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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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: John Mainzer -- 4/19/06
*
* Purpose: This file contains declarations which are normally visible
* only within the H5AC package (just H5AC.c at present).
*
* Source files outside the H5AC package should include
* H5ACprivate.h instead.
*
* The one exception to this rule is testpar/t_cache.c. The
* test code is easier to write if it can look at H5AC_aux_t.
* Indeed, this is the main reason why this file was created.
*
*/
#ifndef H5AC_PACKAGE
#error "Do not include this file outside the H5AC package!"
#endif
#ifndef _H5ACpkg_H
#define _H5ACpkg_H
/* Get package's private header */
#include "H5ACprivate.h" /* Metadata cache */
/* Get needed headers */
#include "H5Cprivate.h" /* Cache */
#include "H5SLprivate.h" /* Skip lists */
#define H5AC_DEBUG_DIRTY_BYTES_CREATION 0
#ifdef H5_HAVE_PARALLEL
/* the following #defined are used to specify the operation required
* at a sync point.
*/
#define H5AC_SYNC_POINT_OP__FLUSH_TO_MIN_CLEAN 0
#define H5AC_SYNC_POINT_OP__FLUSH_CACHE 1
#endif /* H5_HAVE_PARALLEL */
/*-------------------------------------------------------------------------
* It is a bit difficult to set ranges of allowable values on the
* dirty_bytes_threshold field of H5AC_aux_t. The following are
* probably broader than they should be.
*-------------------------------------------------------------------------
*/
#define H5AC__MIN_DIRTY_BYTES_THRESHOLD (int32_t) \
(H5C__MIN_MAX_CACHE_SIZE / 2)
#define H5AC__DEFAULT_DIRTY_BYTES_THRESHOLD (256 * 1024)
#define H5AC__MAX_DIRTY_BYTES_THRESHOLD (int32_t) \
(H5C__MAX_MAX_CACHE_SIZE / 4)
/****************************************************************************
*
* structure H5AC_aux_t
*
* While H5AC has become a wrapper for the cache implemented in H5C.c, there
* are some features of the metadata cache that are specific to it, and which
* therefore do not belong in the more generic H5C cache code.
*
* In particular, there is the matter of synchronizing writes from the
* metadata cache to disk in the PHDF5 case.
*
* Prior to this update, the presumption was that all metadata caches would
* write the same data at the same time since all operations modifying
* metadata must be performed collectively. Given this assumption, it was
* safe to allow only the writes from process 0 to actually make it to disk,
* while metadata writes from all other processes were discarded.
*
* Unfortunately, this presumption is in error as operations that read
* metadata need not be collective, but can change the location of dirty
* entries in the metadata cache LRU lists. This can result in the same
* metadata write operation triggering writes from the metadata caches on
* some processes, but not all (causing a hang), or in different sets of
* entries being written from different caches (potentially resulting in
* metadata corruption in the file).
*
* To deal with this issue, I decided to apply a paradigm shift to the way
* metadata is written to disk.
*
* With this set of changes, only the metadata cache on process 0 is able
* to write metadata to disk, although metadata caches on all other
* processes can read metadata from disk as before.
*
* To keep all the other caches from getting plugged up with dirty metadata,
* process 0 periodically broadcasts a list of entries that it has flushed
* since that last notice, and which are currently clean. The other caches
* mark these entries as clean as well, which allows them to evict the
* entries as needed.
*
* One obvious problem in this approach is synchronizing the broadcasts
* and receptions, as different caches may see different amounts of
* activity.
*
* The current solution is for the caches to track the number of bytes
* of newly generated dirty metadata, and to broadcast and receive
* whenever this value exceeds some user specified threshold.
*
* Maintaining this count is easy for all processes not on process 0 --
* all that is necessary is to add the size of the entry to the total
* whenever there is an insertion, a move of a previously clean entry,
* or whever a previously clean entry is marked dirty in an unprotect.
*
* On process 0, we have to be careful not to count dirty bytes twice.
* If an entry is marked dirty, flushed, and marked dirty again, all
* within a single reporting period, it only th first marking should
* be added to the dirty bytes generated tally, as that is all that
* the other processes will see.
*
* At present, this structure exists to maintain the fields needed to
* implement the above scheme, and thus is only used in the parallel
* case. However, other uses may arise in the future.
*
* Instance of this structure are associated with metadata caches via
* the aux_ptr field of H5C_t (see H5Cpkg.h). The H5AC code is
* responsible for allocating, maintaining, and discarding instances
* of H5AC_aux_t.
*
* The remainder of this header comments documents the individual fields
* of the structure.
*
* JRM - 6/27/05
*
* magic: Unsigned 32 bit integer always set to
* H5AC__H5AC_AUX_T_MAGIC. This field is used to validate
* pointers to instances of H5AC_aux_t.
*
* mpi_comm: MPI communicator associated with the file for which the
* cache has been created.
*
* mpi_rank: MPI rank of this process within mpi_comm.
*
* mpi_size: Number of processes in mpi_comm.
*
* write_permitted: Boolean flag used to control whether the cache
* is permitted to write to file.
*
* dirty_bytes_threshold: Integer field containing the dirty bytes
* generation threashold. Whenever dirty byte creation
* exceeds this value, the metadata cache on process 0
* broadcasts a list of the entries it has flushed since
* the last broadcast (or since the beginning of execution)
* and which are currently clean (if they are still in the
* cache)
*
* Similarly, metadata caches on processes other than process
* 0 will attempt to receive a list of clean entries whenever
* the threshold is exceeded.
*
* dirty_bytes: Integer field containing the number of bytes of dirty
* metadata generated since the beginning of the computation,
* or (more typically) since the last clean entries list
* broadcast. This field is reset to zero after each such
* broadcast.
*
* metadata_write_strategy: Integer code indicating how we will be
* writing the metadata. In the first incarnation of
* this code, all writes were done from process 0. This
* field exists to facilitate experiments with other
* strategies.
*
* dirty_bytes_propagations: This field only exists when the
* H5AC_DEBUG_DIRTY_BYTES_CREATION #define is TRUE.
*
* It is used to track the number of times the cleaned list
* has been propagated from process 0 to the other
* processes.
*
* unprotect_dirty_bytes: This field only exists when the
* H5AC_DEBUG_DIRTY_BYTES_CREATION #define is TRUE.
*
* It is used to track the number of dirty bytes created
* via unprotect operations since the last time the cleaned
* list was propagated.
*
* unprotect_dirty_bytes_updates: This field only exists when the
* H5AC_DEBUG_DIRTY_BYTES_CREATION #define is TRUE.
*
* It is used to track the number of times dirty bytes have
* been created via unprotect operations since the last time
* the cleaned list was propagated.
*
* insert_dirty_bytes: This field only exists when the
* H5AC_DEBUG_DIRTY_BYTES_CREATION #define is TRUE.
*
* It is used to track the number of dirty bytes created
* via insert operations since the last time the cleaned
* list was propagated.
*
* insert_dirty_bytes_updates: This field only exists when the
* H5AC_DEBUG_DIRTY_BYTES_CREATION #define is TRUE.
*
* It is used to track the number of times dirty bytes have
* been created via insert operations since the last time
* the cleaned list was propagated.
*
* move_dirty_bytes: This field only exists when the
* H5AC_DEBUG_DIRTY_BYTES_CREATION #define is TRUE.
*
* It is used to track the number of dirty bytes created
* via move operations since the last time the cleaned
* list was propagated.
*
* move_dirty_bytes_updates: This field only exists when the
* H5AC_DEBUG_DIRTY_BYTES_CREATION #define is TRUE.
*
* It is used to track the number of times dirty bytes have
* been created via move operations since the last time
* the cleaned list was propagated.
*
* Things have changed a bit since the following four fields were defined.
* If metadata_write_strategy is H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY,
* all comments hold as before -- with the caviate that pending further
* coding, the process 0 metadata cache is forbidden to flush entries outside
* of a sync point.
*
* However, for different metadata write strategies, these fields are used
* only to maintain the correct dirty byte count on process zero -- and in
* most if not all cases, this is redundant, as process zero will be barred
* from flushing entries outside of a sync point.
*
* JRM -- 3/16/10
*
* d_slist_ptr: Pointer to an instance of H5SL_t used to maintain a list
* of entries that have been dirtied since the last time they
* were listed in a clean entries broadcast. This list is
* only maintained by the metadata cache on process 0 -- it
* it used to maintain a view of the dirty entries as seen
* by the other caches, so as to keep the dirty bytes count
* in synchronization with them.
*
* Thus on process 0, the dirty_bytes count is incremented
* only if either
*
* 1) an entry is inserted in the metadata cache, or
*
* 2) a previously clean entry is moved, and it does not
* already appear in the dirty entry list, or
*
* 3) a previously clean entry is unprotected with the
* dirtied flag set and the entry does not already appear
* in the dirty entry list.
*
* Entries are added to the dirty entry list whever they cause
* the dirty bytes count to be increased. They are removed
* when they appear in a clean entries broadcast. Note that
* moves must be reflected in the dirty entry list.
*
* To reitterate, this field is only used on process 0 -- it
* should be NULL on all other processes.
*
* d_slist_len: Integer field containing the number of entries in the
* dirty entry list. This field should always contain the
* value 0 on all processes other than process 0. It exists
* primarily for sanity checking.
*
* c_slist_ptr: Pointer to an instance of H5SL_t used to maintain a list
* of entries that were dirty, have been flushed
* to disk since the last clean entries broadcast, and are
* still clean. Since only process 0 can write to disk, this
* list only exists on process 0.
*
* In essence, this slist is used to assemble the contents of
* the next clean entries broadcast. The list emptied after
* each broadcast.
*
* c_slist_len: Integer field containing the number of entries in the clean
* entries list (*c_slist_ptr). This field should always
* contain the value 0 on all processes other than process 0.
* It exists primarily for sanity checking.
*
* The following two fields are used only when metadata_write_strategy
* is H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED.
*
* candidate_slist_ptr: Pointer to an instance of H5SL_t used by process 0
* to construct a list of entries to be flushed at this sync
* point. This list is then broadcast to the other processes,
* which then either flush or mark clean all entries on it.
*
* candidate_slist_len: Integer field containing the number of entries on the
* candidate list. It exists primarily for sanity checking.
*
* write_done: In the parallel test bed, it is necessary to ensure that
* all writes to the server process from cache 0 complete
* before it enters the barrier call with the other caches.
*
* The write_done callback allows t_cache to do this without
* requiring an ACK on each write. Since these ACKs greatly
* increase the run time on some platforms, this is a
* significant optimization.
*
* This field must be set to NULL when the callback is not
* needed.
*
* Note: This field has been extended for use by all processes
* with the addition of support for the distributed
* metadata write strategy.
* JRM -- 5/9/10
*
* sync_point_done: In the parallel test bed, it is necessary to verify
* that the expected writes, and only the expected writes,
* have taken place at the end of each sync point.
*
* The sync_point_done callback allows t_cache to perform
* this verification. The field is set to NULL when the
* callback is not needed.
*
****************************************************************************/
#ifdef H5_HAVE_PARALLEL
#define H5AC__H5AC_AUX_T_MAGIC (unsigned)0x00D0A01
typedef struct H5AC_aux_t
{
uint32_t magic;
MPI_Comm mpi_comm;
int mpi_rank;
int mpi_size;
hbool_t write_permitted;
int32_t dirty_bytes_threshold;
int32_t dirty_bytes;
int32_t metadata_write_strategy;
#if H5AC_DEBUG_DIRTY_BYTES_CREATION
int32_t dirty_bytes_propagations;
int32_t unprotect_dirty_bytes;
int32_t unprotect_dirty_bytes_updates;
int32_t insert_dirty_bytes;
int32_t insert_dirty_bytes_updates;
int32_t move_dirty_bytes;
int32_t move_dirty_bytes_updates;
#endif /* H5AC_DEBUG_DIRTY_BYTES_CREATION */
H5SL_t * d_slist_ptr;
int32_t d_slist_len;
H5SL_t * c_slist_ptr;
int32_t c_slist_len;
H5SL_t * candidate_slist_ptr;
int32_t candidate_slist_len;
void (* write_done)(void);
void (* sync_point_done)(int num_writes,
haddr_t * written_entries_tbl);
} H5AC_aux_t; /* struct H5AC_aux_t */
#endif /* H5_HAVE_PARALLEL */
#endif /* _H5ACpkg_H */
|