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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5Fio.c
* Jan 10 2008
* Quincey Koziol <koziol@hdfgroup.org>
*
* Purpose: File I/O routines.
*
*-------------------------------------------------------------------------
*/
/****************/
/* Module Setup */
/****************/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Package Typedefs */
/********************/
/********************/
/* Local Prototypes */
/********************/
/*********************/
/* Package Variables */
/*********************/
/*****************************/
/* Library Private Variables */
/*****************************/
/*******************/
/* Local Variables */
/*******************/
/*-------------------------------------------------------------------------
* Function: H5F_block_read
*
* Purpose: Reads some data from a file/server/etc into a buffer.
* The data is contiguous. The address is relative to the base
* address for the file.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* matzke@llnl.gov
* Jul 10 1997
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_block_read(const H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size,
hid_t dxpl_id, void *buf/*out*/)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
HDassert(f);
HDassert(f->shared);
HDassert(buf);
HDassert(H5F_addr_defined(addr));
/* Check for attempting I/O on 'temporary' file address */
if(H5F_addr_le(f->shared->tmp_addr, (addr + size)))
HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")
/* Pass through metadata accumulator layer */
if(H5F_accum_read(f, dxpl_id, type, addr, size, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "read through metadata accumulator failed")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_block_read() */
/*-------------------------------------------------------------------------
* Function: H5F_block_write
*
* Purpose: Writes some data from memory to a file/server/etc. The
* data is contiguous. The address is relative to the base
* address.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* matzke@llnl.gov
* Jul 10 1997
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_block_write(const H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size,
hid_t dxpl_id, const void *buf)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
#ifdef QAK
HDfprintf(stderr, "%s: write to addr = %a, size = %Zu\n", FUNC, addr, size);
#endif /* QAK */
HDassert(f);
HDassert(f->shared);
HDassert(f->intent & H5F_ACC_RDWR);
HDassert(buf);
HDassert(H5F_addr_defined(addr));
/* Check for attempting I/O on 'temporary' file address */
if(H5F_addr_le(f->shared->tmp_addr, (addr + size)))
HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")
/* Pass through metadata accumulator layer */
if(H5F_accum_write(f, dxpl_id, type, addr, size, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write through metadata accumulator failed")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_block_write() */
/*-------------------------------------------------------------------------
* Function: H5F_flush_tagged_metadata
*
* Purpose: Flushes metadata with specified tag in the metadata cache
* to disk.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Mike McGreevy
* September 9, 2010
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_flush_tagged_metadata(H5F_t * f, haddr_t tag, hid_t dxpl_id)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Use tag to search for and flush associated metadata */
if(H5AC_flush_tagged_metadata(f, tag, dxpl_id)<0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata")
/* Flush out the metadata accumulator */
if(H5F_accum_flush(f, dxpl_id) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush metadata accumulator")
/* Flush file buffers to disk. */
if(H5FD_flush(f->shared->lf, dxpl_id, FALSE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "low level flush failed")
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5F_flush_tagged_metadata */
/*-------------------------------------------------------------------------
* Function: H5F_evict_tagged_metadata
*
* Purpose: Evicts metadata from the cache with specified tag.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Mike McGreevy
* September 9, 2010
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_evict_tagged_metadata(H5F_t * f, haddr_t tag, hid_t dxpl_id)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Unpin the superblock, as this will be marked for eviction and it can't
be pinned. */
if(H5AC_unpin_entry(f->shared->sblock) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTUNPIN, FAIL, "unable to unpin superblock")
f->shared->sblock = NULL;
/* Evict the object's metadata */
if(H5AC_evict_tagged_metadata(f, tag, dxpl_id)<0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTEXPUNGE, FAIL, "unable to evict tagged metadata")
/* Re-read the superblock. */
if (H5F_super_read(f, dxpl_id) < 0)
HGOTO_ERROR(H5E_FILE, H5E_READERROR, FAIL, "unable to read superblock")
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5F_evict_tagged_metadata */
/*-------------------------------------------------------------------------
* Function: H5F_get_checksums
*
* Purpose: Decode checksum stored in the buffer
* Calculate checksum for the data in the buffer
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Vailin Choi; Sept 2013
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_get_checksums(uint8_t *buf, size_t chk_size, uint32_t *s_chksum/*out*/, uint32_t *c_chksum/*out*/)
{
uint32_t stored_chksum; /* Stored metadata checksum value */
uint32_t computed_chksum; /* Computed metadata checksum value */
const uint8_t *chk_p; /* Pointer into raw data buffer */
FUNC_ENTER_NOAPI_NOINIT_NOERR
/* Check arguments */
HDassert(buf);
HDassert(chk_size);
/* Compute checksum for the buffer */
computed_chksum = H5_checksum_metadata(buf, chk_size - H5_SIZEOF_CHKSUM, 0);
/* Offset to the checksum in the buffer */
chk_p = buf + chk_size - H5_SIZEOF_CHKSUM;
/* Decode the checksum stored in the buffer */
UINT32DECODE(chk_p, stored_chksum);
/* Return the stored checksum */
if(s_chksum)
*s_chksum = stored_chksum;
/* Return the computed checksum */
if(c_chksum)
*c_chksum = computed_chksum;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5F_get_chksums() */
/*-------------------------------------------------------------------------
* Function: H5F_read_check_meatadata
*
* Purpose: Attempts to read and validate a piece of meatadata that has
* checksum as follows:
* a) read the piece of metadata
* b) calculate checksum for the buffer of metadata
* c) decode the checksum stored in the buffer of metadata
d) compare the computed checksum with its stored checksum
* The library will perform (a) to (d) above for "f->read_attempts"
* times or until the checksum comparison in (d) passes.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Vailin Choi; Sept 2013
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_read_check_metadata(const H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t read_size, size_t chk_size,
hid_t dxpl_id, uint8_t *buf/*out*/, uint32_t *chksum/*out*/)
{
size_t tries, max_tries;
uint32_t stored_chksum; /* Stored metadata checksum value */
uint32_t computed_chksum; /* Computed metadata checksum value */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Get the # of read attempts */
max_tries = tries = f->read_attempts;
do {
/* Read header from disk */
if(H5F_block_read(f, type, addr, read_size, dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read metadata")
/* Get stored and computed checksums */
H5F_get_checksums(buf, chk_size, &stored_chksum, &computed_chksum);
/* Verify checksum */
if(stored_chksum == computed_chksum)
break;
} while(--tries);
if(tries == 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "incorrect metadatda checksum after all read attempts (%u) for %u bytes:c_chksum=%u, s_chkum=%u",
max_tries, chk_size, computed_chksum, stored_chksum)
else if((max_tries - tries + 1) > 1)
HDfprintf(stderr, "%s: SUCCESS after %u attempts; type=%u\n", FUNC, max_tries - tries + 1, type);
/* Return the computed checksum */
if(chksum)
*chksum = computed_chksum;
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5F_read_check_metadata */
|
