forked from HDFGroup/hdf5
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathH5EA.c
1029 lines (863 loc) · 40.5 KB
/
H5EA.c
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
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 LICENSE file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5EA.c
*
* Purpose: Implements an "extensible array" for storing elements
* in an array whose high bounds can extend and shrink.
*
* Please see the documentation in:
* doc/html/TechNotes/ExtensibleArray.html for a full
* description of how they work, etc.
*
*-------------------------------------------------------------------------
*/
/**********************/
/* Module Declaration */
/**********************/
#include "H5EAmodule.h" /* This source code file is part of the H5EA module */
/***********************/
/* Other Packages Used */
/***********************/
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector functions */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/* Typedef for generically unprotecting an object */
typedef herr_t (*H5EA__unprotect_func_t)(void *thing, unsigned cache_flags);
/********************/
/* Package Typedefs */
/********************/
/********************/
/* Local Prototypes */
/********************/
static herr_t H5EA__lookup_elmt(const H5EA_t *ea, hsize_t idx, bool will_extend, unsigned thing_acc,
void **thing, uint8_t **thing_elmt_buf, hsize_t *thing_elmt_idx,
H5EA__unprotect_func_t *thing_unprot_func);
static H5EA_t *H5EA__new(H5F_t *f, haddr_t ea_addr, bool from_open, void *ctx_udata);
/*********************/
/* Package Variables */
/*********************/
/* Package initialization variable */
bool H5_PKG_INIT_VAR = false;
/* Extensible array client ID to class mapping */
/* Remember to add client ID to H5EA_cls_id_t in H5EAprivate.h when adding a new
* client class..
*/
const H5EA_class_t *const H5EA_client_class_g[] = {
H5EA_CLS_CHUNK, /* 0 - H5EA_CLS_CHUNK_ID */
H5EA_CLS_FILT_CHUNK, /* 1 - H5EA_CLS_FILT_CHUNK_ID */
H5EA_CLS_TEST, /* ? - H5EA_CLS_TEST_ID */
};
/*****************************/
/* Library Private Variables */
/*****************************/
/*******************/
/* Local Variables */
/*******************/
/* Declare a free list to manage the H5EA_t struct */
H5FL_DEFINE_STATIC(H5EA_t);
/* Declare a PQ free list to manage the element */
H5FL_BLK_DEFINE_STATIC(ea_native_elmt);
/*-------------------------------------------------------------------------
* Function: H5EA__new
*
* Purpose: Allocate and initialize a new extensible array wrapper in memory
*
* Return: Pointer to earray wrapper success
* NULL on failure
*
*-------------------------------------------------------------------------
*/
static H5EA_t *
H5EA__new(H5F_t *f, haddr_t ea_addr, bool from_open, void *ctx_udata)
{
H5EA_t *ea = NULL; /* Pointer to new extensible array */
H5EA_hdr_t *hdr = NULL; /* The extensible array header information */
H5EA_t *ret_value = NULL;
FUNC_ENTER_PACKAGE
/* Check arguments */
assert(f);
assert(H5_addr_defined(ea_addr));
/* Allocate extensible array wrapper */
if (NULL == (ea = H5FL_CALLOC(H5EA_t)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTALLOC, NULL, "memory allocation failed for extensible array info");
/* Lock the array header into memory */
if (NULL == (hdr = H5EA__hdr_protect(f, ea_addr, ctx_udata, H5AC__READ_ONLY_FLAG)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, NULL, "unable to load extensible array header");
/* Check for pending array deletion */
if (from_open && hdr->pending_delete)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTOPENOBJ, NULL, "can't open extensible array pending deletion");
/* Point extensible array wrapper at header and bump it's ref count */
ea->hdr = hdr;
if (H5EA__hdr_incr(ea->hdr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTINC, NULL, "can't increment reference count on shared array header");
/* Increment # of files using this array header */
if (H5EA__hdr_fuse_incr(ea->hdr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTINC, NULL,
"can't increment file reference count on shared array header");
/* Set file pointer for this array open context */
ea->f = f;
/* Set the return value */
ret_value = ea;
done:
if (hdr && H5EA__hdr_unprotect(hdr, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, NULL, "unable to release extensible array header");
if (!ret_value)
if (ea && H5EA_close(ea) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CLOSEERROR, NULL, "unable to close extensible array");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA__new() */
/*-------------------------------------------------------------------------
* Function: H5EA_create
*
* Purpose: Creates a new empty extensible array in the file.
*
* Return: Pointer to earray wrapper on success
* NULL on failure
*
*-------------------------------------------------------------------------
*/
H5EA_t *
H5EA_create(H5F_t *f, const H5EA_create_t *cparam, void *ctx_udata)
{
H5EA_t *ea = NULL; /* Pointer to new extensible array */
haddr_t ea_addr; /* Array header address */
H5EA_t *ret_value = NULL;
FUNC_ENTER_NOAPI(NULL)
/* Check arguments */
assert(f);
assert(cparam);
/* H5EA interface sanity check */
HDcompile_assert(H5EA_NUM_CLS_ID == NELMTS(H5EA_client_class_g));
/* Create extensible array header */
if (HADDR_UNDEF == (ea_addr = H5EA__hdr_create(f, cparam, ctx_udata)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTINIT, NULL, "can't create extensible array header");
/* Allocate and initialize new extensible array wrapper */
if (NULL == (ea = H5EA__new(f, ea_addr, false, ctx_udata)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTINIT, NULL,
"allocation and/or initialization failed for extensible array wrapper");
/* Set the return value */
ret_value = ea;
done:
if (!ret_value)
if (ea && H5EA_close(ea) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CLOSEERROR, NULL, "unable to close extensible array");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA_create() */
/*-------------------------------------------------------------------------
* Function: H5EA_open
*
* Purpose: Opens an existing extensible array in the file.
*
* Return: Pointer to array wrapper on success
* NULL on failure
*
*-------------------------------------------------------------------------
*/
H5EA_t *
H5EA_open(H5F_t *f, haddr_t ea_addr, void *ctx_udata)
{
H5EA_t *ea = NULL; /* Pointer to new extensible array wrapper */
H5EA_t *ret_value = NULL;
FUNC_ENTER_NOAPI(NULL)
/* Check arguments */
assert(f);
assert(H5_addr_defined(ea_addr));
/* Allocate and initialize new extensible array wrapper */
if (NULL == (ea = H5EA__new(f, ea_addr, true, ctx_udata)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTINIT, NULL,
"allocation and/or initialization failed for extensible array wrapper");
/* Set the return value */
ret_value = ea;
done:
if (!ret_value)
if (ea && H5EA_close(ea) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CLOSEERROR, NULL, "unable to close extensible array");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA_open() */
/*-------------------------------------------------------------------------
* Function: H5EA_get_nelmts
*
* Purpose: Query the current number of elements in array
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
H5EA_get_nelmts(const H5EA_t *ea, hsize_t *nelmts)
{
FUNC_ENTER_NOAPI_NOERR
/* Check arguments */
assert(ea);
assert(nelmts);
/* Retrieve the max. index set */
*nelmts = ea->hdr->stats.stored.max_idx_set;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5EA_get_nelmts() */
/*-------------------------------------------------------------------------
* Function: H5EA_get_addr
*
* Purpose: Query the address of the array
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
H5EA_get_addr(const H5EA_t *ea, haddr_t *addr)
{
FUNC_ENTER_NOAPI_NOERR
/* Check arguments */
assert(ea);
assert(ea->hdr);
assert(addr);
/* Retrieve the address of the extensible array's header */
*addr = ea->hdr->addr;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5EA_get_addr() */
/*-------------------------------------------------------------------------
* Function: H5EA__lookup_elmt
*
* Purpose: Retrieve the metadata object and the element buffer for a
* given element in the array.
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5EA__lookup_elmt(const H5EA_t *ea, hsize_t idx, bool will_extend, unsigned thing_acc, void **thing,
uint8_t **thing_elmt_buf, hsize_t *thing_elmt_idx,
H5EA__unprotect_func_t *thing_unprot_func)
{
H5EA_hdr_t *hdr = ea->hdr; /* Header for EA */
H5EA_iblock_t *iblock = NULL; /* Pointer to index block for EA */
H5EA_sblock_t *sblock = NULL; /* Pointer to super block for EA */
H5EA_dblock_t *dblock = NULL; /* Pointer to data block for EA */
H5EA_dblk_page_t *dblk_page = NULL; /* Pointer to data block page for EA */
unsigned iblock_cache_flags = H5AC__NO_FLAGS_SET; /* Flags to unprotecting index block */
unsigned sblock_cache_flags = H5AC__NO_FLAGS_SET; /* Flags to unprotecting super block */
bool stats_changed = false; /* Whether array statistics changed */
bool hdr_dirty = false; /* Whether the array header changed */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* Check arguments */
assert(ea);
assert(hdr);
assert(thing);
assert(thing_elmt_buf);
assert(thing_unprot_func);
/* only the H5AC__READ_ONLY_FLAG may be set in thing_acc */
assert((thing_acc & (unsigned)(~H5AC__READ_ONLY_FLAG)) == 0);
/* Set the shared array header's file context for this operation */
hdr->f = ea->f;
/* Reset the pointers to the 'thing' info */
*thing = NULL;
*thing_elmt_buf = NULL;
*thing_elmt_idx = 0;
*thing_unprot_func = (H5EA__unprotect_func_t)NULL;
/* Check if we should create the index block */
if (!H5_addr_defined(hdr->idx_blk_addr)) {
/* Check if we are allowed to create the thing */
if (0 == (thing_acc & H5AC__READ_ONLY_FLAG)) { /* i.e. r/w access */
/* Create the index block */
hdr->idx_blk_addr = H5EA__iblock_create(hdr, &stats_changed);
if (!H5_addr_defined(hdr->idx_blk_addr))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTCREATE, FAIL, "unable to create index block");
hdr_dirty = true;
} /* end if */
else
HGOTO_DONE(SUCCEED);
} /* end if */
/* Protect index block */
if (NULL == (iblock = H5EA__iblock_protect(hdr, thing_acc)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL,
"unable to protect extensible array index block, address = %llu",
(unsigned long long)hdr->idx_blk_addr);
/* Check if element is in index block */
if (idx < hdr->cparam.idx_blk_elmts) {
/* Set 'thing' info to refer to the index block */
*thing = iblock;
*thing_elmt_buf = (uint8_t *)iblock->elmts;
*thing_elmt_idx = idx;
*thing_unprot_func = (H5EA__unprotect_func_t)H5EA__iblock_unprotect;
} /* end if */
else {
unsigned sblk_idx; /* Which superblock does this index fall in? */
size_t dblk_idx; /* Data block index */
hsize_t elmt_idx; /* Offset of element in super block */
/* Get super block index where element is located */
sblk_idx = H5EA__dblock_sblk_idx(hdr, idx);
/* Adjust index to offset in super block */
elmt_idx = idx - (hdr->cparam.idx_blk_elmts + hdr->sblk_info[sblk_idx].start_idx);
/* Check for data block containing element address in the index block */
if (sblk_idx < iblock->nsblks) {
/* Compute the data block index in index block */
dblk_idx = (size_t)(hdr->sblk_info[sblk_idx].start_dblk +
(elmt_idx / hdr->sblk_info[sblk_idx].dblk_nelmts));
assert(dblk_idx < iblock->ndblk_addrs);
/* Check if the data block has been allocated on disk yet */
if (!H5_addr_defined(iblock->dblk_addrs[dblk_idx])) {
/* Check if we are allowed to create the thing */
if (0 == (thing_acc & H5AC__READ_ONLY_FLAG)) { /* i.e. r/w access */
haddr_t dblk_addr; /* Address of data block created */
hsize_t dblk_off; /* Offset of data block in array */
/* Create data block */
dblk_off = hdr->sblk_info[sblk_idx].start_idx +
(dblk_idx * hdr->sblk_info[sblk_idx].dblk_nelmts);
dblk_addr = H5EA__dblock_create(hdr, iblock, &stats_changed, dblk_off,
hdr->sblk_info[sblk_idx].dblk_nelmts);
if (!H5_addr_defined(dblk_addr))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTCREATE, FAIL,
"unable to create extensible array data block");
/* Set data block address in index block */
iblock->dblk_addrs[dblk_idx] = dblk_addr;
iblock_cache_flags |= H5AC__DIRTIED_FLAG;
} /* end if */
else
HGOTO_DONE(SUCCEED);
} /* end if */
/* Protect data block */
if (NULL == (dblock = H5EA__dblock_protect(hdr, iblock, iblock->dblk_addrs[dblk_idx],
hdr->sblk_info[sblk_idx].dblk_nelmts, thing_acc)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL,
"unable to protect extensible array data block, address = %llu",
(unsigned long long)iblock->dblk_addrs[dblk_idx]);
/* Adjust index to offset in data block */
elmt_idx %= hdr->sblk_info[sblk_idx].dblk_nelmts;
/* Check if there is already a dependency on the header */
if (will_extend && !dblock->has_hdr_depend) {
if (H5EA__create_flush_depend((H5AC_info_t *)hdr, (H5AC_info_t *)dblock) < 0)
HGOTO_ERROR(
H5E_EARRAY, H5E_CANTDEPEND, FAIL,
"unable to create flush dependency between data block and header, index = %llu",
(unsigned long long)idx);
dblock->has_hdr_depend = true;
} /* end if */
/* Set 'thing' info to refer to the data block */
*thing = dblock;
*thing_elmt_buf = (uint8_t *)dblock->elmts;
*thing_elmt_idx = elmt_idx;
*thing_unprot_func = (H5EA__unprotect_func_t)H5EA__dblock_unprotect;
} /* end if */
else {
size_t sblk_off; /* Offset of super block in index block array of super blocks */
/* Calculate offset of super block in index block's array */
sblk_off = sblk_idx - iblock->nsblks;
/* Check if the super block has been allocated on disk yet */
if (!H5_addr_defined(iblock->sblk_addrs[sblk_off])) {
/* Check if we are allowed to create the thing */
if (0 == (thing_acc & H5AC__READ_ONLY_FLAG)) { /* i.e. r/w access */
haddr_t sblk_addr; /* Address of data block created */
/* Create super block */
sblk_addr = H5EA__sblock_create(hdr, iblock, &stats_changed, sblk_idx);
if (!H5_addr_defined(sblk_addr))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTCREATE, FAIL,
"unable to create extensible array super block");
/* Set super block address in index block */
iblock->sblk_addrs[sblk_off] = sblk_addr;
iblock_cache_flags |= H5AC__DIRTIED_FLAG;
} /* end if */
else
HGOTO_DONE(SUCCEED);
} /* end if */
/* Protect super block */
if (NULL == (sblock = H5EA__sblock_protect(hdr, iblock, iblock->sblk_addrs[sblk_off], sblk_idx,
thing_acc)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL,
"unable to protect extensible array super block, address = %llu",
(unsigned long long)iblock->sblk_addrs[sblk_off]);
/* Compute the data block index in super block */
dblk_idx = (size_t)(elmt_idx / sblock->dblk_nelmts);
assert(dblk_idx < sblock->ndblks);
/* Check if the data block has been allocated on disk yet */
if (!H5_addr_defined(sblock->dblk_addrs[dblk_idx])) {
/* Check if we are allowed to create the thing */
if (0 == (thing_acc & H5AC__READ_ONLY_FLAG)) { /* i.e. r/w access */
haddr_t dblk_addr; /* Address of data block created */
hsize_t dblk_off; /* Offset of data block in array */
/* Create data block */
dblk_off = hdr->sblk_info[sblk_idx].start_idx +
(dblk_idx * hdr->sblk_info[sblk_idx].dblk_nelmts);
dblk_addr =
H5EA__dblock_create(hdr, sblock, &stats_changed, dblk_off, sblock->dblk_nelmts);
if (!H5_addr_defined(dblk_addr))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTCREATE, FAIL,
"unable to create extensible array data block");
/* Set data block address in index block */
sblock->dblk_addrs[dblk_idx] = dblk_addr;
sblock_cache_flags |= H5AC__DIRTIED_FLAG;
/* Create flush dependency on header, if extending the array and one doesn't already exist
*/
if (will_extend && !sblock->has_hdr_depend) {
if (H5EA__create_flush_depend((H5AC_info_t *)sblock->hdr, (H5AC_info_t *)sblock) < 0)
HGOTO_ERROR(
H5E_EARRAY, H5E_CANTDEPEND, FAIL,
"unable to create flush dependency between super block and header, address "
"= %llu",
(unsigned long long)sblock->addr);
sblock->has_hdr_depend = true;
} /* end if */
} /* end if */
else
HGOTO_DONE(SUCCEED);
} /* end if */
/* Adjust index to offset in data block */
elmt_idx %= sblock->dblk_nelmts;
/* Check if the data block is paged */
if (sblock->dblk_npages) {
haddr_t dblk_page_addr; /* Address of data block page */
size_t page_idx; /* Index of page within data block */
size_t page_init_idx; /* Index of 'page init' bit */
/* Compute page index */
page_idx = (size_t)elmt_idx / hdr->dblk_page_nelmts;
/* Compute 'page init' index */
page_init_idx = (dblk_idx * sblock->dblk_npages) + page_idx;
/* Adjust index to offset in data block page */
elmt_idx %= hdr->dblk_page_nelmts;
/* Compute data block page address */
dblk_page_addr = sblock->dblk_addrs[dblk_idx] + H5EA_DBLOCK_PREFIX_SIZE(sblock) +
(page_idx * sblock->dblk_page_size);
/* Check if page has been initialized yet */
if (!H5VM_bit_get(sblock->page_init, page_init_idx)) {
/* Check if we are allowed to create the thing */
if (0 == (thing_acc & H5AC__READ_ONLY_FLAG)) { /* i.e. r/w access */
/* Create the data block page */
if (H5EA__dblk_page_create(hdr, sblock, dblk_page_addr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTCREATE, FAIL, "unable to create data block page");
/* Mark data block page as initialized in super block */
H5VM_bit_set(sblock->page_init, page_init_idx, true);
sblock_cache_flags |= H5AC__DIRTIED_FLAG;
} /* end if */
else
HGOTO_DONE(SUCCEED);
} /* end if */
/* Protect data block page */
if (NULL == (dblk_page = H5EA__dblk_page_protect(hdr, sblock, dblk_page_addr, thing_acc)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL,
"unable to protect extensible array data block page, address = %llu",
(unsigned long long)dblk_page_addr);
/* Check if there is already a dependency on the header */
if (will_extend && !dblk_page->has_hdr_depend) {
if (H5EA__create_flush_depend((H5AC_info_t *)hdr, (H5AC_info_t *)dblk_page) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTDEPEND, FAIL,
"unable to create flush dependency between data block page and header, "
"index = %llu",
(unsigned long long)idx);
dblk_page->has_hdr_depend = true;
} /* end if */
/* Set 'thing' info to refer to the data block page */
*thing = dblk_page;
*thing_elmt_buf = (uint8_t *)dblk_page->elmts;
*thing_elmt_idx = elmt_idx;
*thing_unprot_func = (H5EA__unprotect_func_t)H5EA__dblk_page_unprotect;
} /* end if */
else {
/* Protect data block */
if (NULL == (dblock = H5EA__dblock_protect(hdr, sblock, sblock->dblk_addrs[dblk_idx],
sblock->dblk_nelmts, thing_acc)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL,
"unable to protect extensible array data block, address = %llu",
(unsigned long long)sblock->dblk_addrs[dblk_idx]);
/* Check if there is already a dependency on the header */
if (will_extend && !dblock->has_hdr_depend) {
if (H5EA__create_flush_depend((H5AC_info_t *)hdr, (H5AC_info_t *)dblock) < 0)
HGOTO_ERROR(
H5E_EARRAY, H5E_CANTDEPEND, FAIL,
"unable to create flush dependency between data block and header, index = %llu",
(unsigned long long)idx);
dblock->has_hdr_depend = true;
} /* end if */
/* Set 'thing' info to refer to the data block */
*thing = dblock;
*thing_elmt_buf = (uint8_t *)dblock->elmts;
*thing_elmt_idx = elmt_idx;
*thing_unprot_func = (H5EA__unprotect_func_t)H5EA__dblock_unprotect;
} /* end else */
} /* end else */
} /* end else */
/* Sanity checks */
assert(*thing != NULL);
assert(*thing_unprot_func != NULL);
done:
/* Reset 'thing' info on error */
if (ret_value < 0) {
*thing = NULL;
*thing_elmt_buf = NULL;
*thing_elmt_idx = 0;
*thing_unprot_func = (H5EA__unprotect_func_t)NULL;
} /* end if */
/* Check for updating array statistics */
if (stats_changed)
hdr_dirty = true;
/* Check for header modified */
if (hdr_dirty)
if (H5EA__hdr_modified(hdr) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTMARKDIRTY, FAIL,
"unable to mark extensible array header as modified");
/* Release resources */
if (iblock && *thing != iblock && H5EA__iblock_unprotect(iblock, iblock_cache_flags) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, FAIL, "unable to release extensible array index block");
/* (Note: super blocks don't contain elements, so don't have a '*thing != sblock' check) */
if (sblock && H5EA__sblock_unprotect(sblock, sblock_cache_flags) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, FAIL, "unable to release extensible array super block");
if (dblock && *thing != dblock && H5EA__dblock_unprotect(dblock, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, FAIL, "unable to release extensible array data block");
if (dblk_page && *thing != dblk_page && H5EA__dblk_page_unprotect(dblk_page, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, FAIL,
"unable to release extensible array data block page");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA__lookup_elmt() */
/*-------------------------------------------------------------------------
* Function: H5EA_set
*
* Purpose: Set an element of an extensible array
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
H5EA_set(const H5EA_t *ea, hsize_t idx, const void *elmt)
{
H5EA_hdr_t *hdr = ea->hdr; /* Header for EA */
void *thing = NULL; /* Pointer to the array metadata containing the array index we are interested in */
uint8_t *thing_elmt_buf; /* Pointer to the element buffer for the array metadata */
hsize_t thing_elmt_idx; /* Index of the element in the element buffer for the array metadata */
H5EA__unprotect_func_t thing_unprot_func; /* Function pointer for unprotecting the array metadata */
bool will_extend; /* Flag indicating if setting the element will extend the array */
unsigned thing_cache_flags = H5AC__NO_FLAGS_SET; /* Flags for unprotecting array metadata */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Check arguments */
assert(ea);
assert(hdr);
/* Set the shared array header's file context for this operation */
hdr->f = ea->f;
/* Look up the array metadata containing the element we want to set */
will_extend = (idx >= hdr->stats.stored.max_idx_set);
if (H5EA__lookup_elmt(ea, idx, will_extend, H5AC__NO_FLAGS_SET, &thing, &thing_elmt_buf, &thing_elmt_idx,
&thing_unprot_func) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL, "unable to protect array metadata");
/* Sanity check */
assert(thing);
assert(thing_elmt_buf);
assert(thing_unprot_func);
/* Set element in thing's element buffer */
H5MM_memcpy(thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), elmt,
hdr->cparam.cls->nat_elmt_size);
thing_cache_flags |= H5AC__DIRTIED_FLAG;
/* Update max. element set in array, if appropriate */
if (will_extend) {
/* Update the max index for the array */
hdr->stats.stored.max_idx_set = idx + 1;
if (H5EA__hdr_modified(hdr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTMARKDIRTY, FAIL,
"unable to mark extensible array header as modified");
}
done:
/* Release resources */
if (thing && (thing_unprot_func)(thing, thing_cache_flags) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, FAIL, "unable to release extensible array metadata");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA_set() */
/*-------------------------------------------------------------------------
* Function: H5EA_get
*
* Purpose: Get an element of an extensible array
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
H5EA_get(const H5EA_t *ea, hsize_t idx, void *elmt)
{
H5EA_hdr_t *hdr = ea->hdr; /* Header for EA */
void *thing = NULL; /* Pointer to the array metadata containing the array index we are interested in */
H5EA__unprotect_func_t thing_unprot_func =
NULL; /* Function pointer for unprotecting the array metadata */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Check arguments */
assert(ea);
assert(hdr);
/* Check for element beyond max. element in array */
if (idx >= hdr->stats.stored.max_idx_set) {
/* Call the class's 'fill' callback */
if ((hdr->cparam.cls->fill)(elmt, (size_t)1) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTSET, FAIL, "can't set element to class's fill value");
} /* end if */
else {
uint8_t *thing_elmt_buf; /* Pointer to the element buffer for the array metadata */
hsize_t thing_elmt_idx; /* Index of the element in the element buffer for the array metadata */
/* Set the shared array header's file context for this operation */
hdr->f = ea->f;
/* Look up the array metadata containing the element we want to set */
if (H5EA__lookup_elmt(ea, idx, false, H5AC__READ_ONLY_FLAG, &thing, &thing_elmt_buf, &thing_elmt_idx,
&thing_unprot_func) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL, "unable to protect array metadata");
/* Check if the thing holding the element has been created yet */
if (NULL == thing) {
/* Call the class's 'fill' callback */
if ((hdr->cparam.cls->fill)(elmt, (size_t)1) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTSET, FAIL, "can't set element to class's fill value");
} /* end if */
else
/* Get element from thing's element buffer */
H5MM_memcpy(elmt, thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx),
hdr->cparam.cls->nat_elmt_size);
} /* end else */
done:
/* Release thing */
if (thing && (thing_unprot_func)(thing, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, FAIL, "unable to release extensible array metadata");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA_get() */
/*-------------------------------------------------------------------------
* Function: H5EA_depend
*
* Purpose: Make a child flush dependency between the extensible array
* and another piece of metadata in the file.
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
H5EA_depend(H5EA_t *ea, H5AC_proxy_entry_t *parent)
{
H5EA_hdr_t *hdr = ea->hdr; /* Header for EA */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Check arguments */
assert(ea);
assert(hdr);
assert(parent);
/*
* Check to see if a flush dependency between the extensible array
* and another data structure in the file has already been set up.
* If it hasn't, do so now.
*/
if (NULL == hdr->parent) {
/* Sanity check */
assert(hdr->top_proxy);
/* Set the shared array header's file context for this operation */
hdr->f = ea->f;
/* Add the extensible array as a child of the parent (proxy) */
if (H5AC_proxy_entry_add_child(parent, hdr->f, hdr->top_proxy) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTSET, FAIL, "unable to add extensible array as child of proxy");
hdr->parent = parent;
}
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA_depend() */
/*-------------------------------------------------------------------------
* Function: H5EA_close
*
* Purpose: Close an extensible array
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
H5EA_close(H5EA_t *ea)
{
bool pending_delete = false; /* Whether the array is pending deletion */
haddr_t ea_addr = HADDR_UNDEF; /* Address of array (for deletion) */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Check arguments */
assert(ea);
/* Close the header, if it was set */
if (ea->hdr) {
/* Decrement file reference & check if this is the last open extensible array using the shared array
* header */
if (0 == H5EA__hdr_fuse_decr(ea->hdr)) {
/* Set the shared array header's file context for this operation */
ea->hdr->f = ea->f;
/* Shut down anything that can't be put in the header's 'flush' callback */
/* Check for pending array deletion */
if (ea->hdr->pending_delete) {
/* Set local info, so array deletion can occur after decrementing the
* header's ref count
*/
pending_delete = true;
ea_addr = ea->hdr->addr;
} /* end if */
} /* end if */
/* Check for pending array deletion */
if (pending_delete) {
H5EA_hdr_t *hdr; /* Another pointer to extensible array header */
#ifndef NDEBUG
{
unsigned hdr_status = 0; /* Header's status in the metadata cache */
/* Check the header's status in the metadata cache */
if (H5AC_get_entry_status(ea->f, ea_addr, &hdr_status) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTGET, FAIL,
"unable to check metadata cache status for extensible array header");
/* Sanity checks on header */
assert(hdr_status & H5AC_ES__IN_CACHE);
assert(hdr_status & H5AC_ES__IS_PINNED);
assert(!(hdr_status & H5AC_ES__IS_PROTECTED));
}
#endif /* NDEBUG */
/* Lock the array header into memory */
/* (OK to pass in NULL for callback context, since we know the header must be in the cache) */
if (NULL == (hdr = H5EA__hdr_protect(ea->f, ea_addr, NULL, H5AC__NO_FLAGS_SET)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTLOAD, FAIL, "unable to load extensible array header");
/* Set the shared array header's file context for this operation */
hdr->f = ea->f;
/* Decrement the reference count on the array header */
/* (don't put in H5EA_hdr_fuse_decr() as the array header may be evicted
* immediately -QAK)
*/
if (H5EA__hdr_decr(ea->hdr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTDEC, FAIL,
"can't decrement reference count on shared array header");
/* Delete array, starting with header (unprotects header) */
if (H5EA__hdr_delete(hdr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTDELETE, FAIL, "unable to delete extensible array");
} /* end if */
else {
/* Decrement the reference count on the array header */
/* (don't put in H5EA_hdr_fuse_decr() as the array header may be evicted
* immediately -QAK)
*/
if (H5EA__hdr_decr(ea->hdr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTDEC, FAIL,
"can't decrement reference count on shared array header");
} /* end else */
} /* end if */
/* Release the extensible array wrapper */
ea = (H5EA_t *)H5FL_FREE(H5EA_t, ea);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA_close() */
/*-------------------------------------------------------------------------
* Function: H5EA_delete
*
* Purpose: Delete an extensible array
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
H5EA_delete(H5F_t *f, haddr_t ea_addr, void *ctx_udata)
{
H5EA_hdr_t *hdr = NULL; /* The fractal heap header information */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Check arguments */
assert(f);
assert(H5_addr_defined(ea_addr));
/* Lock the array header into memory */
if (NULL == (hdr = H5EA__hdr_protect(f, ea_addr, ctx_udata, H5AC__NO_FLAGS_SET)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTPROTECT, FAIL,
"unable to protect extensible array header, address = %llu", (unsigned long long)ea_addr);
/* Check for files using shared array header */
if (hdr->file_rc)
hdr->pending_delete = true;
else {
/* Set the shared array header's file context for this operation */
hdr->f = f;
/* Delete array now, starting with header (unprotects header) */
if (H5EA__hdr_delete(hdr) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTDELETE, FAIL, "unable to delete extensible array");
hdr = NULL;
}
done:
/* Unprotect the header if an error occurred */
if (hdr && H5EA__hdr_unprotect(hdr, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_EARRAY, H5E_CANTUNPROTECT, FAIL, "unable to release extensible array header");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5EA_delete() */
/*-------------------------------------------------------------------------
* Function: H5EA_iterate
*
* Purpose: Iterate over the elements of an extensible array
* (copied and modified from FA_iterate() in H5FA.c)
*
* Return: H5_ITER_CONT/H5_ITER_ERROR
*
*-------------------------------------------------------------------------
*/
int
H5EA_iterate(H5EA_t *ea, H5EA_operator_t op, void *udata)
{
uint8_t *elmt = NULL;
hsize_t u;
int ret_value = H5_ITER_CONT;
FUNC_ENTER_NOAPI(H5_ITER_ERROR)
/* Check arguments */
assert(ea);
assert(op);
assert(udata);
/* Allocate space for a native array element */
if (NULL == (elmt = H5FL_BLK_MALLOC(ea_native_elmt, ea->hdr->cparam.cls->nat_elmt_size)))
HGOTO_ERROR(H5E_EARRAY, H5E_CANTALLOC, H5_ITER_ERROR,
"memory allocation failed for extensible array element");
/* Iterate over all elements in array */
for (u = 0; u < ea->hdr->stats.stored.max_idx_set && ret_value == H5_ITER_CONT; u++) {
/* Get array element */
if (H5EA_get(ea, u, elmt) < 0)
HGOTO_ERROR(H5E_EARRAY, H5E_CANTGET, H5_ITER_ERROR, "unable to delete fixed array");
/* Make callback */
if ((ret_value = (*op)(u, elmt, udata)) < 0) {
HERROR(H5E_EARRAY, H5E_BADITER, "iteration callback error");
break;
}
}
done:
if (elmt)
elmt = H5FL_BLK_FREE(ea_native_elmt, elmt);