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
|
#include "H5VolUtil.h"
#include "H5VolError.h"
void *safe_calloc(size_t n, size_t s, unsigned long line)
{
if (n == 0)
{
return NULL;
}
void *p = calloc(n, s);
if (!p)
{
fprintf(stderr, "[%s:%ld]Out of memory at calloc (%ld, %ld)\n", __FILE__, line,
(unsigned long)n, (unsigned long)s);
exit(EXIT_FAILURE);
}
return p;
}
void *safe_malloc(size_t n, unsigned long line)
{
if (n == 0)
{
return NULL;
}
void *p = malloc(n);
if (!p)
{
fprintf(stderr, "[%s:%ld]Out of memory at malloc (%zu bytes)\n", __FILE__, line, n);
exit(EXIT_FAILURE);
}
return p;
}
void safe_free(void *p)
{
if (p)
{
free(p);
p = NULL;
}
}
void *safe_ralloc(void *ptr, size_t newsize, unsigned long line)
{
void *p = realloc(ptr, newsize);
if (!p)
{
fprintf(stderr, "[%s:%ld]Out of memory at ralloc to (%ld bytes)\n", __FILE__, line,
(unsigned long)newsize);
exit(EXIT_FAILURE);
}
return p;
}
void gUtilConvert(hsize_t *fromH5, size_t *to, size_t ndims)
{
size_t i = 0;
for (i = 0; i < ndims; i++)
{
to[i] = fromH5[i];
}
}
int gUtilADIOS2GetShape(hid_t space_id, size_t *shape, size_t ndims)
{
if (gUtilADIOS2IsScalar(space_id))
{
// nothing to do
return H5VL_CODE_SUCC;
}
// get num dimensions
hsize_t h5Shape[ndims];
H5Sget_simple_extent_dims(space_id, h5Shape, NULL);
gUtilConvert(h5Shape, shape, ndims);
return H5VL_CODE_SUCC;
}
int gUtilADIOS2GetBlockInfo(hid_t hyperSlab_id, size_t *start, size_t *count, hsize_t ndims)
{
hsize_t npts = H5Sget_select_npoints(hyperSlab_id);
if (0 == npts)
return npts;
else
{
hsize_t s[ndims], e[ndims];
H5Sget_select_bounds(hyperSlab_id, s, e);
hsize_t numElements = 1;
hsize_t k = 0;
for (k = 0; k < ndims; k++)
{
start[k] = s[k];
count[k] = (e[k] - s[k]) + 1;
numElements *= count[k];
}
if (npts == numElements)
return npts; // ok got block
}
return H5VL_CODE_FAIL; // slab has many blocks
/*
NOTE: this is a well wish segment. Reality is hdf5 returns numBlocks =
numPts; 1 pt per block. so cann't apply this method!! hsize_t numBlocks =
H5Sget_select_hyper_nblocks(hyperSlab_id); REQUIRE_SUCC_MSG((1 == numBlocks),
H5VL_CODE_FAIL, "Currently not able to support strides != 1 %ld", numBlocks);
// now numBlocks = 1
hsize_t *blockinfo = (hsize_t *)SAFE_MALLOC(sizeof(hsize_t) * 2 * ndims *
numBlocks); herr_t status = H5Sget_select_hyper_blocklist(hyperSlab_id,
(hsize_t)0, numBlocks, blockinfo);
int i=0;
for (i = 0; i < ndims; i++) {
start[i] = blockinfo[i];
count[i] = blockinfo[ndims + i] - start[i] + 1;
}
*/
}
int gUtilADIOS2IsScalar(hid_t space_id)
{
H5S_class_t stype = H5Sget_simple_extent_type(space_id);
if (H5S_SCALAR == stype)
return H5VL_CODE_SUCC;
return H5VL_CODE_FAIL;
}
int gUtilADIOS2GetDim(hid_t space_id) { return H5Sget_simple_extent_ndims(space_id); }
hid_t gUtilHDF5Type(adios2_type adios2Type)
{
if (adios2Type == adios2_type_int8_t)
return H5T_NATIVE_INT8;
if (adios2Type == adios2_type_int16_t)
return H5T_NATIVE_INT16;
if (adios2Type == adios2_type_int32_t)
return H5T_NATIVE_INT32;
if (adios2Type == adios2_type_int64_t)
return H5T_NATIVE_INT64;
if (adios2Type == adios2_type_uint8_t)
return H5T_NATIVE_UINT8;
if (adios2Type == adios2_type_uint16_t)
return H5T_NATIVE_UINT16;
if (adios2Type == adios2_type_uint32_t)
return H5T_NATIVE_UINT32;
if (adios2Type == adios2_type_uint64_t)
return H5T_NATIVE_UINT64;
if (adios2Type == adios2_type_float)
return H5T_NATIVE_FLOAT;
if (adios2Type == adios2_type_double)
return H5T_NATIVE_DOUBLE;
if (adios2Type == adios2_type_long_double)
return H5T_NATIVE_LDOUBLE;
if (adios2Type == adios2_type_string)
{
hid_t string_t_id = H5Tcopy(H5T_C_S1);
H5Tset_size(string_t_id,
30); // limiting each string to be less than 30 char long
return string_t_id;
}
// unknown types
return -1;
}
adios2_type gUtilADIOS2Type(hid_t h5Type)
{
if (H5Tequal(H5T_NATIVE_INT8, h5Type))
return adios2_type_int8_t;
if (H5Tequal(H5T_NATIVE_INT16, h5Type))
return adios2_type_int16_t;
if (H5Tequal(H5T_NATIVE_INT32, h5Type))
return adios2_type_int32_t;
if (H5Tequal(H5T_NATIVE_INT64, h5Type))
return adios2_type_int64_t;
if (H5Tequal(H5T_NATIVE_UINT8, h5Type))
return adios2_type_uint8_t;
if (H5Tequal(H5T_NATIVE_UINT16, h5Type))
return adios2_type_uint16_t;
if (H5Tequal(H5T_NATIVE_UINT32, h5Type))
return adios2_type_uint32_t;
if (H5Tequal(H5T_NATIVE_UINT64, h5Type))
return adios2_type_uint64_t;
if (H5Tequal(H5T_NATIVE_FLOAT, h5Type))
return adios2_type_float;
if (H5Tequal(H5T_NATIVE_DOUBLE, h5Type))
return adios2_type_double;
if (H5Tequal(H5T_NATIVE_LDOUBLE, h5Type))
return adios2_type_long_double;
if (H5Tget_class(h5Type) == H5T_NATIVE_CHAR)
return adios2_type_string;
if (H5Tget_class(h5Type) == H5T_STRING)
return adios2_type_string;
if (H5Tget_class(h5Type) == H5T_ENUM) //
return adios2_type_uint8_t;
// complex types are not supported in adios2_types
// so return unknown
return adios2_type_unknown;
}
|
