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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Quincey Koziol
* Thursday, September 30, 2004
*
* Purpose: Dataspace I/O functions.
*/
/****************/
/* 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 "H5FLprivate.h" /* Free Lists */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Local Prototypes */
/********************/
static herr_t H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts,
const H5S_t *file_space, const H5S_t *mem_space);
/*********************/
/* Package Variables */
/*********************/
/*******************/
/* Local Variables */
/*******************/
/* Declare a free list to manage sequences of size_t */
H5FL_SEQ_DEFINE(size_t);
/* Declare a free list to manage sequences of hsize_t */
H5FL_SEQ_DEFINE(hsize_t);
/*-------------------------------------------------------------------------
* Function: H5D__select_io
*
* Purpose: Perform I/O directly from application memory and a file
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 27, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, const H5S_t *file_space,
const H5S_t *mem_space)
{
H5S_sel_iter_t mem_iter; /* Memory selection iteration info */
hbool_t mem_iter_init = 0; /* Memory selection iteration info has been initialized */
H5S_sel_iter_t file_iter; /* File selection iteration info */
hbool_t file_iter_init = 0; /* File selection iteration info has been initialized */
hsize_t _mem_off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets in memory */
hsize_t * mem_off = NULL; /* Pointer to sequence offsets in memory */
hsize_t _file_off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets in the file */
hsize_t * file_off = NULL; /* Pointer to sequence offsets in the file */
size_t _mem_len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths in memory */
size_t * mem_len = NULL; /* Pointer to sequence lengths in memory */
size_t _file_len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths in the file */
size_t * file_len = NULL; /* Pointer to sequence lengths in the file */
size_t curr_mem_seq; /* Current memory sequence to operate on */
size_t curr_file_seq; /* Current file sequence to operate on */
size_t mem_nseq; /* Number of sequences generated in the file */
size_t file_nseq; /* Number of sequences generated in memory */
ssize_t tmp_file_len; /* Temporary number of bytes in file sequence */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Check args */
HDassert(io_info);
HDassert(io_info->dset);
HDassert(io_info->store);
HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER));
HDassert(io_info->u.rbuf);
/* Allocate the vector I/O arrays */
if (io_info->dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
if (NULL == (mem_len = H5FL_SEQ_MALLOC(size_t, io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array")
if (NULL == (mem_off = H5FL_SEQ_MALLOC(hsize_t, io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array")
if (NULL == (file_len = H5FL_SEQ_MALLOC(size_t, io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array")
if (NULL == (file_off = H5FL_SEQ_MALLOC(hsize_t, io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array")
} /* end if */
else {
mem_len = _mem_len;
mem_off = _mem_off;
file_len = _file_len;
file_off = _file_off;
} /* end else */
/* Check for only one element in selection */
if (nelmts == 1) {
/* Get offset of first element in selections */
if (H5S_SELECT_OFFSET(file_space, file_off) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve file selection offset")
if (H5S_SELECT_OFFSET(mem_space, mem_off) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve memory selection offset")
/* Set up necessary information for I/O operation */
file_nseq = mem_nseq = 1;
curr_mem_seq = curr_file_seq = 0;
*file_off *= elmt_size;
*mem_off *= elmt_size;
*file_len = *mem_len = elmt_size;
/* Perform I/O on memory and file sequences */
if (io_info->op_type == H5D_IO_OP_READ) {
if ((tmp_file_len =
(*io_info->layout_ops.readvv)(io_info, file_nseq, &curr_file_seq, file_len, file_off,
mem_nseq, &curr_mem_seq, mem_len, mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error")
} /* end if */
else {
HDassert(io_info->op_type == H5D_IO_OP_WRITE);
if ((tmp_file_len =
(*io_info->layout_ops.writevv)(io_info, file_nseq, &curr_file_seq, file_len, file_off,
mem_nseq, &curr_mem_seq, mem_len, mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
} /* end else */
/* Decrement number of elements left to process */
HDassert(((size_t)tmp_file_len % elmt_size) == 0);
} /* end if */
else {
size_t mem_nelem; /* Number of elements used in memory sequences */
size_t file_nelem; /* Number of elements used in file sequences */
/* Initialize file iterator */
if (H5S_select_iter_init(&file_iter, file_space, elmt_size) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
file_iter_init = 1; /* File selection iteration info has been initialized */
/* Initialize memory iterator */
if (H5S_select_iter_init(&mem_iter, mem_space, elmt_size) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
mem_iter_init = 1; /* Memory selection iteration info has been initialized */
/* Initialize sequence counts */
curr_mem_seq = curr_file_seq = 0;
mem_nseq = file_nseq = 0;
/* Loop, until all bytes are processed */
while (nelmts > 0) {
/* Check if more file sequences are needed */
if (curr_file_seq >= file_nseq) {
/* Get sequences for file selection */
if (H5S_SELECT_GET_SEQ_LIST(file_space, H5S_GET_SEQ_LIST_SORTED, &file_iter,
io_info->dxpl_cache->vec_size, nelmts, &file_nseq, &file_nelem,
file_off, file_len) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
/* Start at the beginning of the sequences again */
curr_file_seq = 0;
} /* end if */
/* Check if more memory sequences are needed */
if (curr_mem_seq >= mem_nseq) {
/* Get sequences for memory selection */
if (H5S_SELECT_GET_SEQ_LIST(mem_space, 0, &mem_iter, io_info->dxpl_cache->vec_size, nelmts,
&mem_nseq, &mem_nelem, mem_off, mem_len) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
/* Start at the beginning of the sequences again */
curr_mem_seq = 0;
} /* end if */
/* Perform I/O on memory and file sequences */
if (io_info->op_type == H5D_IO_OP_READ) {
if ((tmp_file_len =
(*io_info->layout_ops.readvv)(io_info, file_nseq, &curr_file_seq, file_len, file_off,
mem_nseq, &curr_mem_seq, mem_len, mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error")
} /* end if */
else {
HDassert(io_info->op_type == H5D_IO_OP_WRITE);
if ((tmp_file_len = (*io_info->layout_ops.writevv)(io_info, file_nseq, &curr_file_seq,
file_len, file_off, mem_nseq,
&curr_mem_seq, mem_len, mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
} /* end else */
/* Decrement number of elements left to process */
HDassert(((size_t)tmp_file_len % elmt_size) == 0);
if (elmt_size == 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "Resulted in division by zero")
nelmts -= ((size_t)tmp_file_len / elmt_size);
} /* end while */
} /* end else */
done:
/* Release file selection iterator */
if (file_iter_init)
if (H5S_SELECT_ITER_RELEASE(&file_iter) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
/* Release memory selection iterator */
if (mem_iter_init)
if (H5S_SELECT_ITER_RELEASE(&mem_iter) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
/* Release vector arrays, if allocated */
if (file_len && file_len != _file_len)
file_len = H5FL_SEQ_FREE(size_t, file_len);
if (file_off && file_off != _file_off)
file_off = H5FL_SEQ_FREE(hsize_t, file_off);
if (mem_len && mem_len != _mem_len)
mem_len = H5FL_SEQ_FREE(size_t, mem_len);
if (mem_off && mem_off != _mem_off)
mem_off = H5FL_SEQ_FREE(hsize_t, mem_off);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__select_io() */
/*-------------------------------------------------------------------------
* Function: H5D__select_read
*
* Purpose: Reads directly from file into application memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, July 23, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__select_read(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts,
const H5S_t *file_space, const H5S_t *mem_space)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Call generic selection operation */
H5_CHECK_OVERFLOW(nelmts, hsize_t, size_t);
if (H5D__select_io(io_info, type_info->src_type_size, (size_t)nelmts, file_space, mem_space) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__select_read() */
/*-------------------------------------------------------------------------
* Function: H5D__select_write
*
* Purpose: Writes directly from application memory into a file
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, July 23, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__select_write(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts,
const H5S_t *file_space, const H5S_t *mem_space)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Call generic selection operation */
H5_CHECK_OVERFLOW(nelmts, hsize_t, size_t);
if (H5D__select_io(io_info, type_info->dst_type_size, (size_t)nelmts, file_space, mem_space) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__select_write() */
|