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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* For generating files for verifying h5repack with external storage. . .
*
* Each case file should follow the format of:
* + h5repack_<NAME>.h5
* + h5repack_<NAME>_ex.h5
* + h5repack_<NAME>_ex-<N>.dat
* ...where NAME idenfities the type, and N is a positive decimal number;
* multiple external files (*.dat) are allowed per file, but they must
* follow the pattern and be in contiguous numerical sequence starting at 0.
*
* Each file typename must be added to the listing for
* `VERIFY_EXTERNAL_CONSOLIDATION` in h5repack.sh
*
* There is no restriction on the name, number, or structure of datasets and
* groups in HDF5 file.
*
* The inluded datatypes should be more than adequate to verify the correctness
* of the behavior -- if one type can be consolidated from external storage,
* then thay all can.
*/
#include "hdf5.h"
#include "H5private.h"
#define MAX_NAME_SIZE 256
#define FILE_INT32LE_1 "h5repack_int32le_1d"
#define FILE_INT32LE_2 "h5repack_int32le_2d"
#define FILE_INT32LE_3 "h5repack_int32le_3d"
#define FILE_UINT8BE "h5repack_uint8be"
#define FILE_F32LE "h5repack_f32le"
#define H5REPACKGENTEST_OOPS { \
ret_value = -1; \
goto done; \
}
#define H5REPACKGENTEST_COMMON_CLEANUP(dcpl, file, space) { \
if ((dcpl) != H5P_DEFAULT && (dcpl) != H5I_INVALID_HID) { \
(void)H5Pclose((dcpl)); \
} \
if ((file) != H5I_INVALID_HID) { (void)H5Fclose((file)); } \
if ((space) != H5I_INVALID_HID) { (void)H5Sclose((space)); } \
}
struct external_def {
hsize_t type_size;
unsigned n_elts_per_file;
unsigned n_elts_total;
};
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Helper function to create and write a dataset to file.
* Returns 0 on success, -1 on failure.
*/
static int
__make_dataset(hid_t file_id, const char *dset_name,
hid_t mem_type_id, hid_t space_id, hid_t dcpl_id, void *wdata) {
hid_t dset_id = H5I_INVALID_HID;
int ret_value = 0;
dset_id = H5Dcreate2(file_id, dset_name, mem_type_id, space_id,
H5P_DEFAULT, dcpl_id,
H5P_DEFAULT);
if (dset_id == H5I_INVALID_HID)
H5REPACKGENTEST_OOPS;
if (H5Dwrite(dset_id, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata) < 0)
H5REPACKGENTEST_OOPS;
done:
if (dset_id != H5I_INVALID_HID)
(void) H5Dclose(dset_id);
return ret_value;
} /* end __make_dataset() */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Helper function to populate the DCPL external storage list.
* Creates external files for the DCPL, with each file name following the
* convention "<filename>_ex-<num>.dat". Will append `n_external_files` to
* the filename list, with each file having space for `n_elts` items of the
* type (of size `elt_size`). The numeric inputs are not sanity-checked.
* Returns 0 on success, -1 on failure.
*/
static int
__set_dcpl_external_list(hid_t dcpl, const char *filename,
unsigned n_elts_per_file, unsigned n_elts_total, hsize_t elt_size) {
char name[MAX_NAME_SIZE];
unsigned n_external_files = 0;
unsigned i = 0;
if (NULL == filename || '\0' == *filename)
return -1;
n_external_files = n_elts_total / n_elts_per_file;
if (n_elts_total != (n_external_files * n_elts_per_file))
return -1;
for (i = 0; i < n_external_files; i++) {
if (HDsnprintf(name, MAX_NAME_SIZE, "%s_ex-%u.dat", filename, i) >= MAX_NAME_SIZE)
return -1;
if (H5Pset_external(dcpl, name, 0, n_elts_per_file * elt_size) < 0)
return -1;
}
return 0;
} /* end __set_dcpl_external_list() */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Generalized utility function to write a file with the specified data and
* dataset configuration. If `ext` is provided, will attempt to use external
* storage.
* Returns 0 on success, -1 on failure.
*/
static int
__make_file(const char *basename, struct external_def *ext,
hid_t type_id, hsize_t rank, hsize_t *dims, void *wdata) {
char filename[MAX_NAME_SIZE];
hid_t file_id = H5I_INVALID_HID;
hid_t dcpl_id = H5P_DEFAULT;
hid_t space_id = H5I_INVALID_HID;
int ret_value = 0;
if (HDsnprintf(filename, MAX_NAME_SIZE, "%s%s.h5", basename, (NULL != ext) ? "_ex" : "") >= MAX_NAME_SIZE)
H5REPACKGENTEST_OOPS;
if (NULL != ext) {
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
if (dcpl_id == H5I_INVALID_HID)
H5REPACKGENTEST_OOPS;
if (__set_dcpl_external_list(dcpl_id, basename, ext->n_elts_per_file, ext->n_elts_total, ext->type_size) < 0)
H5REPACKGENTEST_OOPS;
}
space_id = H5Screate_simple((int)rank, dims, NULL);
if (space_id == H5I_INVALID_HID)
H5REPACKGENTEST_OOPS;
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (file_id == H5I_INVALID_HID)
H5REPACKGENTEST_OOPS;
if (__make_dataset(file_id, "dset", type_id, space_id, dcpl_id, wdata) < 0)
H5REPACKGENTEST_OOPS;
done:
H5REPACKGENTEST_COMMON_CLEANUP(dcpl_id, file_id, space_id);
return ret_value;
} /* end __make_file() */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Returns 0 on success, -1 on failure.
*/
static int
generate_int32le_1d(hbool_t external) {
int32_t wdata[12];
hsize_t dims[] = { 12 };
struct external_def *def_ptr = NULL;
struct external_def def = { (hsize_t) sizeof(int32_t), 6, 12 };
int32_t n = 0;
int ret_value = 0;
/* Generate values
*/
for (n = 0; n < 12; n++) {
wdata[n] = n - 6;
}
def_ptr = (TRUE == external) ? (&def) : NULL;
if (__make_file(FILE_INT32LE_1, def_ptr, H5T_STD_I32LE, 1, dims, wdata) < 0)
ret_value = -1;
return ret_value;
} /* end generate_int32le_1d() */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Returns 0 on success, -1 on failure.
*/
static int
generate_int32le_2d(hbool_t external) {
int32_t wdata[64];
hsize_t dims[] = { 8, 8 };
struct external_def *def_ptr = NULL;
struct external_def def = { (hsize_t) sizeof(int32_t), 64, 64 };
int32_t n = 0;
int ret_value = 0;
/* Generate values
*/
for (n = 0; n < 64; n++) {
wdata[n] = n - 32;
}
def_ptr = (TRUE == external) ? (&def) : NULL;
if (__make_file(FILE_INT32LE_2, def_ptr, H5T_STD_I32LE, 2, dims, wdata) < 0)
ret_value = -1;
return ret_value;
} /* end generate_int32le_2d() */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Returns 0 on success, -1 on failure.
*/
static int
generate_int32le_3d(hbool_t external) {
hsize_t dims[] = { 8, 8, 8 };
int32_t wdata[512]; /* 8^3, from dims */
struct external_def *def_ptr = NULL;
struct external_def def = { (hsize_t) sizeof(int32_t), 512, 512 };
int32_t n = 0;
int i = 0;
int j = 0;
int k = 0;
int ret_value = 0;
/* generate values, alternating positive and negative
*/
for (i = 0, n = 0; i < dims[0]; i++) {
for (j = 0; j < dims[1]; j++) {
for (k = 0; k < dims[2]; k++, n++) {
wdata[n] = (k + j * 512 + i * 4096) * ((n & 1) ? (-1) : (1));
}
}
}
def_ptr = (TRUE == external) ? (&def) : NULL;
if (__make_file(FILE_INT32LE_3, def_ptr, H5T_STD_I32LE, 3, dims, wdata) < 0)
ret_value = -1;
return ret_value;
} /* end generate_int32le_3d() */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Returns 0 on success, -1 on failure.
*/
static int
generate_uint8be(hbool_t external) {
hsize_t dims[] = { 4, 8, 8 };
uint8_t wdata[256]; /* 4*8*8, from dims */
struct external_def *def_ptr = NULL;
struct external_def def = { (hsize_t) sizeof(uint8_t), 64, 256 };
uint8_t n = 0;
int i = 0;
int j = 0;
int k = 0;
int ret_value = 0;
/* Generate values, ping-pong from ends of range
*/
for (i = 0, n = 0; i < dims[0]; i++) {
for (j = 0; j < dims[1]; j++) {
for (k = 0; k < dims[2]; k++, n++) {
wdata[n] = (uint8_t)((n & 1) ? -n : n);
}
}
}
def_ptr = (TRUE == external) ? (&def) : NULL;
if (__make_file(FILE_UINT8BE, def_ptr, H5T_STD_U8BE, 3, dims, wdata) < 0)
ret_value = -1;
return ret_value;
} /* end generate_uint8be() */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Returns 0 on success, -1 on failure.
*/
static int
generate_f32le(hbool_t external) {
hsize_t dims[] = { 12, 6 };
float wdata[72]; /* 12*6, from dims */
struct external_def *def_ptr = NULL;
struct external_def def = { (hsize_t) sizeof(float), 72, 72 };
float n = 0;
int i = 0;
int j = 0;
int k = 0;
int ret_value = 0;
/* Generate values */
for (i = 0, k = 0, n = 0; i < dims[0]; i++) {
for (j = 0; j < dims[1]; j++, k++, n++) {
wdata[k] = n * 801.1f * ((k % 5 == 1) ? (-1) : (1));
}
}
def_ptr = (TRUE == external) ? (&def) : NULL;
if (__make_file(FILE_F32LE, def_ptr, H5T_IEEE_F32LE, 2, dims, wdata) < 0)
ret_value = -1;
return ret_value;
} /* end generate_f32le() */
/* ----------------------------------------------------------------------------
* Create files.
* Return 0 on success, nonzero on failure.
*/
int
main(void) {
int i = 0;
for (i = 0; i < 2; i++) {
hbool_t external = (i & 1) ? TRUE : FALSE;
if (generate_int32le_1d(external) < 0)
HDprintf("A generate_int32le_1d failed!\n");
if (generate_int32le_2d(external) < 0)
HDprintf("A generate_int32le_2d failed!\n");
if (generate_int32le_3d(external) < 0)
HDprintf("A generate_int32le_3d failed!\n");
if (generate_uint8be(external) < 0)
HDprintf("A generate_uint8be failed!\n");
if (generate_f32le(external) < 0)
HDprintf("A generate_f32le failed!\n");
} /* end for external data storage or not */
return EXIT_SUCCESS;
} /* end main() */
|