diff options
| -rw-r--r-- | src/H5Dio.c | 938 |
1 files changed, 639 insertions, 299 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 6d66ae3..06d5a15 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -21,6 +21,7 @@ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Sprivate.h" /* Dataspace functions */ +#include "H5TBprivate.h" /* Threaded, balanced, binary trees (TBBTs) */ #include "H5Vprivate.h" /* Vector and array functions */ /*#define H5D_DEBUG*/ @@ -44,18 +45,36 @@ /* Local typedefs */ -/*information for mapping between file space and memory space*/ +/* Information for mapping between file space and memory space */ + +/* Structure holding information about a file chunk's selection for mapping */ +typedef struct H5D_fchunk_info_t { + hsize_t index; /* "Index" of chunk in dataset (must be first for TBBT routines) */ + H5S_t *space; /* Dataspace describing chunk & selection in it */ + hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */ +} H5D_fchunk_info_t; + +/* Structure holding information about a memory chunk's selection for mapping */ +typedef struct H5D_mchunk_info_t { + hsize_t index; /* "Index" of chunk in dataset (must be first for TBBT routines) */ + H5S_t *space; /* Dataspace describing chunk & selection in it */ +} H5D_mchunk_info_t; + +/* Main structure holding the mapping between file chunks and memory */ typedef struct fm_map { - H5S_t **fspace; /*file spaces for all chunks*/ - H5S_t **mspace; /*memory spaces for all chunks*/ - hsize_t elmt_count; /*indicate which element is being processed*/ - hsize_t nchunks; /*total number of chunks*/ + H5TB_TREE *fsel; /* TBBT containing file dataspaces for all chunks */ + H5TB_TREE *msel; /* TBBT containing memory dataspaces for all chunks */ + hsize_t last_index; /* Index of last chunk operated on */ + H5S_t *last_fchunk; /* Pointer to last file chunk's dataspace */ + H5S_t *last_mchunk; /* Pointer to last memory chunk's dataspace */ + H5S_t *fchunk_tmpl; /* Dataspace template for new file chunks */ + H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */ + unsigned f_ndims; /* Number of dimensions for file dataspace */ H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */ unsigned m_ndims; /* Number of dimensions for memory dataspace */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ - hssize_t *chunk_coords; /*coordinates for all chunks*/ - H5O_layout_t *layout; /*dataset layout information*/ + H5O_layout_t *layout; /* Dataset layout information*/ } fm_map; /* Interface initialization */ @@ -94,11 +113,13 @@ static herr_t H5D_io_assist_mpio(H5P_genplist_t *dx_plist, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, hbool_t *xfer_mode_changed); #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); +static herr_t H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, + const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm); +static herr_t H5D_destroy_chunk_map(fm_map *fm); +static void H5D_free_fchunk_info(void *fchunk_info); +static void H5D_free_mchunk_info(void *mchunk_info); static herr_t H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, - hsize_t chunks[], hsize_t chunk_ptr); + hsize_t chunks[], hsize_t chunk_idx); static herr_t H5D_chunk_cb(void *elem, hid_t type_id, hsize_t ndims, hssize_t *coords, void *fm); static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, @@ -111,6 +132,12 @@ H5FL_BLK_DEFINE(type_elem); /* Declare a free list to manage blocks of type conversion data */ H5FL_BLK_DEFINE(type_conv); +/* Declare a free list to manage the H5D_fchunk_info_t struct */ +H5FL_DEFINE_STATIC(H5D_fchunk_info_t); + +/* Declare a free list to manage the H5D_mchunk_info_t struct */ +H5FL_DEFINE_STATIC(H5D_mchunk_info_t); + /*-------------------------------------------------------------------------- NAME @@ -1419,6 +1446,8 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/) { fm_map fm; /* File<->memory mapping */ + H5TB_NODE *fchunk_node; /* Current node in file chunk TBBT */ + H5TB_NODE *mchunk_node; /* Current node in memory chunk TBBT */ herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; @@ -1439,7 +1468,6 @@ H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_ uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5D_storage_t store; /*union of EFL and chunk pointer in file space */ - hsize_t h; /* Local index variable */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ #endif /*H5_HAVE_PARALLEL*/ @@ -1447,12 +1475,9 @@ 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, 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); + if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping"); /* * If there is no type conversion then read directly into the @@ -1466,22 +1491,47 @@ 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); - /*loop through each chunk, read data*/ - 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.chunk_coords + h*dataset->layout.ndims; + /* Get first node in chunk trees */ + fchunk_node=H5TB_first(fm.fsel->root); + mchunk_node=H5TB_first(fm.msel->root); - status = (sconv->read)(dataset->ent.file, &(dataset->layout), - dc_plist, &store, H5T_get_size(dataset->type), - fm.fspace[h], fm.mspace[h], dxpl_id, buf/*out*/); + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); - /* Check return value from optimized read */ - if (status<0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); - } /* end if */ - } /* end for */ + /* Iterate through chunks to be operated on */ + while(fchunk_node) { + H5D_fchunk_info_t *fchunk_info; /* File chunk information */ + H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */ + + /* Get the actual chunk information from the tree nodes */ + fchunk_info=fchunk_node->data; + mchunk_info=mchunk_node->data; + + /* Pass in chunk's coordinates in a union. */ + store.chunk_coords = fchunk_info->coords; + + /* Perform the actual read operation */ + status = (sconv->read)(dataset->ent.file, &(dataset->layout), + dc_plist, &store, H5T_get_size(dataset->type), + fchunk_info->space, mchunk_info->space, dxpl_id, buf); + + /* Check return value from optimized read */ + if (status<0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); + + /* Get the next chunk nodes in the trees */ + fchunk_node=H5TB_next(fchunk_node); + mchunk_node=H5TB_next(mchunk_node); + + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); + } /* end while */ #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].read_timer), &timer); @@ -1546,109 +1596,136 @@ 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.nchunks; h++) { + + /* Get first node in chunk trees */ + fchunk_node=H5TB_first(fm.fsel->root); + mchunk_node=H5TB_first(fm.msel->root); + + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); + + /* Iterate through chunks to be operated on */ + while(fchunk_node) { hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ + H5D_fchunk_info_t *fchunk_info; /* File chunk information */ + H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */ + + /* Get the actual chunk information from the tree nodes */ + fchunk_info=fchunk_node->data; + mchunk_info=mchunk_node->data; /* Get the number of elements selected in this chunk */ - chunk_nelmts=H5S_get_select_npoints(fm.fspace[h]); + chunk_nelmts=H5S_get_select_npoints(fchunk_info->space); assert(chunk_nelmts<=nelmts); - if(chunk_nelmts > 0) { - /* initialize selection iterator */ - 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.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.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.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 */ - assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); - smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); - - /* - * Gather the data from disk into the data type conversion - * buffer. Also gather data from application to background buffer - * if necessary. - */ + + /* initialize selection iterator */ + if (H5S_select_iter_init(&file_iter, fchunk_info->space, 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, mchunk_info->space, 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, mchunk_info->space, 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 = fchunk_info->coords; + + for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { + /* Go figure out how many elements to read from the file */ + assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); + smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); + + /* + * Gather the data from disk into the data type conversion + * buffer. Also gather data from application to background buffer + * if necessary. + */ #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - /* Sanity check that space is allocated, then read data from it */ - 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.fspace[h], - &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); + /* Sanity check that space is allocated, then read data from it */ + 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, fchunk_info->space, + &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG - H5_timer_end(&(sconv->stats[1].gath_timer), &timer); - sconv->stats[1].gath_nbytes += n * src_type_size; - sconv->stats[1].gath_ncalls++; + H5_timer_end(&(sconv->stats[1].gath_timer), &timer); + sconv->stats[1].gath_nbytes += n * src_type_size; + sconv->stats[1].gath_ncalls++; #endif - if (n!=smine_nelmts) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); + if (n!=smine_nelmts) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); - if (need_bkg) { + if (need_bkg) { #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - n = H5S_select_mgath(buf, dst_type_size, fm.mspace[h], &bkg_iter, - smine_nelmts, dxpl_id, bkg_buf/*out*/); + n = H5S_select_mgath(buf, dst_type_size, mchunk_info->space, &bkg_iter, + smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG - H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); - sconv->stats[1].bkg_nbytes += n * dst_type_size; - sconv->stats[1].bkg_ncalls++; + H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); + sconv->stats[1].bkg_nbytes += n * dst_type_size; + sconv->stats[1].bkg_ncalls++; #endif - if (n!=smine_nelmts) - HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); - } /* end if */ - - /* - * Perform data type conversion. - */ - if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, - tconv_buf, bkg_buf, dxpl_id)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); - - /* - * Scatter the data into memory. - */ + if (n!=smine_nelmts) + HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); + } /* end if */ + + /* + * Perform data type conversion. + */ + if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, + tconv_buf, bkg_buf, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); + + /* + * Scatter the data into memory. + */ #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - status = H5S_select_mscat(tconv_buf, dst_type_size, fm.mspace[h], - &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); + status = H5S_select_mscat(tconv_buf, dst_type_size, mchunk_info->space, + &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG - H5_timer_end(&(sconv->stats[1].scat_timer), &timer); - sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; - sconv->stats[1].scat_ncalls++; + H5_timer_end(&(sconv->stats[1].scat_timer), &timer); + sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; + sconv->stats[1].scat_ncalls++; #endif - if (status<0) - HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); - } /* end for */ - - /* Release selection iterators */ - if(file_iter_init) { - H5S_select_iter_release(&file_iter); - file_iter_init=0; - } /* end if */ - if(mem_iter_init) { - H5S_select_iter_release(&mem_iter); - mem_iter_init=0; - } /* end if */ - if(bkg_iter_init) { - H5S_select_iter_release(&bkg_iter); - bkg_iter_init=0; - } /* end if */ + if (status<0) + HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); + } /* end for */ + + /* Release selection iterators */ + if(file_iter_init) { + H5S_select_iter_release(&file_iter); + file_iter_init=0; } /* end if */ - } /* end for */ + if(mem_iter_init) { + H5S_select_iter_release(&mem_iter); + mem_iter_init=0; + } /* end if */ + if(bkg_iter_init) { + H5S_select_iter_release(&bkg_iter); + bkg_iter_init=0; + } /* end if */ + + /* Get the next chunk nodes in the trees */ + fchunk_node=H5TB_next(fchunk_node); + mchunk_node=H5TB_next(mchunk_node); + + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); + } /* end while */ done: #ifdef H5_HAVE_PARALLEL @@ -1660,7 +1737,7 @@ done: #endif xfer_mode = H5FD_MPIO_COLLECTIVE; if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); + HDONE_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); } /* end if */ #endif /*H5_HAVE_PARALLEL*/ @@ -1678,19 +1755,9 @@ done: if(bkg_iter_init) H5S_select_iter_release(&bkg_iter); - /* Close file space and memory space for each chunk*/ - 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.chunk_coords) - H5MM_free(fm.chunk_coords); - if(fm.fspace) - H5MM_free(fm.fspace); - if(fm.mspace) - H5MM_free(fm.mspace); + /* Release chunk mapping information */ + if(H5D_destroy_chunk_map(&fm) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping"); FUNC_LEAVE_NOAPI(ret_value); } /* H5D_chunk_read() */ @@ -1726,6 +1793,8 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S xfer_mode, hid_t src_id, hid_t dst_id, const void *buf) { fm_map fm; /* File<->memory mapping */ + H5TB_NODE *fchunk_node; /* Current node in file chunk TBBT */ + H5TB_NODE *mchunk_node; /* Current node in memory chunk TBBT */ herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; @@ -1746,7 +1815,6 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5D_storage_t store; /*union of EFL and chunk pointer in file space */ - hsize_t h; /* Local index variable */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ #endif /*H5_HAVE_PARALLEL*/ @@ -1754,12 +1822,9 @@ 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, 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); + if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping"); /* * If there is no type conversion then write directly from the @@ -1769,22 +1834,47 @@ H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - /*loop through each chunk, write data*/ - 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.chunk_coords + h*dataset->layout.ndims; - - status = (sconv->write)(dataset->ent.file, &(dataset->layout), - dc_plist, &store, H5T_get_size(dataset->type), - fm.fspace[h], fm.mspace[h], dxpl_id, buf); - - /* Check return value from optimized write */ - if (status<0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); - } - } + /* Get first node in chunk trees */ + fchunk_node=H5TB_first(fm.fsel->root); + mchunk_node=H5TB_first(fm.msel->root); + + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); + + /* Iterate through chunks to be operated on */ + while(fchunk_node) { + H5D_fchunk_info_t *fchunk_info; /* File chunk information */ + H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */ + + /* Get the actual chunk information from the tree nodes */ + fchunk_info=fchunk_node->data; + mchunk_info=mchunk_node->data; + + /* Pass in chunk's coordinates in a union. */ + store.chunk_coords = fchunk_info->coords; + + /* Perform the actual write operation */ + status = (sconv->write)(dataset->ent.file, &(dataset->layout), + dc_plist, &store, H5T_get_size(dataset->type), + fchunk_info->space, mchunk_info->space, dxpl_id, buf); + + /* Check return value from optimized write */ + if (status<0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); + + /* Get the next chunk nodes in the trees */ + fchunk_node=H5TB_next(fchunk_node); + mchunk_node=H5TB_next(mchunk_node); + + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); + } /* end while */ #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].write_timer), &timer); @@ -1853,110 +1943,136 @@ 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.nchunks; h++) { + + /* Get first node in chunk trees */ + fchunk_node=H5TB_first(fm.fsel->root); + mchunk_node=H5TB_first(fm.msel->root); + + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); + + /* Iterate through chunks to be operated on */ + while(fchunk_node) { hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ + H5D_fchunk_info_t *fchunk_info; /* File chunk information */ + H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */ + + /* Get the actual chunk information from the tree nodes */ + fchunk_info=fchunk_node->data; + mchunk_info=mchunk_node->data; /* Get the number of elements selected in this chunk */ - chunk_nelmts=H5S_get_select_npoints(fm.fspace[h]); + chunk_nelmts=H5S_get_select_npoints(fchunk_info->space); assert(chunk_nelmts<=nelmts); - if(chunk_nelmts > 0) { - - /* initialize selection iterator */ - 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.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.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 */ + + /* initialize selection iterator */ + if (H5S_select_iter_init(&file_iter, fchunk_info->space, 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, mchunk_info->space, 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, fchunk_info->space, 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 = fchunk_info->coords; + + for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { + /* Go figure out how many elements to read from the file */ + assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); + smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); - /*pass in chunk's coordinates in a union*/ - 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 */ - assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); - smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); - - /* - * Gather the data from disk into the data type conversion - * buffer. Also gather data from application to background buffer - * if necessary. - */ + /* + * Gather the data from disk into the data type conversion + * buffer. Also gather data from application to background buffer + * if necessary. + */ #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - n = H5S_select_mgath(buf, src_type_size, fm.mspace[h], &mem_iter, - smine_nelmts, dxpl_id, tconv_buf/*out*/); - + n = H5S_select_mgath(buf, src_type_size, mchunk_info->space, &mem_iter, + smine_nelmts, dxpl_id, tconv_buf/*out*/); + #ifdef H5S_DEBUG - H5_timer_end(&(sconv->stats[1].gath_timer), &timer); - sconv->stats[1].gath_nbytes += n * src_type_size; - sconv->stats[1].gath_ncalls++; + H5_timer_end(&(sconv->stats[1].gath_timer), &timer); + sconv->stats[1].gath_nbytes += n * src_type_size; + sconv->stats[1].gath_ncalls++; #endif - if (n!=smine_nelmts) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); + if (n!=smine_nelmts) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); - if (need_bkg) { + if (need_bkg) { #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), - dc_plist, &store, dst_type_size, fm.fspace[h], - &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); + n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), + dc_plist, &store, dst_type_size, fchunk_info->space, + &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG - H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); - sconv->stats[0].bkg_nbytes += n * dst_type_size; - sconv->stats[0].bkg_ncalls++; + H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); + sconv->stats[0].bkg_nbytes += n * dst_type_size; + sconv->stats[0].bkg_ncalls++; #endif - if (n!=smine_nelmts) - HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); - } /* end if */ - - /* - * Perform data type conversion. - */ - if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, - tconv_buf, bkg_buf, dxpl_id)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); - - /* - * Scatter the data out to the file. - */ + if (n!=smine_nelmts) + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); + } /* end if */ + + /* + * Perform data type conversion. + */ + if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, + tconv_buf, bkg_buf, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); + + /* + * Scatter the data out to the file. + */ #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), - dc_plist, &store, dst_type_size, fm.fspace[h], - &file_iter, smine_nelmts, dxpl_id, tconv_buf); + status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), + dc_plist, &store, dst_type_size, fchunk_info->space, + &file_iter, smine_nelmts, dxpl_id, tconv_buf); #ifdef H5S_DEBUG - H5_timer_end(&(sconv->stats[0].scat_timer), &timer); - sconv->stats[0].scat_nbytes += n * dst_type_size; - sconv->stats[0].scat_ncalls++; + H5_timer_end(&(sconv->stats[0].scat_timer), &timer); + sconv->stats[0].scat_nbytes += n * dst_type_size; + sconv->stats[0].scat_ncalls++; #endif - if (status<0) - HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed"); - } /* end for */ - - /* Release selection iterators */ - if(file_iter_init) { - H5S_select_iter_release(&file_iter); - file_iter_init=0; - } /* end if */ - if(mem_iter_init) { - H5S_select_iter_release(&mem_iter); - mem_iter_init=0; - } /* end if */ - if(bkg_iter_init) { - H5S_select_iter_release(&bkg_iter); - bkg_iter_init=0; - } /* end if */ + if (status<0) + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed"); + } /* end for */ + + /* Release selection iterators */ + if(file_iter_init) { + H5S_select_iter_release(&file_iter); + file_iter_init=0; + } /* end if */ + if(mem_iter_init) { + H5S_select_iter_release(&mem_iter); + mem_iter_init=0; + } /* end if */ + if(bkg_iter_init) { + H5S_select_iter_release(&bkg_iter); + bkg_iter_init=0; } /* end if */ - } /* end for */ + + /* Get the next chunk nodes in the trees */ + fchunk_node=H5TB_next(fchunk_node); + mchunk_node=H5TB_next(mchunk_node); + + /* Sanity check that we either have both file & memory chunk information + * or _don't_ have both file & memory chunk information + * (i.e. don't run out of one kind of chunk before the other) + */ + assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); + } /* end while */ done: #ifdef H5_HAVE_PARALLEL @@ -1968,7 +2084,7 @@ done: #endif xfer_mode = H5FD_MPIO_COLLECTIVE; if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); + HDONE_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); } /* end if */ #endif /*H5_HAVE_PARALLEL*/ @@ -1986,19 +2102,9 @@ done: if(bkg_iter_init) H5S_select_iter_release(&bkg_iter); - /* Close file space and memory space for each chunk*/ - 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.chunk_coords) - H5MM_free(fm.chunk_coords); - if(fm.fspace) - H5MM_free(fm.fspace); - if(fm.mspace) - H5MM_free(fm.mspace); + /* Release chunk mapping information */ + if(H5D_destroy_chunk_map(&fm) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping"); FUNC_LEAVE_NOAPI(ret_value); } /* H5D_chunk_write() */ @@ -2060,7 +2166,7 @@ done: /*------------------------------------------------------------------------- * Function: H5D_chunk_coords_assist * - * Purpose: Compute the coords for a particular chunk (in CHUNK_PTR), + * Purpose: Compute the coords for a particular chunk (in CHUNK_IDX), * based on the size of the dataset's dataspace (given in * NDIMS and CHUNKS), putting the resulting chunk's coordinate * offsets in the COORDS array. @@ -2075,7 +2181,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_t chunk_ptr) +H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_t chunk_idx) { hsize_t tmp; /* Size of "down elements" in each dimension */ size_t i, j; /* Local index variables */ @@ -2086,8 +2192,8 @@ H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_ tmp=1; for(j=i+1; j<ndims; j++) tmp *= chunks[j]; - coords[i] = (hssize_t)(chunk_ptr / tmp); - chunk_ptr = chunk_ptr % tmp; + coords[i] = (hssize_t)(chunk_idx / tmp); + chunk_idx = chunk_idx % tmp; } coords[ndims] = 0; @@ -2096,7 +2202,7 @@ H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_ /*------------------------------------------------------------------------- - * Function: H5D_chunk_mem_file_map + * Function: H5D_create_chunk_map * * Purpose: Creates the mapping between elements selected in each chunk * and the elements in the memory selection. @@ -2113,7 +2219,7 @@ H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_ *------------------------------------------------------------------------- */ static herr_t -H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, +H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm) { H5S_t *tmp_fspace=NULL, /* Temporary file dataspace */ @@ -2124,12 +2230,19 @@ H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_ unsigned f_ndims; /* The number of dimensions of the file's dataspace */ int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */ hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* Dimensionality of file dataspace */ + hsize_t nchunks, last_nchunks; /* Number of chunks in dataset */ + H5TB_NODE *curr_node; /* Current node in TBBT */ char bogus; /* "bogus" buffer to pass to selection iterator */ unsigned u; /* Local index variable */ - hsize_t j; /* Local index variable */ herr_t ret_value = SUCCEED; /*return value */ - FUNC_ENTER_NOINIT(H5D_chunk_mem_file_map); + FUNC_ENTER_NOINIT(H5D_create_chunk_map); + + /* Initialize fm_map structure */ + HDmemset(fm, 0, sizeof(fm_map)); + + /* Get layout for dataset */ + fm->layout = &(dataset->layout); /* Create a file space of a chunk's size, instead of whole file space*/ if(NULL==(tmp_fspace=H5S_create_simple((dataset->layout.ndims-1),dataset->layout.dim,NULL))) @@ -2146,7 +2259,7 @@ H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space"); /* Get dim number and dimensionality for each dataspace */ - f_ndims=dataset->layout.ndims-1; + fm->f_ndims=f_ndims=dataset->layout.ndims-1; if((sm_ndims = H5S_get_simple_extent_ndims(tmp_mspace))<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number"); fm->m_ndims=sm_ndims; @@ -2155,41 +2268,37 @@ H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality"); /* Decide the number of chunks in each dimension*/ - fm->nchunks = 1; + last_nchunks=0; + nchunks=1; for(u=0; u<f_ndims; u++) { fm->chunks[u] = ((f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u]; - fm->nchunks *= fm->chunks[u]; - } + + /* Track total number of chunks in dataset */ + nchunks *= fm->chunks[u]; + + /* Check if the chunk indices will overflow */ + if(nchunks<last_nchunks) + HGOTO_ERROR (H5E_DATASET, H5E_OVERFLOW, FAIL, "too many chunks"); + last_nchunks=nchunks; + } /* end for */ /* Compute the "down" size of 'chunks' information */ if(H5V_array_down(f_ndims,fm->chunks,fm->down_chunks)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes"); - /* Allocate arrays to hold each chunk's dataspace & selection, for both the - * file and memory */ - H5_CHECK_OVERFLOW((sizeof(H5S_t*)*fm->nchunks),hsize_t,size_t); - fm->fspace = (H5S_t**)H5MM_malloc((size_t)(sizeof(H5S_t*)*fm->nchunks)); - fm->mspace = (H5S_t**)H5MM_malloc((size_t)(sizeof(H5S_t*)*fm->nchunks)); - fm->elmt_count = 0; + /* Initialize TBBT's for file & memory chunk selections */ + if((fm->fsel=H5TB_fast_dmake(H5TB_FAST_HSIZE_COMPARE))==NULL) + HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create TBBT for file chunk selections"); + if((fm->msel=H5TB_fast_dmake(H5TB_FAST_HSIZE_COMPARE))==NULL) + HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create TBBT for memory chunk selections"); - /* Allocate array to hold coordinates of each chunk in file's dataspace */ - H5_CHECK_OVERFLOW((sizeof(hsize_t)*fm->nchunks*(f_ndims+1)),hsize_t,size_t); - fm->chunk_coords = (hssize_t*)H5MM_malloc((size_t)(sizeof(hsize_t)*fm->nchunks*(f_ndims+1))); - - /* Make per-chunk copies of memory and chunk dataspaces - * (with each one's selection set to "none" - */ - for(j=0; j<fm->nchunks; j++) { - if((fm->mspace[j] = H5S_copy(tmp_mspace))==NULL) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); - if((fm->fspace[j] = H5S_copy(tmp_fspace))==NULL) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space"); - - /* Initialize chunk_coords for each chunk. each stride is the number of - * file space dimensions, with fast-growing dimension at the last - */ - H5D_chunk_coords_assist(fm->chunk_coords+j*(f_ndims+1), f_ndims, fm->chunks, j); - } + /* Save chunk template information */ + fm->fchunk_tmpl=tmp_fspace; + fm->mchunk_tmpl=tmp_mspace; + + /* Initialize "last chunk" information */ + fm->last_index=(hsize_t)-1; + fm->last_fchunk=fm->last_mchunk=NULL; /* Create temporary datatypes for selection iteration */ if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) @@ -2206,28 +2315,176 @@ H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_ if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_cb, fm)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to iterate file space"); - /* Clean hyperslab span "scratch" information */ - for(j=0; j<fm->nchunks; j++) { - if(H5S_hyper_reset_scratch(fm->fspace[j])<0) + /* Clean file chunks' hyperslab span "scratch" information */ + curr_node=H5TB_first(fm->fsel->root); + while(curr_node) { + H5D_fchunk_info_t *chunk_info; /* Pointer chunk information */ + + /* Get pointer to chunk's information */ + chunk_info=curr_node->data; + assert(chunk_info); + + /* Clean hyperslab span's "scratch" information */ + if(H5S_hyper_reset_scratch(chunk_info->space)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); - if(H5S_hyper_reset_scratch(fm->mspace[j])<0) + + /* Get the next chunk node in the TBBT */ + curr_node=H5TB_next(curr_node); + } /* end while */ + + /* Clean memory chunks' hyperslab span "scratch" information */ + curr_node=H5TB_first(fm->msel->root); + while(curr_node) { + H5D_mchunk_info_t *chunk_info; /* Pointer chunk information */ + + /* Get pointer to chunk's information */ + chunk_info=curr_node->data; + assert(chunk_info); + + /* Clean hyperslab span's "scratch" information */ + if(H5S_hyper_reset_scratch(chunk_info->space)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); - } /* end for */ + + /* Get the next chunk node in the TBBT */ + curr_node=H5TB_next(curr_node); + } /* end while */ done: + /* Release the [potentially partially built] chunk mapping information if an error occurs */ + if(ret_value<0) { + if(tmp_fspace && !fm->fchunk_tmpl) { + if(H5S_close(tmp_fspace)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file chunk dataspace template"); + } /* end if */ + + if(tmp_mspace && !fm->mchunk_tmpl) { + if(H5S_close(tmp_mspace)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template"); + } /* end if */ + + if (H5D_destroy_chunk_map(fm)<0) + HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping"); + } /* end if */ + if(iter_init) { if (H5S_select_iter_release(&(fm->mem_iter))<0) HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); } - if(tmp_fspace) - H5S_close(tmp_fspace); - if(tmp_mspace) - H5S_close(tmp_mspace); if(f_tid!=(-1)) H5Tclose(f_tid); FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_chunk_mem_file_map() */ +} /* end H5D_create_chunk_map() */ + + +/*-------------------------------------------------------------------------- + NAME + H5D_free_fchunk_info + PURPOSE + Internal routine to destroy a file chunk info node (Wrapper for compatibility + with H5TB_dfree) + USAGE + void H5D_free_fchunk_info(fchunk_info) + void *fchunk_info; IN: Pointer to file chunk info to destroy + RETURNS + No return value + DESCRIPTION + Releases all the memory for a file chunk info node. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static void +H5D_free_fchunk_info(void *_fchunk_info) +{ + H5D_fchunk_info_t *fchunk_info=(H5D_fchunk_info_t *)_fchunk_info; + + FUNC_ENTER_NOINIT(H5D_free_fchunk_info); + + assert(fchunk_info); + + H5S_close(fchunk_info->space); + + FUNC_LEAVE_NOAPI_VOID; +} /* H5D_free_fchunk_info() */ + + +/*-------------------------------------------------------------------------- + NAME + H5D_free_mchunk_info + PURPOSE + Internal routine to destroy a file chunk info node (Wrapper for compatibility + with H5TB_dfree) + USAGE + void H5D_free_mchunk_info(mchunk_info) + void *mchunk_info; IN: Pointer to memory chunk info to destroy + RETURNS + No return value + DESCRIPTION + Releases all the memory for a memory chunk info node. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static void +H5D_free_mchunk_info(void *_mchunk_info) +{ + H5D_mchunk_info_t *mchunk_info=(H5D_mchunk_info_t *)_mchunk_info; + + FUNC_ENTER_NOINIT(H5D_free_mchunk_info); + + assert(mchunk_info); + + H5S_close(mchunk_info->space); + + FUNC_LEAVE_NOAPI_VOID; +} /* H5D_free_mchunk_info() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_destroy_chunk_map + * + * Purpose: Destroy chunk mapping information. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Saturday, May 17, 2003 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_destroy_chunk_map(fm_map *fm) +{ + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOINIT(H5D_destroy_chunk_map); + + /* Free the file chunk info tree */ + if(fm->fsel) + H5TB_dfree(fm->fsel,H5D_free_fchunk_info,NULL); + + /* Free the memory chunk info tree */ + if(fm->msel) + H5TB_dfree(fm->msel,H5D_free_mchunk_info,NULL); + + /* Free the file chunk dataspace template */ + if(fm->fchunk_tmpl) + if(H5S_close(fm->fchunk_tmpl)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file chunk dataspace template"); + + /* Free the memory chunk dataspace template */ + if(fm->mchunk_tmpl) + if(H5S_close(fm->mchunk_tmpl)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template"); + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_destroy_chunk_map() */ /*------------------------------------------------------------------------- @@ -2251,9 +2508,11 @@ static herr_t H5D_chunk_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm) { fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ + H5S_t *fspace; /* File chunk's dataspace */ + H5S_t *mspace; /* Memory chunk's dataspace */ hssize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ hssize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ - hsize_t chunk_idx; /* Chunk index */ + hsize_t chunk_index; /* Chunk index */ hsize_t u; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2268,10 +2527,10 @@ H5D_chunk_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *c #endif /* QAK */ /* Calculate the index of this chunk */ - if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_idx)<0) + if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); #ifdef QAK -HDfprintf(stderr,"%s: chunk_idx=%Hu\n",FUNC,chunk_idx); +HDfprintf(stderr,"%s: chunk_index=%Hu\n",FUNC,chunk_index); #endif /* QAK */ /*convert coords from relative to whole file space to relative to its chunk space, @@ -2287,8 +2546,89 @@ HDfprintf(stderr,"%s: chunk_idx=%Hu\n",FUNC,chunk_idx); HDfprintf(stderr,"%Hd%s",coords_in_chunk[u],(u<(ndims-1)?", ":"}\n")); } #endif /* QAK */ + + /* Find correct chunk in file & memory TBBTs */ + if(chunk_index==fm->last_index) { + /* If the chunk index is the same as the last chunk index we used, + * get the cached spaces to operate on. + */ + fspace=fm->last_fchunk; + mspace=fm->last_mchunk; + } /* end if */ + else { + H5TB_NODE *chunk_node; /* TBBT node holding chunk information */ + /* If the chunk index is not the same as the last chunk index we used, + * find the chunk in the tree. + */ + /* Get the chunk node from the TBBT */ + if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))!=NULL) { + /* We found the correct chunk already in the tree */ + + /* Get the file space information from the node */ + fspace=((H5D_fchunk_info_t *)(chunk_node->data))->space; + + /* Look up the memory space information for the chunk */ + if((chunk_node=H5TB_dfind(fm->msel,&chunk_index,NULL))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't find memory chunk info"); + + /* Get the file space information from the node */ + mspace=((H5D_mchunk_info_t *)(chunk_node->data))->space; + } /* end if */ + else { + H5D_fchunk_info_t *new_fchunk_info; /* File chunk information to insert into tree */ + H5D_mchunk_info_t *new_mchunk_info; /* Memory chunk information to insert into tree */ + + /* The correct chunk is not already in the tree, create a new node */ + /* in both the file and memory chunk trees */ + + /* Allocate the file & memory chunk information */ + if (NULL==(new_fchunk_info = H5FL_MALLOC (H5D_fchunk_info_t))) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate file chunk info"); + if (NULL==(new_mchunk_info = H5FL_MALLOC (H5D_mchunk_info_t))) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate memory chunk info"); + + /* Initialize the file chunk information */ + + /* Set the chunk index */ + new_fchunk_info->index=chunk_index; + + /* Copy the template file chunk dataspace */ + if((new_fchunk_info->space = H5S_copy(fm->fchunk_tmpl))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space"); + + /* Compute the chunk's coordinates */ + H5D_chunk_coords_assist(new_fchunk_info->coords, fm->f_ndims, fm->chunks, chunk_index); + + /* Insert the new file chunk into the TBBT tree */ + if(H5TB_dins(fm->fsel,new_fchunk_info,new_fchunk_info)==NULL) + HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert file chunk into TBBT"); + + /* Initialize the memory chunk information */ + + /* Set the chunk index */ + new_mchunk_info->index=chunk_index; + + /* Copy the template memory chunk dataspace */ + if((new_mchunk_info->space = H5S_copy(fm->mchunk_tmpl))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space"); + + /* Insert the new memory chunk into the TBBT tree */ + if(H5TB_dins(fm->msel,new_mchunk_info,new_mchunk_info)==NULL) + HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert memory chunk into TBBT"); + + /* Get the dataspaces for use in this routine */ + fspace=new_fchunk_info->space; + mspace=new_mchunk_info->space; + } /* end else */ + + /* Update the "last chunk seen" information */ + fm->last_index=chunk_index; + fm->last_fchunk=fspace; + fm->last_mchunk=mspace; + } /* end else */ + /* Add point to file selection for chunk */ - if(H5S_hyper_add_span_element(fm->fspace[chunk_idx], (unsigned)ndims, coords_in_chunk)<0) + if(H5S_hyper_add_span_element(fspace, fm->f_ndims, coords_in_chunk)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); /* Get coordinates of selection iterator for memory */ @@ -2304,7 +2644,7 @@ HDfprintf(stderr,"%s: chunk_idx=%Hu\n",FUNC,chunk_idx); } #endif /* QAK */ /* Add point to memory selection for chunk */ - if(H5S_hyper_add_span_element(fm->mspace[chunk_idx], fm->m_ndims, coords_in_mem)<0) + if(H5S_hyper_add_span_element(mspace, fm->m_ndims, coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); /* Move memory selection iterator to next element in selection */ |