
<a href="Performance.html">Performance</a>
|
|
|
|
|
<a href="Debugging.html">Debugging</a>
|
|
|
|
|
<a href="Environment.html">Environment</a>
|
|
|
|
|
<a href="ddl.html">DDL</a>
|
1998-12-22 06:52:56 +08:00
|
|
|
</td></tr>
|
|
|
|
|
</table>
|
|
|
|
|
</center>
|
1998-09-10 06:48:37 +08:00
|
|
|
<hr>
|
2003-03-15 03:12:34 +08:00
|
|
|
<!-- #EndLibraryItem --><!-- #BeginLibraryItem "/ed_libs/Footer.lbi" --><address>
|
|
|
|
|
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
|
|
|
|
|
<br>
|
2003-07-04 03:35:53 +08:00
|
|
|
Describes HDF5 Release 1.4.5, February 2003
|
2003-07-03 05:28:11 +08:00
|
|
|
</address><!-- #EndLibraryItem --><!-- Created: Wed Jun 17 12:29:12 EDT 1998 -->
|
1999-12-14 04:39:48 +08:00
|
|
|
<!-- hhmts start -->
|
2003-03-15 03:12:34 +08:00
|
|
|
Last modified: 13 December 1999
|
1999-12-14 04:39:48 +08:00
|
|
|
<!-- hhmts end -->
|
1998-09-10 06:48:37 +08:00
|
|
|
|
2000-12-09 06:12:36 +08:00
|
|
|
|
2003-03-15 03:12:34 +08:00
|
|
|
</body>
|
1998-08-20 06:46:31 +08:00
|
|
|
</html>
|
