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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* This program illustrates assertion errors when linked
* to HDF5 1.4.1-post2 or 1.4.2-pre3 debug library.
*
* If the assertion errors are ignored, the program eventially causes
* an error in H5Gcreate2 when writing object 83381.
*
* When writing in single file mode, the assertion errors still occur
* but the H5Gcreate2 error does not.
*/
#include "hdf5.h"
#define FILEN "testmeta.h5"
#define MEMB_SIZE 100000000
#define CHUNK_SIZE 512
#define NDATAARRAYS 3
/*#define NPOINTS 2048*/
#define NPOINTS 20
#define NEXTARRAYS 10
#define NWATTRS 2
#define NDATAOBJECTS 100000
int main(void)
{
hid_t file_id, prop_id, memspace_id, type_id;
hid_t group_id;
hid_t dataset_id, dataspace_id;
herr_t status;
hsize_t dims[1];
hsize_t maxdims[1];
float data[NPOINTS];
float floatval;
unsigned numdataobj = 0;
unsigned i, j;
char name[80];
hsize_t start[1] = {0};
hsize_t stride[1] = {1};
hsize_t count[1] = {1};
/* Create a file */
file_id = H5Fcreate(FILEN, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create a dataset to hold the number of data objects */
/* Create the data space */
dataspace_id = H5Screate(H5S_SCALAR);
/* Create dataset */
dataset_id = H5Dcreate2(file_id, "/NumDataObj",
H5T_NATIVE_UINT, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* Write value to NumDataObj dataset */
status = H5Dwrite(dataset_id, H5T_NATIVE_UINT, H5S_ALL,
H5S_ALL, H5P_DEFAULT, &numdataobj);
/* Close the identifiers */
status = H5Dclose(dataset_id);
status = H5Sclose(dataspace_id);
/* Create extendible arrays */
/* Set up for extendible dataset */
prop_id = H5Pcreate(H5P_DATASET_CREATE);
dims[0] = CHUNK_SIZE;
status = H5Pset_chunk(prop_id, 1, dims);
/* Create dataspace */
dims[0]=1;
maxdims[0]=H5S_UNLIMITED;
dataspace_id = H5Screate_simple(1, dims, maxdims);
for(i=0; i<NEXTARRAYS; i++)
{
/* Create dataset */
sprintf(name, "/ExtArray%06d", i);
dataset_id = H5Dcreate2(file_id, name,
H5T_NATIVE_FLOAT, dataspace_id, H5P_DEFAULT, prop_id, H5P_DEFAULT);
/* Close the identifier */
status = H5Dclose(dataset_id);
}
/* Close the identifiers */
status = H5Sclose(dataspace_id);
status = H5Pclose(prop_id);
/* Create group to hold data object data arrays */
group_id = H5Gcreate2(file_id, "/DataArray", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group_id);
for(j=0; j<NDATAOBJECTS; j++)
{
printf("\rWriting Object #%d of %d", j+1, NDATAOBJECTS);
fflush(stdout);
floatval = (float)j;
/* Create group to hold data arrays for this object */
sprintf(name, "/DataArray/%06d", j);
group_id = H5Gcreate2(file_id, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(group_id < 0) {
fprintf(stderr, "Failed to create DataArray group.\n");
status = H5Fclose(file_id);
return -1;
}
/* Loop over data arrays */
for(i=0; i<NDATAARRAYS; i++)
{
/* Create dataspace */
dims[0]=NPOINTS;
maxdims[0]=NPOINTS;
dataspace_id = H5Screate_simple(1 ,dims, maxdims);
/* Create dataset */
sprintf(name, "DataArray%06d", i);
dataset_id = H5Dcreate2(group_id, name,
H5T_NATIVE_FLOAT, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dataset_id < 0) {
fprintf(stderr, "Failed to create DataArray dataset.\n");
status = H5Fclose(file_id);
return -1;
}
/* Write the data array data */
status = H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, H5S_ALL,
H5S_ALL, H5P_DEFAULT, data);
if(status < 0) {
fprintf(stderr, "Failed to write DataArray dataset.\n");
status = H5Fclose(file_id);
return -1;
}
/* Close the identifiers */
status = H5Dclose(dataset_id);
status = H5Sclose(dataspace_id);
}
/* Open NumDataObj dataset */
dataset_id = H5Dopen2(file_id, "/NumDataObj", H5P_DEFAULT);
if(dataset_id < 0) {
fprintf(stderr, "Failed to open NumDataObj dataset.\n");
status = H5Fclose(file_id);
return -1;
}
/* Write value to NumDataObj dataset */
numdataobj = j + 1;
status = H5Dwrite(dataset_id, H5T_NATIVE_UINT, H5S_ALL,
H5S_ALL, H5P_DEFAULT, &numdataobj);
if(status < 0) {
fprintf(stderr, "Failed to write NumDataObj dataset.\n");
status = H5Fclose(file_id);
return -1;
}
/* Close identifiers */
status = H5Dclose(dataset_id);
status = H5Gclose(group_id);
/* Extend attribute arrays */
for(i = 0; i < NEXTARRAYS; i++) {
/* Open extendable dataset */
sprintf(name, "/ExtArray%06d", i);
dataset_id = H5Dopen2(file_id, name, H5P_DEFAULT);
if(dataset_id < 0) {
fprintf(stderr, "Failed to open ExtArray dataset.\n");
status = H5Fclose(file_id);
return -1;
} /* end if */
/* Extend attribute dataset */
dims[0] = (hsize_t)j + 1;
status = H5Dset_extent(dataset_id, dims);
if(status < 0) {
fprintf(stderr, "Failed to extend DataArray dataset.\n");
status = H5Fclose(file_id);
return -1;
} /* end if */
/* Select element and write value to attribute dataset */
dims[0] = 1;
memspace_id = H5Screate_simple(1, dims, dims);
dataspace_id = H5Dget_space(dataset_id);
type_id = H5Dget_type(dataset_id);
start[0] = 0;
status = H5Sselect_hyperslab(memspace_id, H5S_SELECT_SET,
start, stride, count, NULL);
start[0] = (hssize_t)j;
status = H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET,
start, stride, count, NULL);
status = H5Dwrite(dataset_id, type_id, memspace_id,
dataspace_id, H5P_DEFAULT, &floatval);
if(status < 0)
{
fprintf(stderr, "Failed to write DataArray dataset.\n");
status = H5Fclose(file_id);
return -1;
}
/* Close identifiers */
status = H5Tclose(type_id);
status = H5Sclose(dataspace_id);
status = H5Sclose(memspace_id);
status = H5Dclose(dataset_id);
}
}
/* Close the file */
status = H5Fclose(file_id);
printf("\n");
return 0;
}
|
