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
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
|
HDF5 version 1.8.6-pre2 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.5 and
HDF5 1.8.6-*, and contains information on the platforms tested and
known problems in HDF5-1.8.6-*.
For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
Links to the HDF5 1.8.6 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.6 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.6 can be accessed directly at this location:
http://www.hdfgroup.org/HDF5/doc/
New features in the HDF5-1.8.x release series, including brief general
descriptions of some new and modified APIs, are described in the "What's New
in 1.8.0?" document:
http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 1.8.6 (current
release) versus Release 1.8.5":
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
========
- New Features
- Support for New Platforms, Languages, and Compilers
- Bug Fixes since HDF5-1.8.5
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- CMake: Improved CPack packaging, added parallel commands, improved
configuration options (better similarity to configure), added more
tests, better support for use in external cmake projects.
(ADB - 2010/10/07)
- The default configuration setting for official releases is
--enable-production. For unofficial releases, the default configuration
setting has been --disable-production. (AKC - 2010/05/28)
Library
-------
- Added support for thread safety on Windows using the Windows threads
library. Use the HDF5_ENABLE_THREADSAFE option in CMake on a Windows
platform to enable this functionality. This is supported on Windows
Vista and newer Windows operating systems. (MAM - 2010/09/10)
- H5Tset_order and H5Tget_order now support all datatypes. A new byte
order, H5T_ORDER_MIXED, has been added specifically for a compound
datatype and its derived type. (SLU - 2010/8/23)
- Improved performance of metadata I/O by changing the default algorithm
to perform I/O from all processes (instead of just process 0) when using
parallel I/O drivers. (QAK - 2010/07/19)
- Improved performance of I/O on datasets with the same shape, but
different rank. (QAK - 2010/07/19)
- Improved performance of the chunk cache by avoiding unnecessary b-tree
lookups of chunks already in cache. (NAF - 2010/06/15)
Parallel Library
----------------
- None
Tools
-----
- h5diff: Added a new flag: --exclude-path. The specified path to an
object will be excluded when comparing two files or two groups. If a
group is specified to be excluded, all member objects of that group
will be excluded. (JKM - 2010/09/16).
- h5ls: Added a new flag: --no-dangling-links. See --help output for
details. (JKM - 2010/06/15)
- h5ls: Added a new flag --follow-symlinks. See --help output for
details. (JKM - 2010/05/25)
High-Level APIs
---------------
- None
F90 API
-------
- None
C++ API
-------
- None
Support for New Platforms, Languages, and Compilers
===================================================
- Sun C and C++ 5.10 and Sun Fortran 95 8.4.
Bug Fixes since HDF5-1.8.5
==========================
Configuration
-------------
- The default number of MPI processes for testing purposes has been
changed from 3 to 6. (AKC - 2010/11/11)
- Some tests in tools/h5repack may fail in AIX systems when -q32 mode is
used. The error is caused by not requesting enough memory in default.
Added "env LDR_CNTRL=MAXDATA=0x20000000@DSA" into the $RUNSERIAL and
$RUNPARALLE in the AIX config file so that executables are tested with
more memory. (AKC - 2010/11/11)
- Removed recognition of the parallel compilers of LAM(hcc) and
ChMPIon(cmpicc) since we have no access to these two MPI implementations
and cannot verify their correctness. (AKC - 2010/07/14 - Bug 1921)
- PHDF5 was changed to use "mpiexec" instead of mpirun as the default
MPI applications startup command as defined in the MPI-2 definition,
section 4.1. (AKC - 2010/06/11 - Bug 1921)
Library
-------
- Retrieving a link's name by index in the case where the link is external
and the file that the link refers to doesn't exist will now fail
gracefully rather than cause a segmentation fault. (MAM - 2010/11/17)
- Modified metadata accumulator to better track accumulated dirty metadata
in an effort to reduce unnecessary I/O in certain situations and to
fix some other corner cases which were prone to error. (MAM - 2010/10/15)
- Added a new set of unit tests that are run during 'make check' to verify
the behavior of the metadata accumulator. (MAM - 2010/10/15)
- Modified library to always cache symbol table information. Libraries
from version 1.6.3 and earler have a bug which causes them to require
this information for some operations. (NAF - 2010/09/21 - Bug 1864)
- Fixed a bug where the library could generate an assertion/core dump when
a file that had been created with H5Pset_libver_bounds(fapl,
H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) but didn't have a superblock
extension was later reopened. (QAK - 2010/09/16 - Bug 1968)
- Fixed a bug that could occur when getting information for a new-style
group that was previously opened through a file handle that was later
closed. (NAF - 2010/09/15)
- Added define check in H5public.h if stdint.h is supported by the C++
compiler. This define is only available on Windows with VS2010 and using
CMake to build the library. (ADB - 2010/09/13 - Bug 1938)
- When a mandatory filter failed to write data chunks, the dataset
couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure. (SLU - 2010/09/08)
- H5Eset_current_stack now also closes the error stack set as the
default. This is to avoid a potential problem.
(SLU - 2010/09/07 - Bug 1799)
- Corrected situation where 1-D chunked dataset could get created by an
application without calling H5Pset_chunk(). H5Pset_chunk is now
required for creating all chunked datasets. (QAK - 2010/09/02)
- Fixed many memory issues that valgrind exposed. (QAK - 2010/08/24)
- Fixed the bug in the filter's public CAN_APPLY function. The return
value should be htri_t not herr_t. (SLU - 2010/08/05 - Bug 1239)
- Fixed the STDIO VFD to use fseeko64 instead of fseek64 for 64-bit I/O
support. (AKC - 2010/7/30)
- Fixed a bug in the direct I/O driver that could render files with certain
kinds of unaligned data unreadable or corrupt them. (NAF - 2010/07/28)
- valgrind reported an error of copying data to itself when a new attribute
is written. Fixed by taking out the memcpy step in the attribute code.
(SLU - 2010/07/28 - Bug 1956)
- Corrected various issues in the MPI datatype creation code which could
cause resource leaks or incorrect behavior (and may improve the
performance as well). (QAK - 2010/07/19)
- Fixed a bug that could cause file corruption when using non-default sizes
of addresses and/or lengths. This bug could also cause uncorrupted files
with this property to be unreadable. This bug was introduced in 1.8.5.
(NAF - 2010/07/16 - Bug 1951)
Parallel Library
----------------
- None
Tools
-----
- Fixed h5diff to compare member objects and groups recursively when
two files or groups are compared. (JKM - 2010/9/16 - Bug 1975)
- Fixed h5repack to be able to convert a dataset to COMPACT layout.
(JKM - 2010/09/15 - Bug 1896)
- Changed h5ls to not interpret special characters in object or attribute
names for output. (JKM - 2010/06/28 - Bug 1784)
- Revised the order of arguments for h5cc, h5fc, h5c++, h5pcc and h5pfc.
CPPFLAGS, CFLAGS, LDFLAGS, and LIBS have been duplicated with an H5BLD_
prefix to put the flags and paths from the hdf5 build in the correct
places and allow the script user to add entries in CPPFLAGS, CFLAGS,
LDFLAGS, and LIBS that will take precedence over those from the hdf5
build. The user can make these entries persistent by editing
CFLAGSBASE, CPPFLAGSBASE, LDFLAGSBASE, and LIBSBASE near the top of
the script or temporary by setting HDF5_CFLAGS, HDF5_CPPFLAGS,
HDF5_LDFLAGS, or HDF5_LIBS in the environment. The new order of
arguments in these scripts is $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS
$H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args
$shared_link. (LRK - 2010/10/25 - Bug 1973)
F90 API
------
- None
C++ API
------
- None
High-Level APIs:
------
- None
Fortran High-Level APIs:
------
- None
Platforms Tested
================
The following platforms and compilers have been tested for this release.
AIX 6.1 xlc 11.1.0.3
(NCSA BP) xlC 11.1.0.3
xlf 13.1.0.3
mpcc_r 11.1.0.3
mpxlf_r 13.1.0.3
FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
(duty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.4.5 20100803
g++ 4.4.5 20100803
gfortran 4.4.5 20100803
FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.4.5 20100803
g++ 4.4.5 20100803
gfortran 4.4.5 20100803
Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2
#1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
(jam) GNU Fortran (GCC) 4.1.2 20080704
(Red Hat 4.1.2-48) and 4.4.2
PGI C, Fortran, C++ 10.4-0 32-bit
PGI C, Fortran, C++ 10.6-0 32-bit
Intel(R) C Compiler for 32-bit
applications, Version 11.1
Intel(R) C++ Compiler for 32-bit
applications, Version 11.1
Intel(R) Fortran Compiler for 32-bit
applications, Version 11.1
Absoft 32-bit Fortran 95 10.0.7
MPICH mpich2-1.3a2 compiled with
gcc 4.1.2 and PGI Fortran 10.4-0
Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2
#1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
(amani) tested for both 32- and 64-bit binaries
GNU Fortran (GCC) 4.1.2 20080704
(Red Hat 4.1.2-46) and 4.4.2
Intel(R) C, C++, Fortran Compilers for
applications running on Intel(R) 64,
Version 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 and G95 PGI Fortran 10.4-0
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 Sun OS_sparc Patch 124867-16
(linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-07
Sun C++ 5.9 Sun OS_sparc Patch 124863-25
Sun C 5.10 SunOS_sparc Patch 141861-06
Sun Fortran 95 8.4 SunOS_sparc Patch 128231-05
Sun C++ 5.10 SunOS_sparc 128228-10
Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404
92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017
perfctr #2 SMP Intel(R) Fortran Compiler Version 10.1.017
(abe) Open MPI 1.2.2
MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
compiled with icc v10.0.026 and ifort 10.1.017
Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
Visual Studio 2010 (cmake)
Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
Visual Studio 2010 (cmake)
Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
Mac OS X 10.6.3 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
Darwin Kernel Version 10.3.1 GNU Fortran (GCC) 4.5.0 20090910
Intel C, C++ and Fortran compilers 11.1 20100806
Mac OS X 10.6.4 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
Darwin Kernel Version 10.4.0 GNU Fortran (GCC) 4.4.0 20090123
Debian5.06 2.6.26-2-686 #1 SMP i686 GNU/Linux
gcc (Debian 4.3.2-1.1) 4.3.2
GNU Fortran (Debian 4.3.2-1.1) 4.3.2
Debian5.06 2.6.26-2-amd64 #1 SMP x86_64 GNU/Linux
gcc (Debian 4.3.2-1.1) 4.3.2
GNU Fortran (Debian 4.3.2-1.1) 4.3.2
Fedora14 2.6.35.6-48.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux
gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
Fedora14 2.6.35.6-48.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
SUSE 11.3 2.6.34-12-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
SUSE 11.3 2.6.34-12-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
Ubuntu 10.10 2.6.35-22-generic #34-Ubuntu SMP i686 GNU/Linux
gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
Ubuntu 10.10 2.6.35-22-generic #34-Ubuntu SMP x86_64 GNU/Linux
gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
OpenVMS Alpha 8.3 HP C V7.3-009
HP Fortran V8.2-104679-48H9K
HP C++ V7.3-009
Supported Configuration Features Summary
========================================
In the tables below
y = tested and supported
n = not supported or not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
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 y y y
Windows XP n y(4) n(4) y y y
Windows XP x64 n y(4) n(4) y y y
Windows Vista n y(4) n(4) y y y
Windows Vista x64 n y(4) n(4) y y y
OpenVMS Alpha n y n y y n
Mac OS X 10.6 Intel n y n y y y
AIX 6.1 32- and 64-bit n y n y y n
FreeBSD 6.3-STABLE 32&64 bit n y n y y y
RedHat EL5 2.6.18-194 i686 GNU (1)W y y(2) y y y y
RedHat EL5 2.6.18-194 i686 Intel W n y n y y n
RedHat EL5 2.6.18-194 i686 PGI W n y n y y n
SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
SuSe Linux 2.6.16 x86_64 Intel W n y n y y n
SuSe Linux 2.6.16 x86_64 PGI W n y n y y y
SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
SuSe Linux 2.4.21 ia64 Intel C y y y y y n
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.10 32-bit y y y y
Solaris2.10 64-bit y y y y
Windows XP y y(4) y n
Windows XP x64 y y(4) y n
Windows Vista y y(4) y y
Windows Vista x64 y y(4) y y
OpenVMS Alpha n n n n
Mac OS X 10.6 y(5) n y n
AIX 6.1 32- and 64-bit n n n n
FreeBSD 6.3-STABLE 32&64 bit y n y y
RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y
RedHat EL5 2.6.18-128 i686 Intel W y y y n
RedHat EL5 2.6.18-128 i686 PGI W y y y n
SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y
SuSe Linux 2.6.16 x86_64 Intel W y y y n
SuSe Linux 2.6.16 x86_64 PGI W y y y n
SuSe Linux 2.6.16 SGI Altix ia64 C y n
RedHat EL4 2.6.18 Xeon Lustre C y y y n
SuSe Linux 2.4.21 ia64 Intel C y y y n
(1) Fortran compiled with g95.
(2) With PGI and Absoft compilers.
(3) With PGI compiler for Fortran.
(4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported)
(5) C shared libraries will be built only when Fortran is disabeld.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* Parallel test, t_shapesame in testpar, is rather unstable as it continues to
have occasional errors in AIX and quite often in NCSA Abe, it is being built
but is not run automatically in the "make check" command. One would have to
run it by hand to see if it works in a particular machine. AKC - 2011/01/28
* Although OpenVMS Alpha is supported, there are several problems with the C
test suite - getname.c, lheap.c, lheap.c, mtime.c, and stab.c. The test
suite for h5diff also fails. These failures are from the tests, not the
library. We have fixed these failures. But it's too late to put the fixes
into this release. If you install the 1.8.6 library, it should still work
despite of these test failures. If you want the working copy without any
test failure, you can request it from us. SLU - 2011/01/26
* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command
sometimes fails in the perform directory due to the attempt to remove the
executable of h5perf or h5perf_serial by two "parallel" commands. This error
has no consequence on the functionality of the HDF5 library or install. It
is fixed in the next release. AKC - 2011/01/25
* While working on the 1.8.6 release of HDF5, a bug was discovered that can
occur when reading from a dataset in parallel shortly after it has been
written to collectively. The issue was exposed by a new test in the parallel
HDF5 test suite, but had existed before that. We believe the problem lies with
certain MPI implementations and/or filesystems.
We have provided a pure MPI test program, as well as a standalone HDF5
program, that can be used to determine if this is an issue on your system.
They should be run across multiple nodes with a varying number of processes.
These programs can be found at:
http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
* The h5diff tool can display garbage values when variable-length strings in
a compound type dataset are compared. This also occurs with variable-length
string arrays in a compound type dataset. See bug #1989. This will be fixed
in the next release. JKM - 2010/11/05
* The AIX --enable-shared setting does not quite work. It can produce a shared
library, but there cannot be more than one shared library that is
interlinked. This means that the high level APIs will not work which is not
very useful. We hope to have a solution in the next release.
(AKC - 2010/10/15)
* H5Eset_auto can cause a seg fault for a library API call if the application
compiles with -DH5_USE_16_API (see bug 1707). It will be fixed in the
next release. SLU - 2010/10/5
* The library's test dt_arith.c showed a compiler's rounding problem on
Cygwin when converting an unsigned long long to a long double. The
library's own conversion works fine. We defined a macro for Cygwin to
skip this test until we can solve the problem. Please see bug #1813.
SLU - 2010/5/5
* All the VFL drivers aren't backwardly compatible. In H5FDpublic.h, the
structure H5FD_class_t changed in 1.8. A new parameter was added to the
get_eoa and set_eoa callback functions, and a new callback function
get_type_map was added. The public function H5FDrealloc was taken out in
1.8. The problem only happens when users define their own driver for 1.6
and try to plug in a 1.8 library. This will be fixed in 1.10. SLU - 2010/2/2
* MinGW has a missing libstdc++.dll.a library file and will not successfully link
C++ applications/tests. Do not use the enable-cxx configure option. Read all of
the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11
* The PathScale MPI implementation, accessing a Panasas file system, would
cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not
exist. 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 16 processes with data inconsistency at testphdf5
/ dataset_readAll. Parallel tests also failed with 32 and 64 processes with
collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
with MPI IO. CMC - 2009/04/28
* For gcc v4.3 and v4.4 with production mode, if -O3 is used, H5Tinit.c will
fail to compile. A corrupted H5Tinit.c is produced. If -O (same as -O1) is
used, H5Tinit.c compiled okay but test/dt_arith would fail. When -O0 (no
optimization) is used, H5Tinit.c compiles okay and all tests passed.
Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. AKC - 2009/04/20
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
tools/h5copy/testh5copy.sh will fail some of their sub-tests. These
sub-tests are expected to fail and should exit with a non-zero code but
the yod command does not propagate the exit code of the executables. Yod
always returns 0 if it can launch the executable. The test suite shell
expects a non-zero for this particular test. Therefore, it concludes the
test has failed when it receives 0 from yod. To skip all the "failing"
tests for now, change them as shown below.
======== Original tools/h5ls/testh5ls.sh =========
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== Change to ===============================
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
==================================================
======== Original tools/h5copy/testh5copy.sh =========
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
H5LSTEST $FILEOUT
======== Change to ===============================
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
echo SKIP H5LSTEST $FILEOUT
==================================================
AKC - 2008/11/10
* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
message "yod allocation delayed for node recovery." This interferes
with test suites that do not expect to see this message. See the "Red Storm"
section in file INSTALL_parallel for a way to deal with this problem.
AKC - 2008/05/28
* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
use the -mp -O1 compilation flags to build the libraries. A higher level
of optimization causes failures in several HDF5 library tests.
* On mpich 1.2.5 and 1.2.6 on a system using four processors, if more than
two processes contribute no I/O and the application asks to do collective
I/O, we have found that a simple collective write will sometimes hang. This
can be verified with the t_mpi test under testpar.
* A dataset created or rewritten with a v1.6.3 or later library cannot be
read with the v1.6.2 or earlier library when the Fletcher32 EDC filter
is enabled. There was a bug in the calculation of the Fletcher32 checksum
in the library before v1.6.3; the checksum value was not 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 was no
longer the same as before on little-endian system. Library releases after
1.6.4 can still read datasets created or rewritten with an HDF5 library of
v1.6.2 or earlier. SLU - 2005/6/30
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command `poe'. To
work around this, set the environment variable MP_INFOLEVEL to 0 to
minimize the messages and run the tests again. The tests may fail with
messages like "The socket name is already in use", but HDF5 does not use
sockets. This failure is due to problems with the poe command trying to
set up the debug socket. To resolve this problem, check to see whether
there are any old /tmp/s.pedb.* files around. These are sockets used by
the poe command and left behind if the command failed at some point. To
resolve this, ask your system administrator to remove the
old/tmp/s.pedb.* files, and then ask IBM to provide a means to run poe
without the debug socket.
* The --enable-static-exec configure flag will only statically link
libraries if the static version of that library is present. If only the
shared version of a library exists (i.e., most system libraries on
Solaris, AIX, and Mac, for example, only have shared versions), the flag
should still result in a successful compilation, but note that the
installed executables will not be fully static. Thus, the only guarantee
on these systems is that the executable is statically linked with just
the HDF5 library.
* There is a configure error on Altix machines that incorrectly reports
when a version of Szip without an encoder is being used.
* On an SGI Altix SMP ia64 system, the Intel compiler version 10.1 (which
is the default on that system) does not work properly and results in
failures during the make check (in a static build) and the make
installcheck (in a shared build). This appears to be a compiler
optimization problem. Reducing the optimization by setting CFLAGS to
-O1 or below resolves the issue. Using a newer version of the compiler
(11.0) avoids the issue. MAM - 2010/06/01
|