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
|
HDF5 version 1.6.10-pre2 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.10 and
HDF5-1.6.9-*.
It contains information on the platforms tested and known problems in
HDF5-1.6.9-*. For more details, check the HISTORY.txt file in
the HDF5 source.
HDF5 documentation can be found in the distributed release source code
in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server:
ftp://ftp.hdfgroup.org/HDF5/docs/
Documentation for the current release in the HDF5 Release 1.6.x series is
also on the HDF web site:
http://hdfgroup.org/HDF5/doc1.6/
For more information, see the HDF5 home page:
http://hdfgroup.org/products/hdf5/
If you have any questions or comments, please see the HDF Support page
for a list of available resources:
http://hdfgroup.org/services/support.html
CONTENTS
========
- New Features
- Support for New Platforms, Languages and Compilers
- Bug Fixes since HDF5-1.6.10
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
-------------------------
- Changed default Gnu fortran compiler from g95 to gfortran since
gfortran is more likely installed with gcc now. -AKC 2009/07/19-
Library:
--------
- The embedded library information is displayed by H5check_version() if a
version mismatch is detected. Also changed H5check_version() to
suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2
or higher. (Old behavior treated 3 or higher the same as 1, that is
print a warning and allows the program to continue. (AKC - 2009/9/28)
- Embed the content of libhdf5.settings into the hdf5 executables so that
an "orphaned" executables can display (via the Unix strings command, for
example) the library settings used to build the executables.
If a user does not care for the extra library information insert
in the executables, he may turn it off by --disable-embedded-libinfo
during configure. (AKC - 2009/9/30)
Parallel Library:
-----------------
- None
Tools:
------
- h5diff: h5diff treats two INFINITY values different. Fixed by checking
(value==expect) before call ABS(...) at h5diff_array.c. This will
make that (INF==INF) is true (INF is treated as an number instead of
NaN) (PC -- 2009/07/28)
- h5diff: add option "--use-system-epsilon" to print difference if
(|a-b| > EPSILON). Change default to use strict equality
(PC -- 2009/09/12)
F90 API:
--------
- None
C++ API:
--------
- New member functions DataSet::getInMemDataSize() and
Attribute::getInMemDataSize() simplify getting the dataset's or
attribute's data size, in bytes, in memory. (BMR - 2009/07/26)
Support for New Platforms, Languages and Compilers
==================================================
- PathScale compilers are recognized and can build the HDF5 library
properly. AKC - 2009/7/28 -
Bug Fixes since HDF5-1.6.9 Release
==================================
Library
-------
- Fixed a bug where writing and deleting many global heap objects (i.e.
variable length data) would render the file unreadable. Previously
created files exhibiting this problem should now be readable.
NAF - 2009/10/27 - 1483
- Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628
- Fixed incorrect return value for H5Pget_filter_by_id in H5Ppublic.h.
NAF - 2009/09/25 - 1620
- Fixed a bug where properties weren't being compared with the registered
compare callback. NAF - 2009/09/25 - 1555
- Fixed a bug where H5Pget_fitler_by_id would succeed when called for a
filter that wasn't present. NAF - 2009/06/25 - 1250
- Fixed an issue with committed compound datatypes containing a vlen. Also
fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593
Configuration
-------------
- The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to
recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 -
Performance
-----------
Tools
-----
- None
F90 API
-------
- None
C++ API
-------
- The parameter 'size' in CommonFG::getLinkval now has default value
for user's convenience. (BMR - 2009/10/23)
- NULL pointer accessing was fixed, bugzilla 1061. (BMR - 2009/10/05)
- read/write methods of DataSet and Attribute classes were fixed
to handle string correctly. (BMR - 2009/07/26)
Documentation
=============
HDF5 documentation can be found in the distributed release source
code in the subdirectory doc/html/ (start with index.html) or on the
THG (The HDF Group) FTP server:
ftp://ftp.hdfgroup.org/HDF5/docs/
Online documentation for the current release in the HDF5 Release 1.6.x
series can be found on the THG web site:
http://hdfgroup.org/HDF5/doc1.6/
A listing of interface changes from release to release can be found
in the document "HDF5 Software Changes from Release to Release":
http://hdfgroup.org/HDF5/doc1.6/ADGuide/Changes.html
Platforms Tested
================
AIX 5.3 xlc 7.0.0.8
xlf 09.01.0000.0008
xlC 7.0.0.8
mpcc_r 7.0.0.8
mpxlf_r 09.01.0000.0008
FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
(duty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.3.5 20091004
g++ 4.3.5 20091004
FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.4.2 20091006
g++ 4.4.2 20091006
Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 20080704
#1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
(jam) PGI C, Fortran, C++ 8.0-5 32-bit
PGI C, Fortran, C++ 8.0-1 32-bit
Intel(R) C Compiler for 32-bit
applications, Versions 11.0, 11.1
Intel(R) C++ Compiler for 32-bit
applications, Version 11.0, 11.1
Intel(R) Fortran Compiler for 32-bit
applications, Version 11.0, 11.1
Absoft 32-bit Fortran 95 10.0.7
MPICH mpich2-1.0.8 compiled with
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
Linux 2.6.16.46-0.12-debug #1 Intel(R) C++ Version 10.0.025
SMP ia64 GNU/Linux Intel(R) Fortran Itanium(R) Version 10.0.025
(ucar hir1)
Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704
x86_64 GNU/Linux Intel(R) C, C++, Fortran Compilers for
(amani) applications running on Intel(R) 64,
Versions 11.1.
PGI C, Fortran, C++ Version 9.0-4
for 64-bit target on x86-64
MPICH mpich2-1.0.8 compiled with
gcc 4.1.2
Linux 2.6.16.60-0.42.5 #1 Intel(R) C++ Version 10.1.017
SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
(cobalt) SGI MPI 1.38
SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc
Patch 124867-11 2009/04/30
(linew) Sun Fortran 95 8.3 SunOS_sparc
Patch 127000-11 2009/10/06
Sun C++ 5.9 SunOS_sparc
Patch 124863-16 2009/09/15
Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026
92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026
perfctr #2 SMP Open MPI 1.2.2
(abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
compiled with icc v10.0.026 and ifort 10.0.026
IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2
#1 SMP ia64 Intel(R) C++ Version 8.1.037
(NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033
mpich-gm-1.2.7p1..16-intel-8.1.037-r1
Windows XP Visual Studio .NET (with Intel Fortran 9.1)
Visual Studio 2005 (with Intel Fortran 9.1)
cygwin (gcc 3.4.4)
Windows Vista Visual studio 2005
Mac OS X Intel 10.5.6 i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
g95 0.91
Supported Configuration Features Summary
========================================
Key: y = Tested and supported
n = Not supported or not tested in this release
C = Cluster
W = Workstation
( ) = Footnote appears below second table
Platform C F90 F90 C++ zlib SZIP
parallel parallel
Solaris2.10 32-bit n y n y y y
Solaris2.10 64-bit n y n n y y
WinXP CYGWIN n n n y y y
WinXP 2005 n y n y y y
WinXP .Net n y n y y y
WinVista 2005 n n n y y y
Mac OS X 10.4.10 n y n y y y
AIX 5.3 32- and 64-bit n y n y y n
FreeBSD 6.3 32- and 64-bit n n n y y y
RedHat EL5 2.6.18-164 i686 GNU W y y y y y y
RedHat EL5 2.6.18-164 i686 Intel W n y n y y n
RedHat EL5 2.6.18-164 i686 PGI W n y n y y n
RedHat EL5 2.6.16 x86_64 GNU (1) W y y n y y y
RedHat EL5 2.6.16 x86_64 Intel W n y n y y n
RedHat EL5 2.6.16 x86_64 PGI W n y n y y n
RedHat EL 4 2.6.18 Xeon Lustre C y y y y y y
SuSE Linux 2.4.21 ia64 C y y y y y y
SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
Platform Shared Thread-
libraries(4) safe
Solaris2.10 32- and 64-bit y y
WinXP CYGWIN y n
WinXP 2005 y n
WinXP .Net y n
WinVista 2005 y n
Mac OS X 10.5.6 n n
AIX 5.3 32- and 64-bit n n
FreeBSD 6.3 32- and 64-bit y n
RedHat EL5 2.6.18-164 i686 GNU W y y
RedHat EL5 2.6.18-164 i686 Intel W y n
RedHat EL5 2.6.18-164 i686 PGI W n n
RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y
RedHat EL5 2.6.18-164 x86_64 IntelW y n
RedHat EL5 2.6.18-164 x86_64 PGI W n n
RedHat EL4 2.6.18 Xeon Lustre C y n
SuSE Linux 2.4.21 ia64 C y n
SuSe Linux 2.6.16 SGI Altix ia64 C n n
Compiler versions for each platform are listed in the "Platforms Tested"
table found elsewhere in this file (RELEASE.txt). Unless otherwise noted,
compilers used are the system compilers.
Footnotes:
(1) Fortran compiled with g95.
Known Problems
==============
* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used.
The error is due to insufficient memory requested. Request a large amount
of runtime memory by setting the following environment variable for more
memory.
LDR_CNTRL=MAXDATA=0x20000000@DSA
AKC - 2009/10/31
* The PathScale MPI implementation, accessing a Panasas file system, would
cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
existing. This is due to the MPI_File_open() call failing if the amode has
the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
* Parallel tests failed with 15, 16, and 32 processes with data inconsistency
at testphdf5 / dataset_readAll. Parallel tests also failed with 64 processes
with collective abort of all ranks at testphdf5 / collective irregular simple
chunk write. CMC - 2009/04/28
* h5repack may not handle committed datatypes correctly. NAF - 2009/4/20 - 1516/
1466
* When in production mode, any presence of the '-g' flag within CFLAGS is
stripped out during configuration. This currently cannot be overridden.
In order to build with '-g' specified within CFLAGS, use the
--disable-production configure flag in order to configure in development
mode. MAM - 2009/03/09.
* A contiguous or chunked dataset created by a sequential version of HDF5
might not be able to be modified with a parallel version of the library.
Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the
dataset creation property list to avoid the problem. EIP - 2005/09/09
* A dataset created or rewritten with the v1.6.3 library or after can't
be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is
enabled. There was a bug in the calculating code of the Fletcher32
checksum in the library before v1.6.3. The checksum value wasn't consistent
between big-endian and little-endian systems. This bug was fixed in
Release 1.6.3. However, after fixing the bug, the checksum value is no
longer the same as before on little-endian system. HDF5 library releases
after 1.6.4 can still read datasets created or rewritten with an HDF5
library of v1.6.2 or before. SLU - 2005/7/8
* test/big fails sometimes with the message "Possible overlap with another
region." The test selects regions randomly, and this error occurs when
two regions overlap each other; it is a bug in the test and not in
HDF5. Since the error is triggered by a random situation, it will
usually disappear if the test is re-run.
* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but
have a "guard" statement in stdint.h that will #error and skip the rest
of the header file if the C99 option is not used explicitly. Hardsetting
$CC to c99 will resolve the problem. AKC - 2004/12/13
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command poe.
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
and run the tests again.
The tests may also fail with messages like "The socket name is already
in use". HDF5 does not use sockets. This is due to problems of the
poe command trying to set up the debug socket. Check whether there are
many old /tmp/s.pedb.* files staying around. These are sockets used by
the poe command and left behind due to failed commands. Ask your system
administrator to clean them out. Lastly, request IBM to provide a means
to run poe without the debug socket.
* The h5dump tests may fail to match the expected output on some platforms
(e.g. parallel jobs, Windows) where the error messages directed to
"stderr" do not appear in the "right order" with output from stdout.
This is not an error.
* The --enable-static-exec configure flag fails to compile for Solaris
platforms. This is due to the fact that not all of the system
libraries on Solaris are available in a static format.
The --enable-static-exec configure flag also fails to correctly compile
on the IBM SP2 platform for the serial mode. The parallel mode works fine
with this option.
The --enable-static-exec configure flag also fails to correctly compile
on the HPUX 11.00.
It is suggested that you don't use this option on these platforms
during configuration.
* Use the --disable-shared configure flag if building with an Absoft Fortran
compiler.
|