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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#define H5F_PACKAGE
#include "hdf5.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "H5private.h"
#include "H5Iprivate.h"
#include <unistd.h>
#include <fcntl.h>
#include <string.h>
#include <stdlib.h>
#include "H5Fpkg.h"
const char * progname="h5recover";
int d_status;
/* Define valid command line options. */
static const char *s_opts = "hb:j:vnV";
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
{ "backup", require_arg, 'b' },
{ "journal", require_arg, 'j' },
{ "verbose", no_arg, 'v' },
{ "nocopy", no_arg, 'n' },
{ "version", no_arg, 'V' },
{ NULL, 0, '\0' }
};
/*-------------------------------------------------------------------------
* Function: usage()
*
* Purpose: Prints a usage message and then returns.
*
* Return: void
*
* Programmer: Mike McGreevy <mcgreevy@hdfgroup.org>
* Monday, March 10, 2008
*
*-------------------------------------------------------------------------
*/
static void
usage (void)
{
fprintf(stdout, "\
usage: h5recover [OPTIONS] [OBJECTS] [HDF5_FILE]\n\
OBJECTS\n\
-j, --journal [JOURNAL_FILE] journal file name\n\
OPTIONS\n\
-b, --backup [BACKUP_NAME] Specify a name for the backup copy\n\
of the HDF5 file.\n\
default = '[HDF5_FILE].backup'\n\
-n, --nocopy Do not create a backup copy.\n\
-h, --help Print a usage message and exit\n\
-v, --verbose Generate more verbose output\n\
-V, --version Print version number and exit\n");
}
/*-------------------------------------------------------------------------
* Function: leave
*
* Purpose: Shutdown MPI & HDF5 and call exit()
*
* Return: Does not return
*
* Programmer: Quincey Koziol
* Saturday, 31. January 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
leave(int ret)
{
h5tools_close();
exit(ret);
}
/*-------------------------------------------------------------------------
* Function: file_copy()
*
* Purpose: Makes a back up copy of a file.
*
* Return: 0 on success
*
* Programmer: Mike McGreevy <mcgreevy@hdfgroup.org>
* Monday, March 10, 2008
*
*-------------------------------------------------------------------------
*/
static int
file_copy(char * file_from, char * file_to)
{
FILE * from;
FILE * to;
char ch;
/* open source file */
if((from = fopen(file_from, "rb")) == NULL) {
error_msg(progname, "Could not open source file\n");
leave( EXIT_FAILURE );
}
/* open destination file */
if((to = fopen(file_to, "wb")) == NULL) {
error_msg(progname, "Could not open destination file\n");
leave( EXIT_FAILURE );
}
/* copy the file */
while( !feof(from) ) {
ch = fgetc(from);
if( ferror(from) ) {
error_msg(progname, "Error reading source file\n");
leave( EXIT_FAILURE );
} /* end if */
if( !feof(from) )
fputc(ch, to);
if( ferror(to) ) {
error_msg(progname, "Error writing destination file\n");
leave( EXIT_FAILURE );
} /* end if */
} /* end while */
/* close source file */
if( fclose(from) == EOF ) {
error_msg(progname, "Error closing source file\n");
leave( EXIT_FAILURE );
} /* end if */
/* close destination file */
if( fclose(to) == EOF ) {
error_msg(progname, "Error closing destination file\n");
leave( EXIT_FAILURE );
} /* end if */
return 0;
}
/*-------------------------------------------------------------------------
* Function: main()
*
* Purpose: main h5recover program.
*
* Programmer: Mike McGreevy <mcgreevy@hdfgroup.org>
* Monday, March 10, 2008
*
*-------------------------------------------------------------------------
*/
int
main (int argc, const char *argv[])
{
/* ===================== */
/* Variable Declarations */
/* ===================== */
hid_t fid = -1; /* file id number */
hid_t fapl = -1; /* file access property list */
char * file_name = NULL; /* file name */
char * file_name_backup = NULL; /* name of backup file */
char * journal_name = NULL; /* journal name */
unsigned verbose = 0; /* verbose boolean */
int opt; /* option number */
FILE * journal_fp; /* journal file pointer */
int hdf5_fd; /* hdf5 file descriptor */
char * readback; /* array to read into from journal */
char * last_trans_msg; /* array to keep last end_trans msg */
int last_trans_found = 0; /* bool */
char * tok[11]; /* string tokens */
int i; /* iterator */
off_t address; /* address to write to */
haddr_t eoa; /* end of address of file */
uint8_t * body; /* body of journal entry */
size_t size; /* size of journal entry body */
size_t max_size; /* maximum size of journal entry body */
char * p; /* pointer */
hbool_t custom_name = 0; /* bool indicating custom backup name */
hbool_t no_copy = 0; /* bool indicating not to make backup */
H5AC_cache_config_t config; /* cache configuration */
hbool_t check_file = 1; /* boolean indicating whether to check */
uint8_t * compare_buf; /* buffer to read into from hdf5 file */
hid_t status = -1; /* status indicator for retval checking */
char c_old,c_new; /* temporary storage for single characters */
long pos; /* file descriptor position indicator */
long pos_end; /* file descriptor position indicator */
char temp[100]; /* temporary buffer */
H5F_t * f; /* File pointer */
/* ==================== */
/* Command Line Parsing */
/* ==================== */
/* initialize h5tools lib */
h5tools_init();
/* Check for no command line parameters */
if ( argc == 1 ) {
usage();
leave( EXIT_SUCCESS );
} /* end if */
/* parse command line options */
while ( (opt = get_option(argc, argv, s_opts, l_opts) ) != EOF) {
switch ((char)opt) {
case 'h':
usage();
leave( EXIT_SUCCESS );
break;
case 'b':
custom_name = 1;
file_name_backup = strdup ( opt_arg );
break;
case 'n':
no_copy = 1;
break;
case 'j':
journal_name = strdup( opt_arg );
break;
case 'V':
print_version(progname);
leave( EXIT_SUCCESS );
break;
case 'v':
verbose = 1;
break;
default:
usage();
leave( EXIT_FAILURE );
} /* end switch */
} /* end while */
/* check for missing file name */
if (argc <= opt_ind) {
error_msg(progname, "HDF5 file name missing\n");
usage();
leave( EXIT_FAILURE );
}
file_name = HDstrdup(argv[opt_ind]);
/* check for missing journal name */
if ( journal_name == NULL ) {
error_msg(progname, "Journal file name missing\n");
usage();
leave( EXIT_FAILURE );
} /* end if */
/* check for missing backup file name */
if ( custom_name == 1) {
if ( file_name_backup == NULL ) {
error_msg(progname, "Journal file backup name missing\n");
usage();
leave( EXIT_FAILURE );
} /* end if */
} /* end if */
/* ========================================== */
/* Open HDF5 File with Journal Recovered Flag */
/* ========================================== */
/* set up appropriate fapl */
fapl = H5Pcreate(H5P_FILE_ACCESS);
if ( fapl == -1 ) {
error_msg(progname, "Could not create FAPL.\n");
leave( EXIT_FAILURE );
} /* end if */
config.version = 1; /* should be H5C2__CURR_AUTO_SIZE_CTL_VER */
/* get H5AC_cache_config_t configuration from fapl */
if ( H5Pget_mdc_config(fapl, &config) == -1) {
error_msg(progname, "Could not get mdc config from FAPL.\n");
leave( EXIT_FAILURE );
}
/* make sure journal recovered field is set to TRUE in mdc_config */
config.journal_recovered = TRUE;
/* set H5AC_cache_config_t configuration with file recovered */
if ( H5Pset_mdc_config(fapl, &config) == -1) {
error_msg(progname, "Could not set mdc config on FAPL.\n");
leave( EXIT_FAILURE );
} /* end if */
/* open HDF5 file with provided fapl */
fid = H5Fopen(file_name, H5F_ACC_RDWR, fapl);
if ( fid == -1 ) {
error_msg(progname, "Could not open recovered HDF5 file.\n");
leave( EXIT_FAILURE );
} /* end if */
/* =============================== */
/* Make a Backup Copy of HDF5 File */
/* =============================== */
if ( verbose ) printf("\n==============================================\n");
if (no_copy == 0) {
/* make a backup copy of HDF5 file before recovery */
if (custom_name == 1) {
if ( verbose ) printf("Copying HDF5 file <%s> into file <%s>\n", file_name, file_name_backup);
file_copy( /* from */ file_name, /* to */ file_name_backup);
} /* end if */
else {
file_name_backup = HDmalloc(HDstrlen(file_name) + (size_t)10);
HDsnprintf(file_name_backup, HDstrlen(file_name) + (size_t)8, "%s.backup", file_name);
if ( verbose ) printf("Copying HDF5 file <%s> into file <%s>\n", file_name, file_name_backup);
file_copy( /* from */ file_name, /* to */ file_name_backup);
} /* end else */
} /* end if */
/* =========================== */
/* Open HDF5 and Journal Files */
/* =========================== */
/* open the journal file for reading */
journal_fp = fopen(journal_name, "r");
if (journal_fp == NULL) {
error_msg(progname, "Could not open specified journal file\n");
usage();
leave( EXIT_FAILURE );
} /* end if */
/* open hdf5 file for reading and writing */
hdf5_fd = open(file_name, O_RDWR);
if (hdf5_fd == -1) {
error_msg(progname, "Could not open specified hdf5 file\n");
usage();
leave( EXIT_FAILURE );
} /* end if */
/* allocate temporary space to store end transaction messages */
last_trans_msg = HDmalloc((size_t)50);
if (last_trans_msg == NULL) {
error_msg(progname, "Could not allocate space\n");
leave( EXIT_FAILURE);
} /* end if */
if ( verbose ) printf("Recovering file <%s> from journal <%s>\n\n",
file_name, journal_name);
/* ====================================================== */
/* Find the last complete transaction in the journal file */
/* ====================================================== */
fseek(journal_fp, 0, SEEK_END);
while (last_trans_found == 0) {
while (fgetc(journal_fp) != '\n') {
if (ftell(journal_fp) <= 1) {
error_msg(progname, "Journal has no complete transactions\n");
usage();
leave( EXIT_FAILURE );
} /* end if */
fseek(journal_fp, -2, SEEK_CUR);
} /* end while */
if ( fgetc(journal_fp) == '3' ) {
last_trans_found = 1;
fseek(journal_fp, -1, SEEK_CUR);
fgets(last_trans_msg, 50, journal_fp);
} /* end if */
else {
fseek(journal_fp, -3, SEEK_CUR);
} /* end else */
} /* end while */
/* ======================================= */
/* Determine Size of Biggest Journal Entry */
/* ======================================= */
fseek(journal_fp, 0, SEEK_END);
pos_end = ftell(journal_fp);
fseek(journal_fp, 0, SEEK_SET);
c_new = 0;
c_old = 0;
max_size = 0;
/* while journal is not at end of file */
while (ftell(journal_fp) != pos_end) {
c_old = c_new;
c_new = fgetc(journal_fp);
/* if position is at the start of a line */
if (c_old == '\n') {
/* if the line starts with a '2', find out size of entry */
if (c_new == '2') {
pos = ftell(journal_fp);
fgets(temp, 100, journal_fp);
tok[0] = HDstrtok(temp, " ");
if (tok[0] == NULL) {
error_msg(progname, "Could not tokenize entry\n");
leave( EXIT_FAILURE);
} /* end if */
for (i=1; i<8; i++) {
tok[i] = HDstrtok(NULL, " ");
if (tok[i] == NULL) {
error_msg(progname, "Could not tokenize entry\n");
leave( EXIT_FAILURE);
} /* end if */
} /* end for */
size = HDstrtod(tok[3], NULL);
if (max_size < size) {
max_size = size;
} /* end if */
/* jump back to start of line */
fseek(journal_fp, pos, SEEK_SET);
} /* end if */
} /* end if */
} /* end while */
/* ================================================= */
/* Tokenize each journal entry in order to grab data */
/* ================================================= */
max_size = max_size * 3 + 200;
/* allocate space large enough to hold largest journal entry */
readback = HDmalloc( max_size );
if (readback == NULL) {
error_msg(progname, "Could not allocate space to hold entries\n");
leave( EXIT_FAILURE);
} /* end if */
/* read through journal file. recover any journal entries found, up
* through the last transaction number */
fseek(journal_fp, 0, SEEK_SET);
while ( fgets(readback, max_size, journal_fp) != NULL ) {
if (HDstrcmp(readback, last_trans_msg) == 0) {
/* done reading from file */
break;
} /* end if */
if ( readback[0] == '2') { /* journal entry found */
if ( verbose ) printf("Journal entry found.\n");
if ( verbose ) printf("Tokenizing journal entry.\n");
/* divide the journal entry into tokens */
tok[0] = HDstrtok(readback, " ");
if (tok[0] == NULL) {
error_msg(progname, "Could not tokenize journal entry\n");
leave( EXIT_FAILURE);
} /* end if */
if ( verbose ) printf(" token[0] : <%s>\n", tok[0]);
for (i=1; i<10; i++) {
tok[i] = HDstrtok(NULL, " ");
if (tok[i] == NULL) {
error_msg(progname, "Could not tokenize journal entry\n");
leave( EXIT_FAILURE);
} /* end if */
if ( verbose ) printf(" token[%d] : <%s>\n", i, tok[i]);
} /* end for */
/* put all remaining data into last token. */
/* This contains all of the journal entry body */
tok[10] = HDstrtok(NULL, "\n");
if (tok[10] == NULL) {
error_msg(progname, "Could not tokenize journal entry\n");
leave( EXIT_FAILURE);
} /* end if */
if ( verbose ) printf(" token[8] : <hexadecimal body data>\n");
/* ================================== */
/* Convert Items from Character Array */
/* ================================== */
if ( verbose ) printf("Converting data from character strings.\n");
/* convert address from character character string */
address = HDstrtod(tok[8], NULL);
if (address == 0) {
error_msg(progname, "Could not convert address to integer\n");
leave( EXIT_FAILURE);
} /* end if */
if ( verbose ) printf(" address : %llx\n", address);
/* convert size from character string*/
size = HDstrtod(tok[6], NULL);
if (size == 0) {
error_msg(progname, "Could not convert size to double\n");
leave( EXIT_FAILURE);
} /* end if */
/* convert eoa from character character string */
eoa = HDstrtod(tok[4], NULL);
if (eoa == 0) {
error_msg(progname, "Could not convert eoa to integer\n");
leave( EXIT_FAILURE);
} /* end if */
if ( verbose ) printf(" length : %d\n", size);
/* transform body out of hexadecimal character string */
body = HDmalloc(size + 1);
if (body == NULL) {
error_msg(progname, "Could not allocate space for body\n");
leave( EXIT_FAILURE);
} /* end if */
p = &(tok[10])[0];
for (i = 0; i < size; i++) {
body[i] = HDstrtoul(p, NULL, 16);
p = &p[3];
} /* end for */
body[i] = 0;
if ( verbose ) printf(" body : binary body data\n");
/* ================================================ */
/* Write into HDF5 file the recovered journal entry */
/* ================================================ */
if ( verbose ) printf("Writing entry to HDF5 file.\n");
/* perform a write */
status = pwrite(hdf5_fd, body, size, address);
if (status == -1) {
error_msg(progname, "pwrite failed\n");
leave( EXIT_FAILURE );
}
if (status == 0) {
error_msg(progname, "pwrite did not write anything!\n");
leave( EXIT_FAILURE);
}
/* Verify that write occurred correctly */
if ( check_file == 1) {
if ( verbose ) printf("Verifying success of write");
compare_buf = HDmalloc(size + 1);
if (compare_buf == NULL) {
error_msg(progname, "Could not allocate space\n");
leave( EXIT_FAILURE);
} /* end if */
pread(hdf5_fd, compare_buf, size, address);
/* do a quick string compare on two items */
if (HDstrcmp((const char *)body, (const char *)compare_buf) != 0) {
error_msg(progname, "Entry incorrectly written into HDF5 file. Exiting.\n");
printf("Address %llx:\n", (unsigned long_long)address);
printf(" -- from journal: '%s'\n", body);
printf(" -- from HDF5 file: '%s'\n", compare_buf);
leave( EXIT_FAILURE );
} /* end if */
/* compare each individual value of entry */
for (i=0; i<size; i++) {
if (body[i] != compare_buf[i]) {
error_msg(progname, "Entry incorrectly written into HDF5 file. Exiting.\n");
printf("Address %llx\n", (unsigned long_long)(address + i));
printf(" -- from journal: %d\n", body[i]);
printf(" -- from HDF5 file: %d\n", compare_buf[i]);
leave( EXIT_FAILURE );
}
}
if ( verbose ) printf(" .... SUCCESS!\n\n");
free(compare_buf);
}
free(body);
} /* end if */
} /* end while */
fclose(journal_fp);
close(hdf5_fd);
free(last_trans_msg);
free(readback);
free(journal_name);
/* =========================================== */
/* Set EOA Value and Close Recovered HDF5 File */
/* =========================================== */
/* obtain H5F_t pointer */
if (NULL == (f = H5I_object(fid))) {
error_msg(progname, "Could not obtain H5F_t pointer from file id");
leave( EXIT_FAILURE );
} /* end if */
/* set the correct value of the eoa */
if (H5FDset_eoa(f->shared->lf, H5FD_MEM_DEFAULT, eoa) == -1) {
error_msg(progname, "Driver set eoa request failed");
leave( EXIT_FAILURE );
} /* end if */
/* close HDF5 file */
if ( H5Fclose(fid) == -1 ) {
error_msg(progname, "Could not close recovered HDF5 file.\n");
leave( EXIT_FAILURE );
} /* end if */
/* ================ */
/* Cleanup and Exit */
/* ================ */
/* MIKE: Should I remove journal file here, or should that happen
on file close? */
printf("HDF5 file successfuly recovered.\n");
if ( verbose ) printf("==============================================\n\n");
free(file_name);
return 0;
} /* end main */
|