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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5HLprivate.h" /* Local heaps */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Local Prototypes */
/********************/
/*********************/
/* Package Variables */
/*********************/
/*****************************/
/* Library Private Variables */
/*****************************/
/*******************/
/* Local Variables */
/*******************/
/*-------------------------------------------------------------------------
* Function: H5D_layout_set_io_ops
*
* Purpose: Set the I/O operation function pointers for a dataset,
* according to the dataset's layout
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, March 20, 2008
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_layout_set_io_ops(const H5D_t *dataset)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
/* check args */
HDassert(dataset);
/* Set the I/O functions for each layout type */
switch(dataset->shared->layout.type) {
case H5D_CONTIGUOUS:
if(dataset->shared->dcpl_cache.efl.nused > 0)
dataset->shared->layout.ops = H5D_LOPS_EFL;
else
dataset->shared->layout.ops = H5D_LOPS_CONTIG;
break;
case H5D_CHUNKED:
dataset->shared->layout.ops = H5D_LOPS_CHUNK;
/* Set the chunk operations */
/* (Only "B-tree" indexing type currently supported) */
dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BTREE;
break;
case H5D_COMPACT:
dataset->shared->layout.ops = H5D_LOPS_COMPACT;
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method")
} /* end switch */ /*lint !e788 All appropriate cases are covered */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_layout_set_io_ops() */
/*-------------------------------------------------------------------------
* Function: H5D_layout_meta_size
*
* Purpose: Returns the size of the raw message in bytes except raw data
* part for compact dataset. This function doesn't take into
* account message alignment.
*
* Return: Success: Message data size in bytes
* Failure: 0
*
* Programmer: Raymond Lu
* August 14, 2002
*
*-------------------------------------------------------------------------
*/
size_t
H5D_layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t include_compact_data)
{
size_t ret_value;
FUNC_ENTER_NOAPI_NOINIT
/* check args */
HDassert(f);
HDassert(layout);
ret_value = 1 + /* Version number */
1; /* layout class type */
switch(layout->type) {
case H5D_COMPACT:
/* Size of raw data */
ret_value += 2;
if(include_compact_data)
ret_value += layout->storage.u.compact.size;/* data for compact dataset */
break;
case H5D_CONTIGUOUS:
ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */
ret_value += H5F_SIZEOF_SIZE(f); /* Length of data */
break;
case H5D_CHUNKED:
/* Number of dimensions (1 byte) */
HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
ret_value++;
/* Dimension sizes */
ret_value += layout->u.chunk.ndims * 4;
/* B-tree address */
ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, 0, "Invalid layout class")
} /* end switch */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_layout_meta_size() */
/*-------------------------------------------------------------------------
* Function: H5D_layout_oh_create
*
* Purpose: Create layout/pline/efl information for dataset
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Monday, July 27, 2009
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
hid_t dapl_id)
{
H5O_layout_t *layout; /* Dataset's layout information */
const H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */
hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
/* Sanity checking */
HDassert(file);
HDassert(oh);
HDassert(dset);
/* Set some local variables, for convenience */
layout = &dset->shared->layout;
fill_prop = &dset->shared->dcpl_cache.fill;
/* Update the filters message, if this is a chunked dataset */
if(layout->type == H5D_CHUNKED) {
H5O_pline_t *pline; /* Dataset's I/O pipeline information */
pline = &dset->shared->dcpl_cache.pline;
if(pline->nused > 0 && H5O_msg_append_oh(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message")
} /* end if */
/* Initialize the layout information for the new dataset */
if(dset->shared->layout.ops->init && (dset->shared->layout.ops->init)(file, dxpl_id, dset, dapl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize layout information")
/* Indicate that the layout information was initialized */
layout_init = TRUE;
/*
* Allocate storage if space allocate time is early; otherwise delay
* allocation until later.
*/
if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY)
if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
/* Update external storage message, if it's used */
if(dset->shared->dcpl_cache.efl.nused > 0) {
H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */
H5HL_t *heap; /* Pointer to local heap for EFL file names */
size_t heap_size = H5HL_ALIGN(1);
size_t u;
/* Determine size of heap needed to stored the file names */
for(u = 0; u < efl->nused; ++u)
heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1);
/* Create the heap for the EFL file names */
if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap")
/* Pin the heap down in memory */
if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect EFL file name heap")
/* Insert "empty" name first */
if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) {
H5HL_unprotect(heap);
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
} /* end if */
for(u = 0; u < efl->nused; ++u) {
size_t offset; /* Offset of file name in heap */
/* Insert file name into heap */
if((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap,
HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) {
H5HL_unprotect(heap);
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
} /* end if */
/* Store EFL file name offset */
HDassert(0 == efl->slot[u].name_offset);
efl->slot[u].name_offset = offset;
} /* end for */
/* Release the heap */
if(H5HL_unprotect(heap) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect EFL file name heap")
heap = NULL;
/* Insert EFL message into dataset object header */
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message")
} /* end if */
/* Create layout message */
/* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */
/* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout")
done:
/* 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_layout_oh_create() */
/*-------------------------------------------------------------------------
* Function: H5D_layout_oh_read
*
* Purpose: Read layout/pline/efl information for dataset
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Monday, July 27, 2009
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t *plist)
{
htri_t msg_exists; /* Whether a particular type of message exists */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
/* Sanity checking */
HDassert(dataset);
HDassert(plist);
/* Get the optional filters message */
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_PLINE_ID, dxpl_id)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
if(msg_exists) {
/* Retrieve the I/O pipeline message */
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline, dxpl_id))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
/* Set the I/O pipeline info in the property list */
if(H5P_set(plist, H5O_CRT_PIPELINE_NAME, &dataset->shared->dcpl_cache.pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline")
} /* end if */
/*
* Get the raw data layout info. It's actually stored in two locations:
* the storage message of the dataset (dataset->storage) and certain
* values are copied to the dataset create plist so the user can query
* them.
*/
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message")
/* Check for external file list message (which might not exist) */
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
if(msg_exists) {
/* Retrieve the EFL message */
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
/* Set the EFL info in the property list */
if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list")
/* Set the dataset's I/O operations */
dataset->shared->layout.ops = H5D_LOPS_EFL;
} /* end if */
/* Sanity check that the layout operations are set up */
HDassert(dataset->shared->layout.ops);
/* Adjust chunk dimensions to omit datatype size (in last dimension) for creation property */
if(H5D_CHUNKED == dataset->shared->layout.type)
dataset->shared->layout.u.chunk.ndims--;
/* Copy layout to the DCPL */
if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout")
/* Adjust chunk dimensions back again (*sigh*) */
if(H5D_CHUNKED == dataset->shared->layout.type)
dataset->shared->layout.u.chunk.ndims++;
switch(dataset->shared->layout.type) {
case H5D_CONTIGUOUS:
{
hsize_t tmp_size; /* Temporary holder for raw data size */
size_t tmp_sieve_buf_size; /* Temporary holder for sieve buffer size */
/* Compute the size of the contiguous storage for versions of the
* layout message less than version 3 because versions 1 & 2 would
* truncate the dimension sizes to 32-bits of information. - QAK 5/26/04
*/
if(dataset->shared->layout.version < 3) {
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 */
/* Retrieve the number of elements in the dataspace */
if((snelmts = H5S_GET_EXTENT_NPOINTS(dataset->shared->space)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace")
nelmts = (hsize_t)snelmts;
/* Get the datatype's size */
if(0 == (dt_size = H5T_GET_SIZE(dataset->shared->type)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype")
/* Compute the size of the dataset's contiguous storage */
tmp_size = nelmts * dt_size;
/* Check for overflow during multiplication */
if(nelmts != (tmp_size / dt_size))
HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed")
/* Assign the dataset's contiguous storage size */
dataset->shared->layout.storage.u.contig.size = tmp_size;
} else
tmp_size = dataset->shared->layout.storage.u.contig.size;
/* Get the sieve buffer size for the file */
tmp_sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->oloc.file);
/* Adjust the sieve buffer size to the smaller one between the dataset size and the buffer size
* from the file access property. (SLU - 2012/3/30) */
if(tmp_size < tmp_sieve_buf_size)
dataset->shared->cache.contig.sieve_buf_size = tmp_size;
else
dataset->shared->cache.contig.sieve_buf_size = tmp_sieve_buf_size;
}
break;
case H5D_CHUNKED:
/* Initialize the chunk cache for the dataset */
if(H5D_chunk_init(dataset->oloc.file, dxpl_id, dataset, dapl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache")
break;
case H5D_COMPACT:
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method")
} /* end switch */ /*lint !e788 All appropriate cases are covered */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_layout_oh_read() */
/*-------------------------------------------------------------------------
* Function: H5D_layout_oh_write
*
* Purpose: Write layout/pline/efl information for dataset
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Monday, July 27, 2009
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh, unsigned update_flags)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
/* Sanity checking */
HDassert(dataset);
HDassert(oh);
/* Write the layout message to the dataset's header */
if(H5O_msg_write_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_flags, &dataset->shared->layout) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout message")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_layout_oh_write() */
|