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
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
|
HDF5 version 1.9.132 currently under development
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.9.0 and
HDF5 1.9.x snapshot, and contains information on the platforms
tested and known problems in HDF5-1.9.x.
For more details check the HISTORY*.txt files in the HDF5 source.
Links to HDF5 1.9.x source code can be found on The HDF Group's
development FTP server at the following location:
ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots
User documentation for the snapshot can be accessed directly at this location:
http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/
For more information, see the HDF5 home page:
http://www.hdfgroup.org/HDF5/
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 HDF5-1.8.0
- Platforms Tested
- Known Problems
New Features
============
Configuration:
-------------
- Fixed AIX Fortran compiler flags to use appropriate settings for
debugging, profiling, optimization situations. HDFFV-8069. (AKC
2012/09/27)
- Updated to latest autotools and changed all hard *.sh scripts to
configure managed *.sh.in files. Removed overloading of autotools
TESTS variable by examples and tests. Renamed configure.in to
configure.ac. (ADB - 2012/08/23 - HDFFV-8129)
- Added code to display the version information of XL fortran and C++
in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793)
- Configure now generates Makefiles that build in "silent make mode"
by default in which compile and link lines are significantly
simplified for clarity. To override this and view actual compile and
link lines during building, the --disable-silent-rules flag can be used
at configure time, or the 'make' command can be followed by V=1, to
indicate a "verbose" make. (MAM - 2011/4/14).
- Added mpicc and mpif90 as the default C and Fortran compilers for Linux
systems when --enable-parallel is specified but no $CC or $FC is defined.
(AKC - 2011/2/7)
- Added a new configure option, "--enable-unsupported", which can
be used to stop configure from preventing the use of unsupported
configure option combinations, such as c++ in parallel or parallel
HDF5 with threadsafe. Use at your own risk, as it may result in a
library that won't compile or run as expected!
(MAM - 2010/11/17 - Bug 2061)
- PHDF5 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 - 2010/6/11 - Bug 1921)
- Configure now adds appropriate defines for supporting large (64-bit)
files on all systems, where supported, by default, instead of only linux.
This largefile support is controllable with the --enable-largefile
configure option. This is replacing the linux-specific --enable-linux-lfs
option, which has been removed from configure.
(MAM - 2010/05/05 - 1772/1434)
- Upgraded versions of autotools used to generate configuration suite.
We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b.
MAM 2010/04/15.
- Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM
compilers so that the ibm compiler options can be added properly. This
allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be
recognized. AKC 2009/11/26.
- Configuration suite now uses Automake 1.11 and Autoconf 2.64.
MAM 2009/08/11.
- Changed default Gnu fortran compiler from g95 to gfortran since
gfortran is more likely installed with gcc now. -AKC 2009/07/19-
- Added libtool version numbers to generated c++, fortran, and
hl libraries. MAM 2009/04/19.
- Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19.
- Added a Make target of check-all-install to test the correctness of
installing via the prefix= or $DESTDIR options. AKC - 2009/04/14
- Configuration suite now uses Libtool 2.2.6a. MAM 2008/10/24
- Configuration suite now uses Autoconf 2.61, Automake 1.10.1.
MAM 2008/05/05.
- The new configure option "--disable-sharedlib-rpath" disables
embedding the '-Wl,-rpath' information into executables when
shared libraries are produced, and instead solely relies on the
information in LD_LIBRARY_PATH. (MAM - 2008/05/15)
Library:
--------
- The library now supports the data conversion from enumeration to numeric
(integer and floating-point number) datatypes. See Issue 8221.
(SLU - 2012/10/23)
- The data sieve buffer size was for all the datasets in the file. It
could waste memory if any dataset size is smaller than the sieve buffer
size. Now the library picks the smaller one between the dataset size
and the sieve buffer size from the file access property. See Issue 7934.
(SLU - 2012/4/2)
- I added a new parameter of object access property list to the function
H5Rdereference (Issue 2763). It's called H5Rdereference2 now. The former
H5Rdereference function has been deprecated to H5Rdereference1. (SLU -
2011/7/18)
- H5Tcreate now supports string type (fixed-length and variable-length).
(SLU - 2011/05/20)
- Added ability to cache files opened through external links. Added new
public functions H5Pset_elink_file_cache_size(),
H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache().
(NAF - 2011/02/17)
- Removed all old code for Metraowerks compilers, bracketed by
__MWERKS__). Metraowerks compiler is long gone. (AKC - 2010/11/17)
- Added support for threadsafety on windows using the windows threads
library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a
windows platform to enable this functionality. This is supported on
Windows Vista and newer Windows operating systems. (MAM - 2010/09/10)
- 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 - 2010/9/8)
- H5Tset_order and H5Tget_order now support all data types. A new byte
order H5T_ORDER_MIXED has been added specifically for compound datatype
and its derived type. Please see bug #1934. (SLU - 2010/8/23)
- Improved performance of the chunk cache by avoiding unnecessary b-tree
lookups of chunks already in cache. (NAF - 2010/06/15)
- Greatly improved performance of extending a dataset with early
allocation. (NAF - 2010/03/24 - 1637)
- Added support for filtering densely stored groups. Many of the API
functions related to filters have been extended to support dense groups
as well as datasets. Pipeline messages can now be stored in a group's
object header. (NAF/QAK - 2009/10/8)
- 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)
- 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 - 2009/9/15)
- Corrected problem where library would re-write the superblock in a file
opened for R/W access, even when no changes were made to the file.
(QAK - 2009/08/20, Bz#1473)
- Separated "factory" free list class from block free lists. These free
lists are dynamically created and manage blocks of a fixed size.
H5set_free_list_limits() will use the same settings specified for block
free lists for factory free lists. (NAF - 2009/04/08)
- Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29)
- Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a
user-defined callback function for external link traversal.
(NAF - 2009/01/08)
- Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to
allow the user to specify the file access flags used to open the target
file of an external link. (NAF - 2009/01/08)
- Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
individual rdcc configuration for each dataset. Added
H5Dget_access_plist() function to retrieve a dataset access property
list from a dataset. (NAF - 2008/11/12)
- Added H5Iis_valid() function to check if an id is valid without producing
an error message. (NAF - 2008/11/5)
- Added two new public routines: H5Pget_elink_fapl() and
H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13)
- Improved free space tracking in file to be faster. (QAK - 2008/10/06)
- Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
Parallel Library:
-----------------
- Add H5Pget_mpio_no_collective_cause() function that retrive reasons
why the collective I/O was broken during read/write IO access.
(JKM - 2012/08/30 HDFFV-8143)
- Special Collective IO (IO when some processes do not contribute to the
IO) and Complex Derived Datatype MPI functionalities are no longer
conditionally enabled in the library by configure. They are always
enabled in order to take advantage of performance boosts from these
behaviors. Older MPI implementations that do not allow for these
functionalities can no longer by used by HDF5. (MAM - 2011/07/08).
- Modified parallel tests to run with arbitrary number of processes. The
modified tests are testphdf5 (parallel dataset access), t_chunk_alloc
(chunk allocation), and t_posix_compliant (posix compliance). The rest of
the parallel tests already use in the code the number of processes
available in the communicator. (CMC - 2009/04/28)
Fortran Library:
----------------
- Added parallel routine H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27)
- Added for the C API the Fortran wrapper:
h5ocopy_f (MSB - 2012/03/22)
HDF5 Fortran library was enhanced to support Fortran 2003 standard.
The following features are available when the HDF5 library is configured
using --enable-fortran --enable-fortran2003 configure flags AND
if fortran compiler is Fortran2003 compliant:
- Subroutines overloaded with the C_PTR derived type:
h5pget_f
h5pget_fill_value_f
h5pinsert_f
h5pregister_f
h5pset_f
h5pset_fill_value_f
h5rcreate_f
h5rderefrence_f
h5rget_name_f
h5rget_obj_type_f
- Subroutines overloaded with the C_PTR derived type
and simplified signatures:
h5aread_f
h5awrite_f
h5dread_f
h5dwrite_f
- New subroutines
h5dvlen_reclaim_f
h5literate_by_name_f
h5literate_f
h5ovisit_f
h5tconvert_f
- Subroutines with additional optional parameters:
h5pcreate_class_f
(EIP - 2011/10/14)
- Added for the C APIs the Fortran wrappers:
h5dget_access_plist_f
h5iis_valid_f
h5pset_chunk_cache_f
h5pget_chunk_cache_f
(MSB - 2009/04/17)
C++ Library:
------------
- New member functions
+ Overloaded CommonFG::getObjnameByIdx to take char* for name
+ Overloaded CommonFG::getObjTypeByIdx to return type name as a char*.
(BMR - 2010/05/02)
+ DataSet::getInMemDataSize() to simplify getting the dataset's
data size in memory. (BMR - 2009/07/26)
- These member functions were added as wrapper for H5Rdereference to
replace the incorrect IdComponent::dereference().
void H5Object::dereference(H5File& h5file, void* ref)
void H5Object::dereference(H5Object& obj, void* ref)
In addition, these constructors were added to create the associated
objects by way of dereference:
Attribute(H5Object& obj, void* ref);
Attribute(H5File& file, void* ref);
DataSet(H5Object& obj, void* ref);
DataSet(H5File& file, void* ref);
DataType(H5Object& obj, void* ref);
DataType(H5File& file, void* ref);
Group(H5Object& obj, void* ref);
Group(H5File& obj, void* ref);
(BMR - 2008/08/10)
Tools:
------
- h5dump: Added capability for "-a" option to show attributes containing "/"
by using an escape character. For example, for a dataset "/dset"
containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)"
to show the content of the attribute. See details at HDFFV-7523
(PC -- 2012/03/12)
- h5dump: Added ability to apply command options across multiple files using a
wildcard in the filename. Example; "h5dump -H -d Dataset1 tarr*.h5".
HDFFV-7876 (ADB - 2012/03/12).
- h5repack: Improved performance for big chunked datasets (size > 128MB)
when used with layout (-l) or compression (-f) option.
It would perform much better prior to the improvement,
especially for cases that chunk dimentions looks like
"1024x5x1" (compare to "1x5x1024"). When bigger numbers
are toward front and smaller number is toward back in chunk
dimentions. HDFFV-7862 (JKM - 2012/03/01)
- h5dump: Added new option --no-compact-subset. This option will not
interpret the '[' character as starting the compact form of
subsetting. This is useful when the "h5dump error: unable to
open dataset "datset_name"" message is output because a dataset
name contains a '[' character. HDFFV-7689 (ADB - 2012/01/31)
- h5dump: Corrected schema location:
<hdf5:HDF5-File
xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File
http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd">
(ADB - 2011/08/10)
- h5diff: Added new level for -v (verbose) option. The new levels are
1 and 2. So -v1 and -v2 can be specified to view more
information about attributes differences.
Bug#2121 (JKM 2011/3/23)
- h5dump: Added new option --enable-error-stack. This option will display
error stack information in the output stream. This is useful
when the "h5dump: Unable to print data" message is output.
(ADB - 2011/02/24)
- h5diff: Add a new flag --exclude-path. Specified path to an object will
be excluded from comparing the two files or two groups. If group
is specified all the member objects will be excluded.
(JKM - 2010/09/16).
- h5ls: Add new flag --no-dangling-links. (refer to --help for details)
(JKM - 2010/06/15)
- h5ls: Add new flag --follow-symlinks. (refer to --help for details)
(JKM - 2010/05/25)
- h5diff: Add new flag --no-dangling-links. (refer to --help for details)
(JKM - 2010/02/10)
- h5diff: Add new flag --follow-symlinks. (refer to --help for details)
(JKM - 2010/01/25)
- h5diff: fix for displaying garbage value on LE machine for BE data.
(JKM - 2009/11/20)
- h5dump: subsetting now allows default for count. Also trailing ; in short form
can be omitted after last specified value.
(ADB - 2009/09/04)
- h5dump/h5ls: now can display data in region references
using new -R, --region flag.
(ADB - 2009/09/04)
- h5diff: new flag, -c, --compare, list objects that are not comparable.
(PVN - 2009/4/10 - 1368)
- h5diff new flag, -N, --nan, avoids NaNs detection. (PVN - 2009/4/10)
- h5dump correctly specifies XML dtd / schema urls (ADB - 2009/4/3 - 1519)
- h5repack now handles group creation order. (PVN - 2009/4/2 - 1402)
- h5dump: added a printing of the compression ratio of uncompressed and compressed
sizes for cases where compression filters are present. (PVN - 2008/05/01)
- h5dump: added an option to allow a user defined formatting string for printf
regarding floating point numbers. (PVN - 2008/05/06)
- h5dump: support for external links, display the object that the external link
points to. (PVN - 2008/05/12)
- h5repack: add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26)
- h5repack: add 2 options that call H5Pset_alignment in the repacked file. (PVN - 2008/08/29)
- h5ls: added capability to traverse through external links when the -r
(recursive) flag is given. (NAF - 2008/09/16)
- h5ls: added -E option to enable traversal of external links. h5ls will
not traverse external links without this flag being set.
(NAF - 2008/10/06)
- h5diff: added support for long double (PVN - 2008/10/28)
- h5dump: binary output defaults to NATIVE with -b optionally accepting
the form of binary output (NATIVE, FILE, BE, LE). (PVN - 2008/10/30)
- h5diff: return 1 for file differences when both file graphs differ by any object.
Error return code was changed to 2 from -1. (PVN - 2008/10/30)
- h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP
instead (PVN - 2008/10/30)
- h5repack: When user doesn't specify a chunk size, h5repack now defines a default
chunk size as the same size of the size of the hyperslab used to read the chunks.
The size of the hyperslabs are defined as the size of each dimension or a
predefined constant, whatever is smaller. This assures that the chunk
read fits in the chunk cache. (PVN - 2008/11/21)
- 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)
High-Level APIs:
------
- Table: In version 3.0 of Table, "NROWS" (used to store number of records) was
deprecated (PVN - 2008/11/24)
- Added Fortran wrappers for Dimension Scale APIs. HDFFV-3797
h5dsset_scale_f
h5dsattach_scale_f
h5dsdetach_scale_f
h5dsis_attached_f
h5dsis_scale_f
h5dsset_label_f
h5dsget_label_f
h5dsget_scale_name_f
h5dsget_num_scales_f
(EIP for SB - 2011/10/13)
- New API: h5ltpath_valid (Fortran: h5ltpath_valid_f) which checks
if a path is correct and determines if a link resolves to a valid
object and checks that the link does not dangle. (MSB- 2012/3/15)
Documentation
-------------
Support for new platforms, languages and compilers.
=======================================
- Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08)
- PathScale compilers are recognized and can build the HDF5 library
properly. AKC - 2009/7/28 -
Bug Fixes since HDF5-1.8.0 release
==================================
Library
-------
- Fixed an error that could occur when calling H5Ocopy within an
H5Literate callback (and possibly other situations).
(NAF - 2012/7/25 - HDFFV-5853)
- Fixed an error that would occur when copying an object with attribute
creation order tracked and indexed. (NAF - 2012/3/28 - HDFFV-7762)
- Fixed a bug in H5Ocopy(): When copying an opened object, call the
object's flush class action to ensure that cached data is flushed
so that H5Ocopy will get the correct data.
(VC - 2012/3/27 - HDFFV-7853)
- When an application tries to write or read many small data chunks and
runs out of memory, the library had a seg fault. The fix is to
return the error stack with proper information. (SLU - 2012/3/23.
Issue 7785)
- H5Pset_data_transform had seg fault in some cases like x*-100. It
works correctly now and handles other cases like 100-x or 2/x.
(SLU - 2012/3/15. Issue 7922)
- Fixed rare corruption bugs that could occur when using the new object
header format. (NAF - 2012/3/15 - HDFFV-7879)
- Creating a dataset in a read-only file caused seg fault when the file
is closed. It's fixed. The attemp to create a dataset will fail
with the error stack indicating the file is read-only. (SLU -
2012/1/25. Issue 7756)
- Fixed a seg fault that could occur when shrinking a dataset with chunks
larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833)
- Fixed a bug that could cause file corruption when copying named
datatypes to a file using shared messages. (NAF - 2011/11/14)
- Fixed a bug that could cause H5Oget_info to return the wrong address
after copying a named datatype. (NAF - 2011/11/14)
- The library allowed the conversion of strings between ASCII and UTF8
(Issue 7582). We have corrected it to report an error under this
situation. (SLU - 2011/11/8)
- The library had seg fault when it tried to shrink the size of compound type
through H5Tset_size immediately after the type was created (Issue
7618). It's fixed now. (SLU - 2011/10/26)
- Fixed a bug that occurred when using H5Ocopy on a committed datatype
containing an attribute using that committed datatype.
(NAF - 2011/10/13 - Issue 5854)
- #ifdef _WIN32 instances changed to #ifdef H5_HAVE_WIN32_API and added
H5_HAVE_VISUAL_STUDIO checks where necessary. CMake only as configure
never set _WIN32.
- CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
discovered 3 problems in tests and tools' library (Issue 7674):
1. In dsets.c, left shifting an unsigned int for 32 bits or more
caused undefined behavior.
2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow
when the value is negative minimal and is being subtracted one.
3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits
or more caused undefined behavior.
All the problems have been corrected. (SLU - 2011/9/2)
- In v1.6 library, there was EOA for the whole MULTI file saved in the
super block. We took it out in v1.8 library because it's meaningless
for the MULTI file. v1.8 library saves the EOA for the metadata file,
instead. But this caused some backward compatibility problem.
v1.8 library couldn't open the file created with v1.6 library. We
fixed the problem by checking the EOA value to detect the file
created with v1.6 library. (SLU - 2011/6/22)
- When a dataset had filters and reading data failed, the error message
didn't say which filter isn't registered. It's fixed now.
(SLU - 2011/6/3)
- The datatype handler created with H5Tencode/decode used to have the
reference count 0 (zero). I have fixed it. It is 1 (one) now.
(SLU - 2011/2/18)
- Fixed a bug that caused big endian machines to generate corrupt files
when using the scale-offset filter with floating point data or
fill values. Note that such datasets will no longer be readable
by any machine after this patch. (NAF - 2010/02/02 - Bug 2131)
- 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 library to always cache symbol table information. Libraries
version 1.6.3 have a bug which causes them to require this
information for some operations. (NAF - 2010/09/21 - 1864)
- 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)
- H5Eset_current_stack now also closes the error stack to be set as the
default. This is to avoid a potential problem (Bug 1799).
(SLU - 2010/9/7)
- Fixed the bug in the filter's public CAN_APPLY function. The return
value should be htri_t not herr_t (Bug #1239). (SLU - 2010/8/5)
- 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 (Bug #1956). I fixed it by taking out the memcpy step in
the attribute code. (SLU - 2010/07/28)
- 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 - 1951)
- Fixed a file corruption bug that could happen when shrinking a
compressed dataset. (NAF - 2010/05/20)
- Fixed some memory leaks in VL datatype conversion when strings are
used as fill values. (MAM - 2010/05/12 - BZ# 1826)
- Fixed a bug when copying objects with NULL references with the
H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815)
- Files can now be concurrently opened more than once using the core file
driver, as long as the backing store is used. (NAF - 2010/03/09)
- Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External
links will now be expanded if this flag is set.
(NAF - 2010/03/05 - 1733)
- Fixed a bug where the library, when traversing an external link, would
reopen the source file if nothing else worked. (NAF - 2010/03/05)
- Fixed an intermittent bug in the b-tree code which could be triggered
by expanding and shrinking chunked datasets in certain ways.
(NAF - 2010/02/16)
- H5Tdetect_class said a VL string is a string type. But when it's
in a compound type, it said it's a VL type (Bug #1584). I fixed it
to be consistent. It always return string type. (SLU - 2009/12/10)
- 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 an assertion failure that occurred when H5Ocopy was called on a
dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597)
- Fixed incorrect return value for H5Pget_filter_by_id1/2 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)
- Added versioning to H5Z_class_t struct to allow compatibility with 1.6
API. (NAF - 2009/04/20 - 1533)
- Fixed a problem with using data transforms with non-native types in the
file. (NAF - 2009/04/20 - 1548)
- Added direct.h include file to windows section of H5private.h
to fix _getcwd() warning. (ADB - 2009/04/14 - 1536)
- Fixed a bug that prevented external links from working after calling
H5close(). (NAF - 2009/04/10 - 1539)
- Modified library to write cached symbol table information to the
superblock, to allow library versions 1.3.0 to 1.6.3 to read files
created by this version. (NAF - 2009/04/08 - 1423)
- Changed skip lists to use a deterministic algorithm. The library should
now never call rand() or srand(). (NAF - 2009/04/08 - 503)
- Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate
groups when that property was set. (NAF - 2009/04/07 - 1526)
- Fixed a bug that caused files with a user block to grow by the size of
the user block every time they were opened.
(NAF - 2009/03/26 - 1499)
- Fixed a rare problem that could occur with files using the old (pre 1.4)
array datatype. (NAF - 2009/03/23)
- Modified library to be able to open files with corrupt root group symbol
table messages, and correct these errors if they are found. Such
files can only be successfully opened with write access.
(NAF - 2009/03/23 - 1189)
- Removed the long_long #define and replaced all instances with
"long long". This caused problems with third party products. All
currently supported compliers support the type. (ADB - 2009/03/05)
- Fixed various bugs that could prevent the fill value from being written
in certain rare cases. (NAF - 2009/02/26 - 1469)
- Fixed a bug that prevented more than one dataset chunk from being cached
at a time. (NAF - 2009/02/12 - 1015)
- Fixed an assertion failure caused by opening an attribute multiple times
through multiple file handles. (NAF - 2009/02/12 - 1420)
- Fixed a problem that could prevent the user from adding attributes (or
any object header message) in some circumstances.
(NAF - 2009/02/12 - 1427)
- Fixed a bug that could cause problems when an attribute was added to a
committed datatype using the committed datatype's datatype.
(NAF - 2009/02/12)
- Fixed a bug that could cause problems when copying an object with a
shared message in its own object header. (NAF - 2009/01/29)
- Changed H5Tset_order to properly reject H5T_ORDER_NONE for most
datatypes. (NAF - 2009/01/27 - 1443)
- Fixed a bug where H5Tpack wouldn't remove trailing space from an
otherwise packed compound type. (NAF - 2009/01/14)
- Fixed up some old v2 btree assertions that get run in debug mode that
were previously failing on compilation, and removed some of the
more heavily outdated and non-rewritable ones. (MAM - 2008/12/15)
- Fixed a bug that could cause problems when "automatically" unmounting
multiple files. (NAF - 2008/11/17)
- H5Ovisit and H5Ovisit_by_name will now properly terminate when the
callback function returns a positive value on the starting object.
(NAF - 2008/11/03)
- Fixed an error where a null message could be created that was larger
than could be written to the file. (NAF - 2008/10/23)
- Corrected error with family/split/multi VFD not updating driver info
when "latest" version of the file format used. (QAK - 2008/10/14)
- Corrected alignment+threshold errors to work correctly when metadata
aggregation is enabled. (QAK - 2008/10/06)
- Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered
by the library for internal library use. (NAF - 2008/10/06)
- Fixed potential memory leak during compound conversion.
(NAF - 2008/10/06)
- Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also
changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and
the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26)
- Fixed an issue that could cause data to be improperly overwritten
during compound type conversion. (NAF - 2008/09/19)
- Fixed pointer alignment violations that could occur during vlen
conversion. (NAF - 2008/09/16)
- Fixed problem where library could cause a segmentation fault when
an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19)
- Fixed improper shutdown when objects have reference count > 1. The
library now tracks reference count due to the application separately
from that due to internal library routines. (NAF - 2008/08/19)
- Fixed assertion failure caused by incorrect array datatype version.
(NAF - 2008/08/08)
- Fixed an issue where mount point traversal would fail when using
multiple handles for the child. (NAF - 2008/08/07)
- Fixed an issue where mount points were inaccessible when using multiple
file handles for the parent. The mount table is now in the shared
file structure (the parent pointer is still in the top structure).
(NAF - 2008/08/07)
- when an attribute was opened twice and data was written with one of the handles,
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure. SLU - 2008/07/22
- Fixed issue where a group could have a file mounted on it twice.
(QAK - 2008/07/15)
- Fixed a Windows-specific issue in the ohdr test which was causing users
in some timezones to get false errors. This a deficiency in the Windows
mktime() function, and has been handled properly. SJW - 2008/06/19
- Fixed the problem with the searching of target file for H5Lcreate_external().
The searching pattern will depend on whether the target file's
pathname is an absolute or a relative path. Please see the description
in the RM for H5Lcreate_external(). (VC - 2008/04/08)
- Fixed possible file corruption bug when encoding datatype
descriptions for compound datatypes whose size was between
256 & 511 bytes and the file was opened with the "use the
latest format" property enabled (with H5Pset_libver_bounds).
(QAK - 2008/03/13)
- Fixed bug in H5Aget_num_attrs() routine to handle invalid location
ID correctly. (QAK - 2008/03/11)
- H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
(PVN - 2009/01/8)
- Added code to maintain a min_clean_fraction in the metadata cache when
in serial mode. (MAM - 2009/01/9)
Configuration
-------------
- Fixed Makefile issue in which "-Wl," was not properly specified
prior to -rpath when building parallel fortran libraries with
an Intel compiler. (MAM - 2012/03/26)
- Makefiles generated by other packages using h5cc as the compiler
no longer error when 'make' is invoked more than once in order
to 'rebuild' after changes to source. (MAM - 2012/03/26)
- Added --enable-fortran2003 flag to enable Fortran2003 support
in the HDF5 Fortran library. The flag should be used along with the
--enable-fortran flag and takes affect only when Fortran compiler
is Fortran2003 compliant. (EIP - 2011/11/14)
- In Windows platform, the default VFD, was Windows VFD, is restored back
to the SEC2, aka POSIX, VFD. The Windows VFD is deprecated. HDFFV-7740
(AKC 2011/09/26)
- Removed config/ibm-aix6.x. All IBM-AIX settings are in one file,
ibm-aix. (AKC - 2011/4/14)
- Shared C libraries are no longer disabled on Mac when Fortran
is enabled. Shared Fortran libraries are still not supported on Mac,
so configure will disable them by default, but this is overridable
with the new --enable-unsupported configure option. The configure
summary has been updated to reflect the fact that the shared-ness of
the C++/Fortran wrapper libraries may not align with the C library.
(MAM - 04/11/2011 - HDFFV-4353).
- 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 - 2010/7/14 - Bug 1921)
- Removed the following config files, as we no longer support them:
config/dec-osf*, config/hpux11.00, config/irix5.x,
config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos*
MAM - 2009/10/08
- Modified configure and make process to properly preserve user's CFLAGS
(and company) environment variables. Build will now properly use
automake's AM_CFLAGS for any compiler flags set by the configure
process. Configure will no longer modify CFLAGS directly, nor will
setting CFLAGS during make completely replace what configure has set up.
MAM - 2009/10/08
- Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
machine has long retired. AKC - 2009/10/06.
- Added $(EXEEXT) extension to H5detect when it's executed in the
src/Makfile to generate H5Tinit.c so it works correctly on platforms
that require the full extension when running executables.
MAM - 2009/10/01 - BZ #1613
- Configure will now set FC and CXX to "no" when fortran and c++
are not being compiled, respectively, so configure will not run
some of the compiler tests for these languages when they are not
being used. MAM - 2009/10/01
- 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 -
- The --enable-static-exec flag will now properly place the -static flag
on the link line of all installed executables. This will force the
executable to link with static libraries over shared libraries, provided
the static libraries are available. MAM - 2009/08/31 - BZ #1583
- The --includedir=DIR configuration option now works as intended, and can
be used to specify the location to install C header files. The default
location remains unchanged, residing at ${prefix}/include.
MAM - 2009/03/10 - BZ #1381
- Configure no longer removes the '-g' flag from CFLAGS when in production
mode if it has been explicitly set in the CFLAGS environment variable
prior to configuration. MAM - 2009/03/09 - BZ #1401.
- Fixed error with 'make check install' failing due to h5dump
needing other tools built first. MAM - 2008/10/24.
- Wpen using shared szip, it is no longer necessary to specify
the path to the shared szip libraries in LD_LIBRARY_PATH. MAM -
2008/10/24.
- The file libhdf5_fortran.settings is not installed since its content
is included in libhdf5.settings now. AKC - 2008/10/21
- "make DESTDIR=xxx install" failed to install some tools and files
(e.g., h5cc and fortran modules). Fixed. AKC - 2008/10/8.
Performance
-------------
- Removed program perform/benchpar from the enable-build-all list. The
program will be retired or moved to another location. HDFFV-8156
(AKC 2012/10/01)
- Retired program perform/mpi-perf. Its purpose has been incorporated
into h5perf before. (AKC 2012/09/20)
- ifdefs added to tests around include unistd.h and function to simulate
getlogin() on Windows.
(ADB - 2011/08/15)
- perf_serial test added to Windows projects and check batch file.
(ADB - 2009/06/11)
Fortran
--------
- Fixed a typo in return value of the nh5dread_f_c function ( was 1
instead of 0 on success); fixed the return value to make it consistent
with other Fortran functions; cleaned the code from debug statements.
(EIP - 2012/06/23)
- Fixed problem writing/reading control characters to a dataset; writing
a string containing: alerts, backspace, carriage_return, form_feed,
horizontal_tab, vertical_tab, new_line is now tested and working.
(MSB - 2012/09/01)
- Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01)
- Corrected the number of continuation lines in the src files
to be less then 32 lines for F95 compliance. (MSB - 2012/10/01)
Tools
-----
- h5diff: Improved speed when comparing HDF5 files with lots of
attributes. Much slower performance was identified with release version
from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19)
- h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if
source file contains chunked dataset and a chunk dim is bigger than
the dataset dim. Another issue is that the command changed max dims
if chunk dim is smaller than the dataset dim.
These issue occurred when dataset size is smaller than 64k (compact
size limit) Fixed both.
HDFFV-8012 (JKM 2012/09/24)
- h5diff: Fixed not to accumulate attribute difference to dataset
difference in verbose mode (-v, -r), which caused incorrect
difference between dataset and group/datatype object if attribute
exist with any differences. This also lead to fix inconsistent
format indicating difference between dataset and group/datatype
object. HDFFV-5919 (JKM 2012/09/05)
- h5diff: Fixed the incorrect result when comparing attribute data
values and the data type has same class but different size.
HDFFV-7942 (JKM 2012/08/15)
- ph5diff: Fixed intermittent hang issue on a certain operation in
parallel mode. It was detected by daily test for comparing
non-comparable objects, but it could have occurred in other
operations depend on machine condition. HDFFV-8003 (JKM 2012/08/01)
- h5diff: Fixed test failure for "make check" due to failure of
copying test files when performed in HDF5 source tree. Also applied
to other tools.
HDFFV-8107 (JKM 2012/08/01)
- h5diff: Fixed the Function COPY_TESTFILES_TO_TESTDIR() of
testh5diff.sh to better report when there is an error in the file
copying. HDFFV-8105 (AKC -2012/07/22)
- h5diff: Fixed not to check and display dangling link status without
--follow-symlinks option. This also improved performance when
comparing lots of external links without the --follow-symlinks
option. HDFFV-7998 (JKM 2012/04/26)
- h5unjam: Fixed sefgault when used -V (show version) option.
HDFFV-8001 (JKM 2012/04/19)
- h5repack: Fixed a failure when change the chunk size of a specified
chunked dataset with unlimited max dims. HDFFV-7993 (JKM 2012/04/11)
- h5diff: Fixed failure for comparing same named object with different
object types in comparing groups. Prior to the fix, h5diff resulted
in error. After the fix, h5diff detects such case as non-comparable
and display messages accordingly. HDFFV-7664 (JKM 2012/03/28)
- h5diff: If unique objects exists only in one file and try to exclude
the unique objects with --exclude-path option, h5diff missed
excluding some objects.
Fixed to exclude objects correctly in such case.
HDFFV-7837 (JKM 2012/03/20)
- h5dump: Added tools library error stack to properly catch error
information generated within the library.
HDFFV-7958 (ADB 2012/03/12)
- h5dump: Dangling links no longer throw error message, change process
when open link fails.
HDFFV-7839 (ADB 2012/03/12)
- h5diff: When two symbolic dangling links are compared with
--follow-symlinks option, the result should be same. It worked for
comparing two files, but didn't work for comparing two objects.
HDFFV-7835 (JKM 2012/03/09)
- h5dump: Refactored code to remove duplicated functions. Split XML
functions from DDL functions. Corrected indentation and formatting
errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified
all tools call tools_init() in main.
HDFFV-7560 (ADB 2012/02/17)
- h5diff: fixed to prevent from displaying error stack message when
comparing the two dangling symlinks with follow-symlinks option.
HDFFV-7836 (JKM 2012/01/13)
- h5repack: fixed memory leak for handling variable length string in
attribute. HDFFV-7840 (JKM 2012/01/06)
- h5ls: fixed segfault when access region reference data in an
attribute. HDFFV-7838 (JKM 2011/12/29)
- h5diff: fixed segfault over non-comparable attribute with different
dimention or rank, along with '-c' option to display details.
HDFFV-7770 (JKM 2011/10/24)
- Fixed h5diff to display all the comparable object and attribute
regardless of non-comparables. HDFFV-7693 (JKM 2011/09/16)
- Fixed h5repack to update values of references(object and region) of
attributes in h5repack for 1) references, 2) ARRAY of references,
3) VLEN of references, and 4) COMPOUND of references.
(JIRA HDF5 5932) PC -2011/09/14
- h5diff: fixed segfault over dataset with container types
(array,lven) with multiple nested compound types.
(ex: compound->array->compound, compound->vlen->compound)
HDFFV-7712 JKM (2011/09/01)
- h5repack: added macro to handle failure in H5Dread/write when memory
allocation failed inside the library. (PC -- 2011/08/19)
- Fixed h5jam not to allow specifying an HDF5 formatted file as input
file for -u (user block file) option, because the original HDF5 file
will not be accessible if allows. HDFFV-5941 (JKM 2011/08/15)
- Revised command help pages of h5jam and h5unjam. The descriptions
were not up to date and some were missing.
HDFFV-7515 (JKM 2011/08/15)
- h5repack: h5repack failed to copy dataset if the layout is changed
from chunked with unlimited dims to contiguous. HDFFV-7649
(PC -- 2011/07/15)
- h5diff: "--delta" option considers two NaN of the same type are
different, which is wrong based on h5diff description in Reference
Manual. HDFFV-7656 (PC -- 2011/07/15)
- Fixed h5diff to display instructive error message and exit with 1
when mutually exclusive options (-d, -p and --use-system-epsilon)
are used together. HDFFV-7600 (JKM 2011/07/07)
- Fixed h5dump to display the first line of each element into correct
position for multiple dimention array type.
Before this fix, the first line of each element in array were
displayed after the last line of previous element without
moving to the next line (+indentation).
Bug #HDFFV-5878 (JKM 2011/06/15)
- Fixed h5dump to display correct value for H5T_STD_I8LE dataset
on a system (ppc64, linux, Big-Endian, clustering).
Bug #HDFFV-7594 (ABERT & JKM 2011/05/12)
- Fixed h5diff to compare file itself correctly. Previously h5diff
reported either different or not compatible in certain cases even
comparing file itself. This fix also improve performance when
comparing same target objects through verifying the obj&file
addresses before comparing the details in the objects (ex: datasets
or attributes) Bug #HDFFV-5928 (XCAO & JKM 2011/05/06)
- Updated h5dump test case script to prevent entire test failure upon
source directory is read-only. Bug# HDFFV-4342 (JKM 2011/4/12)
- Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in
attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type,
so h5dump is supposed to display -2 instead of 254. It worked
correctly on Little-Endian system , but not on Big-Endian system.
Bug #HDFFV-4358 (JKM 2011/04/08)
- Updated to unify option name to '--enable-error-stack' for printing
HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now.
For h5ls, this replaces "-e/--errors" option, which is deprecated.
Bug#2182 (JKM 2011/3/30)
- Fix h5diff for --use-system-epsilon option: the calculation changed
from ( |a - b| / b ) to ( |a - b| ). This was decided for better
performance. Bug#2184 (JKM 2011/3/24)
- Fixed output for H5T_REFERENCE in h5dump. According to the BNF document
the output of a H5T_REFERENCE should be followed by the type;
<reference> ::= H5T_REFERENCE { <ref_type> }
<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG
Previously this was only displayed if the -R option was used.
Bug#1725 (ADB 2011/3/28)
- Fix h5diff issues for #1: h5diff compared attributes correctly only
when two objects have the same number of attributes and attribute
names are identical, #2: didn't display useful information about
attribute difference. Bug#2121 (JKM 2011/3/17)
- Fixed memory leak for h5diff when accessing symbolic links with
--follow-symlink option. Bug#2214 (JKM 2011/3/18)
- Fixed memory leak for h5diff when access variable length string
data. Bug#2216 (JKM 2011/3/18)
- Fixed and improved help page for -a option of h5ls.
Bug#1904 (JKM 2011/3/11)
- Fixed h5dump not to include attribute values in the output file when
h5dump "-y -o output_file" options were used. The problem was introduced
in HDF5 1.8.6 by showing data pointed by region references. (XCAO 2011/3/9)
- Fixed h5copy to be able to copy any object into the same HDF5 file.
Previously h5copy displayed error message when target file is same
as source file. (XCAO 2011/3/8)
- Fixed h5dump for skipping some values for long array type dataset on
Windows. This issue only occurred on Windows due to the different
return behavior from _vsnprintf() funtion. Bug#2161 (JKM 2011/3/3)
- Fixed h5dump for skipping array indices every certain number
when the array type dataset is relatively big. The certain number
varies according to the size of array. Bug#2092 (JKM 2011/2/15).
- Fixed h5diff for the segfault when compares compound datasets
with combination of fixed length string types and vlen string types
in certain orders. bug#2089 (JKM 2010/12/28)
- Improve h5diff performance. 1) use HDmemcmp() before comparing each
elements. 2) replace expensive H5Tequals() calls 3) retrieve datatype
information at dataset level not each element level for compound
datasets
- Fixed h5ls to display nested compound type with curly bracket
when -S (--simple) option is used with -l (--label), so it shows
which member (in curly bracket) belong to which nested compound type
and make the output make sense. bug#1979 (JKM 2010/11/09)
- Fixed h5diff to handle variable-length strings in a compound dataset
correctly. (also variable-length string array in a compound dataset)
Garbage values were displayed when h5diff compared multiple
variable-length strings in a compound type dataset.
Bug#1989 (JKM 2010/10/28)
- Fixed h5copy to fail gracefully when copying object to non-exist
group without -p option. Bug#2040 (JKM 2010/10/18)
- Fixed to compare member objects and groups recursively when two
files or groups are specified to be compared. Bug#1975
(JKM 2010/9/16)
- Make h5repack be able to convert a layout to COMPACT for small size
dataset as default. bug#1896 (JKM 2010/09/15)
- Change h5ls not to manipulate special characters in object name or
attribute name for smart display. bug#1784 (JKM 2010/06/28)
- Fixed h5ls to return exit code 1 (error) when non-existent file is
specified. bug#1793. (JKM 2010/04/27)
- h5copy failed to copy dangling link when the link is specified
directly. bug#1817. (JKM 2010/04/22)
- h5repack lost attributes from a dataset of reference type. bug#1726.
(JKM 2010/3/25)
- h5repack sets NULL for object reference value for group or
named datatype. bug#1814. (JKM 2010/03/19)
- h5diff: fixed incorrect behavior (hang) in parallel mode when
specify invalid options (ex: -v and -q) (JKM 2010/02/17)
- h5dump/h5ls display buffer resize fixed in tools library.
(ADB - 2009/07/21 - 1520)
- Fixed many problems that could occur when using h5repack with named
datatypes. (NAF - 2009/4/20 - 1516/1466)
- h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets
that have a datatype datum size greater than H5TOOLS_BUFSIZE, a
constant defined as 1024Kb, such as array types with large
dimensions (PVN - 2009/4/1 - 1501)
- h5import: By selecting a compression type, a big endian byte order was being
selected (PVN - 2009/3/11 - 1462)
- zip_perf.c had missing argument on one of the open() calls. Fixed.
(AKC - 2008/12/9)
- h5dump now checks for uniqueness of committed datatypes.
(NAF - 2008/10/15)
- Fixed unnecessary indentation of committed datatypes in h5dump.
(NAF - 2008/10/15)
- Fixed bugs in h5stat:segmemtation fault when printing groups and
print warning message when traversal of objects is unsuccessful.
(see bug #1253) (VC- 2008/10/13)
- Fixed bug in h5ls that prevented relative group listings (like
"h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03)
- Fixed bug in h5diff that prevented datasets & attributes with
variable-length string elements from comparing correctly.
(QAK - 2008/02/28)
- h5import bug on Windows w/binary datasets. fread in windows needs a
binary file to be open with 'rb' instead of 'r' otherwise it
terminates execution if an end of file character is found on the
input file. Besides that the binary file generated needs to be open
with 'wb' , otherwise an end of line character is read twice.
(PVN - 2008/02/19)
- Fixed bug in h5dump that caused binary output to be made only for the first
dataset, when several datasets were requested. (PVN - 2008/04/07)
- h5dump: when doing binary output (-b), the stdout printing of attributes
was done incorrectly. Removed printing of attributes when doing binary
output. PVN - 2008/06/05
High-Level APIs:
------
- Fixed problem with H5TBdelete_record destroying all data following the deletion
of a row. (MSB- 2012/7/26)
- Fixed H5LTget_attribute_string not closing an object identifier when an
error occurs. (MSB- 2012/7/21)
- Fixed the H5LTdtype_to_text function. It had some memory problems when
dealing with some complicated data types. HDFFVI-7701 (SLU - 2011/10/19)
- Fixed a bug in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale
caused by using H5Tget_native_type function to determine the native
type for reading REFERENCE_LIST attribute. The bug was exposed
on Mac PPC.
(EIP - 2010/05/22 -1851)
- Fixed a bug in the H5DSdetach_scale function when 0 bytes
were allocated after the last reference to a dim. scale
was removed from the list of references in a VL element of the
DIMENSION_LIST attribute; modified the function to comply
with the Spec: DIMENSION_LIST attribute is deleted now when no
dimension scales left attached.
(EIP - 2010/05/14 -1822)
- Fixed a bug where the H5TB API would forget the order of fields when
added out of offset order. (NAF - 2009/10/27 - 1582)
- H5DSis_attached failed to account for different platform types. Added a
get native type call. (ADB - 2009/9/29 - 1562)
- Dimension scales: The scale index return value in H5DSiterate_scales was not always
incremented. (PVN - 2009/4/8 - 1538)
Fortran High-Level APIs:
------
- Lite: The h5ltget_attribute_string_f used to return the C NULL character in the
returned character buffer. The returned Fortran charactor buffer now does
not return the C NULL character. (MSB - 2012/3/23)
- Lite: The h5ltget_dataset_info_f function (gets information about a dataset)
was not correctly returning the dimension array. (PVN - 2009/3/23)
- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions
had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522
Documentation
-------------
F90 APIs
--------
- Modified the h5open_f and h5close_f subroutines to not to call H5open
and H5close correspodningly. While the H5open call just adds overhead,
the H5close call called by an Fortran application shuts down the HDF5
library making it unaccessible to the application.
HDFFV-915 (EIP & SB - 2011/10/13)
C++ APIs
--------
- The constructor PropList::PropList(id) was fixed to act properly
according to the nature of 'id'. When 'id' is a property class id,
a new property list will be created. When 'id' id a property list id,
a copy of the property list will be made. (BMR - 2010/5/9)
- The parameters 'size' and 'bufsize' in CommonFG::getLinkval and
CommonFG::getComment, respectively, now have default values 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)
- Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20)
- Fixed bug in PropList::getClassName to use portable HDfree instead
of free. (BMR - 2008/04/20)
- Fixed a design bug which allowed an Attribute object to create/modify
attributes (bugzilla #1068). The API class hierarchy was revised
to address the problem. Classes AbstractDS and Attribute are moved
out of H5Object. Class Attribute now multiply inherits from
IdComponent and AbstractDs and class DataSet from H5Object and
AbstractDs. In addition, the data member IdComponent::id was
moved into subclasses: Attribute, DataSet, DataSpace, DataType,
H5File, Group, and PropList. (BMR - 2008/08/10)
- IdComponent::dereference was incorrect and replaced as described
in "New Features" section.
(BMR - 2008/08/10)
Platforms Tested
================
AIX 5.3 xlc 10.1.0.5
(NASA G-ADA) xlC 10.1.0.5
xlf90 12.1.0.6
FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
(loyalty) gcc 4.6.1 20110422
g++ 4.6.1 20110422
gfortran 4.6.1 20110422
FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
(freedom) gcc 4.6.1 20110422
g++ 4.6.1 20110422
gfortran 4.6.1 20110422
Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2
#1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704
(jam) (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
MPICH mpich2-1.3.1 compiled with
gcc 4.1.2 and gfortran 4.1.2
Linux 2.6.18-238.12.1.el5 gcc 4.1.2 and 4.4.2
#1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704
(koala) (Red Hat 4.1.2-46) and 4.4.2
tested for both 32- and 64-bit binaries
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 mpich2-1.3.1 compiled with
gcc 4.1.2 and gfortran 4.1.2
SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806
2.6.32.19-0.3.1.1982.0.PTF- Intel(R) Fortran Version 11.1 20100806
default #1 SMP SGI MPT 2.01
SGI Altix UV
(NCSA ember)
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
127000-13
Sun C++ 5.9 Sun OS_sparc Patch 124863-62
Sun C 5.10 SunOS_sparc Patch 141861-07
Sun Fortran 95 8.4 SunOS_sparc Patch
128231-06
Sun C++ 5.10 SunOS_sparc 128228-11
Windows 7 Visual Studio 2010 w/ Intel Fortran 12 (cmake)
Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
Windows 7 x64 Visual Studio 2010 w/ Intel Fortran 12 (cmake)
Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
MAC OS 10.5 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
GNU Fortran (GCC) 4.3.0 20070810
Alpha Open VMS 7.3
Supported Configuration Features Summary
========================================
In the tables below
y = tested and supported
n = not supported or not tested in this release
x = not working in this release
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
W or C indicates workstation or cluster, respectively.
Platform C F90 F90 C++ zlib SZIP
parallel parallel
SunOS5.10 64-bit n y n y y y
SunOS5.10 32-bit n y n y y y
Windows 7 y y n y y y
Windows 7 x64 y y n y y y
Mac OS X 10.5 Intel n y n y y y
FreeBSD 8.2 32- and 64-bit n y n y y y
RedHat EL4 2.6.9 i686 GNU W y(2) y(4) y(2) y y y
RedHat EL4 2.6.9 i686 Intel W n y n y y n
RedHat EL4 2.6.9 i686 PGI W n y n y y n
SuSe Linux 2.6.16 x86_64 GNU (5) W y(2) y n y y y
SuSe Linux 2.6.16 x86_64 Int (5) W n y n y n n
SuSe Linux 2.6.16 x86_64 PGI (5) W n y n y n n
RHL9 Linux 2.4 Xeon Lustre Intel C n y n y y n
RHEL3 Linux 2.4 Xeon Intel W n y n n y n
RHEL4 Linux 2.6 Xeon Lustre Int C n y n y y n
SuSE Linux 2.4 ia64 Intel C y(1) y y y y y
SuSe Linux 2.6.5
SGI Altix ia64 Intel C n y n y n y
Alpha OpenVMS 7.3.2 n y n y n n
Platform Shared Shared Shared static- Thread-
C libs F90 libs C++ libs exec safe
SunOS 5.10 32-bit y y y x y
SunOS 5.10 64-bit y y y x y
Windows 7 y y y y y
Windows 7 x64 y y y y y
Mac OS X 10.5 Intel y y y x n
FreeBSD 8.2 32- and 64-bit y y y y y
RHEL4 2.6.9 i686 GNU W y y(4) y x y
RHEL4 2.6.9 i686 Intel W y y y x n
RHEL4 2.6.9 i686 PGI W y y y x n
SuSE Linux 2.6.16 x86_64 GNU (5) W y y y x y
SuSE Linux 2.6.16 x86_64 Intel(5) W y y y x n
SuSE Linux 2.6.16 x86_64 PGI(5) W y y y x n
RHL9 Linux 2.4 Xeon Lustre Intel C y y y x n
RHEL3 Linux 2.4 Xeon Intel W y n n x n
RHEL4 Linux 2.6 Xeon Lustre Intel C y y y x n
SuSE Linux 2.4 ia64 Intel C y y y x n
SuSe Linux 2.6.5
SGI Altix ia64 Intel C n n n x n
Notes: (1) Using mpich 1.2.6.
(2) Using mpich2 1.0.6.
(3) Using Visual Studio 2008 (Cygwin shared libraries are not supported)
(4) With PGI and Absoft compilers.
(5) AMD Opteron x86_64
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
complains with this message:
"/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
The reason is that __func__ is a predefined identifier in C99 standard. The
HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
C++ compiler doesn't support __func__, thus fails to compile the C++ test.
But 5.11 C++ compiler does. To check whether your Sun C++ compiler knows this
identifier, try to compile the following simple C++ program:
#include<stdio.h>
int main(void)
{
printf("%s\n", __func__);
return 0;
}
(SLU - 2012/11/5)
* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
ports (and probably gcc releases after that).
(QAK - 2012/10/19)
* The data conversion test dt_arith.c has failures (segmentation fault) from
"long double" to other datatypes during hard conversion when the library
is built with the default GCC 4.2.1 on Mac Lion system. It only happens
with optimization (-O3, -O2, and -O1). Some newer versions of GCC do not
have this problem. Users should disable optimization or try newer version
of GCC. (Issue 8017. SLU - 2012/6/12)
* The data conversion test dt_arith.c fails in "long double" to integer
conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library
is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal
(3.2.2 on Fedora) doesn't have the problem. Users should lower down the
optimization level (-O1 or -O0) by defining CFLAGS in the command line of
"configure" like:
CFLAGS=-O1 ./configure
It will overwrite the library's default optimization level. (Issue 7829.
SLU - 2012/2/7)
* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10)
* 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/
* Parallel mode in AIX will fail some of the testcheck_version.sh tests where
it treats "exit(134) the same as if process 0 had received an abort signal.
This is fixed and will be available in the next release. AKC - 2009/11/3
* 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 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 SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
tests failed with MPI-IO file locking message. AKC - 2007/6/25.
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use
-mp -O1 compilation flags to build the libraries. Higher level of optimization
causes failures in several HDF5 library tests.
* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
shared libraries (tested for 1.8.0-beta2)
* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass
and the parallel tests also pass with lots of non-fatal error messages.
* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test
* configuring with --enable-debug=all produces compiler errors on most
platforms. Users who want to run HDF5 in debug mode should use
--enable-debug rather than --enable-debug=all to enable debugging
information on most modules.
* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
double to (unsigned) long long and from (unsigned)long long to long double.
* On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3
optimization flag.
* On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to
HDF5 data generated on VAX. Scaleoffset filter only supports IEEE standard
for floating-point data.
* On Cray X1, a lone colon on the command line of h5dump --xml (as in
the testh5dumpxml.sh script) is misinterpereted by the operating system
and causes an error.
* On mpich 1.2.5 and 1.2.6, we found that if more than two processes
contribute no IO and the application asks to do IO with collective, we found
that when using 4 processors, a simple collective write will be hung
sometimes. This can be verified with t_mpi test under testpar.
* The 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(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. The library release
after 1.6.4 can still read the dataset created or rewritten with the library
of v1.6.2 or before. SLU - 2005/6/30
* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron
processor, there's a bug in the compiler for optimization(-O2). The library
failed in several tests but all related to multi driver. The problem has
been reported to the vendor.
* 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 fail with messages like "The socket name is already
in use". HDF5 does not use sockets (except for stream-VFD). This is
due to problems of the poe command trying to set up the debug socket.
Check if there are many old /tmp/s.pedb.* 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 mean to run poe without the debug socket.
* The C++ library's tests fails when compiling with PGI C++ compiler. The
workaround until the problem is correctly handled is to use the
flag "--instantiate=local" prior to the configure and build steps, as:
setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher
* The stream-vfd test uses ip port 10007 for testing. If another
application is already using that port address, the test will hang
indefinitely and has to be terminated by the kill command. To try the
test again, change the port address in test/stream_test.c to one not
being used in the host.
* 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.
* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
compilation. The ANSI version of the compiler complains about not being
able to handle the `long long' datatype with the warning:
warning: ANSI C does not support `long long'
This warning is innocuous and can be safely ignored.
* Certain platforms give false negatives when testing h5ls:
- Cray J90 and Cray T90IEEE give errors during testing when displaying
some floating-point values. These are benign differences due to
the different precision in the values displayed and h5ls appears to
be dumping floating-point numbers correctly.
* Not all platforms behave correctly with szip's shared libraries. Szip is
disabled in these cases, and a message is relayed at configure time. Static
libraries should be working on all systems that support szip, and should be
used when shared libraries are unavailable. There is also a configure error
on Altix machines that incorrectly reports when a version of szip without
an encoder is being used.
* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library,
compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90
complaining about exit subroutine. Comment out the line
IF (total_error .ne. 0) CALL exit (total_error)
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8
* On at least one system, (SDSC DataStar), the scheduler (in this case
LoadLeveler) sends job status updates to standard error when you run
any executable that was compiled with the parallel compilers.
This causes problems when running "make check" on parallel builds, as
many of the tool tests function by saving the output from test runs,
and comparing it to an exemplar.
The best solution is to reconfigure the target system so it no longer
inserts the extra text. However, this may not be practical.
In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
the configure and build. This will cause "make check" to continue after
detecting errors in the tool tests. However, in the case of SDSC DataStar,
it also leaves you with some 150 "failed" tests to examine by hand.
A second solution is to write a script to run serial tests and filter
out the text added by the scheduler. A sample script used on SDSC
DataStar is given below, but you will probably have to customize it
for your installation.
Observe that the basic idea is to insert the script as the first item
on the command line which executes the the test. The script then
executes the test and filters out the offending text before passing
it on.
#!/bin/csh
set STDOUT_FILE=~/bin/serial_filter.stdout
set STDERR_FILE=~/bin/serial_filter.stderr
rm -f $STDOUT_FILE $STDERR_FILE
($* > $STDOUT_FILE) >& $STDERR_FILE
set RETURN_VALUE=$status
cat $STDOUT_FILE
tail +3 $STDERR_FILE
exit $RETURN_VALUE
You get the HDF make files and test scipts to execute your filter script
by setting the environment variable "RUNSERIAL" to the full path of the
script prior to running configure for parallel builds. Remember to
"unsetenv RUNSERIAL" before running configure for a serial build.
Note that the RUNSERIAL environment variable exists so that we can
can prefix serial runs as necessary on the target system. On DataStar,
no prefix is necessary. However on an MPICH system, the prefix might
have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
get the serial tests to run at all.
In such cases, you will have to include the regular prefix in your
filter script.
* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
is turn on. The value of the reference in the destination attriubte is
wrong. This H5Ocopy problem will affect h5copy tool
|
