diff options
Diffstat (limited to 'src/H5Distore.c')
| -rw-r--r-- | src/H5Distore.c | 106 |
1 files changed, 60 insertions, 46 deletions
diff --git a/src/H5Distore.c b/src/H5Distore.c index 3979746..7e27d1e 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -1964,9 +1964,8 @@ H5D_istore_lock(const H5D_io_info_t *io_info, H5D_istore_ud1_t *udata, done: /* Release the fill buffer info, if it's been initialized */ - if(fb_info_init) - if(H5D_fill_term(&fb_info) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "Can't release fill buffer info") + if(fb_info_init && H5D_fill_term(&fb_info) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "Can't release fill buffer info") /* Release the chunk allocated, on error */ if(!ret_value) @@ -2524,45 +2523,25 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D_istore_chunkmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],hsize_t down_chunks[]) +H5D_istore_chunkmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[], + hsize_t down_chunks[]) { - H5D_t *dset=io_info->dset; /* Local pointer to dataset info */ -#if 0 - const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ - H5D_rdcc_ent_t *ent; /*cache entry */ - H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ - H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ -#endif + H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ H5D_istore_it_ud5_t udata; - hid_t dxpl_id = io_info->dxpl_id; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_chunkmap, FAIL) HDassert(dset); -#if 0 - /* Fill the DXPL cache values for later use */ - if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") - - /* Construct dataset I/O info */ - H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,NULL); - - /* Search for cached chunks that haven't been written out */ - for(ent = rdcc->head; ent; ent = ent->next) { - /* Flush the chunk out to disk, to make certain the size is correct later */ - if (H5D_istore_flush_entry(&io_info, ent, FALSE)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") - } /* end for */ -#endif - - HDmemset(&udata, 0, sizeof udata); + /* Set up user data for B-tree callback */ + HDmemset(&udata, 0, sizeof(udata)); udata.common.mesg = &dset->shared->layout; udata.down_chunks = down_chunks; udata.chunk_addr = chunk_addr; - if (H5B_iterate(dset->oloc.file, dxpl_id, H5B_ISTORE, H5D_istore_iter_chunkmap, dset->shared->layout.u.chunk.addr, &udata)<0) + /* Build mapping of chunk addresses and indices */ + if(H5B_iterate(dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, H5D_istore_iter_chunkmap, dset->shared->layout.u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to iterate over chunk B-tree") done: @@ -2935,7 +2914,7 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) #endif /* H5_HAVE_PARALLEL */ } /* end if */ - /* Release the chunk if we need to re-allocate it each time */ + /* Release the fill buffer if we need to re-allocate it each time */ if(fb_info_init && fb_info.has_vlen_fill_type && pline->nused > 0) H5D_fill_release(&fb_info); } /* end if */ @@ -2969,9 +2948,8 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) done: /* Release the fill buffer info, if it's been initialized */ - if(fb_info_init) - if(H5D_fill_term(&fb_info) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") + if(fb_info_init && H5D_fill_term(&fb_info) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_allocate() */ @@ -3347,8 +3325,11 @@ herr_t H5D_istore_initialize_by_extent(H5D_io_info_t *io_info) { H5S_t *space_chunk = NULL; /* Dataspace for a chunk */ - const H5O_layout_t *layout = &(io_info->dset->shared->layout); /* Dataset's layout */ + H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ + const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ H5D_storage_t store; /* Dataset storage information */ + H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ + hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* Current dataspace dimensions */ hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Current chunk dimensions */ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Logical location of the chunks */ @@ -3371,7 +3352,7 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info) HDassert(H5F_addr_defined(layout->u.chunk.addr)); /* Go get the rank & dimensions */ - if((srank = H5S_get_simple_extent_dims(io_info->dset->shared->space, dset_dims, NULL)) < 0) + if((srank = H5S_get_simple_extent_dims(dset->shared->space, dset_dims, NULL)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") H5_ASSIGN_OVERFLOW(rank, srank, int, unsigned); @@ -3423,19 +3404,26 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info) } /* end if */ if(found) { - const H5O_fill_t *fill = &io_info->dset->shared->dcpl_cache.fill; /* Fill value information */ + H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */ + hssize_t nelmts; /* Number of data elements */ hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */ uint8_t *chunk; /* The file chunk */ unsigned idx_hint; /* Which chunk we're dealing with */ - hsize_t bytes_kept; /* Bytes kept in chunk */ hsize_t bytes_accessed; /* Bytes accessed in chunk */ + /* Initialize the fill value buffer, if necessary */ + if(!fb_info_init) { + if(H5D_fill_init(&fb_info, NULL, FALSE, NULL, NULL, NULL, NULL, + &dset->shared->dcpl_cache.fill, + dset->shared->type, dset->shared->type_id, (size_t)(bytes_per_chunk / layout->u.chunk.dim[rank]), + io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info") + fb_info_init = TRUE; + } /* end if */ + /* Compute the # of elements to leave with existing value, in each dimension */ - /* And, the number of bytes in the chunk being accessed */ - for(u = 0, bytes_kept = layout->u.chunk.dim[rank]; u < rank; u++) { + for(u = 0; u < rank; u++) count[u] = MIN(layout->u.chunk.dim[u], (dset_dims[u] - chunk_offset[u])); - bytes_kept *= count[u]; - } /* end for */ #ifdef H5D_ISTORE_DEBUG HDfputs("cache:initialize:offset:[", stdout); @@ -3465,17 +3453,41 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info) if(NULL == (chunk = H5D_istore_lock(io_info, NULL, FALSE, &idx_hint))) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk") + /* Fill the selection in the memory buffer */ /* Use the size of the elements in the chunk directly instead of */ /* relying on the fill.size, which might be set to 0 if there is */ /* no fill-value defined for the dataset -QAK */ - H5_CHECK_OVERFLOW(dset_dims[rank], hsize_t, size_t); - if(H5S_select_fill(fill->buf, (size_t)dset_dims[rank], space_chunk, chunk) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed") + + /* Get the number of elements in the selection */ + nelmts = H5S_GET_SELECT_NPOINTS(space_chunk); + HDassert(nelmts >= 0); + H5_CHECK_OVERFLOW(nelmts, hssize_t, size_t); + + /* Check for VL datatype & non-default fill value */ + if(fb_info.has_vlen_fill_type) + /* Re-fill the buffer to use for this I/O operation */ + if(H5D_fill_refill_vl(&fb_info, (size_t)nelmts, io_info->dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") + + /* Create a selection iterator for scattering the elements to memory buffer */ + if(H5S_select_iter_init(&chunk_iter, space_chunk, layout->u.chunk.dim[rank]) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunk selection information") + + /* Scatter the data into memory */ + if(H5D_select_mscat(fb_info.fill_buf, space_chunk, &chunk_iter, (size_t)nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) { + H5S_SELECT_ITER_RELEASE(&chunk_iter); + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed") + } /* end if */ + + /* Release the selection iterator */ + if(H5S_SELECT_ITER_RELEASE(&chunk_iter) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") + /* The number of bytes accessed in the chunk */ /* (i.e. the bytes replaced with fill values) */ - bytes_accessed = bytes_per_chunk - bytes_kept; + bytes_accessed = nelmts * layout->u.chunk.dim[rank]; /* Release lock on chunk */ H5_CHECK_OVERFLOW(bytes_accessed, hsize_t, size_t); @@ -3500,6 +3512,8 @@ done: /* Release resources */ if(space_chunk && H5S_close(space_chunk) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") + if(fb_info_init && H5D_fill_term(&fb_info) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_initialize_by_extent() */ |