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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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: Robb Matzke <matzke@llnl.gov>
* Wednesday, May 13, 1998
*
* Purpose: Repartitions a file family. This program can be used to
* split a single file into a family of files, join a family of
* files into a single file, or copy one family to another while
* changing the size of the family members. It can also be used
* to copy a single file to a single file with holes.
*/
/* See H5private.h for how to include system headers */
#include "hdf5.h"
#include "H5private.h"
#ifndef FALSE
#define FALSE 0
#endif
#ifndef TRUE
#define TRUE 1
#endif
#define NAMELEN 4096
#define GB *1024 * 1024 * 1024
#ifndef MIN
#define MIN(X, Y) ((X) < (Y) ? (X) : (Y))
#endif
#ifndef MIN3
#define MIN3(X, Y, Z) MIN(MIN(X, Y), Z)
#endif
/*Make these 2 private properties(defined in H5Fprivate.h) available to h5repart.
*The first one updates the member file size in the superblock. The second one
*change file driver from family to sec2. */
#define H5F_ACS_FAMILY_NEWSIZE_NAME "family_newsize"
#define H5F_ACS_FAMILY_TO_SEC2_NAME "family_to_sec2"
/*-------------------------------------------------------------------------
* Function: usage
*
* Purpose: Prints a usage message.
*
* Return: void
*
* Programmer: Robb Matzke
* Wednesday, May 13, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
usage(const char *progname)
{
HDfprintf(stderr, "usage: %s [-v] [-V] [-[b|m] N[g|m|k]] [-family_to_sec2] SRC DST\n", progname);
HDfprintf(stderr, " -v Produce verbose output\n");
HDfprintf(stderr, " -V Print a version number and exit\n");
HDfprintf(stderr, " -b N The I/O block size, defaults to 1kB\n");
HDfprintf(stderr, " -m N The destination member size or 1GB\n");
HDfprintf(stderr, " -family_to_sec2 Change file driver from family to sec2\n");
HDfprintf(stderr, " SRC The name of the source file\n");
HDfprintf(stderr, " DST The name of the destination files\n");
HDfprintf(stderr, "Sizes may be suffixed with `g' for GB, `m' for MB or "
"`k' for kB.\n");
HDfprintf(stderr, "File family names include an integer printf "
"format such as `%%d'\n");
HDexit(EXIT_FAILURE);
}
/*-------------------------------------------------------------------------
* Function: get_size
*
* Purpose: Reads a size option of the form `-XNS' where `X' is any
* letter, `N' is a multi-character positive decimal number, and
* `S' is an optional suffix letter in the set [GgMmk]. The
* option may also be split among two arguments as: `-X NS'.
* The input value of ARGNO is the argument number for the
* switch in the ARGV vector and ARGC is the number of entries
* in that vector.
*
* Return: Success: The value N multiplied according to the
* suffix S. On return ARGNO will be the number
* of the next argument to process.
*
* Failure: Calls usage() which exits with a non-zero
* status.
*
* Programmer: Robb Matzke
* Wednesday, May 13, 1998
*-------------------------------------------------------------------------
*/
static off_t
get_size(const char *progname, int *argno, int argc, char *argv[])
{
off_t retval = -1;
char *suffix;
if (isdigit((int)(argv[*argno][2]))) {
retval = HDstrtol(argv[*argno] + 2, &suffix, 10);
(*argno)++;
}
else if (argv[*argno][2] || *argno + 1 >= argc) {
usage(progname);
}
else {
retval = HDstrtol(argv[*argno + 1], &suffix, 0);
if (suffix == argv[*argno + 1])
usage(progname);
*argno += 2;
}
if (suffix && suffix[0] && !suffix[1]) {
switch (*suffix) {
case 'G':
case 'g':
retval *= 1024 * 1024 * 1024;
break;
case 'M':
case 'm':
retval *= 1024 * 1024;
break;
case 'k':
retval *= 1024;
break;
default:
usage(progname);
}
}
else if (suffix && suffix[0]) {
usage(progname);
}
return retval;
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: Split an hdf5 file
*
* Return: Success:
*
* Failure:
*
* Programmer: Robb Matzke
* Wednesday, May 13, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main(int argc, char *argv[])
{
const char *prog_name; /*program name */
size_t blk_size = 1024; /*size of each I/O block */
char * buf = NULL; /*I/O block buffer */
size_t n, i; /*counters */
ssize_t nio; /*I/O return value */
int argno = 1; /*program argument number */
int src, dst = -1; /*source & destination files */
int need_seek = FALSE; /*destination needs to seek? */
int need_write; /*data needs to be written? */
h5_stat_t sb; /*temporary file stat buffer */
int verbose = FALSE; /*display file names? */
const char *src_gen_name; /*general source name */
char * src_name = NULL; /*source member name */
int src_is_family; /*is source name a family name? */
int src_membno = 0; /*source member number */
const char *dst_gen_name; /*general destination name */
char * dst_name = NULL; /*destination member name */
int dst_is_family; /*is dst name a family name? */
int dst_membno = 0; /*destination member number */
off_t left_overs = 0; /*amount of zeros left over */
off_t src_offset = 0; /*offset in source member */
off_t dst_offset = 0; /*offset in destination member */
off_t src_size; /*source logical member size */
off_t src_act_size; /*source actual member size */
off_t dst_size = 1 GB; /*destination logical memb size */
hid_t fapl; /*file access property list */
hid_t file;
hsize_t hdsize; /*destination logical memb size */
hbool_t family_to_sec2 = FALSE; /*change family to sec2 driver? */
/*
* Get the program name from argv[0]. Use only the last component.
*/
if ((prog_name = HDstrrchr(argv[0], '/')))
prog_name++;
else
prog_name = argv[0];
/*
* Parse switches.
*/
while (argno < argc && '-' == argv[argno][0]) {
if (!HDstrcmp(argv[argno], "-v")) {
verbose = TRUE;
argno++;
}
else if (!HDstrcmp(argv[argno], "-V")) {
HDprintf("This is %s version %u.%u release %u\n", prog_name, H5_VERS_MAJOR, H5_VERS_MINOR,
H5_VERS_RELEASE);
HDexit(EXIT_SUCCESS);
}
else if (!HDstrcmp(argv[argno], "-family_to_sec2")) {
family_to_sec2 = TRUE;
argno++;
}
else if ('b' == argv[argno][1]) {
blk_size = (size_t)get_size(prog_name, &argno, argc, argv);
}
else if ('m' == argv[argno][1]) {
dst_size = get_size(prog_name, &argno, argc, argv);
}
else {
usage(prog_name);
} /* end if */
} /* end while */
/* allocate names */
if (NULL == (src_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char))))
HDexit(EXIT_FAILURE);
if (NULL == (dst_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char))))
HDexit(EXIT_FAILURE);
/*
* Get the name for the source file and open the first member. The size
* of the first member determines the logical size of all the members.
*/
if (argno >= argc)
usage(prog_name);
src_gen_name = argv[argno++];
HDsprintf(src_name, src_gen_name, src_membno);
src_is_family = strcmp(src_name, src_gen_name);
if ((src = HDopen(src_name, O_RDONLY, 0)) < 0) {
HDperror(src_name);
HDexit(EXIT_FAILURE);
}
if (HDfstat(src, &sb) < 0) {
HDperror("fstat");
HDexit(EXIT_FAILURE);
}
src_size = src_act_size = sb.st_size;
if (verbose)
HDfprintf(stderr, "< %s\n", src_name);
/*
* Get the name for the destination file and open the first member.
*/
if (argno >= argc)
usage(prog_name);
dst_gen_name = argv[argno++];
HDsprintf(dst_name, dst_gen_name, dst_membno);
dst_is_family = HDstrcmp(dst_name, dst_gen_name);
if ((dst = HDopen(dst_name, O_RDWR | O_CREAT | O_TRUNC, 0666)) < 0) {
HDperror(dst_name);
HDexit(EXIT_FAILURE);
}
if (verbose)
HDfprintf(stderr, "> %s\n", dst_name);
/* No more arguments */
if (argno < argc)
usage(prog_name);
/* Now the real work, split the file */
buf = (char *)HDmalloc(blk_size);
while (src_offset < src_size) {
/* Read a block. The amount to read is the minimum of:
* 1. The I/O block size
* 2. What's left to write in the destination member
* 3. Left over zeros or what's left in the source member.
*/
n = blk_size;
if (dst_is_family)
n = (size_t)MIN((off_t)n, dst_size - dst_offset);
if (left_overs) {
n = (size_t)MIN((off_t)n, left_overs);
left_overs = left_overs - (off_t)n;
need_write = FALSE;
}
else if (src_offset < src_act_size) {
n = (size_t)MIN((off_t)n, src_act_size - src_offset);
if ((nio = HDread(src, buf, n)) < 0) {
HDperror("read");
HDexit(EXIT_FAILURE);
}
else if ((size_t)nio != n) {
HDfprintf(stderr, "%s: short read\n", src_name);
HDexit(EXIT_FAILURE);
}
for (i = 0; i < n; i++) {
if (buf[i])
break;
}
need_write = (i < n);
}
else {
n = 0;
left_overs = src_size - src_act_size;
need_write = FALSE;
}
/*
* If the block contains non-zero data then write it to the
* destination, otherwise just remember that we'll have to do a seek
* later in the destination when we finally get non-zero data.
*/
if (need_write) {
if (need_seek && HDlseek(dst, dst_offset, SEEK_SET) < 0) {
HDperror("HDlseek");
HDexit(EXIT_FAILURE);
}
if ((nio = HDwrite(dst, buf, n)) < 0) {
HDperror("write");
HDexit(EXIT_FAILURE);
}
else if ((size_t)nio != n) {
HDfprintf(stderr, "%s: short write\n", dst_name);
HDexit(EXIT_FAILURE);
}
need_seek = FALSE;
}
else {
need_seek = TRUE;
}
/*
* Update the source offset and open the next source family member if
* necessary. The source stream ends at the first member which
* cannot be opened because it doesn't exist. At the end of the
* source stream, update the destination offset and break out of the
* loop. The destination offset must be updated so we can fix
* trailing holes.
*/
src_offset = src_offset + (off_t)n;
if (src_offset == src_act_size) {
HDclose(src);
if (!src_is_family) {
dst_offset = dst_offset + (off_t)n;
break;
}
HDsprintf(src_name, src_gen_name, ++src_membno);
if ((src = HDopen(src_name, O_RDONLY)) < 0 && ENOENT == errno) {
dst_offset = dst_offset + (off_t)n;
break;
}
else if (src < 0) {
HDperror(src_name);
HDexit(EXIT_FAILURE);
}
if (HDfstat(src, &sb) < 0) {
HDperror("fstat");
HDexit(EXIT_FAILURE);
}
src_act_size = sb.st_size;
if (src_act_size > src_size) {
HDfprintf(stderr, "%s: member truncated to %lu bytes\n", src_name, (unsigned long)src_size);
}
src_offset = 0;
if (verbose)
HDfprintf(stderr, "< %s\n", src_name);
}
/*
* Update the destination offset, opening a new member if one will be
* needed. The first member is extended to the logical member size
* but other members might be smaller if they end with a hole.
*/
dst_offset = dst_offset + (off_t)n;
if (dst_is_family && dst_offset == dst_size) {
if (0 == dst_membno) {
if (HDlseek(dst, dst_size - 1, SEEK_SET) < 0) {
HDperror("HDHDlseek");
HDexit(EXIT_FAILURE);
}
if (HDread(dst, buf, 1) < 0) {
HDperror("read");
HDexit(EXIT_FAILURE);
}
if (HDlseek(dst, dst_size - 1, SEEK_SET) < 0) {
HDperror("HDlseek");
HDexit(EXIT_FAILURE);
}
if (HDwrite(dst, buf, 1) < 0) {
HDperror("write");
HDexit(EXIT_FAILURE);
}
}
HDclose(dst);
HDsprintf(dst_name, dst_gen_name, ++dst_membno);
if ((dst = HDopen(dst_name, O_RDWR | O_CREAT | O_TRUNC, 0666)) < 0) {
HDperror(dst_name);
HDexit(EXIT_FAILURE);
}
dst_offset = 0;
need_seek = FALSE;
if (verbose)
HDfprintf(stderr, "> %s\n", dst_name);
}
}
/*
* Make sure the last family member is the right size and then close it.
* The last member can't end with a hole or hdf5 will think that the
* family has been truncated.
*/
if (need_seek) {
if (HDlseek(dst, dst_offset - 1, SEEK_SET) < 0) {
HDperror("HDlseek");
HDexit(EXIT_FAILURE);
}
if (HDread(dst, buf, 1) < 0) {
HDperror("read");
HDexit(EXIT_FAILURE);
}
if (HDlseek(dst, dst_offset - 1, SEEK_SET) < 0) {
HDperror("HDlseek");
HDexit(EXIT_FAILURE);
}
if (HDwrite(dst, buf, 1) < 0) {
HDperror("write");
HDexit(EXIT_FAILURE);
}
}
HDclose(dst);
/* Modify family driver information saved in superblock through private property.
* These private properties are for this tool only. */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
HDperror("H5Pcreate");
HDexit(EXIT_FAILURE);
}
if (family_to_sec2) {
/* The user wants to change file driver from family to sec2. Open the file
* with sec2 driver. This property signals the library to ignore the family
* driver information saved in the superblock. */
if (H5Pset(fapl, H5F_ACS_FAMILY_TO_SEC2_NAME, &family_to_sec2) < 0) {
HDperror("H5Pset");
HDexit(EXIT_FAILURE);
}
}
else {
/* Modify family size saved in superblock through private property. It signals
* library to save the new member size(specified in command line) in superblock.
* This private property is for this tool only. */
if (H5Pset_fapl_family(fapl, H5F_FAMILY_DEFAULT, H5P_DEFAULT) < 0) {
HDperror("H5Pset_fapl_family");
HDexit(EXIT_FAILURE);
}
/* Set the property of the new member size as hsize_t */
hdsize = (hsize_t)dst_size;
if (H5Pset(fapl, H5F_ACS_FAMILY_NEWSIZE_NAME, &hdsize) < 0) {
HDperror("H5Pset");
HDexit(EXIT_FAILURE);
}
}
/* If the new file is a family file, try to open file for "read and write" to
* flush metadata. Flushing metadata will update the superblock to the new
* member size. If the original file is a family file and the new file is a sec2
* file, the property FAMILY_TO_SEC2 will signal the library to switch to sec2
* driver when the new file is opened. If the original file is a sec2 file and the
* new file can only be a sec2 file, reopen the new file should fail. There's
* nothing to do in this case. */
H5E_BEGIN_TRY { file = H5Fopen(dst_gen_name, H5F_ACC_RDWR, fapl); }
H5E_END_TRY;
if (file >= 0) {
if (H5Fclose(file) < 0) {
HDperror("H5Fclose");
HDexit(EXIT_FAILURE);
} /* end if */
} /* end if */
if (H5Pclose(fapl) < 0) {
HDperror("H5Pclose");
HDexit(EXIT_FAILURE);
} /* end if */
/* Free resources and return */
HDfree(src_name);
HDfree(dst_name);
HDfree(buf);
return EXIT_SUCCESS;
} /* end main */
|