diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 140 |
1 files changed, 72 insertions, 68 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 72f9b75..4ece1b4 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -96,7 +96,7 @@ H5D_io_assist_mpio(H5P_genplist_t *dx_plist, hbool_t doing_mpio, H5FD_mpio_xfer_ #endif /*H5_HAVE_PARALLEL*/ static herr_t H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, - const H5S_t *mem_space, fm_map *fm_struct); + const H5S_t *mem_space, fm_map *fm); static herr_t H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_t chunk_ptr); static herr_t H5D_chunk_cb(void *elem, hid_t type_id, hsize_t ndims, @@ -231,7 +231,7 @@ H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_t /* Set up type conversion function */ if (NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL, dxpl_id))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); - } else if (!H5T_IS_NOOP(tpath)) { + } else if (!H5T_path_noop(tpath)) { if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill_type, H5T_COPY_ALL)))<0 || (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(buf_type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); @@ -604,7 +604,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, */ if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL, dxpl_id))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); - } else if (!H5T_IS_NOOP(tpath)) { + } else if (!H5T_path_noop(tpath)) { if ((src_id=H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 || (dst_id=H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); @@ -830,7 +830,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, */ if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL, dxpl_id))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); - } else if (!H5T_IS_NOOP(tpath)) { + } else if (!H5T_path_noop(tpath)) { if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 || (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); @@ -958,7 +958,7 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ - if (H5T_IS_NOOP(tpath)) { + if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif @@ -1018,11 +1018,11 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ - if (tpath->cdata.need_bkg) { + if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); - need_bkg = MAX(tpath->cdata.need_bkg, need_bkg); + need_bkg = MAX(H5T_path_bkg(tpath), need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ @@ -1197,7 +1197,7 @@ H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5 * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ - if (H5T_IS_NOOP(tpath)) { + if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif @@ -1254,11 +1254,11 @@ H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5 * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ - if (tpath->cdata.need_bkg) { + if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); - need_bkg = MAX (tpath->cdata.need_bkg, need_bkg); + need_bkg = MAX (H5T_path_bkg(tpath), need_bkg); } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { /* Old data is retrieved into background buffer for VL datatype. The * data is used later for freeing heap objects. */ @@ -1404,7 +1404,7 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ #endif /*H5_HAVE_PARALLEL*/ xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/) { - fm_map fm_struct; + fm_map fm; /* File<->memory mapping */ herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; @@ -1434,17 +1434,17 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ FUNC_ENTER_NOINIT(H5D_chunk_read); /* Initialize fm_map*/ - HDmemset(&fm_struct, 0, sizeof(fm_map)); - fm_struct.layout = &(dataset->layout); + HDmemset(&fm, 0, sizeof(fm_map)); + fm.layout = &(dataset->layout); /* Map elements between file and memory for each chunk*/ - H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm_struct); + H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm); /* * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ - if (H5T_IS_NOOP(tpath)) { + if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif @@ -1453,15 +1453,15 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ dataset->layout.type==H5D_COMPACT); /*loop through each chunk, read data*/ - for(h=0; h<fm_struct.nchunks; h++) { - if(H5S_get_select_npoints(fm_struct.fspace[h]) > 0) { + for(h=0; h<fm.nchunks; h++) { + if(H5S_get_select_npoints(fm.fspace[h]) > 0) { /*pass in chunk's coordinates in a union. LAYOUT puts datatype size as an extra dimension, * have to take it out.*/ - store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; status = (sconv->read)(dataset->ent.file, &(dataset->layout), dc_plist, &store, H5T_get_size(dataset->type), - fm_struct.fspace[h], fm_struct.mspace[h], dxpl_id, buf/*out*/); + fm.fspace[h], fm.mspace[h], dxpl_id, buf/*out*/); /* Check return value from optimized read */ if (status<0) @@ -1504,11 +1504,11 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ - if (tpath->cdata.need_bkg) { + if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); - need_bkg = MAX(tpath->cdata.need_bkg, need_bkg); + need_bkg = MAX(H5T_path_bkg(tpath), need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ @@ -1525,26 +1525,26 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ } /* end if */ /* Loop over all the chunks, performing I/O on each */ - for(h=0; h<fm_struct.nchunks; h++) { + for(h=0; h<fm.nchunks; h++) { hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ /* Get the number of elements selected in this chunk */ - chunk_nelmts=H5S_get_select_npoints(fm_struct.fspace[h]); + chunk_nelmts=H5S_get_select_npoints(fm.fspace[h]); assert(chunk_nelmts<=nelmts); if(chunk_nelmts > 0) { /* initialize selection iterator */ - if (H5S_select_iter_init(&file_iter, fm_struct.fspace[h], src_type_size)<0) + if (H5S_select_iter_init(&file_iter, fm.fspace[h], src_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); file_iter_init=1; /*file selection iteration info has been initialized */ - if (H5S_select_iter_init(&mem_iter, fm_struct.mspace[h], dst_type_size)<0) + if (H5S_select_iter_init(&mem_iter, fm.mspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); mem_iter_init=1; /*file selection iteration info has been initialized */ - if (H5S_select_iter_init(&bkg_iter, fm_struct.mspace[h], dst_type_size)<0) + if (H5S_select_iter_init(&bkg_iter, fm.mspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); bkg_iter_init=1; /*file selection iteration info has been initialized */ /*pass in chunk's coordinates in a union*/ - store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ @@ -1563,7 +1563,7 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), - dc_plist, &store, src_type_size, fm_struct.fspace[h], + dc_plist, &store, src_type_size, fm.fspace[h], &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG @@ -1578,7 +1578,7 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - n = H5S_select_mgath(buf, dst_type_size, fm_struct.mspace[h], &bkg_iter, + n = H5S_select_mgath(buf, dst_type_size, fm.mspace[h], &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); @@ -1602,7 +1602,7 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - status = H5S_select_mscat(tconv_buf, dst_type_size, fm_struct.mspace[h], + status = H5S_select_mscat(tconv_buf, dst_type_size, fm.mspace[h], &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].scat_timer), &timer); @@ -1658,16 +1658,18 @@ done: H5S_select_iter_release(&bkg_iter); /* Close file space and memory space for each chunk*/ - for(h=0; h<fm_struct.nchunks; h++) { - if(fm_struct.mspace[h]) - H5S_close(fm_struct.mspace[h]); - if(fm_struct.fspace[h]) - H5S_close(fm_struct.fspace[h]); + for(h=0; h<fm.nchunks; h++) { + if(fm.mspace[h]) + H5S_close(fm.mspace[h]); + if(fm.fspace[h]) + H5S_close(fm.fspace[h]); } - if(fm_struct.fspace) - H5MM_free(fm_struct.fspace); - if(fm_struct.mspace) - H5MM_free(fm_struct.mspace); + if(fm.chunk_coords) + H5MM_free(fm.chunk_coords); + if(fm.fspace) + H5MM_free(fm.fspace); + if(fm.mspace) + H5MM_free(fm.mspace); FUNC_LEAVE_NOAPI(ret_value); } /* H5D_chunk_read() */ @@ -1702,7 +1704,7 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S #endif /*H5_HAVE_PARALLEL*/ xfer_mode, hid_t src_id, hid_t dst_id, const void *buf) { - fm_map fm_struct; + fm_map fm; /* File<->memory mapping */ herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; @@ -1732,30 +1734,30 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S FUNC_ENTER_NOINIT(H5D_chunk_write); /* Initialize fm_map*/ - HDmemset(&fm_struct, 0, sizeof(fm_map)); - fm_struct.layout = &(dataset->layout); + HDmemset(&fm, 0, sizeof(fm_map)); + fm.layout = &(dataset->layout); /* Map elements between file and memory for each chunk*/ - H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm_struct); + H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm); /* * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ - if (H5T_IS_NOOP(tpath)) { + if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /*loop through each chunk, write data*/ - for(h=0; h<fm_struct.nchunks; h++) { - if(H5S_get_select_npoints(fm_struct.fspace[h]) > 0) { + for(h=0; h<fm.nchunks; h++) { + if(H5S_get_select_npoints(fm.fspace[h]) > 0) { /*pass in chunk's coordinates in a union. LAYOUT puts datatype size as an extra dimension, * have to take it out.*/ - store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; status = (sconv->write)(dataset->ent.file, &(dataset->layout), dc_plist, &store, H5T_get_size(dataset->type), - fm_struct.fspace[h], fm_struct.mspace[h], dxpl_id, buf); + fm.fspace[h], fm.mspace[h], dxpl_id, buf); /* Check return value from optimized write */ if (status<0) @@ -1798,11 +1800,11 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ - if (tpath->cdata.need_bkg) { + if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); - need_bkg = MAX (tpath->cdata.need_bkg, need_bkg); + need_bkg = MAX (H5T_path_bkg(tpath), need_bkg); } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { /* Old data is retrieved into background buffer for VL datatype. The * data is used later for freeing heap objects. */ @@ -1823,27 +1825,27 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S } /* end if */ /* Loop over all the chunks, performing I/O on each */ - for(h=0; h<fm_struct.nchunks; h++) { + for(h=0; h<fm.nchunks; h++) { hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ /* Get the number of elements selected in this chunk */ - chunk_nelmts=H5S_get_select_npoints(fm_struct.fspace[h]); + chunk_nelmts=H5S_get_select_npoints(fm.fspace[h]); assert(chunk_nelmts<=nelmts); if(chunk_nelmts > 0) { /* initialize selection iterator */ - if (H5S_select_iter_init(&file_iter, fm_struct.fspace[h], dst_type_size)<0) + if (H5S_select_iter_init(&file_iter, fm.fspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); file_iter_init=1; /*file selection iteration info has been initialized */ - if (H5S_select_iter_init(&mem_iter, fm_struct.mspace[h], src_type_size)<0) + if (H5S_select_iter_init(&mem_iter, fm.mspace[h], src_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); mem_iter_init=1; /*file selection iteration info has been initialized */ - if (H5S_select_iter_init(&bkg_iter, fm_struct.fspace[h], dst_type_size)<0) + if (H5S_select_iter_init(&bkg_iter, fm.fspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); bkg_iter_init=1; /*file selection iteration info has been initialized */ /*pass in chunk's coordinates in a union*/ - store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ @@ -1858,7 +1860,7 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - n = H5S_select_mgath(buf, src_type_size, fm_struct.mspace[h], &mem_iter, + n = H5S_select_mgath(buf, src_type_size, fm.mspace[h], &mem_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG @@ -1874,7 +1876,7 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S H5_timer_begin(&timer); #endif n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), - dc_plist, &store, dst_type_size, fm_struct.fspace[h], + dc_plist, &store, dst_type_size, fm.fspace[h], &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG @@ -1900,7 +1902,7 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S H5_timer_begin(&timer); #endif status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), - dc_plist, &store, dst_type_size, fm_struct.fspace[h], + dc_plist, &store, dst_type_size, fm.fspace[h], &file_iter, smine_nelmts, dxpl_id, tconv_buf); #ifdef H5S_DEBUG @@ -1957,16 +1959,18 @@ done: H5S_select_iter_release(&bkg_iter); /* Close file space and memory space for each chunk*/ - for(h=0; h<fm_struct.nchunks; h++) { - if(fm_struct.mspace[h]) - H5S_close(fm_struct.mspace[h]); - if(fm_struct.fspace[h]) - H5S_close(fm_struct.fspace[h]); + for(h=0; h<fm.nchunks; h++) { + if(fm.mspace[h]) + H5S_close(fm.mspace[h]); + if(fm.fspace[h]) + H5S_close(fm.fspace[h]); } - if(fm_struct.fspace) - H5MM_free(fm_struct.fspace); - if(fm_struct.mspace) - H5MM_free(fm_struct.mspace); + if(fm.chunk_coords) + H5MM_free(fm.chunk_coords); + if(fm.fspace) + H5MM_free(fm.fspace); + if(fm.mspace) + H5MM_free(fm.mspace); FUNC_LEAVE_NOAPI(ret_value); } /* H5D_chunk_write() */ |