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
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
1852
1853
1854
1855
1856
1857
1858
1859
1860
1861
1862
1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
1881
1882
1883
1884
1885
1886
1887
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
2029
2030
2031
2032
2033
2034
2035
2036
2037
2038
2039
2040
2041
2042
2043
2044
2045
2046
2047
2048
2049
2050
2051
2052
2053
2054
2055
2056
2057
2058
2059
2060
2061
2062
2063
2064
2065
2066
2067
2068
2069
2070
2071
2072
2073
2074
2075
2076
2077
2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
2089
2090
2091
2092
2093
2094
2095
2096
2097
2098
2099
2100
2101
2102
2103
2104
2105
2106
2107
2108
2109
2110
2111
2112
2113
2114
2115
2116
2117
2118
2119
2120
2121
2122
2123
2124
2125
2126
2127
2128
2129
2130
2131
2132
2133
2134
2135
2136
2137
2138
2139
2140
2141
2142
2143
2144
2145
2146
2147
2148
2149
2150
2151
2152
2153
2154
2155
2156
2157
2158
2159
2160
2161
2162
2163
2164
2165
2166
2167
2168
2169
2170
2171
2172
2173
2174
2175
2176
2177
2178
2179
2180
2181
2182
2183
2184
2185
2186
2187
2188
2189
2190
2191
2192
2193
2194
2195
2196
2197
2198
2199
2200
2201
2202
2203
2204
2205
2206
2207
2208
2209
2210
2211
2212
2213
2214
2215
2216
2217
2218
2219
2220
2221
2222
2223
2224
2225
2226
2227
2228
2229
2230
2231
2232
2233
2234
2235
2236
2237
2238
2239
2240
2241
2242
2243
2244
2245
2246
2247
2248
2249
2250
2251
2252
2253
2254
2255
2256
2257
2258
2259
2260
2261
2262
2263
2264
2265
2266
2267
2268
2269
2270
2271
2272
2273
2274
2275
2276
2277
2278
2279
2280
2281
2282
2283
2284
2285
2286
2287
2288
2289
2290
2291
2292
2293
2294
2295
2296
2297
2298
2299
2300
2301
2302
2303
2304
2305
2306
2307
2308
2309
2310
2311
2312
2313
2314
2315
2316
2317
2318
2319
2320
2321
2322
2323
2324
2325
2326
2327
2328
2329
2330
2331
2332
2333
2334
2335
2336
2337
2338
2339
2340
2341
2342
2343
2344
2345
2346
2347
2348
2349
2350
2351
2352
2353
2354
2355
2356
2357
2358
2359
2360
2361
2362
2363
2364
2365
2366
2367
2368
2369
2370
2371
2372
2373
2374
2375
2376
2377
2378
2379
2380
2381
2382
2383
2384
2385
2386
2387
2388
2389
2390
2391
2392
2393
2394
2395
2396
2397
2398
2399
2400
2401
2402
2403
2404
2405
2406
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416
2417
2418
2419
2420
2421
2422
2423
2424
2425
2426
2427
2428
2429
2430
2431
2432
2433
2434
2435
2436
2437
2438
2439
2440
2441
2442
2443
2444
2445
2446
2447
2448
2449
2450
2451
2452
2453
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/****************/
/* Module Setup */
/****************/
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
/* Interface initialization */
#define H5_INTERFACE_INIT_FUNC H5D__init_interface
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5FOprivate.h" /* File objects */
#include "H5Iprivate.h" /* IDs */
#include "H5Lprivate.h" /* Links */
#include "H5MMprivate.h" /* Memory management */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/* Struct for holding callback info during H5D_flush operation */
typedef struct {
const H5F_t *f; /* Pointer to file being flushed */
hid_t dxpl_id; /* DXPL for I/O operations */
} H5D_flush_ud_t;
/********************/
/* Local Prototypes */
/********************/
/* General stuff */
static herr_t H5D__get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache);
static H5D_shared_t *H5D__new(hid_t dcpl_id, hbool_t creating,
hbool_t vl_type);
static herr_t H5D__init_type(H5F_t *file, const H5D_t *dset, hid_t type_id,
const H5T_t *type);
static herr_t H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space);
static herr_t H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset,
hid_t dapl_id);
static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id);
static herr_t H5D__init_storage(const H5D_t *dataset, hbool_t full_overwrite,
hsize_t old_dim[], hid_t dxpl_id);
/*********************/
/* Package Variables */
/*********************/
/* Define a "default" dataset transfer property list cache structure to use for default DXPLs */
H5D_dxpl_cache_t H5D_def_dxpl_cache;
/* Declare a free list to manage blocks of VL data */
H5FL_BLK_DEFINE(vlen_vl_buf);
/* Declare a free list to manage other blocks of VL data */
H5FL_BLK_DEFINE(vlen_fl_buf);
/*****************************/
/* Library Private Variables */
/*****************************/
/*******************/
/* Local Variables */
/*******************/
/* Declare a free list to manage the H5D_t and H5D_shared_t structs */
H5FL_DEFINE_STATIC(H5D_t);
H5FL_DEFINE_STATIC(H5D_shared_t);
/* Declare the external PQ free list for the sieve buffer information */
H5FL_BLK_EXTERN(sieve_buf);
/* Declare the external free list to manage the H5D_chunk_info_t struct */
H5FL_EXTERN(H5D_chunk_info_t);
/* Define a static "default" dataset structure to use to initialize new datasets */
static H5D_shared_t H5D_def_dset;
/* Dataset ID class */
static const H5I_class_t H5I_DATASET_CLS[1] = {{
H5I_DATASET, /* ID class value */
H5I_CLASS_REUSE_IDS, /* Class flags */
0, /* # of reserved IDs for class */
(H5I_free_t)H5D_close /* Callback routine for closing objects of this class */
}};
/*-------------------------------------------------------------------------
* Function: H5D_init
*
* Purpose: Initialize the interface from some other layer.
*
* Return: Success: non-negative
*
* Failure: negative
*
* Programmer: Quincey Koziol
* Saturday, March 4, 2000
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_init(void)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
/* FUNC_ENTER() does all the work */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_init() */
/*--------------------------------------------------------------------------
NAME
H5D__init_interface -- Initialize interface-specific information
USAGE
herr_t H5D__init_interface()
RETURNS
Non-negative on success/Negative on failure
DESCRIPTION
Initializes any interface-specific data or routines.
NOTES
Care must be taken when using the H5P functions, since they can cause
a deadlock in the library when the library is attempting to terminate -QAK
--------------------------------------------------------------------------*/
static herr_t
H5D__init_interface(void)
{
H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Initialize the atom group for the dataset IDs */
if(H5I_register_type(H5I_DATASET_CLS) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize interface")
/* Reset the "default dataset" information */
HDmemset(&H5D_def_dset, 0, sizeof(H5D_shared_t));
/* Get the default dataset creation property list values and initialize the
* default dataset with them.
*/
if(NULL == (def_dcpl = (H5P_genplist_t *)H5I_object(H5P_LST_DATASET_CREATE_g)))
HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list")
/* Get the default data storage layout */
if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve layout")
/* Get the default dataset creation properties */
if(H5P_get(def_dcpl, H5D_CRT_EXT_FILE_LIST_NAME, &H5D_def_dset.dcpl_cache.efl) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve external file list")
if(H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.dcpl_cache.fill) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value")
if(H5P_get(def_dcpl, H5O_CRT_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve pipeline filter")
/* Reset the "default DXPL cache" information */
HDmemset(&H5D_def_dxpl_cache, 0, sizeof(H5D_dxpl_cache_t));
/* Get the default DXPL cache information */
if(H5D__get_dxpl_cache_real(H5P_DATASET_XFER_DEFAULT, &H5D_def_dxpl_cache) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve default DXPL info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__init_interface() */
/*-------------------------------------------------------------------------
* Function: H5D_term_interface
*
* Purpose: Terminate this interface.
*
* Return: Success: Positive if anything was done that might
* affect other interfaces; zero otherwise.
*
* Failure: Negative.
*
* Programmer: Robb Matzke
* Friday, November 20, 1998
*
*-------------------------------------------------------------------------
*/
int
H5D_term_interface(void)
{
int n=0;
FUNC_ENTER_NOAPI_NOINIT_NOERR
if(H5_interface_initialize_g) {
if((n=H5I_nmembers(H5I_DATASET))>0) {
/* The dataset API uses the "force" flag set to true because it
* is using the "file objects" (H5FO) API functions to track open
* objects in the file. Using the H5FO code means that dataset
* IDs can have reference counts >1, when an existing dataset is
* opened more than once. However, the H5I code does not attempt
* to close objects with reference counts>1 unless the "force" flag
* is set to true.
*
* At some point (probably after the group and datatypes use the
* the H5FO code), the H5FO code might need to be switched around
* to storing pointers to the objects being tracked (H5D_t, H5G_t,
* etc) and reference count those itself instead of relying on the
* reference counting in the H5I layer. Then, the "force" flag can
* be put back to false.
*
* Setting the "force" flag to true for all the interfaces won't
* work because the "file driver" (H5FD) APIs use the H5I reference
* counting to avoid closing a file driver out from underneath an
* open file...
*
* QAK - 5/13/03
*/
H5I_clear_type(H5I_DATASET, TRUE, FALSE);
} else {
H5I_dec_type_ref(H5I_DATASET);
H5_interface_initialize_g = 0;
n = 1; /*H5I*/
}
}
FUNC_LEAVE_NOAPI(n)
} /* end H5D_term_interface() */
/*--------------------------------------------------------------------------
NAME
H5D__get_dxpl_cache_real
PURPOSE
Get all the values for the DXPL cache.
USAGE
herr_t H5D__get_dxpl_cache_real(dxpl_id, cache)
hid_t dxpl_id; IN: DXPL to query
H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Query all the values from a DXPL that are needed by internal routines
within the library.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5D__get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache)
{
H5P_genplist_t *dx_plist; /* Data transfer property list */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Check args */
HDassert(cache);
/* Get the dataset transfer property list */
if(NULL == (dx_plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
/* Get maximum temporary buffer size */
if(H5P_get(dx_plist, H5D_XFER_MAX_TEMP_BUF_NAME, &cache->max_temp_buf) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve maximum temporary buffer size")
/* Get temporary buffer pointer */
if(H5P_get(dx_plist, H5D_XFER_TCONV_BUF_NAME, &cache->tconv_buf) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve temporary buffer pointer")
/* Get background buffer pointer */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_NAME, &cache->bkgr_buf) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer pointer")
/* Get background buffer type */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &cache->bkgr_buf_type) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
/* Get B-tree split ratios */
if(H5P_get(dx_plist, H5D_XFER_BTREE_SPLIT_RATIO_NAME, &cache->btree_split_ratio) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve B-tree split ratios")
/* Get I/O vector size */
if(H5P_get(dx_plist, H5D_XFER_HYPER_VECTOR_SIZE_NAME, &cache->vec_size) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve I/O vector size")
#ifdef H5_HAVE_PARALLEL
/* Collect Parallel I/O information for possible later use */
if(H5P_get(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &cache->xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve parallel transfer method")
if(H5P_get(dx_plist, H5D_XFER_MPIO_COLLECTIVE_OPT_NAME, &cache->coll_opt_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve collective transfer option")
#endif /* H5_HAVE_PARALLEL */
/* Get error detection properties */
if(H5P_get(dx_plist, H5D_XFER_EDC_NAME, &cache->err_detect) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve error detection info")
/* Get filter callback function */
if(H5P_get(dx_plist, H5D_XFER_FILTER_CB_NAME, &cache->filter_cb) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve filter callback function")
/* Get the data transform property */
if(H5P_get(dx_plist, H5D_XFER_XFORM_NAME, &cache->data_xform_prop) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve data transform info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__get_dxpl_cache_real() */
/*--------------------------------------------------------------------------
NAME
H5D__get_dxpl_cache
PURPOSE
Get all the values for the DXPL cache.
USAGE
herr_t H5D__get_dxpl_cache(dxpl_id, cache)
hid_t dxpl_id; IN: DXPL to query
H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Query all the values from a DXPL that are needed by internal routines
within the library.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The CACHE pointer should point at already allocated memory to place
non-default property list info. If a default property list is used, the
CACHE pointer will be changed to point at the default information.
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5D__get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t **cache)
{
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(cache);
/* Check for the default DXPL */
if(dxpl_id==H5P_DATASET_XFER_DEFAULT)
*cache=&H5D_def_dxpl_cache;
else
if(H5D__get_dxpl_cache_real(dxpl_id,*cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't retrieve DXPL values")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D__get_dxpl_cache() */
/*-------------------------------------------------------------------------
* Function: H5D__create_named
*
* Purpose: Internal routine to create a new dataset.
*
* Return: Success: Non-NULL, pointer to new dataset object.
*
* Failure: NULL
*
* Programmer: Quincey Koziol
* Thursday, April 5, 2007
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D__create_named(const H5G_loc_t *loc, const char *name, hid_t type_id,
const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id,
hid_t dxpl_id)
{
H5O_obj_create_t ocrt_info; /* Information for object creation */
H5D_obj_create_t dcrt_info; /* Information for dataset creation */
H5D_t *ret_value; /* Return value */
FUNC_ENTER_PACKAGE
/* Check arguments */
HDassert(loc);
HDassert(name && *name);
HDassert(type_id != H5P_DEFAULT);
HDassert(space);
HDassert(lcpl_id != H5P_DEFAULT);
HDassert(dcpl_id != H5P_DEFAULT);
HDassert(dapl_id != H5P_DEFAULT);
HDassert(dxpl_id != H5P_DEFAULT);
/* Set up dataset creation info */
dcrt_info.type_id = type_id;
dcrt_info.space = space;
dcrt_info.dcpl_id = dcpl_id;
dcrt_info.dapl_id = dapl_id;
/* Set up object creation information */
ocrt_info.obj_type = H5O_TYPE_DATASET;
ocrt_info.crt_info = &dcrt_info;
ocrt_info.new_obj = NULL;
/* Create the new dataset and link it to its parent group */
if(H5L_link_object(loc, name, &ocrt_info, lcpl_id, dapl_id, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create and link to dataset")
HDassert(ocrt_info.new_obj);
/* Set the return value */
ret_value = (H5D_t *)ocrt_info.new_obj;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__create_named() */
/*-------------------------------------------------------------------------
* Function: H5D__get_space_status
*
* Purpose: Returns the status of data space allocation.
*
* Return:
* Success: Non-negative
*
* Failture: Negative
*
* Programmer: Raymond Lu
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id)
{
H5S_t *space; /* Dataset's dataspace */
hsize_t space_allocated; /* The number of bytes allocated for chunks */
hssize_t snelmts; /* Temporary holder for number of elements in dataspace */
hsize_t nelmts; /* Number of elements in dataspace */
size_t dt_size; /* Size of datatype */
hsize_t full_size; /* The number of bytes in the dataset when fully populated */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
HDassert(dset);
/* Get the dataset's dataspace */
space = dset->shared->space;
HDassert(space);
/* Get the total number of elements in dataset's dataspace */
if((snelmts = H5S_GET_EXTENT_NPOINTS(space)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace")
nelmts = (hsize_t)snelmts;
/* Get the size of the dataset's datatype */
if(0 == (dt_size = H5T_GET_SIZE(dset->shared->type)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype")
/* Compute the maximum size of the dataset in bytes */
full_size = nelmts * dt_size;
/* Check for overflow during multiplication */
if(nelmts != (full_size / dt_size))
HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed")
/* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */
if(H5D__get_storage_size(dset, dxpl_id, &space_allocated) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of dataset's storage")
/* Decide on how much of the space is allocated */
if(space_allocated == 0)
*allocation = H5D_SPACE_STATUS_NOT_ALLOCATED;
else if(space_allocated == full_size)
*allocation = H5D_SPACE_STATUS_ALLOCATED;
else {
/* Should only happen for chunked datasets currently */
HDassert(dset->shared->layout.type == H5D_CHUNKED);
*allocation = H5D_SPACE_STATUS_PART_ALLOCATED;
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__get_space_status() */
/*-------------------------------------------------------------------------
* Function: H5D__new
*
* Purpose: Creates a new, empty dataset structure
*
* Return: Success: Pointer to a new dataset descriptor.
*
* Failure: NULL
*
* Programmer: Quincey Koziol
* Monday, October 12, 1998
*
*-------------------------------------------------------------------------
*/
static H5D_shared_t *
H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type)
{
H5D_shared_t *new_dset = NULL; /* New dataset object */
H5P_genplist_t *plist; /* Property list created */
H5D_shared_t *ret_value; /* Return value */
FUNC_ENTER_STATIC
/* Allocate new shared dataset structure */
if(NULL == (new_dset = H5FL_MALLOC(H5D_shared_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Copy the default dataset information */
HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t));
/* If we are using the default dataset creation property list, during creation
* don't bother to copy it, just increment the reference count
*/
if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) {
if(H5I_inc_ref(dcpl_id, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment default DCPL ID")
new_dset->dcpl_id = dcpl_id;
} /* end if */
else {
/* Get the property list */
if(NULL == (plist = (H5P_genplist_t *)H5I_object(dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list")
new_dset->dcpl_id = H5P_copy_plist(plist, FALSE);
} /* end else */
/* Set return value */
ret_value = new_dset;
done:
if(ret_value == NULL)
if(new_dset != NULL) {
if(new_dset->dcpl_id != 0 && H5I_dec_ref(new_dset->dcpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "can't decrement temporary datatype ID")
new_dset = H5FL_FREE(H5D_shared_t, new_dset);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__new() */
/*-------------------------------------------------------------------------
* Function: H5D__init_type
*
* Purpose: Copy a datatype for a dataset's use, performing all the
* necessary adjustments, etc.
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Thursday, June 24, 2004
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type)
{
htri_t relocatable; /* Flag whether the type is relocatable */
htri_t immutable; /* Flag whether the type is immutable */
hbool_t use_latest_format; /* Flag indicating the newest file format should be used */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Sanity checking */
HDassert(file);
HDassert(dset);
HDassert(type);
/* Check whether the datatype is relocatable */
if((relocatable = H5T_is_relocatable(type)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?")
/* Check whether the datatype is immutable */
if((immutable = H5T_is_immutable(type)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?")
/* Get the file's 'use the latest version of the format' flag */
use_latest_format = H5F_USE_LATEST_FORMAT(file);
/* Copy the datatype if it's a custom datatype or if it'll change when it's location is changed */
if(!immutable || relocatable || use_latest_format) {
/* Copy datatype for dataset */
if((dset->shared->type = H5T_copy(type, H5T_COPY_ALL)) == NULL)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy datatype")
/* Mark any datatypes as being on disk now */
if(H5T_set_loc(dset->shared->type, file, H5T_LOC_DISK) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't set datatype location")
/* Set the latest format, if requested */
if(use_latest_format)
if(H5T_set_latest_version(dset->shared->type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype")
/* Get a datatype ID for the dataset's datatype */
if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type, FALSE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type")
} /* end if */
/* Not a custom datatype, just use it directly */
else {
if(H5I_inc_ref(type_id, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment datatype ID")
/* Use existing datatype */
dset->shared->type_id = type_id;
dset->shared->type = (H5T_t *)type; /* (Cast away const OK - QAK) */
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__init_type() */
/*-------------------------------------------------------------------------
* Function: H5D__init_space
*
* Purpose: Copy a dataspace for a dataset's use, performing all the
* necessary adjustments, etc.
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Tuesday, July 24, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space)
{
hbool_t use_latest_format; /* Flag indicating the newest file format should be used */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Sanity checking */
HDassert(file);
HDassert(dset);
HDassert(space);
/* Get the file's 'use the latest version of the format' flag */
use_latest_format = H5F_USE_LATEST_FORMAT(file);
/* Copy dataspace for dataset */
if(NULL == (dset->shared->space = H5S_copy(space, FALSE, TRUE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataspace")
/* Set the latest format, if requested */
if(use_latest_format)
if(H5S_set_latest_version(dset->shared->space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype")
/* Set the dataset's dataspace to 'all' selection */
if(H5S_select_all(dset->shared->space, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set all selection")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__init_space() */
/*-------------------------------------------------------------------------
* Function: H5D__update_oh_info
*
* Purpose: Create and fill object header for dataset
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Programmer: Bill Wendling
* Thursday, October 31, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id)
{
H5O_t *oh = NULL; /* Pointer to dataset's object header */
size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */
H5O_loc_t *oloc = NULL; /* Dataset's object location */
H5O_layout_t *layout; /* Dataset's layout information */
H5T_t *type; /* Dataset's datatype */
hbool_t use_latest_format; /* Flag indicating the newest file format should be used */
H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */
H5D_fill_value_t fill_status; /* Fill value status */
hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */
hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Sanity checking */
HDassert(file);
HDassert(dset);
/* Set some local variables, for convenience */
oloc = &dset->oloc;
layout = &dset->shared->layout;
type = dset->shared->type;
fill_prop = &dset->shared->dcpl_cache.fill;
/* Get the file's 'use the latest version of the format' flag */
use_latest_format = H5F_USE_LATEST_FORMAT(file);
/* Retrieve "defined" status of fill value */
if(H5P_is_fill_value_defined(fill_prop, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* Special case handling for variable-length types */
if(H5T_detect_class(type, H5T_VLEN, FALSE)) {
/* If the default fill value is chosen for variable-length types, always write it */
if(fill_prop->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_DEFAULT) {
/* Update dataset creation property */
fill_prop->fill_time = H5D_FILL_TIME_ALLOC;
/* Note that the fill value changed */
fill_changed = TRUE;
} /* end if */
/* Don't allow never writing fill values with variable-length types */
if(fill_prop->fill_time == H5D_FILL_TIME_NEVER)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined")
} /* end if */
/* Determine whether fill value is defined or not */
if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) {
/* Convert fill value buffer to dataset's datatype */
if(fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(fill_prop, type, &fill_changed, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type")
fill_prop->fill_defined = TRUE;
} else if(fill_status == H5D_FILL_VALUE_UNDEFINED) {
fill_prop->fill_defined = FALSE;
} else
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine if fill value is defined")
/* Check for invalid fill & allocation time setting */
if(fill_prop->fill_defined == FALSE && fill_prop->fill_time == H5D_FILL_TIME_ALLOC)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "fill value writing on allocation set, but no fill value defined")
/* Check if the fill value info changed */
if(fill_changed) {
H5P_genplist_t *dc_plist; /* Dataset's creation property list */
/* Get dataset's property list object */
HDassert(dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT);
if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list")
/* Update dataset creation property */
if(H5P_set(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value info")
} /* end if */
/* Add the dataset's raw data size to the size of the header, if the raw data will be stored as compact */
if(layout->type == H5D_COMPACT)
ohdr_size += layout->storage.u.compact.size;
/* Create an object header for the dataset */
if(H5O_create(file, dxpl_id, ohdr_size, (size_t)1, dset->shared->dcpl_id, oloc/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header")
HDassert(file == dset->oloc.file);
/* Pin the object header */
if(NULL == (oh = H5O_pin(oloc, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header")
/* Write the dataspace header message */
if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message")
/* Write the datatype header message */
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message")
/* Write new fill value message */
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update new fill value header message")
/* If there is valid information for the old fill value struct, add it */
/* (only if we aren't trying to write the latest version of the file format) */
if(fill_prop->buf && !use_latest_format) {
H5O_fill_t old_fill_prop; /* Copy of fill value property, for writing as "old" fill value */
/* Shallow copy the fill value property */
/* (we only want to make certain that the shared component isnt' modified) */
HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
/* Reset shared component info */
H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop);
/* Write old fill value */
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message")
} /* end if */
/* Update/create the layout (and I/O pipeline & EFL) messages */
if(H5D__layout_oh_create(file, dxpl_id, oh, dset, dapl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout/pline/efl header message")
/* Indicate that the layout information was initialized */
layout_init = TRUE;
#ifdef H5O_ENABLE_BOGUS
{
H5P_genplist_t *dc_plist; /* Dataset's creation property list */
/* Get dataset's property list object */
if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list")
/* Check whether to add a "bogus" message */
if(H5P_exist_plist(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME) > 0) {
uint8_t bogus_flags = 0; /* Flags for creating "bogus" message */
/* Retrieve "bogus" message flags */
if(H5P_get(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME, &bogus_flags) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus message options")
/* Add a "bogus" message (for error testing). */
if(H5O_bogus_oh(file, dxpl_id, oh, (unsigned)bogus_flags) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create 'bogus' message")
} /* end if */
}
#endif /* H5O_ENABLE_BOGUS */
/* Add a modification time message, if using older format. */
/* (If using the latest format, the modification time is part of the object
* header and doesn't use a separate message -QAK)
*/
if(!use_latest_format)
if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message")
done:
/* Release pointer to object header itself */
if(oh != NULL)
if(H5O_unpin(oh) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header")
/* Error cleanup */
if(ret_value < 0) {
if(dset->shared->layout.type == H5D_CHUNKED && layout_init) {
if(H5D__chunk_dest(file, dxpl_id, dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
} /* end if */
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__update_oh_info() */
/*-------------------------------------------------------------------------
* Function: H5D__create
*
* Purpose: Creates a new dataset with name NAME in file F and associates
* with it a datatype TYPE for each element as stored in the
* file, dimensionality information or dataspace SPACE, and
* other miscellaneous properties CREATE_PARMS. All arguments
* are deep-copied before being associated with the new dataset,
* so the caller is free to subsequently modify them without
* affecting the dataset.
*
* Return: Success: Pointer to a new dataset
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
hid_t dapl_id, hid_t dxpl_id)
{
const H5T_t *type; /* Datatype for dataset */
H5D_t *new_dset = NULL;
H5P_genplist_t *dc_plist = NULL; /* New Property list */
hbool_t has_vl_type = FALSE; /* Flag to indicate a VL-type for dataset */
hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */
H5G_loc_t dset_loc; /* Dataset location */
H5D_t *ret_value; /* Return value */
FUNC_ENTER_PACKAGE
/* check args */
HDassert(file);
HDassert(H5I_DATATYPE == H5I_get_type(type_id));
HDassert(space);
HDassert(H5I_GENPROP_LST == H5I_get_type(dcpl_id));
HDassert(H5I_GENPROP_LST == H5I_get_type(dxpl_id));
/* Get the dataset's datatype */
if(NULL == (type = (const H5T_t *)H5I_object(type_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype")
/* Check if the datatype is "sensible" for use in a dataset */
if(H5T_is_sensible(type) != TRUE)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible")
/* Check if the datatype is/contains a VL-type */
if(H5T_detect_class(type, H5T_VLEN, FALSE))
has_vl_type = TRUE;
/* Check if the dataspace has an extent set (or is NULL) */
if(!H5S_has_extent(space))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "dataspace extent has not been set.")
/* Initialize the dataset object */
if(NULL == (new_dset = H5FL_CALLOC(H5D_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Set up & reset dataset location */
dset_loc.oloc = &(new_dset->oloc);
dset_loc.path = &(new_dset->path);
H5G_loc_reset(&dset_loc);
/* Initialize the shared dataset space */
if(NULL == (new_dset->shared = H5D__new(dcpl_id, TRUE, has_vl_type)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Copy & initialize datatype for dataset */
if(H5D__init_type(file, new_dset, type_id, type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy datatype")
/* Copy & initialize dataspace for dataset */
if(H5D__init_space(file, new_dset, space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy dataspace")
/* Set the dataset's checked_filters flag to enable writing */
new_dset->shared->checked_filters = TRUE;
/* Check if the dataset has a non-default DCPL & get important values, if so */
if(new_dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) {
H5O_layout_t *layout; /* Dataset's layout information */
H5O_pline_t *pline; /* Dataset's I/O pipeline information */
H5O_fill_t *fill; /* Dataset's fill value info */
/* Check if the filters in the DCPL can be applied to this dataset */
if(H5Z_can_apply(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset")
/* Make the "set local" filter callbacks for this dataset */
if(H5Z_set_local(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters")
/* Get new dataset's property list object */
if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(new_dset->shared->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list")
/* Retrieve the properties we need */
pline = &new_dset->shared->dcpl_cache.pline;
if(H5P_get(dc_plist, H5O_CRT_PIPELINE_NAME, pline) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter")
layout = &new_dset->shared->layout;
if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout")
if(pline->nused > 0 && H5D_CHUNKED != layout->type)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout")
fill = &new_dset->shared->dcpl_cache.fill;
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill value info")
/* Check if the alloc_time is the default and error out */
if(fill->alloc_time == H5D_ALLOC_TIME_DEFAULT)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "invalid space allocation state")
/* Don't allow compact datasets to allocate space later */
if(layout->type == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation")
/* If MPI VFD is used, no filter support yet. */
if(IS_H5FD_MPI(file) && pline->nused > 0)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet")
/* Get the dataset's external file list information */
if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->shared->dcpl_cache.efl) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list")
} /* end if */
/* Set the latest version of the layout, pline & fill messages, if requested */
if(H5F_USE_LATEST_FORMAT(file)) {
/* Set the latest version for the I/O pipeline message */
if(H5O_pline_set_latest_version(&new_dset->shared->dcpl_cache.pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of I/O filter pipeline")
/* Set the latest version for the fill value message */
if(H5O_fill_set_latest_version(&new_dset->shared->dcpl_cache.fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of fill value")
} /* end if */
/* Check if this dataset is going into a parallel file and set space allocation time */
if(IS_H5FD_MPI(file))
new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY;
/* Set the dataset's I/O operations */
if(H5D__layout_set_io_ops(new_dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize I/O operations")
/* Create the layout information for the new dataset */
if((new_dset->shared->layout.ops->construct)(file, new_dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to construct layout information")
/* Update the dataset's object header info. */
if(H5D__update_oh_info(file, dxpl_id, new_dset, dapl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache")
/* Indicate that the layout information was initialized */
layout_init = TRUE;
/* Add the dataset to the list of opened objects in the file */
if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count")
if(H5FO_insert(new_dset->oloc.file, new_dset->oloc.addr, new_dset->shared, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects")
new_dset->shared->fo_count = 1;
/* Success */
ret_value = new_dset;
done:
if(!ret_value && new_dset && new_dset->shared) {
if(new_dset->shared) {
if(new_dset->shared->layout.type == H5D_CHUNKED && layout_init) {
if(H5D__chunk_dest(file, dxpl_id, new_dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy chunk cache")
} /* end if */
if(new_dset->shared->space && H5S_close(new_dset->shared->space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace")
if(new_dset->shared->type && H5I_dec_ref(new_dset->shared->type_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype")
if(H5F_addr_defined(new_dset->oloc.addr)) {
if(H5O_dec_rc_by_loc(&(new_dset->oloc), dxpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement refcount on newly created object")
if(H5O_close(&(new_dset->oloc)) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header")
if(file) {
if(H5O_delete(file, dxpl_id, new_dset->oloc.addr) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTDELETE, NULL, "unable to delete object header")
} /* end if */
} /* end if */
if(new_dset->shared->dcpl_id != 0 && H5I_dec_ref(new_dset->shared->dcpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list")
new_dset->shared = H5FL_FREE(H5D_shared_t, new_dset->shared);
} /* end if */
new_dset->oloc.file = NULL;
new_dset = H5FL_FREE(H5D_t, new_dset);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__create() */
/*
*-------------------------------------------------------------------------
* Function: H5D_open
*
* Purpose: Checks if dataset is already open, or opens a dataset for
* access.
*
* Return: Success: Dataset ID
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Friday, December 20, 2002
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
{
H5D_shared_t *shared_fo = NULL;
H5D_t *dataset = NULL;
H5D_t *ret_value; /* Return value */
FUNC_ENTER_NOAPI(NULL)
/* check args */
HDassert(loc);
/* Allocate the dataset structure */
if(NULL == (dataset = H5FL_CALLOC(H5D_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Shallow copy (take ownership) of the object location object */
if(H5O_loc_copy(&(dataset->oloc), loc->oloc, H5_COPY_SHALLOW) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy object location")
/* Shallow copy (take ownership) of the group hier. path */
if(H5G_name_copy(&(dataset->path), loc->path, H5_COPY_SHALLOW) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path")
/* Check if dataset was already open */
if(NULL == (shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr))) {
/* Clear any errors from H5FO_opened() */
H5E_clear_stack(NULL);
/* Open the dataset object */
if(H5D__open_oid(dataset, dapl_id, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found")
/* Add the dataset to the list of opened objects in the file */
if(H5FO_insert(dataset->oloc.file, dataset->oloc.addr, dataset->shared, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects")
/* Increment object count for the object in the top file */
if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count")
/* We're the first dataset to use the the shared info */
dataset->shared->fo_count = 1;
} /* end if */
else {
/* Point to shared info */
dataset->shared = shared_fo;
/* Increment # of datasets using shared information */
shared_fo->fo_count++;
/* Check if the object has been opened through the top file yet */
if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) {
/* Open the object through this top file */
if(H5O_open(&(dataset->oloc)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open object header")
} /* end if */
/* Increment object count for the object in the top file */
if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count")
} /* end else */
ret_value = dataset;
done:
if(ret_value == NULL) {
/* Free the location--casting away const*/
if(dataset) {
if(shared_fo == NULL) /* Need to free shared fo */
dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared);
H5O_loc_free(&(dataset->oloc));
H5G_name_free(&(dataset->path));
dataset = H5FL_FREE(H5D_t, dataset);
} /* end if */
if(shared_fo)
shared_fo->fo_count--;
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_open() */
/*-------------------------------------------------------------------------
* Function: H5D__open_oid
*
* Purpose: Opens a dataset for access.
*
* Return: Dataset pointer on success, NULL on failure
*
* Programmer: Quincey Koziol
* Monday, October 12, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id)
{
H5P_genplist_t *plist; /* Property list */
H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */
unsigned alloc_time_state; /* Allocation time state */
htri_t msg_exists; /* Whether a particular type of message exists */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* check args */
HDassert(dataset);
/* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */
if(NULL == (dataset->shared = H5D__new(H5P_DATASET_CREATE_DEFAULT, FALSE, FALSE)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Open the dataset object */
if(H5O_open(&(dataset->oloc)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open")
/* Get the type and space */
if(NULL == (dataset->shared->type = (H5T_t *)H5O_msg_read(&(dataset->oloc), H5O_DTYPE_ID, NULL, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load type info from dataset header")
if(H5T_set_loc(dataset->shared->type, dataset->oloc.file, H5T_LOC_DISK) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid datatype location")
if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc), dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header")
/* Get a datatype ID for the dataset's datatype */
if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type, FALSE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type")
/* Get dataset creation property list object */
if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list")
/* Get the layout/pline/efl message information */
if(H5D__layout_oh_read(dataset, dxpl_id, dapl_id, plist) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout/pline/efl info")
/* Point at dataset's copy, to cache it for later */
fill_prop = &dataset->shared->dcpl_cache.fill;
/* Try to get the new fill value message from the object header */
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_NEW_ID, dxpl_id)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
if(msg_exists) {
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop, dxpl_id))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
} /* end if */
else {
/* For backward compatibility, try to retrieve the old fill value message */
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_ID, dxpl_id)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
if(msg_exists) {
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop, dxpl_id))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
} /* end if */
else {
/* Set the space allocation time appropriately, based on the type of dataset storage */
switch(dataset->shared->layout.type) {
case H5D_COMPACT:
fill_prop->alloc_time = H5D_ALLOC_TIME_EARLY;
break;
case H5D_CONTIGUOUS:
fill_prop->alloc_time = H5D_ALLOC_TIME_LATE;
break;
case H5D_CHUNKED:
fill_prop->alloc_time = H5D_ALLOC_TIME_INCR;
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet")
} /* end switch */ /*lint !e788 All appropriate cases are covered */
} /* end else */
/* If "old" fill value size is 0 (undefined), map it to -1 */
if(fill_prop->size == 0)
fill_prop->size = (ssize_t)-1;
} /* end if */
alloc_time_state = 0;
if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY)
|| (dataset->shared->layout.type == H5D_CONTIGUOUS && fill_prop->alloc_time == H5D_ALLOC_TIME_LATE)
|| (dataset->shared->layout.type == H5D_CHUNKED && fill_prop->alloc_time == H5D_ALLOC_TIME_INCR))
alloc_time_state = 1;
/* Set revised fill value properties, if they are different from the defaults */
if(H5P_fill_value_cmp(&H5D_def_dset.dcpl_cache.fill, fill_prop, sizeof(H5O_fill_t))) {
if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set fill value")
if(H5P_set(plist, H5D_CRT_ALLOC_TIME_STATE_NAME, &alloc_time_state) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set allocation time state")
} /* end if */
/*
* Make sure all storage is properly initialized.
* This is important only for parallel I/O where the space must
* be fully allocated before I/O can happen.
*/
if((H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR)
&& !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage)
&& IS_H5FD_MPI(dataset->oloc.file)) {
if(H5D__alloc_storage(dataset, dxpl_id, H5D_ALLOC_OPEN, FALSE, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage")
} /* end if */
done:
if(ret_value < 0) {
if(H5F_addr_defined(dataset->oloc.addr) && H5O_close(&(dataset->oloc)) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header")
if(dataset->shared) {
if(dataset->shared->space && H5S_close(dataset->shared->space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
if(dataset->shared->type) {
if(dataset->shared->type_id > 0) {
if(H5I_dec_ref(dataset->shared->type_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype")
} /* end if */
else {
if(H5T_close(dataset->shared->type) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype")
} /* end else */
} /* end if */
} /* end if */
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__open_oid() */
/*-------------------------------------------------------------------------
* Function: H5D_close
*
* Purpose: Insures that all data has been saved to the file, closes the
* dataset object header, and frees all resources used by the
* descriptor.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_close(H5D_t *dataset)
{
unsigned free_failed = FALSE;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
/* check args */
HDassert(dataset && dataset->oloc.file && dataset->shared);
HDassert(dataset->shared->fo_count > 0);
/* Dump debugging info */
#ifdef H5D_CHUNK_DEBUG
H5D__chunk_stats(dataset, FALSE);
#endif /* H5D_CHUNK_DEBUG */
dataset->shared->fo_count--;
if(dataset->shared->fo_count == 0) {
/* Flush the dataset's information. Continue to close even if it fails. */
if(H5D__flush_real(dataset, H5AC_dxpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info")
/* Free the data sieve buffer, if it's been allocated */
if(dataset->shared->cache.contig.sieve_buf) {
HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */
dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf);
} /* end if */
/* Free cached information for each kind of dataset */
switch(dataset->shared->layout.type) {
case H5D_CONTIGUOUS:
break;
case H5D_CHUNKED:
/* Check for skip list for iterating over chunks during I/O to close */
if(dataset->shared->cache.chunk.sel_chunks) {
HDassert(H5SL_count(dataset->shared->cache.chunk.sel_chunks) == 0);
H5SL_close(dataset->shared->cache.chunk.sel_chunks);
dataset->shared->cache.chunk.sel_chunks = NULL;
} /* end if */
/* Check for cached single chunk dataspace */
if(dataset->shared->cache.chunk.single_space) {
(void)H5S_close(dataset->shared->cache.chunk.single_space);
dataset->shared->cache.chunk.single_space = NULL;
} /* end if */
/* Check for cached single element chunk info */
if(dataset->shared->cache.chunk.single_chunk_info) {
dataset->shared->cache.chunk.single_chunk_info = H5FL_FREE(H5D_chunk_info_t, dataset->shared->cache.chunk.single_chunk_info);
dataset->shared->cache.chunk.single_chunk_info = NULL;
} /* end if */
/* Flush and destroy chunks in the cache. Continue to close even if
* it fails. */
if(H5D__chunk_dest(dataset->oloc.file, H5AC_dxpl_id, dataset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
break;
case H5D_COMPACT:
/* Free the buffer for the raw data for compact datasets */
dataset->shared->layout.storage.u.compact.buf = H5MM_xfree(dataset->shared->layout.storage.u.compact.buf);
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HDassert("not implemented yet" && 0);
#ifdef NDEBUG
HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
#endif /* NDEBUG */
} /* end switch */ /*lint !e788 All appropriate cases are covered */
/*
* Release datatype, dataspace and creation property list -- there isn't
* much we can do if one of these fails, so we just continue.
*/
free_failed = (unsigned)(H5I_dec_ref(dataset->shared->type_id) < 0 || H5S_close(dataset->shared->space) < 0 ||
H5I_dec_ref(dataset->shared->dcpl_id) < 0);
/* Remove the dataset from the list of opened objects in the file */
if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object")
if(H5FO_delete(dataset->oloc.file, H5AC_dxpl_id, dataset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects")
/* Close the dataset object */
/* (This closes the file, if this is the last object open) */
if(H5O_close(&(dataset->oloc)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header")
/*
* Free memory. Before freeing the memory set the file pointer to NULL.
* We always check for a null file pointer in other H5D functions to be
* sure we're not accessing an already freed dataset (see the HDassert()
* above).
*/
dataset->oloc.file = NULL;
dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared);
} /* end if */
else {
/* Decrement the ref. count for this object in the top file */
if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object")
/* Check reference count for this object in the top file */
if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) {
if(H5O_close(&(dataset->oloc)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close")
} /* end if */
else
/* Free object location (i.e. "unhold" the file if appropriate) */
if(H5O_loc_free(&(dataset->oloc)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "problem attempting to free location")
} /* end else */
/* Release the dataset's path info */
if(H5G_name_free(&(dataset->path)) < 0)
free_failed = TRUE;
/* Free the dataset's memory structure */
dataset = H5FL_FREE(H5D_t, dataset);
/* Check if anything failed in the middle... */
if(free_failed)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free a component of the dataset, but the dataset was freed anyway.")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_close() */
/*-------------------------------------------------------------------------
* Function: H5D_oloc
*
* Purpose: Returns a pointer to the object location for a dataset.
*
* Return: Success: Ptr to location
* Failure: NULL
*
* Programmer: Robb Matzke
* Friday, April 24, 1998
*
*-------------------------------------------------------------------------
*/
H5O_loc_t *
H5D_oloc(H5D_t *dataset)
{
/* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */
FUNC_ENTER_NOAPI_NOINIT_NOERR
FUNC_LEAVE_NOAPI(dataset ? &(dataset->oloc) : (H5O_loc_t *)NULL)
} /* end H5D_oloc() */
/*-------------------------------------------------------------------------
* Function: H5D_nameof
*
* Purpose: Returns a pointer to the group hier. path for a dataset.
*
* Return: Success: Ptr to entry
* Failure: NULL
*
* Programmer: Quincey Koziol
* Monday, September 12, 2005
*
*-------------------------------------------------------------------------
*/
H5G_name_t *
H5D_nameof(H5D_t *dataset)
{
/* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */
FUNC_ENTER_NOAPI_NOINIT_NOERR
FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : (H5G_name_t *)NULL)
} /* end H5D_nameof() */
/*-------------------------------------------------------------------------
* Function: H5D_typeof
*
* Purpose: Returns a pointer to the dataset's datatype. The datatype
* is not copied.
*
* Return: Success: Ptr to the dataset's datatype, uncopied.
* Failure: NULL
*
* Programmer: Robb Matzke
* Thursday, June 4, 1998
*
*-------------------------------------------------------------------------
*/
H5T_t *
H5D_typeof(const H5D_t *dset)
{
/* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */
FUNC_ENTER_NOAPI_NOINIT_NOERR
HDassert(dset);
HDassert(dset->shared);
HDassert(dset->shared->type);
FUNC_LEAVE_NOAPI(dset->shared->type)
} /* end H5D_typeof() */
/*-------------------------------------------------------------------------
* Function: H5D__alloc_storage
*
* Purpose: Allocate storage for the raw data of a dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Friday, January 16, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc,
hbool_t full_overwrite, hsize_t old_dim[])
{
H5F_t *f = dset->oloc.file; /* The dataset's file pointer */
H5O_layout_t *layout; /* The dataset's layout information */
hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */
hbool_t addr_set = FALSE; /* Flag to indicate that the dataset's storage address was set */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* check args */
HDassert(dset);
HDassert(f);
/* If the data is stored in external files, don't set an address for the layout
* We assume that external storage is already
* allocated by the caller, or at least will be before I/O is performed.
*/
if(!(H5S_NULL == H5S_GET_EXTENT_TYPE(dset->shared->space) || dset->shared->dcpl_cache.efl.nused > 0)) {
/* Get a pointer to the dataset's layout information */
layout = &(dset->shared->layout);
switch(layout->type) {
case H5D_CONTIGUOUS:
if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) {
/* Check if we have a zero-sized dataset */
if(layout->storage.u.contig.size > 0) {
/* Reserve space in the file for the entire array */
if(H5D__contig_alloc(f, dxpl_id, &layout->storage.u.contig/*out*/) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage")
/* Indicate that we should initialize storage space */
must_init_space = TRUE;
} /* end if */
else
layout->storage.u.contig.addr = HADDR_UNDEF;
/* Indicate that we set the storage addr */
addr_set = TRUE;
} /* end if */
break;
case H5D_CHUNKED:
if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) {
/* Create the root of the B-tree that describes chunked storage */
if(H5D__chunk_create(dset /*in,out*/, dxpl_id) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
/* Indicate that we set the storage addr */
addr_set = TRUE;
/* Indicate that we should initialize storage space */
must_init_space = TRUE;
} /* end if */
/* If space allocation is set to 'early' and we are extending
* the dataset, indicate that space should be allocated, so the
* B-tree gets expanded. -QAK
*/
if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY
&& time_alloc == H5D_ALLOC_EXTEND)
must_init_space = TRUE;
break;
case H5D_COMPACT:
/* Check if space is already allocated */
if(NULL == layout->storage.u.compact.buf) {
/* Reserve space in layout header message for the entire array.
* Starting from the 1.8.7 release, we allow dataspace to have
* zero dimension size. So the storage size can be zero.
* SLU 2011/4/4 */
if(layout->storage.u.compact.size > 0) {
if(NULL == (layout->storage.u.compact.buf = H5MM_malloc(layout->storage.u.compact.size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset")
if(!full_overwrite)
HDmemset(layout->storage.u.compact.buf, 0, layout->storage.u.compact.size);
layout->storage.u.compact.dirty = TRUE;
/* Indicate that we should initialize storage space */
must_init_space = TRUE;
} else {
layout->storage.u.compact.dirty = FALSE;
must_init_space = FALSE;
}
} /* end if */
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HDassert("not implemented yet" && 0);
#ifdef NDEBUG
HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
#endif /* NDEBUG */
} /* end switch */ /*lint !e788 All appropriate cases are covered */
/* Check if we need to initialize the space */
if(must_init_space) {
if(layout->type == H5D_CHUNKED) {
/* If we are doing incremental allocation and the B-tree got
* created during a H5Dwrite call, don't initialize the storage
* now, wait for the actual writes to each block and let the
* low-level chunking routines handle initialize the fill-values.
* Otherwise, pass along the space initialization call and let
* the low-level chunking routines sort out whether to write
* fill values to the chunks they allocate space for. Yes,
* this is icky. -QAK
*/
if(!(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR && time_alloc == H5D_ALLOC_WRITE))
if(H5D__init_storage(dset, full_overwrite, old_dim, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value")
} /* end if */
else {
H5D_fill_value_t fill_status; /* The fill value status */
/* Check the dataset's fill-value status */
if(H5P_is_fill_value_defined(&dset->shared->dcpl_cache.fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If we are filling the dataset on allocation or "if set" and
* the fill value _is_ set, do that now */
if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC ||
(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
if(H5D__init_storage(dset, full_overwrite, old_dim, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value")
} /* end if */
} /* end else */
} /* end if */
/* If we set the address (and aren't in the middle of creating the
* dataset), mark the layout header message for later writing to
* the file. (this improves forward compatibility).
*/
/* (The layout message is already in the dataset's object header, this
* operation just sets the address and makes it constant)
*/
if(time_alloc != H5D_ALLOC_CREATE && addr_set)
/* Mark the layout as dirty, for later writing to the file */
if(H5D__mark(dset, dxpl_id, H5D_MARK_LAYOUT) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark dataspace as dirty")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__alloc_storage() */
/*-------------------------------------------------------------------------
* Function: H5D__init_storage
*
* Purpose: Initialize the data for a new dataset. If a selection is
* defined for SPACE then initialize only that part of the
* dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Monday, October 5, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__init_storage(const H5D_t *dset, hbool_t full_overwrite, hsize_t old_dim[],
hid_t dxpl_id)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
HDassert(dset);
switch (dset->shared->layout.type) {
case H5D_COMPACT:
/* If we will be immediately overwriting the values, don't bother to clear them */
if(!full_overwrite) {
/* Fill the compact dataset storage */
if(H5D__compact_fill(dset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize compact dataset storage")
} /* end if */
break;
case H5D_CONTIGUOUS:
/* Don't write default fill values to external files */
/* If we will be immediately overwriting the values, don't bother to clear them */
if((dset->shared->dcpl_cache.efl.nused == 0 || dset->shared->dcpl_cache.fill.buf) && !full_overwrite)
if(H5D__contig_fill(dset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset")
break;
case H5D_CHUNKED:
/*
* Allocate file space
* for all chunks now and initialize each chunk with the fill value.
*/
{
hsize_t zero_dim[H5O_LAYOUT_NDIMS] = {0};
/* Use zeros for old dimensions if not specified */
if(old_dim == NULL)
old_dim = zero_dim;
if(H5D__chunk_allocate(dset, dxpl_id, full_overwrite, old_dim) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset")
break;
} /* end block */
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HDassert("not implemented yet" && 0);
#ifdef NDEBUG
HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
#endif /* NDEBUG */
} /* end switch */ /*lint !e788 All appropriate cases are covered */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__init_storage() */
/*-------------------------------------------------------------------------
* Function: H5D__get_storage_size
*
* Purpose: Determines how much space has been reserved to store the raw
* data of a dataset.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__get_storage_size(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
switch(dset->shared->layout.type) {
case H5D_CHUNKED:
if((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) {
if(H5D__chunk_allocated(dset, dxpl_id, storage_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve chunked dataset allocated size")
} /* end if */
else
*storage_size = 0;
break;
case H5D_CONTIGUOUS:
/* Datasets which are not allocated yet are using no space on disk */
if((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage))
*storage_size = dset->shared->layout.storage.u.contig.size;
else
*storage_size = 0;
break;
case H5D_COMPACT:
*storage_size = dset->shared->layout.storage.u.compact.size;
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset type")
} /*lint !e788 All appropriate cases are covered */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__get_storage_size() */
/*-------------------------------------------------------------------------
* Function: H5D__get_offset
*
* Purpose: Private function for H5D__get_offset. Returns the address
* of dataset in file.
*
* Return: Success: the address of dataset
*
* Failure: HADDR_UNDEF
*
* Programmer: Raymond Lu
* November 6, 2002
*
*-------------------------------------------------------------------------
*/
haddr_t
H5D__get_offset(const H5D_t *dset)
{
haddr_t ret_value = HADDR_UNDEF;
FUNC_ENTER_PACKAGE
HDassert(dset);
switch(dset->shared->layout.type) {
case H5D_CHUNKED:
case H5D_COMPACT:
break;
case H5D_CONTIGUOUS:
/* If dataspace hasn't been allocated or dataset is stored in
* an external file, the value will be HADDR_UNDEF. */
if(dset->shared->dcpl_cache.efl.nused == 0 || H5F_addr_defined(dset->shared->layout.storage.u.contig.addr))
/* Return the absolute dataset offset from the beginning of file. */
ret_value = dset->shared->layout.storage.u.contig.addr + H5F_BASE_ADDR(dset->oloc.file);
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type")
} /*lint !e788 All appropriate cases are covered */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__get_offset() */
/*-------------------------------------------------------------------------
* Function: H5D__iterate
*
* Purpose: Internal version of H5Diterate()
*
* Return: Returns the return value of the last operator if it was non-zero,
* or zero if all elements were processed. Otherwise returns a
* negative value.
*
* Programmer: Quincey Koziol
* Tuesday, November 22, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t op,
void *operator_data)
{
herr_t ret_value;
FUNC_ENTER_PACKAGE_NOERR
/* Check args */
HDassert(buf);
HDassert(H5I_DATATYPE == H5I_get_type(type_id));
HDassert(space);
HDassert(H5S_has_extent(space));
HDassert(op);
ret_value = H5S_select_iterate(buf, type_id, space, op, operator_data);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__iterate() */
/*-------------------------------------------------------------------------
* Function: H5D_vlen_reclaim
*
* Purpose: Frees the buffers allocated for storing variable-length data
* in memory. Only frees the VL data in the selection defined in the
* dataspace. The dataset transfer property list is required to find the
* correct allocation/free methods for the VL data in the buffer.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 22, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_vlen_reclaim(hid_t type_id, H5S_t *space, hid_t plist_id, void *buf)
{
H5T_vlen_alloc_info_t _vl_alloc_info; /* VL allocation info buffer */
H5T_vlen_alloc_info_t *vl_alloc_info = &_vl_alloc_info; /* VL allocation info */
herr_t ret_value;
FUNC_ENTER_NOAPI(FAIL)
/* Check args */
HDassert(H5I_DATATYPE == H5I_get_type(type_id));
HDassert(space);
HDassert(H5P_isa_class(plist_id, H5P_DATASET_XFER));
HDassert(buf);
/* Get the allocation info */
if(H5T_vlen_get_alloc_info(plist_id,&vl_alloc_info) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to retrieve VL allocation info")
/* Call H5D__iterate with args, etc. */
ret_value = H5D__iterate(buf, type_id, space ,H5T_vlen_reclaim, vl_alloc_info);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_vlen_reclaim() */
/*-------------------------------------------------------------------------
* Function: H5D__vlen_get_buf_size_alloc
*
* Purpose: This routine makes certain there is enough space in the temporary
* buffer for the new data to read in. All the VL data read in is actually
* placed in this buffer, overwriting the previous data. Needless to say,
* this data is not actually usable.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, August 17, 1999
*
*-------------------------------------------------------------------------
*/
void *
H5D__vlen_get_buf_size_alloc(size_t size, void *info)
{
H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)info;
void *ret_value; /* Return value */
FUNC_ENTER_PACKAGE_NOERR
/* Get a temporary pointer to space for the VL data */
if((vlen_bufsize->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize->vl_tbuf, size)) != NULL)
vlen_bufsize->size += size;
/* Set return value */
ret_value = vlen_bufsize->vl_tbuf;
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__vlen_get_buf_size_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D__vlen_get_buf_size
*
* Purpose: This routine checks the number of bytes required to store a single
* element from a dataset in memory, creating a selection with just the
* single element selected to read in the element and using a custom memory
* allocator for any VL data encountered.
* The *size value is modified according to how many bytes are
* required to store the element in memory.
*
* Implementation: This routine actually performs the read with a custom
* memory manager which basically just counts the bytes requested and
* uses a temporary memory buffer (through the H5FL API) to make certain
* enough space is available to perform the read. Then the temporary
* buffer is released and the number of bytes allocated is returned.
* Kinda kludgy, but easier than the other method of trying to figure out
* the sizes without actually reading the data in... - QAK
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, August 17, 1999
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
herr_t
H5D__vlen_get_buf_size(void UNUSED *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t *point, void *op_data)
{
H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data;
H5T_t *dt; /* Datatype for operation */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
HDassert(op_data);
HDassert(H5I_DATATYPE == H5I_get_type(type_id));
/* Check args */
if(NULL == (dt = (H5T_t *)H5I_object(type_id)))
HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a datatype")
/* Make certain there is enough fixed-length buffer available */
if(NULL == (vlen_bufsize->fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->fl_tbuf, H5T_get_size(dt))))
HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't resize tbuf")
/* Select point to read in */
if(H5S_select_elements(vlen_bufsize->fspace, H5S_SELECT_SET, (size_t)1, point) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't select point")
/* Read in the point (with the custom VL memory allocator) */
if(H5D__read(vlen_bufsize->dset, type_id, vlen_bufsize->mspace, vlen_bufsize->fspace, vlen_bufsize->xfer_pid, vlen_bufsize->fl_tbuf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__vlen_get_buf_size() */
/*-------------------------------------------------------------------------
* Function: H5D__check_filters
*
* Purpose: Check if the filters have be initialized for the dataset
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, October 11, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__check_filters(H5D_t *dataset)
{
H5O_fill_t *fill; /* Dataset's fill value */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(dataset);
/* Check if the filters in the DCPL will need to encode, and if so, can they?
*
* Filters need encoding if fill value is defined and a fill policy is set
* that requires writing on an extend.
*/
fill = &dataset->shared->dcpl_cache.fill;
if(!dataset->shared->checked_filters) {
H5D_fill_value_t fill_status; /* Whether the fill value is defined */
/* Retrieve the "defined" status of the fill value */
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Couldn't retrieve fill value from dataset.")
/* See if we can check the filter status */
if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) {
if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
/* Filters must have encoding enabled. Ensure that all filters can be applied */
if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters")
dataset->shared->checked_filters = TRUE;
} /* end if */
} /* end if */
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__check_filters() */
/*-------------------------------------------------------------------------
* Function: H5D__set_extent
*
* Purpose: Based on H5D_extend, allows change to a lower dimension,
* calls H5S_set_extent and H5D__chunk_prune_by_extent instead
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* April 9, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id)
{
H5S_t *space; /* Dataset's dataspace */
int rank; /* Dataspace # of dimensions */
hsize_t curr_dims[H5O_LAYOUT_NDIMS];/* Current dimension sizes */
htri_t changed; /* Whether the dataspace changed size */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(dset);
HDassert(size);
/* Check if we are allowed to modify this file */
if(0 == (H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR))
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file")
/* Check if we are allowed to modify the space; only datasets with chunked and external storage are allowed to be modified */
if(H5D_COMPACT == dset->shared->layout.type)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "dataset has compact storage")
if(H5D_CONTIGUOUS == dset->shared->layout.type && 0 == dset->shared->dcpl_cache.efl.nused)
HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "dataset has contiguous storage")
/* Check if the filters in the DCPL will need to encode, and if so, can they? */
if(H5D__check_filters(dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't apply filters")
/* Get the data space */
space = dset->shared->space;
/* Check if we are shrinking or expanding any of the dimensions */
if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
/* Modify the size of the data space */
if((changed = H5S_set_extent(space, size)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space")
/* Don't bother updating things, unless they've changed */
if(changed) {
hbool_t shrink = FALSE; /* Flag to indicate a dimension has shrank */
hbool_t expand = FALSE; /* Flag to indicate a dimension has grown */
unsigned u; /* Local index variable */
/* Determine if we are shrinking and/or expanding any dimensions */
for(u = 0; u < (unsigned)rank; u++) {
if(size[u] < curr_dims[u])
shrink = TRUE;
if(size[u] > curr_dims[u])
expand = TRUE;
} /* end for */
/*-------------------------------------------------------------------------
* Modify the dataset storage
*-------------------------------------------------------------------------
*/
/* Update the index values for the cached chunks for this dataset */
if(H5D_CHUNKED == dset->shared->layout.type) {
if(H5D__chunk_set_info(dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to update # of chunks")
if(H5D__chunk_update_cache(dset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices")
} /* end if */
/* Allocate space for the new parts of the dataset, if appropriate */
if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY)
if(H5D__alloc_storage(dset, dxpl_id, H5D_ALLOC_EXTEND, FALSE, curr_dims) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset storage")
/*-------------------------------------------------------------------------
* Remove chunk information in the case of chunked datasets
* This removal takes place only in case we are shrinking the dateset
* and if the chunks are written
*-------------------------------------------------------------------------
*/
if(shrink && H5D_CHUNKED == dset->shared->layout.type &&
(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) {
/* Remove excess chunks */
if(H5D__chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks")
} /* end if */
/* Mark the dataspace as dirty, for later writing to the file */
if(H5D__mark(dset, dxpl_id, H5D_MARK_SPACE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark dataspace as dirty")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__set_extent() */
/*-------------------------------------------------------------------------
* Function: H5D__flush_sieve_buf
*
* Purpose: Flush any dataset sieve buffer info cached in memory
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* July 27, 2009
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(dataset);
/* Flush the raw data buffer, if we have a dirty one */
if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) {
HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */
/* Write dirty data sieve buffer to file */
if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc,
dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed")
/* Reset sieve buffer dirty flag */
dataset->shared->cache.contig.sieve_dirty = FALSE;
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__flush_sieve_buf() */
/*-------------------------------------------------------------------------
* Function: H5D__flush_real
*
* Purpose: Flush any dataset information cached in memory
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* December 6, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__flush_real(H5D_t *dataset, hid_t dxpl_id)
{
H5O_t *oh = NULL; /* Pointer to dataset's object header */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(dataset);
/* Check for metadata changes that will require updating the object's modification time */
if(dataset->shared->layout_dirty || dataset->shared->space_dirty) {
unsigned update_flags = H5O_UPDATE_TIME; /* Modification time flag */
/* Pin the object header */
if(NULL == (oh = H5O_pin(&dataset->oloc, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header")
/* Update the layout on disk, if it's been changed */
if(dataset->shared->layout_dirty) {
if(H5D__layout_oh_write(dataset, dxpl_id, oh, update_flags) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout/pline/efl info")
dataset->shared->layout_dirty = FALSE;
/* Reset the "update the modification time" flag, so we only do it once */
update_flags = 0;
} /* end if */
/* Update the dataspace on disk, if it's been changed */
if(dataset->shared->space_dirty) {
if(H5S_write(dataset->oloc.file, dxpl_id, oh, update_flags, dataset->shared->space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace")
dataset->shared->space_dirty = FALSE;
/* Reset the "update the modification time" flag, so we only do it once */
update_flags = 0;
} /* end if */
/* _Somebody_ should have update the modification time! */
HDassert(update_flags == 0);
} /* end if */
/* Flush cached raw data for each kind of dataset layout */
if(dataset->shared->layout.ops->flush &&
(dataset->shared->layout.ops->flush)(dataset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush raw data")
done:
/* Release pointer to object header */
if(oh != NULL)
if(H5O_unpin(oh) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__flush_real() */
/*-------------------------------------------------------------------------
* Function: H5D__mark
*
* Purpose: Mark some aspect of a dataset as dirty
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* July 4, 2008
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__mark(const H5D_t *dataset, hid_t UNUSED dxpl_id, unsigned flags)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_NOERR
/* Check args */
HDassert(dataset);
HDassert(!(flags & (unsigned)~(H5D_MARK_SPACE | H5D_MARK_LAYOUT)));
/* Mark aspects of the dataset as dirty */
if(flags & H5D_MARK_SPACE)
dataset->shared->space_dirty = TRUE;
if(flags & H5D_MARK_LAYOUT)
dataset->shared->layout_dirty = TRUE;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mark() */
/*-------------------------------------------------------------------------
* Function: H5D__flush_cb
*
* Purpose: Flush any dataset information cached in memory
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* November 8, 2007
*
*-------------------------------------------------------------------------
*/
static int
H5D__flush_cb(void *_dataset, hid_t UNUSED id, void *_udata)
{
H5D_t *dataset = (H5D_t *)_dataset; /* Dataset pointer */
H5D_flush_ud_t *udata = (H5D_flush_ud_t *)_udata; /* User data for callback */
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_STATIC
/* Check args */
HDassert(dataset);
/* Check for dataset in same file */
if(udata->f == dataset->oloc.file) {
/* Flush the dataset's information */
if(H5D__flush_real(dataset, udata->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to flush cached dataset info")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__flush_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_flush
*
* Purpose: Flush any dataset information cached in memory
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Ray Lu
* August 14, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_flush(const H5F_t *f, hid_t dxpl_id)
{
H5D_flush_ud_t udata; /* User data for callback */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
/* Check args */
HDassert(f);
/* Set user data for callback */
udata.f = f;
udata.dxpl_id = dxpl_id;
/* Iterate over all the open datasets */
if(H5I_iterate(H5I_DATASET, H5D__flush_cb, &udata, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to flush cached dataset info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_flush() */
|