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
|
/****************************************************************************
* NCSA HDF *
* Software Development Group *
* National Center for Supercomputing Applications *
* University of Illinois at Urbana-Champaign *
* 605 E. Springfield, Champaign IL 61820 *
* *
* For conditions of distribution and use, see the accompanying *
* hdf/COPYING file. *
* *
****************************************************************************/
/*
* This file contains private information about the H5S module
*/
#ifndef _H5Sprivate_H
#define _H5Sprivate_H
#include "H5Spublic.h"
/* Private headers needed by this file */
#include "H5private.h"
#include "H5Dpublic.h"
#include "H5Fprivate.h"
#include "H5Oprivate.h"
#include "H5Pprivate.h"
#define H5S_RESERVED_ATOMS 2
/* Flags to indicate special dataspace features are active */
#define H5S_VALID_MAX 0x01
#define H5S_VALID_PERM 0x02
/* Flags for H5S_find */
#define H5S_CONV_PAR_IO_POSSIBLE 0x0001
/* The storage options are mutually exclusive */
/* (2-bits reserved for storage type currently) */
#define H5S_CONV_STORAGE_COMPACT 0x0000 /* i.e. '0' */
#define H5S_CONV_STORAGE_CONTIGUOUS 0x0002 /* i.e. '1' */
#define H5S_CONV_STORAGE_CHUNKED 0x0004 /* i.e. '2' */
#define H5S_CONV_STORAGE_MASK 0x0006
/* Forward references of common typedefs */
typedef struct H5S_t H5S_t;
typedef struct H5S_pnt_node_t H5S_pnt_node_t;
typedef struct H5S_hyper_span_t H5S_hyper_span_t;
typedef struct H5S_hyper_span_info_t H5S_hyper_span_info_t;
/* Point selection iteration container */
typedef struct {
hsize_t elmt_left; /* Number of elements left to iterate over */
H5S_pnt_node_t *curr; /* Pointer to next node to output */
} H5S_point_iter_t;
/* New Hyperslab selection iteration container */
typedef struct {
hsize_t elmt_left; /* Number of elements left to iterate over */
H5S_hyper_span_info_t *spans; /* Pointer to copy of the span tree */
H5S_hyper_span_t **span; /* Array of pointers to span nodes */
hssize_t *off; /* Offset in span node */
hssize_t *pos; /* Position to start iterating at */
} H5S_hyper_iter_t;
/* "All" selection iteration container */
typedef struct {
hsize_t elmt_left; /* Number of elements left to iterate over */
hsize_t offset; /* Next element to output */
} H5S_all_iter_t;
/* Selection iteration container */
typedef union {
H5S_point_iter_t pnt; /* Point selection iteration information */
H5S_hyper_iter_t hyp; /* New Hyperslab selection iteration information */
H5S_all_iter_t all; /* "All" selection iteration information */
} H5S_sel_iter_t;
/*
* Data space conversions usually take place in two halves. One half
* transfers data points between memory and a data type conversion array
* where the points are contiguous, and the other half transfers points
* between the type conversion array and the file.
*/
typedef struct H5S_fconv_t {
/* Identification */
const char *name;
H5S_sel_type type;
/* Initialize file element numbering information */
herr_t (*init)(const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter);
/* Determine optimal number of elements to transfer */
hsize_t (*avail)(const H5S_t *file_space, const H5S_sel_iter_t *file_iter,
hsize_t max);
/* Gather elements from disk to type conversion buffer */
hsize_t (*gath)(H5F_t *f, const struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
hsize_t nelmts, hid_t dxpl_id, void *tconv_buf/*out*/);
/* Scatter elements from type conversion buffer to disk */
herr_t (*scat)(H5F_t *f, const struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
hsize_t nelmts, hid_t dxpl_id, const void *tconv_buf);
} H5S_fconv_t;
typedef struct H5S_mconv_t {
/* Identification */
const char *name;
H5S_sel_type type;
/* Initialize memory element numbering information */
herr_t (*init)(const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter);
/* Gather elements from app buffer to type conversion buffer */
hsize_t (*gath)(const void *buf, size_t elmt_size,
const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
hsize_t nelmts, void *tconv_buf/*out*/);
/* Scatter elements from type conversion buffer to application buffer */
herr_t (*scat)(const void *tconv_buf, size_t elmt_size,
const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
hsize_t nelmts, void *buf/*out*/);
} H5S_mconv_t;
typedef struct H5S_conv_t {
const H5S_fconv_t *f;
const H5S_mconv_t *m;
/*
* If there is no data type conversion then it might be possible to
* transfer data points between application memory and the file in one
* step without going through the data type conversion buffer.
*/
/* Read from file to application w/o intermediate scratch buffer */
herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, void *buf/*out*/);
/* Write directly from app buffer to file */
herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf);
#ifdef H5S_DEBUG
struct {
H5_timer_t scat_timer; /*time spent scattering */
hsize_t scat_nbytes; /*scatter throughput */
hsize_t scat_ncalls; /*number of calls */
H5_timer_t gath_timer; /*time spent gathering */
hsize_t gath_nbytes; /*gather throughput */
hsize_t gath_ncalls; /*number of calls */
H5_timer_t bkg_timer; /*time for background */
hsize_t bkg_nbytes; /*background throughput */
hsize_t bkg_ncalls; /*number of calls */
H5_timer_t read_timer; /*time for read calls */
hsize_t read_nbytes; /*total bytes read */
hsize_t read_ncalls; /*number of calls */
H5_timer_t write_timer; /*time for write calls */
hsize_t write_nbytes; /*total bytes written */
hsize_t write_ncalls; /*number of calls */
} stats[2]; /* 0=output, 1=input */
#endif
} H5S_conv_t;
/* Conversion information for the various data space selection types */
__DLLVAR__ const H5S_fconv_t H5S_POINT_FCONV[];
__DLLVAR__ const H5S_mconv_t H5S_POINT_MCONV[];
__DLLVAR__ const H5S_fconv_t H5S_ALL_FCONV[];
__DLLVAR__ const H5S_mconv_t H5S_ALL_MCONV[];
__DLLVAR__ const H5S_fconv_t H5S_HYPER_FCONV[];
__DLLVAR__ const H5S_mconv_t H5S_HYPER_MCONV[];
/* We get the declaration of H5G_entry_t from the H5Oprivate.h file */
__DLL__ H5S_t *H5S_create(H5S_class_t type);
__DLL__ H5S_t *H5S_copy(const H5S_t *src);
__DLL__ herr_t H5S_close(H5S_t *ds);
__DLL__ H5S_conv_t *H5S_find(const H5S_t *mem_space, const H5S_t *file_space,
unsigned flags);
__DLL__ H5S_class_t H5S_get_simple_extent_type(const H5S_t *ds);
__DLL__ hssize_t H5S_get_simple_extent_npoints(const H5S_t *ds);
__DLL__ hsize_t H5S_get_npoints_max(const H5S_t *ds);
__DLL__ int H5S_get_simple_extent_ndims(const H5S_t *ds);
__DLL__ int H5S_get_simple_extent_dims(const H5S_t *ds, hsize_t dims[]/*out*/,
hsize_t max_dims[]/*out*/);
__DLL__ herr_t H5S_set_extent_simple (H5S_t *space, unsigned rank, const hsize_t *dims,
const hsize_t *max);
__DLL__ herr_t H5S_modify(struct H5G_entry_t *ent, const H5S_t *space);
__DLL__ H5S_t *H5S_read(struct H5G_entry_t *ent);
__DLL__ int H5S_cmp(const H5S_t *ds1, const H5S_t *ds2);
__DLL__ htri_t H5S_is_simple(const H5S_t *sdim);
__DLL__ unsigned H5S_nelem(const H5S_t *space);
__DLL__ int H5S_get_hyperslab(const H5S_t *ds, hssize_t offset[]/*out*/,
hsize_t size[]/*out*/, hsize_t stride[]/*out*/);
__DLL__ herr_t H5S_select_copy(H5S_t *dst, const H5S_t *src);
__DLL__ herr_t H5S_extent_release(H5S_t *space);
__DLL__ herr_t H5S_select_release(H5S_t *space);
__DLL__ hssize_t H5S_get_select_npoints(const H5S_t *space);
__DLL__ int H5S_extend(H5S_t *space, const hsize_t *size);
__DLL__ herr_t H5S_set_extent(H5S_t *space, const hsize_t *size);
__DLL__ htri_t H5S_select_valid(const H5S_t *space);
__DLL__ herr_t H5S_debug(H5F_t *f, const void *_mesg, FILE *stream,
int indent, int fwidth);
__DLL__ hssize_t H5S_select_serial_size(const H5S_t *space);
__DLL__ herr_t H5S_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ htri_t H5S_select_contiguous(const H5S_t *space);
__DLL__ htri_t H5S_select_single(const H5S_t *space);
__DLL__ htri_t H5S_select_regular(const H5S_t *space);
__DLL__ htri_t H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2);
__DLL__ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
__DLL__ herr_t H5S_sel_iter_release(const H5S_t *space,
H5S_sel_iter_t *sel_iter);
__DLL__ herr_t H5S_select_fill(const void *fill, size_t fill_size,
const H5S_t *space, void *buf);
/* Needed for internal use of selections in H5Fistore code */
__DLL__ herr_t H5S_select_all(H5S_t *space);
__DLL__ herr_t H5S_select_hyperslab (H5S_t *space, H5S_seloper_t op, const hssize_t start[],
const hsize_t stride[], const hsize_t count[],
const hsize_t block[]);
#ifdef H5_HAVE_PARALLEL
/* MPI-IO function to check whether its possible to transfer directly from app buffer to file */
__DLL__ htri_t H5S_all_opt_possible(const H5S_t *mem_space,
const H5S_t *file_space, const unsigned flags);
/* MPI-IO function to read directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
const struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
void *buf/*out*/);
/* MPI-IO function to write directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
const struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
const void *buf);
#ifndef _H5S_IN_H5S_C
/* Global var whose value comes from environment variable */
__DLLVAR__ hbool_t H5_mpi_opt_types_g;
#endif /* _H5S_IN_H5S_C */
#endif /* H5_HAVE_PARALLEL */
#endif /* _H5Sprivate_H */
|
