/src/hdf5/src/H5Dscatgath.c
Line | Count | Source |
1 | | /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * |
2 | | * Copyright by The HDF Group. * |
3 | | * All rights reserved. * |
4 | | * * |
5 | | * This file is part of HDF5. The full HDF5 copyright notice, including * |
6 | | * terms governing use, modification, and redistribution, is contained in * |
7 | | * the LICENSE file, which can be found at the root of the source code * |
8 | | * distribution tree, or in https://www.hdfgroup.org/licenses. * |
9 | | * If you do not have access to either file, you may request a copy from * |
10 | | * help@hdfgroup.org. * |
11 | | * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ |
12 | | |
13 | | /****************/ |
14 | | /* Module Setup */ |
15 | | /****************/ |
16 | | |
17 | | #include "H5Dmodule.h" /* This source code file is part of the H5D module */ |
18 | | |
19 | | /***********/ |
20 | | /* Headers */ |
21 | | /***********/ |
22 | | #include "H5private.h" /* Generic Functions */ |
23 | | #include "H5CXprivate.h" /* API Contexts */ |
24 | | #include "H5Dpkg.h" /* Dataset functions */ |
25 | | #include "H5Eprivate.h" /* Error handling */ |
26 | | #include "H5FLprivate.h" /* Free Lists */ |
27 | | #include "H5MMprivate.h" /* Memory management */ |
28 | | |
29 | | /****************/ |
30 | | /* Local Macros */ |
31 | | /****************/ |
32 | | |
33 | | /* Macro to determine if we're using H5D__compound_opt_read() */ |
34 | | #define H5D__SCATGATH_USE_CMPD_OPT_READ(DSET_INFO, IN_PLACE_TCONV) \ |
35 | 0 | ((DSET_INFO)->type_info.cmpd_subset && H5T_SUBSET_FALSE != (DSET_INFO)->type_info.cmpd_subset->subset && \ |
36 | 0 | !(IN_PLACE_TCONV)) |
37 | | |
38 | | /* Macro to determine if we're using H5D__compound_opt_write() */ |
39 | | #define H5D__SCATGATH_USE_CMPD_OPT_WRITE(DSET_INFO, IN_PLACE_TCONV) \ |
40 | 0 | ((DSET_INFO)->type_info.cmpd_subset && H5T_SUBSET_DST == (DSET_INFO)->type_info.cmpd_subset->subset && \ |
41 | 0 | (DSET_INFO)->type_info.dst_type_size == (DSET_INFO)->type_info.cmpd_subset->copy_size && \ |
42 | 0 | !(IN_PLACE_TCONV)) |
43 | | |
44 | | /******************/ |
45 | | /* Local Typedefs */ |
46 | | /******************/ |
47 | | |
48 | | /********************/ |
49 | | /* Local Prototypes */ |
50 | | /********************/ |
51 | | static herr_t H5D__scatter_file(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, |
52 | | H5S_sel_iter_t *file_iter, size_t nelmts, const void *buf); |
53 | | static size_t H5D__gather_file(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, |
54 | | H5S_sel_iter_t *file_iter, size_t nelmts, void *buf); |
55 | | static herr_t H5D__compound_opt_read(size_t nelmts, H5S_sel_iter_t *iter, const H5D_type_info_t *type_info, |
56 | | uint8_t *tconv_buf, void *user_buf /*out*/); |
57 | | static herr_t H5D__compound_opt_write(size_t nelmts, const H5D_type_info_t *type_info, void *tconv_buf); |
58 | | |
59 | | /*********************/ |
60 | | /* Package Variables */ |
61 | | /*********************/ |
62 | | |
63 | | /*******************/ |
64 | | /* Local Variables */ |
65 | | /*******************/ |
66 | | |
67 | | /* Declare extern free list to manage the H5S_sel_iter_t struct */ |
68 | | H5FL_EXTERN(H5S_sel_iter_t); |
69 | | |
70 | | /* Declare extern free list to manage sequences of size_t */ |
71 | | H5FL_SEQ_EXTERN(size_t); |
72 | | |
73 | | /* Declare extern free list to manage sequences of hsize_t */ |
74 | | H5FL_SEQ_EXTERN(hsize_t); |
75 | | |
76 | | /*------------------------------------------------------------------------- |
77 | | * Function: H5D__scatter_file |
78 | | * |
79 | | * Purpose: Scatters dataset elements from the type conversion buffer BUF |
80 | | * to the file F where the data points are arranged according to |
81 | | * the file dataspace FILE_SPACE and stored according to |
82 | | * LAYOUT and EFL. Each element is ELMT_SIZE bytes. |
83 | | * The caller is requesting that NELMTS elements are copied. |
84 | | * |
85 | | * Return: Non-negative on success/Negative on failure |
86 | | * |
87 | | *------------------------------------------------------------------------- |
88 | | */ |
89 | | static herr_t |
90 | | H5D__scatter_file(const H5D_io_info_t *_io_info, const H5D_dset_io_info_t *_dset_info, H5S_sel_iter_t *iter, |
91 | | size_t nelmts, const void *_buf) |
92 | 0 | { |
93 | 0 | H5D_io_info_t tmp_io_info; /* Temporary I/O info object */ |
94 | 0 | H5D_dset_io_info_t tmp_dset_info; /* Temporary I/O info object */ |
95 | 0 | hsize_t *off = NULL; /* Pointer to sequence offsets */ |
96 | 0 | hsize_t mem_off; /* Offset in memory */ |
97 | 0 | size_t mem_curr_seq; /* "Current sequence" in memory */ |
98 | 0 | size_t dset_curr_seq; /* "Current sequence" in dataset */ |
99 | 0 | size_t *len = NULL; /* Array to store sequence lengths */ |
100 | 0 | size_t orig_mem_len, mem_len; /* Length of sequence in memory */ |
101 | 0 | size_t nseq; /* Number of sequences generated */ |
102 | 0 | size_t nelem; /* Number of elements used in sequences */ |
103 | 0 | size_t dxpl_vec_size; /* Vector length from API context's DXPL */ |
104 | 0 | size_t vec_size; /* Vector length */ |
105 | 0 | herr_t ret_value = SUCCEED; /* Return value */ |
106 | |
|
107 | 0 | FUNC_ENTER_PACKAGE |
108 | | |
109 | | /* Check args */ |
110 | 0 | assert(_io_info); |
111 | 0 | assert(_dset_info); |
112 | 0 | assert(_dset_info->dset); |
113 | 0 | assert(_dset_info->store); |
114 | 0 | assert(iter); |
115 | 0 | assert(nelmts > 0); |
116 | 0 | assert(_buf); |
117 | | |
118 | | /* Set up temporary I/O info object */ |
119 | 0 | H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info)); |
120 | 0 | H5MM_memcpy(&tmp_dset_info, _dset_info, sizeof(*_dset_info)); |
121 | 0 | tmp_io_info.op_type = H5D_IO_OP_WRITE; |
122 | 0 | tmp_dset_info.buf.cvp = _buf; |
123 | 0 | tmp_io_info.dsets_info = &tmp_dset_info; |
124 | | |
125 | | /* Get info from API context */ |
126 | 0 | if (H5CX_get_vec_size(&dxpl_vec_size) < 0) |
127 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve I/O vector size"); |
128 | | |
129 | | /* Allocate the vector I/O arrays */ |
130 | 0 | if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) |
131 | 0 | vec_size = dxpl_vec_size; |
132 | 0 | else |
133 | 0 | vec_size = H5D_IO_VECTOR_SIZE; |
134 | 0 | if (NULL == (len = H5FL_SEQ_MALLOC(size_t, vec_size))) |
135 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array"); |
136 | 0 | if (NULL == (off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) |
137 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array"); |
138 | | |
139 | | /* Loop until all elements are written */ |
140 | 0 | while (nelmts > 0) { |
141 | | /* Get list of sequences for selection to write */ |
142 | 0 | if (H5S_SELECT_ITER_GET_SEQ_LIST(iter, vec_size, nelmts, &nseq, &nelem, off, len) < 0) |
143 | 0 | HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); |
144 | | |
145 | | /* Reset the current sequence information */ |
146 | 0 | mem_curr_seq = dset_curr_seq = 0; |
147 | 0 | orig_mem_len = mem_len = nelem * iter->elmt_size; |
148 | 0 | mem_off = 0; |
149 | | |
150 | | /* Write sequence list out */ |
151 | 0 | if ((*tmp_dset_info.layout_ops.writevv)(&tmp_io_info, &tmp_dset_info, nseq, &dset_curr_seq, len, off, |
152 | 0 | (size_t)1, &mem_curr_seq, &mem_len, &mem_off) < 0) |
153 | 0 | HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); |
154 | | |
155 | | /* Update buffer */ |
156 | 0 | tmp_dset_info.buf.cvp = (const uint8_t *)tmp_dset_info.buf.cvp + orig_mem_len; |
157 | | |
158 | | /* Decrement number of elements left to process */ |
159 | 0 | nelmts -= nelem; |
160 | 0 | } /* end while */ |
161 | | |
162 | 0 | done: |
163 | | /* Release resources, if allocated */ |
164 | 0 | if (len) |
165 | 0 | len = H5FL_SEQ_FREE(size_t, len); |
166 | 0 | if (off) |
167 | 0 | off = H5FL_SEQ_FREE(hsize_t, off); |
168 | |
|
169 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
170 | 0 | } /* H5D__scatter_file() */ |
171 | | |
172 | | /*------------------------------------------------------------------------- |
173 | | * Function: H5D__gather_file |
174 | | * |
175 | | * Purpose: Gathers data points from file F and accumulates them in the |
176 | | * type conversion buffer BUF. The LAYOUT argument describes |
177 | | * how the data is stored on disk and EFL describes how the data |
178 | | * is organized in external files. ELMT_SIZE is the size in |
179 | | * bytes of a datum which this function treats as opaque. |
180 | | * FILE_SPACE describes the dataspace of the dataset on disk |
181 | | * and the elements that have been selected for reading (via |
182 | | * hyperslab, etc). This function will copy at most NELMTS |
183 | | * elements. |
184 | | * |
185 | | * Return: Success: Number of elements copied. |
186 | | * Failure: 0 |
187 | | * |
188 | | *------------------------------------------------------------------------- |
189 | | */ |
190 | | static size_t |
191 | | H5D__gather_file(const H5D_io_info_t *_io_info, const H5D_dset_io_info_t *_dset_info, H5S_sel_iter_t *iter, |
192 | | size_t nelmts, void *_buf /*out*/) |
193 | 0 | { |
194 | 0 | H5D_io_info_t tmp_io_info; /* Temporary I/O info object */ |
195 | 0 | H5D_dset_io_info_t tmp_dset_info; /* Temporary I/O info object */ |
196 | 0 | hsize_t *off = NULL; /* Pointer to sequence offsets */ |
197 | 0 | hsize_t mem_off; /* Offset in memory */ |
198 | 0 | size_t mem_curr_seq; /* "Current sequence" in memory */ |
199 | 0 | size_t dset_curr_seq; /* "Current sequence" in dataset */ |
200 | 0 | size_t *len = NULL; /* Pointer to sequence lengths */ |
201 | 0 | size_t orig_mem_len, mem_len; /* Length of sequence in memory */ |
202 | 0 | size_t nseq; /* Number of sequences generated */ |
203 | 0 | size_t nelem; /* Number of elements used in sequences */ |
204 | 0 | size_t dxpl_vec_size; /* Vector length from API context's DXPL */ |
205 | 0 | size_t vec_size; /* Vector length */ |
206 | 0 | size_t ret_value = nelmts; /* Return value */ |
207 | |
|
208 | 0 | FUNC_ENTER_PACKAGE |
209 | | |
210 | | /* Check args */ |
211 | 0 | assert(_io_info); |
212 | 0 | assert(_dset_info); |
213 | 0 | assert(_dset_info->dset); |
214 | 0 | assert(_dset_info->store); |
215 | 0 | assert(iter); |
216 | 0 | assert(nelmts > 0); |
217 | 0 | assert(_buf); |
218 | | |
219 | | /* Set up temporary I/O info object */ |
220 | 0 | H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info)); |
221 | 0 | H5MM_memcpy(&tmp_dset_info, _dset_info, sizeof(*_dset_info)); |
222 | 0 | tmp_io_info.op_type = H5D_IO_OP_READ; |
223 | 0 | tmp_dset_info.buf.vp = _buf; |
224 | 0 | tmp_io_info.dsets_info = &tmp_dset_info; |
225 | | |
226 | | /* Get info from API context */ |
227 | 0 | if (H5CX_get_vec_size(&dxpl_vec_size) < 0) |
228 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't retrieve I/O vector size"); |
229 | | |
230 | | /* Allocate the vector I/O arrays */ |
231 | 0 | if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) |
232 | 0 | vec_size = dxpl_vec_size; |
233 | 0 | else |
234 | 0 | vec_size = H5D_IO_VECTOR_SIZE; |
235 | 0 | if (NULL == (len = H5FL_SEQ_MALLOC(size_t, vec_size))) |
236 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, 0, "can't allocate I/O length vector array"); |
237 | 0 | if (NULL == (off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) |
238 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, 0, "can't allocate I/O offset vector array"); |
239 | | |
240 | | /* Loop until all elements are read */ |
241 | 0 | while (nelmts > 0) { |
242 | | /* Get list of sequences for selection to read */ |
243 | 0 | if (H5S_SELECT_ITER_GET_SEQ_LIST(iter, vec_size, nelmts, &nseq, &nelem, off, len) < 0) |
244 | 0 | HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); |
245 | | |
246 | | /* Reset the current sequence information */ |
247 | 0 | mem_curr_seq = dset_curr_seq = 0; |
248 | 0 | orig_mem_len = mem_len = nelem * iter->elmt_size; |
249 | 0 | mem_off = 0; |
250 | | |
251 | | /* Read sequence list in */ |
252 | 0 | if ((*tmp_dset_info.layout_ops.readvv)(&tmp_io_info, &tmp_dset_info, nseq, &dset_curr_seq, len, off, |
253 | 0 | (size_t)1, &mem_curr_seq, &mem_len, &mem_off) < 0) |
254 | 0 | HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); |
255 | | |
256 | | /* Update buffer */ |
257 | 0 | tmp_dset_info.buf.vp = (uint8_t *)tmp_dset_info.buf.vp + orig_mem_len; |
258 | | |
259 | | /* Decrement number of elements left to process */ |
260 | 0 | nelmts -= nelem; |
261 | 0 | } /* end while */ |
262 | | |
263 | 0 | done: |
264 | | /* Release resources, if allocated */ |
265 | 0 | if (len) |
266 | 0 | len = H5FL_SEQ_FREE(size_t, len); |
267 | 0 | if (off) |
268 | 0 | off = H5FL_SEQ_FREE(hsize_t, off); |
269 | |
|
270 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
271 | 0 | } /* H5D__gather_file() */ |
272 | | |
273 | | /*------------------------------------------------------------------------- |
274 | | * Function: H5D__scatter_mem |
275 | | * |
276 | | * Purpose: Scatters NELMTS data points from the scatter buffer |
277 | | * TSCAT_BUF to the application buffer BUF. Each element is |
278 | | * ELMT_SIZE bytes and they are organized in application memory |
279 | | * according to SPACE. |
280 | | * |
281 | | * Return: Non-negative on success/Negative on failure |
282 | | * |
283 | | *------------------------------------------------------------------------- |
284 | | */ |
285 | | herr_t |
286 | | H5D__scatter_mem(const void *_tscat_buf, H5S_sel_iter_t *iter, size_t nelmts, void *_buf /*out*/) |
287 | 0 | { |
288 | 0 | uint8_t *buf = (uint8_t *)_buf; /* Get local copies for address arithmetic */ |
289 | 0 | const uint8_t *tscat_buf = (const uint8_t *)_tscat_buf; |
290 | 0 | hsize_t *off = NULL; /* Pointer to sequence offsets */ |
291 | 0 | size_t *len = NULL; /* Pointer to sequence lengths */ |
292 | 0 | size_t curr_len; /* Length of bytes left to process in sequence */ |
293 | 0 | size_t nseq; /* Number of sequences generated */ |
294 | 0 | size_t curr_seq; /* Current sequence being processed */ |
295 | 0 | size_t nelem; /* Number of elements used in sequences */ |
296 | 0 | size_t dxpl_vec_size; /* Vector length from API context's DXPL */ |
297 | 0 | size_t vec_size; /* Vector length */ |
298 | 0 | herr_t ret_value = SUCCEED; /* Number of elements scattered */ |
299 | |
|
300 | 0 | FUNC_ENTER_PACKAGE |
301 | | |
302 | | /* Check args */ |
303 | 0 | assert(tscat_buf); |
304 | 0 | assert(iter); |
305 | 0 | assert(nelmts > 0); |
306 | 0 | assert(buf); |
307 | | |
308 | | /* Get info from API context */ |
309 | 0 | if (H5CX_get_vec_size(&dxpl_vec_size) < 0) |
310 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve I/O vector size"); |
311 | | |
312 | | /* Allocate the vector I/O arrays */ |
313 | 0 | if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) |
314 | 0 | vec_size = dxpl_vec_size; |
315 | 0 | else |
316 | 0 | vec_size = H5D_IO_VECTOR_SIZE; |
317 | 0 | if (NULL == (len = H5FL_SEQ_MALLOC(size_t, vec_size))) |
318 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array"); |
319 | 0 | if (NULL == (off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) |
320 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array"); |
321 | | |
322 | | /* Loop until all elements are written */ |
323 | 0 | while (nelmts > 0) { |
324 | | /* Get list of sequences for selection to write */ |
325 | 0 | if (H5S_SELECT_ITER_GET_SEQ_LIST(iter, vec_size, nelmts, &nseq, &nelem, off, len) < 0) |
326 | 0 | HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); |
327 | | |
328 | | /* Loop, while sequences left to process */ |
329 | 0 | for (curr_seq = 0; curr_seq < nseq; curr_seq++) { |
330 | | /* Get the number of bytes in sequence */ |
331 | 0 | curr_len = len[curr_seq]; |
332 | |
|
333 | 0 | H5MM_memcpy(buf + off[curr_seq], tscat_buf, curr_len); |
334 | | |
335 | | /* Advance offset in destination buffer */ |
336 | 0 | tscat_buf += curr_len; |
337 | 0 | } /* end for */ |
338 | | |
339 | | /* Decrement number of elements left to process */ |
340 | 0 | nelmts -= nelem; |
341 | 0 | } /* end while */ |
342 | | |
343 | 0 | done: |
344 | | /* Release resources, if allocated */ |
345 | 0 | if (len) |
346 | 0 | len = H5FL_SEQ_FREE(size_t, len); |
347 | 0 | if (off) |
348 | 0 | off = H5FL_SEQ_FREE(hsize_t, off); |
349 | |
|
350 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
351 | 0 | } /* H5D__scatter_mem() */ |
352 | | |
353 | | /*------------------------------------------------------------------------- |
354 | | * Function: H5D__gather_mem |
355 | | * |
356 | | * Purpose: Gathers dataset elements from application memory BUF and |
357 | | * copies them into the gather buffer TGATH_BUF. |
358 | | * Each element is ELMT_SIZE bytes and arranged in application |
359 | | * memory according to SPACE. |
360 | | * The caller is requesting that exactly NELMTS be gathered. |
361 | | * |
362 | | * Return: Success: Number of elements copied. |
363 | | * Failure: 0 |
364 | | * |
365 | | *------------------------------------------------------------------------- |
366 | | */ |
367 | | size_t |
368 | | H5D__gather_mem(const void *_buf, H5S_sel_iter_t *iter, size_t nelmts, void *_tgath_buf /*out*/) |
369 | 0 | { |
370 | 0 | const uint8_t *buf = (const uint8_t *)_buf; /* Get local copies for address arithmetic */ |
371 | 0 | uint8_t *tgath_buf = (uint8_t *)_tgath_buf; |
372 | 0 | hsize_t *off = NULL; /* Pointer to sequence offsets */ |
373 | 0 | size_t *len = NULL; /* Pointer to sequence lengths */ |
374 | 0 | size_t curr_len; /* Length of bytes left to process in sequence */ |
375 | 0 | size_t nseq; /* Number of sequences generated */ |
376 | 0 | size_t curr_seq; /* Current sequence being processed */ |
377 | 0 | size_t nelem; /* Number of elements used in sequences */ |
378 | 0 | size_t dxpl_vec_size; /* Vector length from API context's DXPL */ |
379 | 0 | size_t vec_size; /* Vector length */ |
380 | 0 | size_t ret_value = nelmts; /* Number of elements gathered */ |
381 | |
|
382 | 0 | FUNC_ENTER_PACKAGE |
383 | | |
384 | | /* Check args */ |
385 | 0 | assert(buf); |
386 | 0 | assert(iter); |
387 | 0 | assert(nelmts > 0); |
388 | 0 | assert(tgath_buf); |
389 | | |
390 | | /* Get info from API context */ |
391 | 0 | if (H5CX_get_vec_size(&dxpl_vec_size) < 0) |
392 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't retrieve I/O vector size"); |
393 | | |
394 | | /* Allocate the vector I/O arrays */ |
395 | 0 | if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) |
396 | 0 | vec_size = dxpl_vec_size; |
397 | 0 | else |
398 | 0 | vec_size = H5D_IO_VECTOR_SIZE; |
399 | 0 | if (NULL == (len = H5FL_SEQ_MALLOC(size_t, vec_size))) |
400 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, 0, "can't allocate I/O length vector array"); |
401 | 0 | if (NULL == (off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) |
402 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, 0, "can't allocate I/O offset vector array"); |
403 | | |
404 | | /* Loop until all elements are written */ |
405 | 0 | while (nelmts > 0) { |
406 | | /* Get list of sequences for selection to write */ |
407 | 0 | if (H5S_SELECT_ITER_GET_SEQ_LIST(iter, vec_size, nelmts, &nseq, &nelem, off, len) < 0) |
408 | 0 | HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); |
409 | | |
410 | | /* Loop, while sequences left to process */ |
411 | 0 | for (curr_seq = 0; curr_seq < nseq; curr_seq++) { |
412 | | /* Get the number of bytes in sequence */ |
413 | 0 | curr_len = len[curr_seq]; |
414 | |
|
415 | 0 | H5MM_memcpy(tgath_buf, buf + off[curr_seq], curr_len); |
416 | | |
417 | | /* Advance offset in gather buffer */ |
418 | 0 | tgath_buf += curr_len; |
419 | 0 | } /* end for */ |
420 | | |
421 | | /* Decrement number of elements left to process */ |
422 | 0 | nelmts -= nelem; |
423 | 0 | } /* end while */ |
424 | | |
425 | 0 | done: |
426 | | /* Release resources, if allocated */ |
427 | 0 | if (len) |
428 | 0 | len = H5FL_SEQ_FREE(size_t, len); |
429 | 0 | if (off) |
430 | 0 | off = H5FL_SEQ_FREE(hsize_t, off); |
431 | |
|
432 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
433 | 0 | } /* H5D__gather_mem() */ |
434 | | |
435 | | /*------------------------------------------------------------------------- |
436 | | * Function: H5D__scatgath_read |
437 | | * |
438 | | * Purpose: Perform scatter/gather ead from a contiguous [piece of a] dataset. |
439 | | * |
440 | | * Return: Non-negative on success/Negative on failure |
441 | | * |
442 | | *------------------------------------------------------------------------- |
443 | | */ |
444 | | herr_t |
445 | | H5D__scatgath_read(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info) |
446 | 0 | { |
447 | 0 | void *buf; /* Local pointer to application buffer */ |
448 | 0 | void *tmp_buf; /* Buffer to use for type conversion */ |
449 | 0 | H5S_sel_iter_t *mem_iter = NULL; /* Memory selection iteration info*/ |
450 | 0 | bool mem_iter_init = false; /* Memory selection iteration info has been initialized */ |
451 | 0 | H5S_sel_iter_t *bkg_iter = NULL; /* Background iteration info*/ |
452 | 0 | bool bkg_iter_init = false; /* Background iteration info has been initialized */ |
453 | 0 | H5S_sel_iter_t *file_iter = NULL; /* File selection iteration info*/ |
454 | 0 | bool file_iter_init = false; /* File selection iteration info has been initialized */ |
455 | 0 | hsize_t smine_start; /* Strip mine start loc */ |
456 | 0 | size_t smine_nelmts; /* Elements per strip */ |
457 | 0 | bool in_place_tconv; /* Whether to perform in-place type_conversion */ |
458 | 0 | herr_t ret_value = SUCCEED; /* Return value */ |
459 | |
|
460 | 0 | FUNC_ENTER_PACKAGE |
461 | | |
462 | | /* Sanity check */ |
463 | 0 | assert(io_info); |
464 | 0 | assert(dset_info); |
465 | 0 | assert(dset_info->mem_space); |
466 | 0 | assert(dset_info->file_space); |
467 | 0 | assert(dset_info->buf.vp); |
468 | | |
469 | | /* Set buf pointer */ |
470 | 0 | buf = dset_info->buf.vp; |
471 | | |
472 | | /* Check for NOOP read */ |
473 | 0 | if (dset_info->nelmts == 0) |
474 | 0 | HGOTO_DONE(SUCCEED); |
475 | | |
476 | | /* Check for in-place type conversion */ |
477 | 0 | in_place_tconv = dset_info->layout_io_info.contig_piece_info && |
478 | 0 | dset_info->layout_io_info.contig_piece_info->in_place_tconv; |
479 | | |
480 | | /* Check if we should disable in-place type conversion for performance. Do so if we can use the optimized |
481 | | * compound read function, if this is not a selection I/O operation (so we have normal size conversion |
482 | | * buffers), and the either entire I/O operation can fit in the type conversion buffer or we need to use a |
483 | | * background buffer (and therefore could not do the I/O in one operation with in-place conversion |
484 | | * anyways). */ |
485 | 0 | if (in_place_tconv && H5D__SCATGATH_USE_CMPD_OPT_READ(dset_info, false) && |
486 | 0 | (io_info->use_select_io != H5D_SELECTION_IO_MODE_ON) && |
487 | 0 | (dset_info->type_info.need_bkg || (dset_info->nelmts <= dset_info->type_info.request_nelmts))) |
488 | 0 | in_place_tconv = false; |
489 | | |
490 | | /* Allocate the iterators */ |
491 | 0 | if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
492 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate memory iterator"); |
493 | 0 | if (NULL == (bkg_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
494 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate background iterator"); |
495 | 0 | if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
496 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate file iterator"); |
497 | | |
498 | | /* Figure out the strip mine size. */ |
499 | 0 | if (H5S_select_iter_init(file_iter, dset_info->file_space, dset_info->type_info.src_type_size, |
500 | 0 | H5S_SEL_ITER_GET_SEQ_LIST_SORTED) < 0) |
501 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); |
502 | 0 | file_iter_init = true; /*file selection iteration info has been initialized */ |
503 | 0 | if (H5S_select_iter_init(mem_iter, dset_info->mem_space, dset_info->type_info.dst_type_size, 0) < 0) |
504 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); |
505 | 0 | mem_iter_init = true; /*file selection iteration info has been initialized */ |
506 | 0 | if (H5S_select_iter_init(bkg_iter, dset_info->mem_space, dset_info->type_info.dst_type_size, 0) < 0) |
507 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); |
508 | 0 | bkg_iter_init = true; /*file selection iteration info has been initialized */ |
509 | | |
510 | | /* Start strip mining... */ |
511 | 0 | for (smine_start = 0; smine_start < dset_info->nelmts; smine_start += smine_nelmts) { |
512 | 0 | size_t n; /* Elements operated on */ |
513 | |
|
514 | 0 | assert(H5S_SELECT_ITER_NELMTS(file_iter) == (dset_info->nelmts - smine_start)); |
515 | | |
516 | | /* Determine strip mine size. First check if we're doing in-place type conversion */ |
517 | 0 | if (in_place_tconv) { |
518 | | /* If this is not a selection I/O operation and there is a background buffer, we cannot exceed |
519 | | * request_nelmts. It could be part of a selection I/O operation if this read is used to fill in |
520 | | * a nonexistent chunk */ |
521 | 0 | assert(!H5D__SCATGATH_USE_CMPD_OPT_READ(dset_info, in_place_tconv)); |
522 | 0 | if (dset_info->type_info.need_bkg && (io_info->use_select_io != H5D_SELECTION_IO_MODE_ON)) |
523 | 0 | smine_nelmts = |
524 | 0 | (size_t)MIN(dset_info->type_info.request_nelmts, (dset_info->nelmts - smine_start)); |
525 | 0 | else { |
526 | 0 | assert(smine_start == 0); |
527 | 0 | smine_nelmts = dset_info->nelmts; |
528 | 0 | } |
529 | | |
530 | | /* Calculate buffer position in user buffer */ |
531 | 0 | tmp_buf = (uint8_t *)buf + dset_info->layout_io_info.contig_piece_info->buf_off + |
532 | 0 | (smine_start * dset_info->type_info.dst_type_size); |
533 | 0 | } |
534 | 0 | else { |
535 | | /* Do type conversion using intermediate buffer */ |
536 | 0 | tmp_buf = io_info->tconv_buf; |
537 | | |
538 | | /* Go figure out how many elements to read from the file */ |
539 | 0 | smine_nelmts = |
540 | 0 | (size_t)MIN(dset_info->type_info.request_nelmts, (dset_info->nelmts - smine_start)); |
541 | 0 | } |
542 | | |
543 | | /* |
544 | | * Gather the data from disk into the datatype conversion |
545 | | * buffer. Also gather data from application to background buffer |
546 | | * if necessary. |
547 | | */ |
548 | | |
549 | | /* Fill background buffer here unless we will use H5D__compound_opt_read(). Must do this before |
550 | | * the read so the read buffer doesn't get wiped out if we're using in-place type conversion */ |
551 | 0 | if ((H5T_BKG_YES == dset_info->type_info.need_bkg) && |
552 | 0 | !H5D__SCATGATH_USE_CMPD_OPT_READ(dset_info, in_place_tconv)) { |
553 | 0 | n = H5D__gather_mem(buf, bkg_iter, smine_nelmts, io_info->bkg_buf /*out*/); |
554 | 0 | if (n != smine_nelmts) |
555 | 0 | HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); |
556 | 0 | } |
557 | | |
558 | | /* |
559 | | * Gather data |
560 | | */ |
561 | 0 | n = H5D__gather_file(io_info, dset_info, file_iter, smine_nelmts, tmp_buf /*out*/); |
562 | 0 | if (n != smine_nelmts) |
563 | 0 | HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); |
564 | | |
565 | | /* If the source and destination are compound types and subset of each other |
566 | | * and no conversion is needed, copy the data directly into user's buffer and |
567 | | * bypass the rest of steps. |
568 | | */ |
569 | 0 | if (H5D__SCATGATH_USE_CMPD_OPT_READ(dset_info, in_place_tconv)) { |
570 | 0 | if (H5D__compound_opt_read(smine_nelmts, mem_iter, &dset_info->type_info, tmp_buf, buf /*out*/) < |
571 | 0 | 0) |
572 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed"); |
573 | 0 | } /* end if */ |
574 | 0 | else { |
575 | | /* |
576 | | * Perform datatype conversion. |
577 | | */ |
578 | 0 | if (H5T_convert(dset_info->type_info.tpath, dset_info->type_info.src_type, |
579 | 0 | dset_info->type_info.dst_type, smine_nelmts, (size_t)0, (size_t)0, tmp_buf, |
580 | 0 | io_info->bkg_buf) < 0) |
581 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed"); |
582 | | |
583 | | /* Do the data transform after the conversion (since we're using type mem_type) */ |
584 | 0 | if (!dset_info->type_info.is_xform_noop) { |
585 | 0 | H5Z_data_xform_t *data_transform; /* Data transform info */ |
586 | | |
587 | | /* Retrieve info from API context */ |
588 | 0 | if (H5CX_get_data_transform(&data_transform) < 0) |
589 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info"); |
590 | | |
591 | 0 | if (H5Z_xform_eval(data_transform, tmp_buf, smine_nelmts, dset_info->type_info.mem_type) < 0) |
592 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Error performing data transform"); |
593 | 0 | } |
594 | | |
595 | | /* Scatter the data into memory if this was not an in-place conversion */ |
596 | 0 | if (!in_place_tconv) |
597 | 0 | if (H5D__scatter_mem(tmp_buf, mem_iter, smine_nelmts, buf /*out*/) < 0) |
598 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); |
599 | 0 | } /* end else */ |
600 | 0 | } /* end for */ |
601 | | |
602 | 0 | done: |
603 | | /* Release selection iterators */ |
604 | 0 | if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0) |
605 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
606 | 0 | if (file_iter) |
607 | 0 | file_iter = H5FL_FREE(H5S_sel_iter_t, file_iter); |
608 | 0 | if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) |
609 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
610 | 0 | if (mem_iter) |
611 | 0 | mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter); |
612 | 0 | if (bkg_iter_init && H5S_SELECT_ITER_RELEASE(bkg_iter) < 0) |
613 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
614 | 0 | if (bkg_iter) |
615 | 0 | bkg_iter = H5FL_FREE(H5S_sel_iter_t, bkg_iter); |
616 | |
|
617 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
618 | 0 | } /* end H5D__scatgath_read() */ |
619 | | |
620 | | /*------------------------------------------------------------------------- |
621 | | * Function: H5D__scatgath_write |
622 | | * |
623 | | * Purpose: Perform scatter/gather write to a contiguous [piece of a] dataset. |
624 | | * |
625 | | * Return: Non-negative on success/Negative on failure |
626 | | * |
627 | | *------------------------------------------------------------------------- |
628 | | */ |
629 | | herr_t |
630 | | H5D__scatgath_write(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info) |
631 | 0 | { |
632 | 0 | const void *buf; /* Local pointer to application buffer */ |
633 | 0 | void *tmp_buf; /* Buffer to use for type conversion */ |
634 | 0 | H5S_sel_iter_t *mem_iter = NULL; /* Memory selection iteration info*/ |
635 | 0 | bool mem_iter_init = false; /* Memory selection iteration info has been initialized */ |
636 | 0 | H5S_sel_iter_t *bkg_iter = NULL; /* Background iteration info*/ |
637 | 0 | bool bkg_iter_init = false; /* Background iteration info has been initialized */ |
638 | 0 | H5S_sel_iter_t *file_iter = NULL; /* File selection iteration info*/ |
639 | 0 | bool file_iter_init = false; /* File selection iteration info has been initialized */ |
640 | 0 | hsize_t smine_start; /* Strip mine start loc */ |
641 | 0 | size_t smine_nelmts; /* Elements per strip */ |
642 | 0 | bool in_place_tconv; /* Whether to perform in-place type_conversion */ |
643 | 0 | herr_t ret_value = SUCCEED; /* Return value */ |
644 | |
|
645 | 0 | FUNC_ENTER_PACKAGE |
646 | | |
647 | | /* Sanity check */ |
648 | 0 | assert(io_info); |
649 | 0 | assert(dset_info); |
650 | 0 | assert(dset_info->mem_space); |
651 | 0 | assert(dset_info->file_space); |
652 | 0 | assert(dset_info->buf.cvp); |
653 | | |
654 | | /* Set buf pointer */ |
655 | 0 | buf = dset_info->buf.cvp; |
656 | | |
657 | | /* Check for NOOP write */ |
658 | 0 | if (dset_info->nelmts == 0) |
659 | 0 | HGOTO_DONE(SUCCEED); |
660 | | |
661 | | /* Check for in-place type conversion */ |
662 | 0 | in_place_tconv = dset_info->layout_io_info.contig_piece_info && |
663 | 0 | dset_info->layout_io_info.contig_piece_info->in_place_tconv; |
664 | | |
665 | | /* Check if we should disable in-place type conversion for performance. Do so if we can use the optimized |
666 | | * compound write function, if this is not a selection I/O operation (so we have normal size conversion |
667 | | * buffers), and the either entire I/O operation can fit in the type conversion buffer or we need to use a |
668 | | * background buffer (and therefore could not do the I/O in one operation with in-place conversion |
669 | | * anyways). */ |
670 | 0 | if (in_place_tconv && H5D__SCATGATH_USE_CMPD_OPT_WRITE(dset_info, false) && |
671 | 0 | (io_info->use_select_io != H5D_SELECTION_IO_MODE_ON) && |
672 | 0 | (dset_info->type_info.need_bkg || (dset_info->nelmts <= dset_info->type_info.request_nelmts))) |
673 | 0 | in_place_tconv = false; |
674 | | |
675 | | /* Allocate the iterators */ |
676 | 0 | if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
677 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate memory iterator"); |
678 | 0 | if (NULL == (bkg_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
679 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate background iterator"); |
680 | 0 | if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
681 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate file iterator"); |
682 | | |
683 | | /* Figure out the strip mine size. */ |
684 | 0 | if (H5S_select_iter_init(file_iter, dset_info->file_space, dset_info->type_info.dst_type_size, |
685 | 0 | H5S_SEL_ITER_GET_SEQ_LIST_SORTED) < 0) |
686 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); |
687 | 0 | file_iter_init = true; /*file selection iteration info has been initialized */ |
688 | 0 | if (H5S_select_iter_init(mem_iter, dset_info->mem_space, dset_info->type_info.src_type_size, 0) < 0) |
689 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); |
690 | 0 | mem_iter_init = true; /*file selection iteration info has been initialized */ |
691 | 0 | if (H5S_select_iter_init(bkg_iter, dset_info->file_space, dset_info->type_info.dst_type_size, |
692 | 0 | H5S_SEL_ITER_GET_SEQ_LIST_SORTED) < 0) |
693 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); |
694 | 0 | bkg_iter_init = true; /*file selection iteration info has been initialized */ |
695 | | |
696 | | /* Start strip mining... */ |
697 | 0 | for (smine_start = 0; smine_start < dset_info->nelmts; smine_start += smine_nelmts) { |
698 | 0 | size_t n; /* Elements operated on */ |
699 | |
|
700 | 0 | assert(H5S_SELECT_ITER_NELMTS(file_iter) == (dset_info->nelmts - smine_start)); |
701 | | |
702 | | /* Determine strip mine size. First check if we're doing in-place type conversion */ |
703 | 0 | if (in_place_tconv) { |
704 | | /* If this is not a selection I/O operation and there is a background buffer, we cannot exceed |
705 | | * request_nelmts. It could be part of a selection I/O operation if this is used to write the |
706 | | * fill value to a cached chunk that will immediately be evicted. */ |
707 | 0 | assert(!H5D__SCATGATH_USE_CMPD_OPT_WRITE(dset_info, in_place_tconv)); |
708 | 0 | if (dset_info->type_info.need_bkg && (io_info->use_select_io != H5D_SELECTION_IO_MODE_ON)) |
709 | 0 | smine_nelmts = |
710 | 0 | (size_t)MIN(dset_info->type_info.request_nelmts, (dset_info->nelmts - smine_start)); |
711 | 0 | else { |
712 | 0 | assert(smine_start == 0); |
713 | 0 | smine_nelmts = dset_info->nelmts; |
714 | 0 | } |
715 | | |
716 | | /* Calculate buffer position in user buffer */ |
717 | | /* Use "vp" field of union to twiddle away const. OK because if we're doing this it means the |
718 | | * user explicitly allowed us to modify this buffer via H5Pset_modify_write_buf(). */ |
719 | 0 | tmp_buf = (uint8_t *)dset_info->buf.vp + dset_info->layout_io_info.contig_piece_info->buf_off + |
720 | 0 | (smine_start * dset_info->type_info.src_type_size); |
721 | 0 | } |
722 | 0 | else { |
723 | | /* Do type conversion using intermediate buffer */ |
724 | 0 | tmp_buf = io_info->tconv_buf; |
725 | | |
726 | | /* Go figure out how many elements to read from the file */ |
727 | 0 | smine_nelmts = |
728 | 0 | (size_t)MIN(dset_info->type_info.request_nelmts, (dset_info->nelmts - smine_start)); |
729 | | |
730 | | /* |
731 | | * Gather data from application buffer into the datatype conversion |
732 | | * buffer. Also gather data from the file into the background buffer |
733 | | * if necessary. |
734 | | */ |
735 | 0 | n = H5D__gather_mem(buf, mem_iter, smine_nelmts, tmp_buf /*out*/); |
736 | 0 | if (n != smine_nelmts) |
737 | 0 | HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed"); |
738 | 0 | } |
739 | | |
740 | | /* If the source and destination are compound types and the destination is |
741 | | * is a subset of the source and no conversion is needed, copy the data |
742 | | * directly from user's buffer and bypass the rest of steps. If the source |
743 | | * is a subset of the destination, the optimization is done in conversion |
744 | | * function H5T_conv_struct_opt to protect the background data. |
745 | | */ |
746 | 0 | if (H5D__SCATGATH_USE_CMPD_OPT_WRITE(dset_info, in_place_tconv)) { |
747 | 0 | if (H5D__compound_opt_write(smine_nelmts, &dset_info->type_info, tmp_buf) < 0) |
748 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed"); |
749 | |
|
750 | 0 | } /* end if */ |
751 | 0 | else { |
752 | 0 | if (H5T_BKG_YES == dset_info->type_info.need_bkg) { |
753 | 0 | n = H5D__gather_file(io_info, dset_info, bkg_iter, smine_nelmts, io_info->bkg_buf /*out*/); |
754 | 0 | if (n != smine_nelmts) |
755 | 0 | HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); |
756 | 0 | } /* end if */ |
757 | | |
758 | | /* Do the data transform before the type conversion (since |
759 | | * transforms must be done in the memory type). */ |
760 | 0 | if (!dset_info->type_info.is_xform_noop) { |
761 | 0 | H5Z_data_xform_t *data_transform; /* Data transform info */ |
762 | | |
763 | | /* Retrieve info from API context */ |
764 | 0 | if (H5CX_get_data_transform(&data_transform) < 0) |
765 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info"); |
766 | | |
767 | 0 | if (H5Z_xform_eval(data_transform, tmp_buf, smine_nelmts, dset_info->type_info.mem_type) < 0) |
768 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Error performing data transform"); |
769 | 0 | } |
770 | | |
771 | | /* |
772 | | * Perform datatype conversion. |
773 | | */ |
774 | 0 | if (H5T_convert(dset_info->type_info.tpath, dset_info->type_info.src_type, |
775 | 0 | dset_info->type_info.dst_type, smine_nelmts, (size_t)0, (size_t)0, tmp_buf, |
776 | 0 | io_info->bkg_buf) < 0) |
777 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed"); |
778 | 0 | } /* end else */ |
779 | | |
780 | | /* |
781 | | * Scatter the data out to the file. |
782 | | */ |
783 | 0 | if (H5D__scatter_file(io_info, dset_info, file_iter, smine_nelmts, tmp_buf) < 0) |
784 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed"); |
785 | 0 | } /* end for */ |
786 | | |
787 | 0 | done: |
788 | | /* Release selection iterators */ |
789 | 0 | if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0) |
790 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
791 | 0 | if (file_iter) |
792 | 0 | file_iter = H5FL_FREE(H5S_sel_iter_t, file_iter); |
793 | 0 | if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) |
794 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
795 | 0 | if (mem_iter) |
796 | 0 | mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter); |
797 | 0 | if (bkg_iter_init && H5S_SELECT_ITER_RELEASE(bkg_iter) < 0) |
798 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
799 | 0 | if (bkg_iter) |
800 | 0 | bkg_iter = H5FL_FREE(H5S_sel_iter_t, bkg_iter); |
801 | |
|
802 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
803 | 0 | } /* end H5D__scatgath_write() */ |
804 | | |
805 | | /*------------------------------------------------------------------------- |
806 | | * Function: H5D__scatgath_read_select |
807 | | * |
808 | | * Purpose: Perform scatter/gather read from a list of dataset pieces |
809 | | * |
810 | | * Return: Non-negative on success/Negative on failure |
811 | | * |
812 | | *------------------------------------------------------------------------- |
813 | | */ |
814 | | herr_t |
815 | | H5D__scatgath_read_select(H5D_io_info_t *io_info) |
816 | 0 | { |
817 | 0 | H5S_t **tmp_mem_spaces = NULL; /* Memory spaces to use for read from disk */ |
818 | 0 | H5S_sel_iter_t *mem_iter = NULL; /* Memory selection iteration info */ |
819 | 0 | bool mem_iter_init = false; /* Memory selection iteration info has been initialized */ |
820 | 0 | void **tmp_bufs = NULL; /* Buffers to use for read from disk */ |
821 | 0 | void *tmp_bkg_buf = NULL; /* Temporary background buffer pointer */ |
822 | 0 | size_t tconv_bytes_used = 0; /* Number of bytes used so far in conversion buffer */ |
823 | 0 | size_t bkg_bytes_used = 0; /* Number of bytes used so far in background buffer */ |
824 | 0 | size_t i; /* Local index variable */ |
825 | 0 | herr_t ret_value = SUCCEED; /* Return value */ |
826 | |
|
827 | 0 | FUNC_ENTER_PACKAGE |
828 | | |
829 | | /* Sanity check */ |
830 | 0 | assert(io_info); |
831 | 0 | assert(io_info->count > 0); |
832 | 0 | assert(io_info->mem_spaces || io_info->pieces_added == 0); |
833 | 0 | assert(io_info->file_spaces || io_info->pieces_added == 0); |
834 | 0 | assert(io_info->addrs || io_info->pieces_added == 0); |
835 | 0 | assert(io_info->element_sizes || io_info->pieces_added == 0); |
836 | 0 | assert(io_info->rbufs || io_info->pieces_added == 0); |
837 | | |
838 | | /* Allocate list of buffers (within the tconv buf) */ |
839 | 0 | if (NULL == (tmp_bufs = H5MM_malloc(io_info->pieces_added * sizeof(void *)))) |
840 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for temporary buffer list"); |
841 | | |
842 | | /* Allocate the iterator */ |
843 | 0 | if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
844 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate memory iterator"); |
845 | | |
846 | | /* Allocate list of block memory spaces */ |
847 | | /*!FIXME delay doing this until we find the first mem space that is non-contiguous or doesn't start at 0 |
848 | | */ |
849 | 0 | if (NULL == (tmp_mem_spaces = H5MM_malloc(io_info->pieces_added * sizeof(H5S_t *)))) |
850 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, |
851 | 0 | "memory allocation failed for temporary memory space list"); |
852 | | |
853 | | /* Build read operation to tconv buffer */ |
854 | 0 | for (i = 0; i < io_info->pieces_added; i++) { |
855 | 0 | H5D_dset_io_info_t *dset_info = io_info->sel_pieces[i]->dset_info; |
856 | |
|
857 | 0 | assert(io_info->sel_pieces[i]->piece_points > 0); |
858 | | |
859 | | /* Check if this piece is involved in type conversion */ |
860 | 0 | if (dset_info->type_info.is_xform_noop && dset_info->type_info.is_conv_noop) { |
861 | | /* No type conversion, just copy the mem space and buffer */ |
862 | 0 | tmp_mem_spaces[i] = io_info->mem_spaces[i]; |
863 | 0 | tmp_bufs[i] = io_info->rbufs[i]; |
864 | 0 | } |
865 | 0 | else { |
866 | | /* Create block memory space */ |
867 | 0 | if (NULL == |
868 | 0 | (tmp_mem_spaces[i] = H5S_create_simple(1, &io_info->sel_pieces[i]->piece_points, NULL))) { |
869 | 0 | memset(&tmp_mem_spaces[i], 0, (io_info->pieces_added - i) * sizeof(tmp_mem_spaces[0])); |
870 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "unable to create simple memory dataspace"); |
871 | 0 | } |
872 | | |
873 | | /* Check for in-place type conversion */ |
874 | 0 | if (io_info->sel_pieces[i]->in_place_tconv) |
875 | | /* Set buffer to point to read buffer + offset */ |
876 | 0 | tmp_bufs[i] = (uint8_t *)(io_info->rbufs[i]) + io_info->sel_pieces[i]->buf_off; |
877 | 0 | else { |
878 | | /* Set buffer to point into type conversion buffer */ |
879 | 0 | tmp_bufs[i] = io_info->tconv_buf + tconv_bytes_used; |
880 | 0 | tconv_bytes_used += |
881 | 0 | io_info->sel_pieces[i]->piece_points * |
882 | 0 | MAX(dset_info->type_info.src_type_size, dset_info->type_info.dst_type_size); |
883 | 0 | assert(tconv_bytes_used <= io_info->tconv_buf_size); |
884 | 0 | } |
885 | | |
886 | | /* Fill background buffer here unless we will use H5D__compound_opt_read(). Must do this before |
887 | | * the read so the read buffer doesn't get wiped out if we're using in-place type conversion */ |
888 | 0 | if (!H5D__SCATGATH_USE_CMPD_OPT_READ(dset_info, io_info->sel_pieces[i]->in_place_tconv)) { |
889 | | /* Check for background buffer */ |
890 | 0 | if (dset_info->type_info.need_bkg) { |
891 | 0 | assert(io_info->bkg_buf); |
892 | | |
893 | | /* Calculate background buffer position */ |
894 | 0 | tmp_bkg_buf = io_info->bkg_buf + bkg_bytes_used; |
895 | 0 | bkg_bytes_used += |
896 | 0 | io_info->sel_pieces[i]->piece_points * dset_info->type_info.dst_type_size; |
897 | 0 | assert(bkg_bytes_used <= io_info->bkg_buf_size); |
898 | | |
899 | | /* Gather data from read buffer to background buffer if necessary */ |
900 | 0 | if (H5T_BKG_YES == dset_info->type_info.need_bkg) { |
901 | | /* Initialize memory iterator */ |
902 | 0 | assert(!mem_iter_init); |
903 | 0 | if (H5S_select_iter_init(mem_iter, io_info->mem_spaces[i], |
904 | 0 | dset_info->type_info.dst_type_size, 0) < 0) |
905 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, |
906 | 0 | "unable to initialize memory selection information"); |
907 | 0 | mem_iter_init = true; /* Memory selection iteration info has been initialized */ |
908 | |
|
909 | 0 | if ((size_t)io_info->sel_pieces[i]->piece_points != |
910 | 0 | H5D__gather_mem(io_info->rbufs[i], mem_iter, |
911 | 0 | (size_t)io_info->sel_pieces[i]->piece_points, |
912 | 0 | tmp_bkg_buf /*out*/)) |
913 | 0 | HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); |
914 | | |
915 | | /* Reset selection iterator */ |
916 | 0 | assert(mem_iter_init); |
917 | 0 | if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) |
918 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
919 | 0 | mem_iter_init = false; |
920 | 0 | } |
921 | 0 | } |
922 | 0 | } |
923 | 0 | } |
924 | 0 | } |
925 | | |
926 | | /* Read data from all pieces */ |
927 | 0 | H5_CHECK_OVERFLOW(io_info->pieces_added, size_t, uint32_t); |
928 | 0 | if (H5F_shared_select_read(io_info->f_sh, H5FD_MEM_DRAW, (uint32_t)io_info->pieces_added, tmp_mem_spaces, |
929 | 0 | io_info->file_spaces, io_info->addrs, io_info->element_sizes, tmp_bufs) < 0) |
930 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "selection read failed"); |
931 | | |
932 | | /* Reset bkg_bytes_used */ |
933 | 0 | bkg_bytes_used = 0; |
934 | | |
935 | | /* Perform type conversion and scatter data to memory buffers for datasets that need this */ |
936 | 0 | for (i = 0; i < io_info->pieces_added; i++) { |
937 | 0 | H5D_dset_io_info_t *dset_info = io_info->sel_pieces[i]->dset_info; |
938 | |
|
939 | 0 | assert(tmp_mem_spaces[i]); |
940 | | |
941 | | /* Check if this piece is involved in type conversion */ |
942 | 0 | if (tmp_mem_spaces[i] != io_info->mem_spaces[i]) { |
943 | 0 | H5_CHECK_OVERFLOW(io_info->sel_pieces[i]->piece_points, hsize_t, size_t); |
944 | | |
945 | | /* Initialize memory iterator */ |
946 | 0 | assert(!mem_iter_init); |
947 | 0 | if (H5S_select_iter_init(mem_iter, io_info->mem_spaces[i], dset_info->type_info.dst_type_size, |
948 | 0 | 0) < 0) |
949 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, |
950 | 0 | "unable to initialize memory selection information"); |
951 | 0 | mem_iter_init = true; /* Memory selection iteration info has been initialized */ |
952 | | |
953 | | /* If the source and destination are compound types and subset of each other |
954 | | * and no conversion is needed, copy the data directly into user's buffer and |
955 | | * bypass the rest of steps. |
956 | | */ |
957 | 0 | if (H5D__SCATGATH_USE_CMPD_OPT_READ(dset_info, io_info->sel_pieces[i]->in_place_tconv)) { |
958 | 0 | if (H5D__compound_opt_read((size_t)io_info->sel_pieces[i]->piece_points, mem_iter, |
959 | 0 | &dset_info->type_info, tmp_bufs[i], io_info->rbufs[i] /*out*/) < 0) |
960 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed"); |
961 | 0 | } |
962 | 0 | else { |
963 | | /* Check for background buffer */ |
964 | 0 | if (dset_info->type_info.need_bkg) { |
965 | 0 | assert(io_info->bkg_buf); |
966 | | |
967 | | /* Calculate background buffer position */ |
968 | 0 | tmp_bkg_buf = io_info->bkg_buf + bkg_bytes_used; |
969 | 0 | bkg_bytes_used += |
970 | 0 | io_info->sel_pieces[i]->piece_points * dset_info->type_info.dst_type_size; |
971 | 0 | assert(bkg_bytes_used <= io_info->bkg_buf_size); |
972 | 0 | } |
973 | | |
974 | | /* |
975 | | * Perform datatype conversion. |
976 | | */ |
977 | 0 | if (H5T_convert(dset_info->type_info.tpath, dset_info->type_info.src_type, |
978 | 0 | dset_info->type_info.dst_type, (size_t)io_info->sel_pieces[i]->piece_points, |
979 | 0 | (size_t)0, (size_t)0, tmp_bufs[i], tmp_bkg_buf) < 0) |
980 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed"); |
981 | | |
982 | | /* Do the data transform after the conversion (since we're using type mem_type) */ |
983 | 0 | if (!dset_info->type_info.is_xform_noop) { |
984 | 0 | H5Z_data_xform_t *data_transform; /* Data transform info */ |
985 | | |
986 | | /* Retrieve info from API context */ |
987 | 0 | if (H5CX_get_data_transform(&data_transform) < 0) |
988 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info"); |
989 | | |
990 | 0 | if (H5Z_xform_eval(data_transform, tmp_bufs[i], |
991 | 0 | (size_t)io_info->sel_pieces[i]->piece_points, |
992 | 0 | dset_info->type_info.mem_type) < 0) |
993 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Error performing data transform"); |
994 | 0 | } |
995 | | |
996 | | /* Scatter the data into memory if this was not an in-place conversion */ |
997 | 0 | if (!io_info->sel_pieces[i]->in_place_tconv) |
998 | 0 | if (H5D__scatter_mem(tmp_bufs[i], mem_iter, (size_t)io_info->sel_pieces[i]->piece_points, |
999 | 0 | io_info->rbufs[i] /*out*/) < 0) |
1000 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); |
1001 | 0 | } |
1002 | | |
1003 | | /* Release selection iterator */ |
1004 | 0 | assert(mem_iter_init); |
1005 | 0 | if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) |
1006 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
1007 | 0 | mem_iter_init = false; |
1008 | 0 | } |
1009 | 0 | } |
1010 | | |
1011 | 0 | done: |
1012 | | /* Release and free selection iterator */ |
1013 | 0 | if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) |
1014 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
1015 | 0 | if (mem_iter) |
1016 | 0 | mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter); |
1017 | | |
1018 | | /* Free tmp_bufs */ |
1019 | 0 | H5MM_free(tmp_bufs); |
1020 | 0 | tmp_bufs = NULL; |
1021 | | |
1022 | | /* Clear and free tmp_mem_spaces */ |
1023 | 0 | if (tmp_mem_spaces) { |
1024 | 0 | for (i = 0; i < io_info->pieces_added; i++) |
1025 | 0 | if (tmp_mem_spaces[i] != io_info->mem_spaces[i] && tmp_mem_spaces[i] && |
1026 | 0 | H5S_close(tmp_mem_spaces[i]) < 0) |
1027 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "Can't close dataspace"); |
1028 | 0 | H5MM_free(tmp_mem_spaces); |
1029 | 0 | tmp_mem_spaces = NULL; |
1030 | 0 | } |
1031 | |
|
1032 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
1033 | 0 | } /* end H5D__scatgath_read_select() */ |
1034 | | |
1035 | | /*------------------------------------------------------------------------- |
1036 | | * Function: H5D__scatgath_write_select |
1037 | | * |
1038 | | * Purpose: Perform scatter/gather write to a list of dataset pieces. |
1039 | | * |
1040 | | * Return: Non-negative on success/Negative on failure |
1041 | | * |
1042 | | *------------------------------------------------------------------------- |
1043 | | */ |
1044 | | herr_t |
1045 | | H5D__scatgath_write_select(H5D_io_info_t *io_info) |
1046 | 0 | { |
1047 | 0 | H5S_t **write_mem_spaces = NULL; /* Memory spaces to use for write to disk */ |
1048 | 0 | size_t spaces_added = 0; /* Number of spaces added to write_mem_spaces */ |
1049 | 0 | H5S_sel_iter_t *mem_iter = NULL; /* Memory selection iteration info */ |
1050 | 0 | bool mem_iter_init = false; /* Memory selection iteration info has been initialized */ |
1051 | 0 | const void **write_bufs = NULL; /* Buffers to use for write to disk */ |
1052 | 0 | size_t tconv_bytes_used = 0; /* Number of bytes used so far in conversion buffer */ |
1053 | 0 | size_t bkg_bytes_used = 0; /* Number of bytes used so far in background buffer */ |
1054 | 0 | H5S_t **bkg_mem_spaces = NULL; /* Array of memory spaces for read to background buffer */ |
1055 | 0 | H5S_t **bkg_file_spaces = NULL; /* Array of file spaces for read to background buffer */ |
1056 | 0 | haddr_t *bkg_addrs = NULL; /* Array of file addresses for read to background buffer */ |
1057 | 0 | size_t *bkg_element_sizes = NULL; /* Array of element sizes for read to background buffer */ |
1058 | 0 | void **bkg_bufs = NULL; /* Array background buffers for read of existing file contents */ |
1059 | 0 | size_t bkg_pieces = 0; /* Number of pieces that need to read the background data from disk */ |
1060 | 0 | size_t i; /* Local index variable */ |
1061 | 0 | herr_t ret_value = SUCCEED; /* Return value */ |
1062 | |
|
1063 | 0 | FUNC_ENTER_PACKAGE |
1064 | | |
1065 | | /* Sanity check */ |
1066 | 0 | assert(io_info); |
1067 | 0 | assert(io_info->count > 0); |
1068 | 0 | assert(io_info->mem_spaces || io_info->pieces_added == 0); |
1069 | 0 | assert(io_info->file_spaces || io_info->pieces_added == 0); |
1070 | 0 | assert(io_info->addrs || io_info->pieces_added == 0); |
1071 | 0 | assert(io_info->element_sizes || io_info->pieces_added == 0); |
1072 | 0 | assert(io_info->wbufs || io_info->pieces_added == 0); |
1073 | | |
1074 | | /* Allocate list of buffers (within the tconv buf) */ |
1075 | 0 | if (NULL == (write_bufs = (const void **)H5MM_malloc(io_info->pieces_added * sizeof(const void *)))) |
1076 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for temporary buffer list"); |
1077 | | |
1078 | | /* Allocate the iterator */ |
1079 | 0 | if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t))) |
1080 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate memory iterator"); |
1081 | | |
1082 | | /* Allocate list of block memory spaces */ |
1083 | | /*!FIXME delay doing this until we find the first mem space that is non-contiguous or doesn't start at 0 |
1084 | | */ |
1085 | 0 | if (NULL == (write_mem_spaces = H5MM_malloc(io_info->pieces_added * sizeof(H5S_t *)))) |
1086 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, |
1087 | 0 | "memory allocation failed for temporary memory space list"); |
1088 | | |
1089 | | /* Build operations to read data to background buffer and to write data */ |
1090 | 0 | for (i = 0; i < io_info->pieces_added; i++) { |
1091 | 0 | H5D_dset_io_info_t *dset_info = io_info->sel_pieces[i]->dset_info; |
1092 | |
|
1093 | 0 | assert(io_info->sel_pieces[i]->piece_points > 0); |
1094 | | |
1095 | | /* Check if this piece is involved in type conversion */ |
1096 | 0 | if (dset_info->type_info.is_xform_noop && dset_info->type_info.is_conv_noop) { |
1097 | | /* No type conversion, just copy the mem space and buffer */ |
1098 | 0 | write_mem_spaces[i] = io_info->mem_spaces[i]; |
1099 | 0 | spaces_added++; |
1100 | 0 | write_bufs[i] = io_info->wbufs[i]; |
1101 | 0 | } |
1102 | 0 | else { |
1103 | 0 | void *tmp_write_buf; /* To sidestep const warnings */ |
1104 | 0 | void *tmp_bkg_buf = NULL; |
1105 | |
|
1106 | 0 | H5_CHECK_OVERFLOW(io_info->sel_pieces[i]->piece_points, hsize_t, size_t); |
1107 | | |
1108 | | /* Initialize memory iterator */ |
1109 | 0 | assert(!mem_iter_init); |
1110 | 0 | if (H5S_select_iter_init(mem_iter, io_info->mem_spaces[i], dset_info->type_info.src_type_size, |
1111 | 0 | 0) < 0) |
1112 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, |
1113 | 0 | "unable to initialize memory selection information"); |
1114 | 0 | mem_iter_init = true; /* Memory selection iteration info has been initialized */ |
1115 | | |
1116 | | /* Create block memory space */ |
1117 | 0 | if (NULL == |
1118 | 0 | (write_mem_spaces[i] = H5S_create_simple(1, &io_info->sel_pieces[i]->piece_points, NULL))) |
1119 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "unable to create simple memory dataspace"); |
1120 | 0 | spaces_added++; |
1121 | | |
1122 | | /* Check for in-place type conversion */ |
1123 | 0 | if (io_info->sel_pieces[i]->in_place_tconv) { |
1124 | 0 | H5_flexible_const_ptr_t flex_buf; |
1125 | | |
1126 | | /* Set buffer to point to write buffer + offset */ |
1127 | | /* Use cast to union to twiddle away const. OK because if we're doing this it means the user |
1128 | | * explicitly allowed us to modify this buffer via H5Pset_modify_write_buf(). */ |
1129 | 0 | flex_buf.cvp = io_info->wbufs[i]; |
1130 | 0 | tmp_write_buf = (uint8_t *)flex_buf.vp + io_info->sel_pieces[i]->buf_off; |
1131 | 0 | } |
1132 | 0 | else { |
1133 | | /* Set buffer to point into type conversion buffer */ |
1134 | 0 | tmp_write_buf = io_info->tconv_buf + tconv_bytes_used; |
1135 | 0 | tconv_bytes_used += |
1136 | 0 | io_info->sel_pieces[i]->piece_points * |
1137 | 0 | MAX(dset_info->type_info.src_type_size, dset_info->type_info.dst_type_size); |
1138 | 0 | assert(tconv_bytes_used <= io_info->tconv_buf_size); |
1139 | | |
1140 | | /* Gather data from application buffer into the datatype conversion buffer */ |
1141 | 0 | if ((size_t)io_info->sel_pieces[i]->piece_points != |
1142 | 0 | H5D__gather_mem(io_info->wbufs[i], mem_iter, (size_t)io_info->sel_pieces[i]->piece_points, |
1143 | 0 | tmp_write_buf /*out*/)) |
1144 | 0 | HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed"); |
1145 | 0 | } |
1146 | | |
1147 | | /* Set buffer for writing to disk (from type conversion buffer) */ |
1148 | 0 | write_bufs[i] = (const void *)tmp_write_buf; |
1149 | | |
1150 | | /* If the source and destination are compound types and the destination is a subset of |
1151 | | * the source and no conversion is needed, copy the data directly into the type |
1152 | | * conversion buffer and bypass the rest of steps. If the source is a subset of the |
1153 | | * destination, the optimization is done in conversion function H5T_conv_struct_opt to |
1154 | | * protect the background data. |
1155 | | */ |
1156 | 0 | if (H5D__SCATGATH_USE_CMPD_OPT_WRITE(dset_info, io_info->sel_pieces[i]->in_place_tconv)) { |
1157 | 0 | if (H5D__compound_opt_write((size_t)io_info->sel_pieces[i]->piece_points, |
1158 | 0 | &dset_info->type_info, tmp_write_buf) < 0) |
1159 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed"); |
1160 | |
|
1161 | 0 | } /* end if */ |
1162 | 0 | else { |
1163 | | /* Check for background buffer */ |
1164 | 0 | if (dset_info->type_info.need_bkg) { |
1165 | 0 | assert(io_info->bkg_buf); |
1166 | | |
1167 | | /* Calculate background buffer position */ |
1168 | 0 | tmp_bkg_buf = io_info->bkg_buf + bkg_bytes_used; |
1169 | 0 | bkg_bytes_used += |
1170 | 0 | io_info->sel_pieces[i]->piece_points * dset_info->type_info.dst_type_size; |
1171 | 0 | assert(bkg_bytes_used <= io_info->bkg_buf_size); |
1172 | 0 | } |
1173 | | |
1174 | | /* Set up background buffer read operation if necessary */ |
1175 | 0 | if (H5T_BKG_YES == dset_info->type_info.need_bkg) { |
1176 | 0 | assert(io_info->must_fill_bkg); |
1177 | | |
1178 | | /* Allocate arrays of parameters for selection read to background buffer if necessary */ |
1179 | 0 | if (!bkg_mem_spaces) { |
1180 | 0 | assert(!bkg_file_spaces && !bkg_addrs && !bkg_element_sizes && !bkg_bufs); |
1181 | 0 | if (NULL == (bkg_mem_spaces = H5MM_malloc(io_info->pieces_added * sizeof(H5S_t *)))) |
1182 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, |
1183 | 0 | "memory allocation failed for memory space list"); |
1184 | 0 | if (NULL == (bkg_file_spaces = H5MM_malloc(io_info->pieces_added * sizeof(H5S_t *)))) |
1185 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, |
1186 | 0 | "memory allocation failed for file space list"); |
1187 | 0 | if (NULL == (bkg_addrs = H5MM_malloc(io_info->pieces_added * sizeof(haddr_t)))) |
1188 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, |
1189 | 0 | "memory allocation failed for piece address list"); |
1190 | 0 | if (NULL == (bkg_element_sizes = H5MM_malloc(io_info->pieces_added * sizeof(size_t)))) |
1191 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, |
1192 | 0 | "memory allocation failed for element size list"); |
1193 | 0 | if (NULL == (bkg_bufs = H5MM_malloc(io_info->pieces_added * sizeof(const void *)))) |
1194 | 0 | HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, |
1195 | 0 | "memory allocation failed for write buffer list"); |
1196 | 0 | } |
1197 | | |
1198 | | /* Use same (block) memory space, file space, address, and element size as write operation |
1199 | | */ |
1200 | 0 | assert(bkg_mem_spaces && bkg_file_spaces && bkg_addrs && bkg_element_sizes && bkg_bufs); |
1201 | 0 | bkg_mem_spaces[bkg_pieces] = write_mem_spaces[i]; |
1202 | 0 | bkg_file_spaces[bkg_pieces] = io_info->file_spaces[i]; |
1203 | 0 | bkg_addrs[bkg_pieces] = io_info->addrs[i]; |
1204 | 0 | bkg_element_sizes[bkg_pieces] = io_info->element_sizes[i]; |
1205 | | |
1206 | | /* Use previously calculated background buffer position */ |
1207 | 0 | bkg_bufs[bkg_pieces] = tmp_bkg_buf; |
1208 | | |
1209 | | /* Add piece */ |
1210 | 0 | bkg_pieces++; |
1211 | 0 | } |
1212 | 0 | else { |
1213 | | /* Perform type conversion here to avoid second loop if no dsets use the background buffer |
1214 | | */ |
1215 | | /* Do the data transform before the type conversion (since |
1216 | | * transforms must be done in the memory type). */ |
1217 | 0 | if (!dset_info->type_info.is_xform_noop) { |
1218 | 0 | H5Z_data_xform_t *data_transform; /* Data transform info */ |
1219 | | |
1220 | | /* Retrieve info from API context */ |
1221 | 0 | if (H5CX_get_data_transform(&data_transform) < 0) |
1222 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info"); |
1223 | | |
1224 | 0 | if (H5Z_xform_eval(data_transform, tmp_write_buf, |
1225 | 0 | (size_t)io_info->sel_pieces[i]->piece_points, |
1226 | 0 | dset_info->type_info.mem_type) < 0) |
1227 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Error performing data transform"); |
1228 | 0 | } |
1229 | | |
1230 | | /* |
1231 | | * Perform datatype conversion. |
1232 | | */ |
1233 | 0 | if (H5T_convert(dset_info->type_info.tpath, dset_info->type_info.src_type, |
1234 | 0 | dset_info->type_info.dst_type, |
1235 | 0 | (size_t)io_info->sel_pieces[i]->piece_points, (size_t)0, (size_t)0, |
1236 | 0 | tmp_write_buf, tmp_bkg_buf) < 0) |
1237 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed"); |
1238 | 0 | } |
1239 | 0 | } |
1240 | | |
1241 | | /* Release selection iterator */ |
1242 | 0 | assert(mem_iter_init); |
1243 | 0 | if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) |
1244 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
1245 | 0 | mem_iter_init = false; |
1246 | 0 | } |
1247 | 0 | } |
1248 | | |
1249 | 0 | assert(spaces_added == io_info->pieces_added); |
1250 | | |
1251 | | /* Gather data to background buffer if necessary */ |
1252 | 0 | if (io_info->must_fill_bkg) { |
1253 | 0 | size_t j = 0; /* Index into array of background buffers */ |
1254 | | |
1255 | | /* Read data */ |
1256 | 0 | H5_CHECK_OVERFLOW(bkg_pieces, size_t, uint32_t); |
1257 | 0 | if (H5F_shared_select_read(io_info->f_sh, H5FD_MEM_DRAW, (uint32_t)bkg_pieces, bkg_mem_spaces, |
1258 | 0 | bkg_file_spaces, bkg_addrs, bkg_element_sizes, bkg_bufs) < 0) |
1259 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "selection read to background buffer failed"); |
1260 | | |
1261 | | /* Perform type conversion on pieces with background buffers that were just read */ |
1262 | 0 | for (i = 0; i < io_info->pieces_added; i++) { |
1263 | 0 | H5D_dset_io_info_t *dset_info = io_info->sel_pieces[i]->dset_info; |
1264 | |
|
1265 | 0 | if ((H5T_BKG_YES == dset_info->type_info.need_bkg) && |
1266 | 0 | !H5D__SCATGATH_USE_CMPD_OPT_WRITE(dset_info, io_info->sel_pieces[i]->in_place_tconv)) { |
1267 | | /* Non-const write_buf[i]. Use pointer math here to avoid const warnings. When |
1268 | | * there's a background buffer write_buf[i] always points inside the non-const tconv |
1269 | | * buf so this is OK. */ |
1270 | 0 | void *tmp_write_buf = |
1271 | 0 | (void *)((uint8_t *)io_info->tconv_buf + |
1272 | 0 | ((const uint8_t *)write_bufs[i] - (const uint8_t *)io_info->tconv_buf)); |
1273 | | |
1274 | | /* Do the data transform before the type conversion (since |
1275 | | * transforms must be done in the memory type). */ |
1276 | 0 | if (!dset_info->type_info.is_xform_noop) { |
1277 | 0 | H5Z_data_xform_t *data_transform; /* Data transform info */ |
1278 | | |
1279 | | /* Retrieve info from API context */ |
1280 | 0 | if (H5CX_get_data_transform(&data_transform) < 0) |
1281 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info"); |
1282 | | |
1283 | 0 | if (H5Z_xform_eval(data_transform, tmp_write_buf, |
1284 | 0 | (size_t)io_info->sel_pieces[i]->piece_points, |
1285 | 0 | dset_info->type_info.mem_type) < 0) |
1286 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Error performing data transform"); |
1287 | 0 | } |
1288 | | |
1289 | | /* |
1290 | | * Perform datatype conversion. |
1291 | | */ |
1292 | 0 | assert(j < bkg_pieces); |
1293 | 0 | if (H5T_convert(dset_info->type_info.tpath, dset_info->type_info.src_type, |
1294 | 0 | dset_info->type_info.dst_type, (size_t)io_info->sel_pieces[i]->piece_points, |
1295 | 0 | (size_t)0, (size_t)0, tmp_write_buf, bkg_bufs[j]) < 0) |
1296 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed"); |
1297 | | |
1298 | | /* Advance to next background buffer */ |
1299 | 0 | j++; |
1300 | 0 | } |
1301 | 0 | } |
1302 | | |
1303 | 0 | assert(j == bkg_pieces); |
1304 | 0 | } |
1305 | | |
1306 | | /* Write data to disk */ |
1307 | 0 | H5_CHECK_OVERFLOW(io_info->pieces_added, size_t, uint32_t); |
1308 | 0 | if (H5F_shared_select_write(io_info->f_sh, H5FD_MEM_DRAW, (uint32_t)io_info->pieces_added, |
1309 | 0 | write_mem_spaces, io_info->file_spaces, io_info->addrs, |
1310 | 0 | io_info->element_sizes, write_bufs) < 0) |
1311 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "selection write failed"); |
1312 | | |
1313 | 0 | done: |
1314 | | /* Release and free selection iterator */ |
1315 | 0 | if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) |
1316 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator"); |
1317 | 0 | if (mem_iter) |
1318 | 0 | mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter); |
1319 | | |
1320 | | /* Free write_bufs */ |
1321 | 0 | H5MM_free(write_bufs); |
1322 | 0 | write_bufs = NULL; |
1323 | | |
1324 | | /* Clear and free write_mem_spaces */ |
1325 | 0 | if (write_mem_spaces) { |
1326 | 0 | for (i = 0; i < spaces_added; i++) { |
1327 | 0 | assert(write_mem_spaces[i]); |
1328 | 0 | if (write_mem_spaces[i] != io_info->mem_spaces[i] && H5S_close(write_mem_spaces[i]) < 0) |
1329 | 0 | HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "Can't close dataspace"); |
1330 | 0 | } |
1331 | 0 | H5MM_free(write_mem_spaces); |
1332 | 0 | write_mem_spaces = NULL; |
1333 | 0 | } |
1334 | | |
1335 | | /* Free background buffer parameter arrays */ |
1336 | 0 | H5MM_free(bkg_mem_spaces); |
1337 | 0 | bkg_mem_spaces = NULL; |
1338 | 0 | H5MM_free(bkg_file_spaces); |
1339 | 0 | bkg_file_spaces = NULL; |
1340 | 0 | H5MM_free(bkg_addrs); |
1341 | 0 | bkg_addrs = NULL; |
1342 | 0 | H5MM_free(bkg_element_sizes); |
1343 | 0 | bkg_element_sizes = NULL; |
1344 | 0 | H5MM_free(bkg_bufs); |
1345 | 0 | bkg_bufs = NULL; |
1346 | |
|
1347 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
1348 | 0 | } /* end H5D__scatgath_write_select() */ |
1349 | | |
1350 | | /*------------------------------------------------------------------------- |
1351 | | * Function: H5D__compound_opt_read |
1352 | | * |
1353 | | * Purpose: A special optimization case when the source and |
1354 | | * destination members are a subset of each other, and |
1355 | | * the order is the same, and no conversion is needed. |
1356 | | * For example: |
1357 | | * struct source { struct destination { |
1358 | | * TYPE1 A; --> TYPE1 A; |
1359 | | * TYPE2 B; --> TYPE2 B; |
1360 | | * TYPE3 C; --> TYPE3 C; |
1361 | | * }; TYPE4 D; |
1362 | | * TYPE5 E; |
1363 | | * }; |
1364 | | * or |
1365 | | * struct destination { struct source { |
1366 | | * TYPE1 A; <-- TYPE1 A; |
1367 | | * TYPE2 B; <-- TYPE2 B; |
1368 | | * TYPE3 C; <-- TYPE3 C; |
1369 | | * }; TYPE4 D; |
1370 | | * TYPE5 E; |
1371 | | * }; |
1372 | | * The optimization is simply moving data to the appropriate |
1373 | | * places in the buffer. |
1374 | | * |
1375 | | * Return: Non-negative on success/Negative on failure |
1376 | | * |
1377 | | *------------------------------------------------------------------------- |
1378 | | */ |
1379 | | static herr_t |
1380 | | H5D__compound_opt_read(size_t nelmts, H5S_sel_iter_t *iter, const H5D_type_info_t *type_info, |
1381 | | uint8_t *tconv_buf, void *user_buf /*out*/) |
1382 | 0 | { |
1383 | 0 | uint8_t *ubuf = (uint8_t *)user_buf; /* Cast for pointer arithmetic */ |
1384 | 0 | uint8_t *xdbuf; /* Pointer into dataset buffer */ |
1385 | 0 | hsize_t *off = NULL; /* Pointer to sequence offsets */ |
1386 | 0 | size_t *len = NULL; /* Pointer to sequence lengths */ |
1387 | 0 | size_t src_stride, dst_stride, copy_size; |
1388 | 0 | size_t dxpl_vec_size; /* Vector length from API context's DXPL */ |
1389 | 0 | size_t vec_size; /* Vector length */ |
1390 | 0 | herr_t ret_value = SUCCEED; /* Return value */ |
1391 | |
|
1392 | 0 | FUNC_ENTER_PACKAGE |
1393 | | |
1394 | | /* Check args */ |
1395 | 0 | assert(nelmts > 0); |
1396 | 0 | assert(iter); |
1397 | 0 | assert(type_info); |
1398 | 0 | assert(type_info->cmpd_subset); |
1399 | 0 | assert(H5T_SUBSET_SRC == type_info->cmpd_subset->subset || |
1400 | 0 | H5T_SUBSET_DST == type_info->cmpd_subset->subset); |
1401 | 0 | assert(user_buf); |
1402 | | |
1403 | | /* Get info from API context */ |
1404 | 0 | if (H5CX_get_vec_size(&dxpl_vec_size) < 0) |
1405 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve I/O vector size"); |
1406 | | |
1407 | | /* Allocate the vector I/O arrays */ |
1408 | 0 | if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) |
1409 | 0 | vec_size = dxpl_vec_size; |
1410 | 0 | else |
1411 | 0 | vec_size = H5D_IO_VECTOR_SIZE; |
1412 | 0 | if (NULL == (len = H5FL_SEQ_MALLOC(size_t, vec_size))) |
1413 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array"); |
1414 | 0 | if (NULL == (off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) |
1415 | 0 | HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array"); |
1416 | | |
1417 | | /* Get source & destination strides */ |
1418 | 0 | src_stride = type_info->src_type_size; |
1419 | 0 | dst_stride = type_info->dst_type_size; |
1420 | | |
1421 | | /* Get the size, in bytes, to copy for each element */ |
1422 | 0 | copy_size = type_info->cmpd_subset->copy_size; |
1423 | | |
1424 | | /* Loop until all elements are written */ |
1425 | 0 | xdbuf = tconv_buf; |
1426 | 0 | while (nelmts > 0) { |
1427 | 0 | size_t nseq; /* Number of sequences generated */ |
1428 | 0 | size_t curr_seq; /* Current sequence being processed */ |
1429 | 0 | size_t elmtno; /* Element counter */ |
1430 | | |
1431 | | /* Get list of sequences for selection to write */ |
1432 | 0 | if (H5S_SELECT_ITER_GET_SEQ_LIST(iter, vec_size, nelmts, &nseq, &elmtno, off, len) < 0) |
1433 | 0 | HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); |
1434 | | |
1435 | | /* Loop, while sequences left to process */ |
1436 | 0 | for (curr_seq = 0; curr_seq < nseq; curr_seq++) { |
1437 | 0 | size_t curr_off; /* Offset of bytes left to process in sequence */ |
1438 | 0 | size_t curr_len; /* Length of bytes left to process in sequence */ |
1439 | 0 | size_t curr_nelmts; /* Number of elements to process in sequence */ |
1440 | 0 | uint8_t *xubuf; |
1441 | 0 | size_t i; /* Local index variable */ |
1442 | | |
1443 | | /* Get the number of bytes and offset in sequence */ |
1444 | 0 | curr_len = len[curr_seq]; |
1445 | 0 | H5_CHECK_OVERFLOW(off[curr_seq], hsize_t, size_t); |
1446 | 0 | curr_off = (size_t)off[curr_seq]; |
1447 | | |
1448 | | /* Decide the number of elements and position in the buffer. */ |
1449 | 0 | curr_nelmts = curr_len / dst_stride; |
1450 | 0 | xubuf = ubuf + curr_off; |
1451 | | |
1452 | | /* Copy the data into the right place. */ |
1453 | 0 | for (i = 0; i < curr_nelmts; i++) { |
1454 | 0 | memmove(xubuf, xdbuf, copy_size); |
1455 | | |
1456 | | /* Update pointers */ |
1457 | 0 | xdbuf += src_stride; |
1458 | 0 | xubuf += dst_stride; |
1459 | 0 | } /* end for */ |
1460 | 0 | } /* end for */ |
1461 | | |
1462 | | /* Decrement number of elements left to process */ |
1463 | 0 | nelmts -= elmtno; |
1464 | 0 | } /* end while */ |
1465 | | |
1466 | 0 | done: |
1467 | | /* Release resources, if allocated */ |
1468 | 0 | if (len) |
1469 | 0 | len = H5FL_SEQ_FREE(size_t, len); |
1470 | 0 | if (off) |
1471 | 0 | off = H5FL_SEQ_FREE(hsize_t, off); |
1472 | |
|
1473 | 0 | FUNC_LEAVE_NOAPI(ret_value) |
1474 | 0 | } /* end H5D__compound_opt_read() */ |
1475 | | |
1476 | | /*------------------------------------------------------------------------- |
1477 | | * Function: H5D__compound_opt_write |
1478 | | * |
1479 | | * Purpose: A special optimization case when the source and |
1480 | | * destination members are a subset of each other, and |
1481 | | * the order is the same, and no conversion is needed. |
1482 | | * For example: |
1483 | | * struct source { struct destination { |
1484 | | * TYPE1 A; --> TYPE1 A; |
1485 | | * TYPE2 B; --> TYPE2 B; |
1486 | | * TYPE3 C; --> TYPE3 C; |
1487 | | * }; TYPE4 D; |
1488 | | * TYPE5 E; |
1489 | | * }; |
1490 | | * or |
1491 | | * struct destination { struct source { |
1492 | | * TYPE1 A; <-- TYPE1 A; |
1493 | | * TYPE2 B; <-- TYPE2 B; |
1494 | | * TYPE3 C; <-- TYPE3 C; |
1495 | | * }; TYPE4 D; |
1496 | | * TYPE5 E; |
1497 | | * }; |
1498 | | * The optimization is simply moving data to the appropriate |
1499 | | * places in the buffer. |
1500 | | * |
1501 | | * |
1502 | | * Return: Non-negative on success/Negative on failure |
1503 | | * |
1504 | | *------------------------------------------------------------------------- |
1505 | | */ |
1506 | | static herr_t |
1507 | | H5D__compound_opt_write(size_t nelmts, const H5D_type_info_t *type_info, void *tconv_buf) |
1508 | 0 | { |
1509 | 0 | uint8_t *xsbuf, *xdbuf; /* Source & destination pointers into dataset buffer */ |
1510 | 0 | size_t src_stride, dst_stride; /* Strides through source & destination datatypes */ |
1511 | 0 | size_t i; /* Local index variable */ |
1512 | |
|
1513 | 0 | FUNC_ENTER_PACKAGE_NOERR |
1514 | | |
1515 | | /* Check args */ |
1516 | 0 | assert(nelmts > 0); |
1517 | 0 | assert(type_info); |
1518 | | |
1519 | | /* Initialize values for loop */ |
1520 | 0 | src_stride = type_info->src_type_size; |
1521 | 0 | dst_stride = type_info->dst_type_size; |
1522 | | |
1523 | | /* Loop until all elements are written */ |
1524 | 0 | xsbuf = tconv_buf; |
1525 | 0 | xdbuf = tconv_buf; |
1526 | 0 | for (i = 0; i < nelmts; i++) { |
1527 | 0 | memmove(xdbuf, xsbuf, dst_stride); |
1528 | | |
1529 | | /* Update pointers */ |
1530 | 0 | xsbuf += src_stride; |
1531 | 0 | xdbuf += dst_stride; |
1532 | 0 | } /* end for */ |
1533 | |
|
1534 | 0 | FUNC_LEAVE_NOAPI(SUCCEED) |
1535 | 0 | } /* end H5D__compound_opt_write() */ |