1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
|
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html>
<head>
<title>Debugging HDF5 Applications</title>
<!-- #BeginLibraryItem "/ed_libs/styles_UG.lbi" -->
<!--
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-->
<!-- #EndLibraryItem --></head>
<body bgcolor="#FFFFFF">
<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.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="../RM/RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="../UG/index.html">HDF5 User's Guide for Release 1.8</a> <br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
And in this document, the
<a href="../H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>
<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>
</td></tr>
</table>
</center>
<hr>
<!-- #EndLibraryItem --><h1>Debugging HDF5 Applications</h1>
<h2>Introduction</h2>
<p>The HDF5 library contains a number of debugging features to
make programmers' lives easier including the ability to print
detailed error messages, check invariant conditions, display
timings and other statistics, and trace API function calls and
return values.
<dl>
<dt><b>Error Messages</b>
<dd>Error messages are normally displayed automatically on the
standard error stream and include a stack trace of the library
including file names, line numbers, and function names. The
application has complete control over how error messages are
displayed and can disable the display on a permanent or
temporary basis. Refer to the documentation for the H5E error
handling package.
<br><br>
<dt><b>Invariant Conditions</b>
<dd>Unless <code>NDEBUG</code> is defined during compiling, the
library will include code to verify that invariant conditions
have the expected values. When a problem is detected the
library will display the file and line number within the
library and the invariant condition that failed. A core dump
may be generated for post mortem debugging. The code to
perform these checks can be included on a per-package bases.
<br><br>
<dt><b>Timings and Statistics</b>
<dd>The library can be configured to accumulate certain
statistics about things like cache performance, datatype
conversion, data space conversion, and data filters. The code
is included on a per-package basis and enabled at runtime by
an environment variable.
<br><br>
<dt><b>API Tracing</b>
<dd>All API calls made by an application can be displayed and
include formal argument names and actual values and the
function return value. This code is also conditionally
included at compile time and enabled at runtime.
</dl>
<p>The statistics and tracing can be displayed on any output
stream (including streams opened by the shell) with output from
different packages even going to different streams.
<h2>Error Messages</h2>
<p>By default any API function that fails will print an error
stack to the standard error stream.
<p>
<center>
<table border align=center width="100%">
<tr>
<td>
<p><code><pre>
HDF5-DIAG: Error detected in thread 0. Back trace follows.
#000: H5F.c line 1245 in H5Fopen(): unable to open file
major(04): File interface
minor(10): Unable to open file
#001: H5F.c line 846 in H5F_open(): file does not exist
major(04): File interface
minor(10): Unable to open file
</pre></code>
</td>
</tr>
</table>
</center>
<p>The error handling package (H5E) is described
<a href="Errors.html">elsewhere</a>.
<h2>Invariant Conditions</h2>
<p>To include checks for invariant conditions the library should
be configured with <code>--disable-production</code>, the
default for versions before 1.2. The library designers have made
every attempt to handle error conditions gracefully but an
invariant condition assertion may fail in certain cases. The
output from a failure usually looks something like this:
<p>
<center>
<table border align=center width="100%">
<tr>
<td>
<p><code><pre>
Assertion failed: H5.c:123: i<NELMTS(H5_debug_g)
IOT Trap, core dumped.
</pre></code>
</td>
</tr>
</table>
</center>
<h2>Timings and Statistics</h2>
<p>Code to accumulate statistics is included at compile time by
using the <code>--enable-debug</code> configure switch. The
switch can be followed by an equal sign and a comma-separated
list of package names or else a default list is used.
<p>
<center>
<table border align=center width="80%">
<tr>
<th>Name</th>
<th>Default</th>
<th>Description</th>
</tr>
<tr>
<td align=center>a</td>
<td align=center>No</td>
<td>Attributes</td>
</tr>
<tr>
<td align=center>ac</td>
<td align=center>Yes</td>
<td>Meta data cache</td>
</tr>
<tr>
<td align=center>b</td>
<td align=center>Yes</td>
<td>B-Trees</td>
</tr>
<tr>
<td align=center>d</td>
<td align=center>Yes</td>
<td>Datasets</td>
</tr>
<tr>
<td align=center>e</td>
<td align=center>Yes</td>
<td>Error handling</td>
</tr>
<tr>
<td align=center>f</td>
<td align=center>Yes</td>
<td>Files</td>
</tr>
<tr>
<td align=center>g</td>
<td align=center>Yes</td>
<td>Groups</td>
</tr>
<tr>
<td align=center>hg</td>
<td align=center>Yes</td>
<td>Global heap</td>
</tr>
<tr>
<td align=center>hl</td>
<td align=center>No</td>
<td>Local heaps</td>
</tr>
<tr>
<td align=center>i</td>
<td align=center>Yes</td>
<td>Interface abstraction</td>
</tr>
<tr>
<td align=center>mf</td>
<td align=center>No</td>
<td>File memory management</td>
</tr>
<tr>
<td align=center>mm</td>
<td align=center>Yes</td>
<td>Library memory managment</td>
</tr>
<tr>
<td align=center>o</td>
<td align=center>No</td>
<td>Object headers and messages</td>
</tr>
<tr>
<td align=center>p</td>
<td align=center>Yes</td>
<td>Property lists</td>
</tr>
<tr>
<td align=center>s</td>
<td align=center>Yes</td>
<td>Data spaces</td>
</tr>
<tr>
<td align=center>t</td>
<td align=center>Yes</td>
<td>Datatypes</td>
</tr>
<tr>
<td align=center>v</td>
<td align=center>Yes</td>
<td>Vectors</td>
</tr>
<tr>
<td align=center>z</td>
<td align=center>Yes</td>
<td>Raw data filters</td>
</tr>
</table>
</center>
<p>In addition to including the code at compile time the
application must enable each package at runtime. This is done
by listing the package names in the <code>HDF5_DEBUG</code>
environment variable. That variable may also contain file
descriptor numbers (the default is `2') which control the output
for all following packages up to the next file number. The
word <code>all</code> refers to all packages. Any word my be
preceded by a minus sign to turn debugging off for the package.
<p>
<center>
<table border align=center width="100%">
<caption align=top><b>Sample debug specifications</b></caption>
<tr valign=top>
<td><code>all</code></td>
<td>This causes debugging output from all packages to be
sent to the standard error stream.</td>
</tr>
<tr valign=top>
<td><code>all -t -s</code></td>
<td>Debugging output for all packages except datatypes
and data spaces will appear on the standard error
stream.</td>
</tr>
<tr valign=top>
<td><code>-all ac 255 t,s</code></td>
<td>This disables all debugging even if the default was to
debug something, then output from the meta data cache is
send to the standard error stream and output from data
types and spaces is sent to file descriptor 255 which
should be redirected by the shell.</td>
</tr>
</table>
</center>
<p>The components of the <code>HDF5_DEBUG</code> value may be
separated by any non-lowercase letter.
<h2>API Tracing</h2>
<p>The HDF5 library can trace API calls by printing the
function name, the argument names and their values, and the
return value. Some people like to see lots of output during
program execution instead of using a good symbolic debugger, and
this feature is intended for their consumption. For example,
the output from <code>h5ls foo</code> after turning on tracing,
includes:
<p>
<center>
<table border align=center width="100%">
<tr>
<td>
<code><pre>
H5Tcopy(type=184549388) = 184549419 (type);
H5Tcopy(type=184549392) = 184549424 (type);
H5Tlock(type=184549424) = SUCCEED;
H5Tcopy(type=184549393) = 184549425 (type);
H5Tlock(type=184549425) = SUCCEED;
H5Fopen(filename="foo", flags=0, access=H5P_DEFAULT) = FAIL;
HDF5-DIAG: Error detected in thread 0. Back trace follows.
#000: H5F.c line 1245 in H5Fopen(): unable to open file
major(04): File interface
minor(10): Unable to open file
#001: H5F.c line 846 in H5F_open(): file does not exist
major(04): File interface
minor(10): Unable to open file
</pre></code>
</td>
</tr>
</table>
</center>
<p>The code that performs the tracing must be included in the
library by specifying the <code>--enable-trace</code>
configuration switch (the default for versions before 1.2). Then
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>
$ ../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
modified.</p>
<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.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="../RM/RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="../UG/index.html">HDF5 User's Guide for Release 1.8</a> <br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
And in this document, the
<a href="../H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>
<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>
</td></tr>
</table>
</center>
<hr>
<!-- #EndLibraryItem --><address>
THG Help Desk: <img src="../Graphics/help.png" align=top height=16>
<br>
Describes HDF5 Release 1.4.5, February 2003
</address>
<!-- Created: Wed Jun 17 12:29:12 EDT 1998 -->
<!-- hhmts start -->
Last modified: 13 December 1999
<!-- hhmts end -->
</body>
</html>
|
