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
|
/*
* Copyright (C) 2000 NCSA
* All rights reserved.
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Thursday, September 28, 2000
*
* Purpose: Provides I/O facilities for sequences of bytes stored with various
* layout policies. These routines are similar to the H5Farray.c routines,
* these deal in terms of byte offsets and lengths, not coordinates and
* hyperslab sizes.
*
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h>
#include <H5FDprivate.h> /*file driver */
#include <H5Iprivate.h>
#include <H5MFprivate.h>
#include <H5MMprivate.h> /*memory management */
#include <H5Oprivate.h>
#include <H5Pprivate.h>
#include <H5Vprivate.h>
/* MPIO driver functions are needed for some special checks */
#include <H5FDmpio.h>
/* Interface initialization */
#define PABLO_MASK H5Fseq_mask
#define INTERFACE_INIT NULL
static intn interface_initialize_g = 0;
/*-------------------------------------------------------------------------
* Function: H5F_seq_read
*
* Purpose: Reads a sequence of bytes from a file dataset into a buffer in
* in memory. The data is read from file F and the array's size and
* storage information is in LAYOUT. External files are described
* according to the external file list, EFL. The sequence offset is
* FILE_OFFSET in the file (offsets are
* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
* total size of the file array is implied in the LAYOUT argument.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, September 28, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const H5O_fill_t *fill,
const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
hsize_t seq_len, hsize_t file_offset, void *buf/*out*/)
{
hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
intn ndims;
haddr_t addr; /*address in file */
intn i; /*counters */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif
FUNC_ENTER(H5F_seq_read, FAIL);
/* Check args */
assert(f);
assert(layout);
assert(buf);
#ifdef H5_HAVE_PARALLEL
{
/* Get the transfer mode */
H5D_xfer_t *dxpl;
H5FD_mpio_dxpl_t *dx;
if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
xfer_mode = dx->xfer_mode;
}
}
/* Collective MPIO access is unsupported for non-contiguous datasets */
if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
"collective access on non-contiguous datasets not supported yet");
}
#endif
switch (layout->type) {
case H5D_CONTIGUOUS:
/* Filters cannot be used for contiguous data. */
if (pline && pline->nfilters>0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"filters are not allowed for contiguous data");
}
/*
* Initialize loop variables. The loop is a multi-dimensional loop
* that counts from SIZE down to zero and IDX is the counter. Each
* element of IDX is treated as a digit with IDX[0] being the least
* significant digit.
*/
if (efl && efl->nused>0) {
addr = 0;
} else {
addr = layout->addr;
}
addr += file_offset;
/*
* Now begin to walk through the array, copying data from disk to
* memory.
*/
#ifdef H5_HAVE_PARALLEL
if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
/*
* Currently supports same number of collective access. Need to
* be changed LATER to combine all reads into one collective MPIO
* call.
*/
unsigned long max, min, temp;
temp = seq_len;
assert(temp==seq_len); /* verify no overflow */
MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
H5FD_mpio_communicator(f->shared->lf));
MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
if (max != min)
HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
"collective access with unequal number of blocks not supported yet");
}
#endif
/* Read directly from file if the dataset is in an external file */
/* Note: We can't use data sieve buffers for datasets in external files
* because the 'addr' of all external files is set to 0 (above) and
* all datasets in external files would alias to the same set of
* file offsets, totally mixing up the data sieve buffer information. -QAK
*/
if (efl && efl->nused>0) {
if (H5O_efl_read(f, efl, addr, seq_len, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"external data read failed");
}
} else {
if (H5F_contig_read(f, H5FD_MEM_DRAW, addr, seq_len, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"block read failed");
}
} /* end else */
break;
case H5D_CHUNKED:
/*
* This method is unable to access external raw data files
*/
if (efl && efl->nused>0) {
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
"chunking and external files are mutually exclusive");
}
/* Compute the file offset coordinates and hyperslab size */
if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
#ifdef QAK
/* The library shouldn't be reading partial elements currently */
assert(seq_len%elmt_size!=0);
assert(addr%elmt_size!=0);
#endif /* QAK */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
printf("%s: file_offset=%d\n",FUNC,(int)file_offset);
count++;
}
}
#endif /* QAK */
/* Set location in dataset from the file_offset */
addr=file_offset;
/* Convert the bytes into elements */
seq_len/=elmt_size;
addr/=elmt_size;
/* Compute the hyperslab offset from the address given */
for(i=ndims-1; i>=0; i--) {
coords[i]=addr%dset_dims[i];
addr/=dset_dims[i];
} /* end for */
coords[ndims]=0; /* No offset for element info */
/* Compute the hyperslab size from the length given */
for(i=ndims-1; i>=0; i--) {
/* Check if the hyperslab is wider than the width of the dimension */
if(seq_len>dset_dims[i]) {
if (0!=coords[i])
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
hslab_size[i]=dset_dims[i];
} /* end if */
else
hslab_size[i]=seq_len;
/* Fold the length into the length in the next highest dimension */
seq_len/=dset_dims[i];
/* Make certain the hyperslab sizes don't go less than 1 */
if(seq_len<1)
seq_len=1;
} /* end for */
hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
for(i=0; i<=ndims; i++)
printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
for(i=0; i<=ndims; i++)
printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
count++;
}
}
#endif /* QAK */
if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
hslab_size, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
}
break;
default:
assert("not implemented yet" && 0);
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
} /* end switch() */
FUNC_LEAVE(SUCCEED);
} /* H5F_seq_read() */
/*-------------------------------------------------------------------------
* Function: H5F_seq_write
*
* Purpose: Writes a sequence of bytes to a file dataset from a buffer in
* in memory. The data is written to file F and the array's size and
* storage information is in LAYOUT. External files are described
* according to the external file list, EFL. The sequence offset is
* FILE_OFFSET in the file (offsets are
* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
* total size of the file array is implied in the LAYOUT argument.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Monday, October 9, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const H5O_fill_t *fill,
const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
hsize_t seq_len, hsize_t file_offset, const void *buf)
{
hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
intn ndims;
haddr_t addr; /*address in file */
intn i; /*counters */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif
FUNC_ENTER(H5F_seq_write, FAIL);
/* Check args */
assert(f);
assert(layout);
assert(buf);
#ifdef H5_HAVE_PARALLEL
{
/* Get the transfer mode */
H5D_xfer_t *dxpl;
H5FD_mpio_dxpl_t *dx;
if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
xfer_mode = dx->xfer_mode;
}
}
/* Collective MPIO access is unsupported for non-contiguous datasets */
if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
"collective access on non-contiguous datasets not supported yet");
}
#endif
switch (layout->type) {
case H5D_CONTIGUOUS:
/* Filters cannot be used for contiguous data. */
if (pline && pline->nfilters>0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"filters are not allowed for contiguous data");
}
/*
* Initialize loop variables. The loop is a multi-dimensional loop
* that counts from SIZE down to zero and IDX is the counter. Each
* element of IDX is treated as a digit with IDX[0] being the least
* significant digit.
*/
if (efl && efl->nused>0) {
addr = 0;
} else {
addr = layout->addr;
}
addr += file_offset;
/*
* Now begin to walk through the array, copying data from disk to
* memory.
*/
#ifdef H5_HAVE_PARALLEL
if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
/*
* Currently supports same number of collective access. Need to
* be changed LATER to combine all reads into one collective MPIO
* call.
*/
unsigned long max, min, temp;
temp = seq_len;
assert(temp==seq_len); /* verify no overflow */
MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
H5FD_mpio_communicator(f->shared->lf));
MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
if (max != min)
HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"collective access with unequal number of blocks not supported yet");
}
#endif
/* Write directly to file if the dataset is in an external file */
/* Note: We can't use data sieve buffers for datasets in external files
* because the 'addr' of all external files is set to 0 (above) and
* all datasets in external files would alias to the same set of
* file offsets, totally mixing up the data sieve buffer information. -QAK
*/
if (efl && efl->nused>0) {
if (H5O_efl_write(f, efl, addr, seq_len, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"external data write failed");
}
} else {
if (H5F_contig_write(f, H5FD_MEM_DRAW, addr, seq_len, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}
} /* end else */
break;
case H5D_CHUNKED:
/*
* This method is unable to access external raw data files
*/
if (efl && efl->nused>0) {
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
"chunking and external files are mutually exclusive");
}
/* Compute the file offset coordinates and hyperslab size */
if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%lu\n",FUNC,(int)elmt_size,(int)addr,(unsigned long)seq_len);
printf("%s: file_offset=%d\n",FUNC,(int)file_offset);
count++;
}
}
#endif /* QAK */
#ifdef QAK
/* The library shouldn't be reading partial elements currently */
assert((seq_len%elmt_size)!=0);
assert((addr%elmt_size)!=0);
#endif /* QAK */
/* Set location in dataset from the file_offset */
addr=file_offset;
/* Convert the bytes into elements */
seq_len/=elmt_size;
addr/=elmt_size;
/* Compute the hyperslab offset from the address given */
for(i=ndims-1; i>=0; i--) {
coords[i]=addr%dset_dims[i];
addr/=dset_dims[i];
} /* end for */
coords[ndims]=0; /* No offset for element info */
/* Compute the hyperslab size from the length given */
for(i=ndims-1; i>=0; i--) {
/* Check if the hyperslab is wider than the width of the dimension */
if(seq_len>dset_dims[i]) {
if (0!=coords[i])
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
hslab_size[i]=dset_dims[i];
} /* end if */
else
hslab_size[i]=seq_len;
/* Fold the length into the length in the next highest dimension */
seq_len/=dset_dims[i];
/* Make certain the hyperslab sizes don't go less than 1 */
if(seq_len<1)
seq_len=1;
} /* end for */
hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
for(i=0; i<=ndims; i++)
printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
for(i=0; i<=ndims; i++)
printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
count++;
}
}
#endif /* QAK */
if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
hslab_size, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
}
break;
default:
assert("not implemented yet" && 0);
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
} /* end switch() */
FUNC_LEAVE(SUCCEED);
} /* H5F_seq_write() */
|
