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
|
HDF5 version 1.13.4-1 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.13.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
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 and languages
- Bug Fixes since HDF5-1.13.2
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Add new CMake configuration variable HDF5_USE_GNU_DIRS
HDF5_USE_GNU_DIRS (default OFF) selects the use of GNU Coding Standard install
directory variables by including the CMake module, GNUInstallDirs(see CMake
documentation for details). The HDF_DIR_PATHS macro in the HDFMacros.cmake file
sets various PATH variables for use during the build, test and install processes.
By default, the historical settings for these variables will be used.
(ADB - 2022/10/21, GH-2175, GH-1716)
- Update CMake minimum version to 3.18
Updated CMake minimum version from 3.12 to 3.18 and removed version checks
which were added for Windows features not yet available in version 3.12. Also
removed configure macros and code checks for old style code compile checks.
(ADB - 2022/08/29, HDFFV-11329)
Library:
--------
- Added multi dataset I/O feature
Added H5Dread_multi, H5Dread_multi_async, H5Dwrite_multi, and
H5Dwrite_multi_async API routines to allow I/O on multiple datasets with a
single API call. Added H5Dread_multi_f and H5Dwrite_multi_f Fortran
wrappers. Updated VOL callbacks for dataset I/O to support multi dataset
I/O.
(NAF - 2022/10/19)
Parallel Library:
-----------------
-
Fortran Library:
----------------
- Added pointer based H5Dfill_f API
Added Fortran H5Dfill_f, which is fully equivalent to the C API. It accepts pointers,
fill value datatype and datatype of dataspace elements.
(MSB - 2022/10/10, HDFFV-10734.)
C++ Library:
------------
-
Java Library:
-------------
-
Tools:
------
-
High-Level APIs:
----------------
-
C Packet Table API:
-------------------
-
Internal header file:
---------------------
-
Documentation:
--------------
- Doxygen User Guide documentation is available when configured and generated.
The resulting documentation files will be in the share/html subdirectory
of the HDF5 install directory.
(ADB - 2022/08/09)
Support for new platforms, languages and compilers
==================================================
-
Bug Fixes since HDF5-1.13.2 release
===================================
Library
-------
- Fixed an issue with variable length attributes
Previously, if a variable length attribute was held open while its file
was opened through another handle, the same attribute was opened through
the second file handle, and the second file and attribute handles were
closed, attempting to write to the attribute through the first handle
would cause an error.
(NAF - 2022/10/24)
- Fixed an issue with hyperslab selections
Previously, when combining hyperslab selections, it was possible for the
library to produce an incorrect combined selection.
(NAF - 2022/09/25)
- Fixed an issue with attribute type conversion with compound datatypes
Previously, when performing type conversion for attribute I/O with a
compound datatype, the library would not fill the background buffer with
the contents of the destination, potentially causing data to be lost when
only writing to a subset of the compound fields.
(NAF - 2022/08/22, GitHub #2016)
- Memory leak
A memory leak was observed with variable-length fill value in
H5O_fill_convert() function in H5Ofill.c. The leak is
manifested by running valgrind on test/set_extent.c.
Previously, fill->buf is used for datatype conversion
if it is large enough and the variable-length information
is therefore lost. A buffer is now allocated regardless
so that the element in fill->buf can later be reclaimed.
(VC - 2022/10/10, HDFFV-10840)
Java Library
------------
- Improve variable-length datatype handling in JNI.
The existing JNI read-write functions could handle variable-length datatypes
that were simple variable-length datatype with an atomic sub-datatype. More
complex combinations could not be handled. Reworked the JNI read-write functions
to recursively inspect datatypes for variable-length sub-datatypes.
(ADB - 2022/10/12, HDFFV-8701,10375)
Configuration
-------------
-
Tools
-----
-
Performance
-------------
-
Fortran API
-----------
-
High-Level Library
------------------
-
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
-
Platforms Tested
===================
Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
#1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35)
(cmake and autotools)
Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1
#36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1
Ubuntu 20.04 Ubuntu clang version 10.0.0-4
(cmake and autotools)
Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16
#1 SMP x86_64 GNU/Linux Cray clang 14.0.0
(crusher) GCC 11.2.0
(cmake)
Linux 5.3.18-24-cray_shasta_c cray-mpich/8.1.12
#1 SMP x86_64 GNU/Linux Cray clang 13.0.0
(spock) AMD clang 13.0.0
GCC 8.2.0, 11.2.0
(cmake)
Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5
#1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5)
(stria) GCC 7.2.0 (Spack GCC)
(cmake)
Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 12.0.1
(vortex) GCC 8.3.1
XL 16.1.1
(cmake)
Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1
(lassen) GCC 7.3.1
XL 16.1.1.2
(cmake)
Linux-4.12.14-150.75-default cray-mpich/7.7.10
#1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0
(cori) Intel (R) Version 19.0.3.199
(cmake)
Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
#1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0,
Version 7.2.0, Version 8.3.0, Version 9.1.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
GNU C (gcc) and C++ (g++) 4.8.5 compilers
with NAG Fortran Compiler Release 6.1(Tozai)
Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
with NAG Fortran Compiler Release 6.1(Tozai)
MPICH 3.1.4 compiled with GCC 4.9.3
MPICH 3.3 compiled with GCC 7.2.0
OpenMPI 2.1.6 compiled with icc 18.0.1
OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Version 19.10-0
(autotools and cmake)
Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0
#1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1
(quartz) GCC 7.3.0, 8.1.0
Intel 16.0.4, 18.0.2, 19.0.4
Linux-3.10.0-1160.71.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(skybridge) Intel/19.1
(cmake)
Linux-3.10.0-1160.66.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(attaway) Intel/19.1
(cmake)
Linux-3.10.0-1160.59.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux Intel/19.1
(chama) (cmake)
macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11)
Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0
(macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609
macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9)
Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
(bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228
macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4)
64-bit gfortran GNU Fortran (GCC) 6.3.0
(bear) Intel icc/icpc/ifort version 19.0.4.233 20190416
macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2)
64-bit gfortran GNU Fortran (GCC) 7.4.0
(kite) Intel icc/icpc/ifort version 17.0.2
Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011test) Intel icc/icpc/ifort version 16.0.2
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
Centos6 Version 4.4.7 20120313
(platypus) Version 4.9.3, 5.3.0, 6.2.0
MPICH 3.1.4 compiled with GCC 4.9.3
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Version 19.10-0
Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake)
Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake)
Visual Studio 2019 w/ clang 12.0.0
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2021 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
Known Problems
==============
Setting a variable-length dataset fill value will leak the memory allocated
for the p field of the hvl_t struct. A fix is in progress for this.
HDFFV-10840
CMake files do not behave correctly with paths containing spaces.
Do not use spaces in paths because the required escaping for handling spaces
results in very complex and fragile build files.
ADB - 2019/05/07
At present, metadata cache images may not be generated by parallel
applications. Parallel applications can read files with metadata cache
images, but since this is a collective operation, a deadlock is possible
if one or more processes do not participate.
CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
The subsetting option in ph5diff currently will fail and should be avoided.
The subsetting option works correctly in serial h5diff.
Several tests currently fail on certain platforms:
MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms.
MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with
cray-mpich on theta and with XL compilers on ppc64le platforms.
MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
The issues with the gif tool are:
HDFFV-10592 CVE-2018-17433
HDFFV-10593 CVE-2018-17436
HDFFV-11048 CVE-2020-10809
These CVE issues have not yet been addressed and can be avoided by not building
the gif tool. Disable building the High-Level tools with these options:
autotools: --disable-hltools
cmake: HDF5_BUILD_HL_TOOLS=OFF
|