diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5Dbtree.c | 19 | ||||
| -rw-r--r-- | src/H5Dchunk.c | 256 | ||||
| -rw-r--r-- | src/H5Ddeprec.c | 11 | ||||
| -rw-r--r-- | src/H5Dint.c | 33 | ||||
| -rw-r--r-- | src/H5Dio.c | 2 | ||||
| -rw-r--r-- | src/H5Dlayout.c | 2 | ||||
| -rw-r--r-- | src/H5Dpkg.h | 5 | ||||
| -rw-r--r-- | src/H5private.h | 2 |
8 files changed, 197 insertions, 133 deletions
diff --git a/src/H5Dbtree.c b/src/H5Dbtree.c index 6ca826c..9cc15c0 100644 --- a/src/H5Dbtree.c +++ b/src/H5Dbtree.c @@ -87,6 +87,12 @@ typedef struct H5D_btree_it_ud_t { void *udata; /* User data for chunk callback routine */ } H5D_btree_it_ud_t; +/* B-tree callback info for debugging */ +typedef struct H5D_btree_dbg_t { + H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ + unsigned ndims; /* Number of dimensions */ +} H5D_btree_dbg_t; + /********************/ /* Local Prototypes */ @@ -743,7 +749,7 @@ H5D_btree_debug_key(FILE *stream, int indent, int fwidth, const void *_key, const void *_udata) { const H5D_btree_key_t *key = (const H5D_btree_key_t *)_key; - const unsigned *ndims = (const unsigned *)_udata; + const H5D_btree_dbg_t *udata = (const H5D_btree_dbg_t *)_udata; unsigned u; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_btree_debug_key) @@ -753,7 +759,7 @@ H5D_btree_debug_key(FILE *stream, int indent, int fwidth, const void *_key, HDfprintf(stream, "%*s%-*s %u bytes\n", indent, "", fwidth, "Chunk size:", (unsigned)key->nbytes); HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth, "Filter mask:", key->filter_mask); HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:"); - for(u = 0; u < *ndims; u++) + for(u = 0; u < udata->ndims; u++) HDfprintf(stream, "%s%Hd", u?", ":"", key->offset[u]); HDfputs("}\n", stream); @@ -1437,7 +1443,7 @@ herr_t H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth, unsigned ndims) { - H5D_chunk_common_ud_t udata; /* User data for B-tree callback */ + H5D_btree_dbg_t udata; /* User data for B-tree callback */ H5O_storage_chunk_t storage; /* Storage information for B-tree callback */ hbool_t shared_init = FALSE; /* Whether B-tree shared info is initialized */ herr_t ret_value = SUCCEED; /* Return value */ @@ -1454,9 +1460,10 @@ H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent shared_init = TRUE; /* Set up user data for callback */ - udata.layout = NULL; - udata.storage = &storage; - udata.offset = NULL; + udata.common.layout = NULL; + udata.common.storage = &storage; + udata.common.offset = NULL; + udata.ndims = ndims; /* Dump the records for the B-tree */ (void)H5B_debug(f, dxpl_id, addr, stream, indent, fwidth, H5B_BTREE, &udata); diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 7485717..03a3785 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -3083,10 +3083,13 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) +H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, + hsize_t old_dim[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ const H5D_chunk_ops_t *ops = dset->shared->layout.storage.u.chunk.ops; /* Chunk operations */ + hsize_t min_unalloc[H5O_LAYOUT_NDIMS]; /* First chunk in each dimension that is unallocated */ + hsize_t max_unalloc[H5O_LAYOUT_NDIMS]; /* Last chunk in each dimension that is unallocated */ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */ size_t orig_chunk_size; /* Original size of chunk in bytes */ unsigned filter_mask = 0; /* Filter mask for chunks that have them */ @@ -3107,6 +3110,8 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ int space_ndims; /* Dataset's space rank */ hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */ + const uint32_t *chunk_dim = layout->u.chunk.dim; /* Convenience pointer to chunk dimensions */ + int op_dim; /* Current operationg dimension */ 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 */ hid_t data_dxpl_id; /* DXPL ID to use for raw data I/O operations */ @@ -3124,6 +3129,15 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info") space_dim[space_ndims] = layout->u.chunk.dim[space_ndims]; + /* Check if any space dimensions are 0, if so we do not have to do anything + */ + for(op_dim=0; op_dim<space_ndims; op_dim++) + if(space_dim[op_dim] == 0) { + /* Reset any cached chunk info for this dataset */ + H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); + HGOTO_DONE(SUCCEED) + } /* end if */ + #ifdef H5_HAVE_PARALLEL /* Retrieve MPI parameters */ if(IS_H5FD_MPI(dset->oloc.file)) { @@ -3208,135 +3222,161 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = &dset->shared->layout.storage.u.chunk; - /* Reset the chunk offset indices */ - HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0]))); + /* Calculate the minimum and maximum chunk offsets in each dimension */ + for(op_dim=0; op_dim<space_ndims; op_dim++) { + min_unalloc[op_dim] = ((old_dim[op_dim] + chunk_dim[op_dim] - 1) + / chunk_dim[op_dim]) * chunk_dim[op_dim]; + if(space_dim[op_dim] == 0) + max_unalloc[op_dim] = 0; + else + max_unalloc[op_dim] = ((space_dim[op_dim] - 1) / chunk_dim[op_dim]) + * chunk_dim[op_dim]; + } /* end for */ /* Loop over all chunks */ - carry = FALSE; - while(!carry) { + /* The algorithm is: + * For each dimension: + * -Allocate all chunks in the new dataspace that are beyond the original + * dataspace in the operating dimension, except those that have already + * been allocated. + * + * This is accomplished mainly using the min_unalloc and max_unalloc arrays. + * min_unalloc represents the lowest offset in each dimension of chunks that + * have not been allocated (whether or not they need to be). max_unalloc + * represents the highest offset in each dimension of chunks in the new + * dataset that have not been allocated by this routine (they may have been + * allocated previously). + * + * Every time the algorithm finishes allocating chunks allocated beyond a + * certain dimension, max_unalloc is updated in order to avoid allocating + * those chunks again. + */ + for(op_dim=0; op_dim<space_ndims; op_dim++) { H5D_chunk_ud_t udata; /* User data for querying chunk info */ int i; /* Local index variable */ - /* Get the chunk's info */ - if(H5D_chunk_get_info(dset, dxpl_id, chunk_offset, &udata) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") - - /* Check if the chunk exists yet on disk */ - if(!H5F_addr_defined(udata.addr)) { - const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */ - H5D_rdcc_ent_t *ent; /* Cache entry */ - hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */ - unsigned u; /* Local index variable */ - - /* Didn't find the chunk on disk */ - chunk_exists = FALSE; - - /* Look for chunk in cache */ - for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) { - /* Assume a match */ - chunk_exists = TRUE; - for(u = 0; u < layout->u.chunk.ndims; u++) - if(ent->offset[u] != chunk_offset[u]) { - chunk_exists = FALSE; /* Reset if no match */ - break; - } /* end if */ - } /* end for */ - - /* Chunk wasn't in cache either, create it now */ - if(!chunk_exists) { - size_t chunk_size; /* Size of chunk in bytes, possibly filtered */ - - /* Check for VL datatype & non-default fill value */ - if(fb_info_init && fb_info.has_vlen_fill_type) { - /* Sanity check */ - HDassert(should_fill); + /* Check if allocation along this dimension is really necessary */ + if(min_unalloc[op_dim] > max_unalloc[op_dim]) + carry = TRUE; + else { + /* Reset the chunk offset indices */ + HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0]))); + chunk_offset[op_dim] = min_unalloc[op_dim]; - /* Fill the buffer with VL datatype fill values */ - if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") + carry = FALSE; + } /* end if */ - /* Check if there are filters which need to be applied to the chunk */ - if(pline->nused > 0) { - size_t buf_size = orig_chunk_size; - size_t nbytes = fb_info.fill_buf_size; + while(!carry) { + size_t chunk_size; /* Size of chunk in bytes, possibly filtered */ - /* Push the chunk through the filters */ - if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &fb_info.fill_buf) < 0) - HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed") +#ifndef NDEBUG + /* None of the chunks should be allocated */ + if(H5D_chunk_get_info(dset, dxpl_id, chunk_offset, &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") + HDassert(!H5F_addr_defined(udata.addr)); +#endif /* NDEBUG */ + + /* Check for VL datatype & non-default fill value */ + if(fb_info_init && fb_info.has_vlen_fill_type) { + /* Sanity check */ + HDassert(should_fill); + + /* Fill the buffer with VL datatype fill values */ + if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") + + /* Check if there are filters which need to be applied to the chunk */ + if(pline->nused > 0) { + size_t buf_size = orig_chunk_size; + size_t nbytes = fb_info.fill_buf_size; + + /* Push the chunk through the filters */ + if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &fb_info.fill_buf) < 0) + HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 - /* Check for the chunk expanding too much to encode in a 32-bit value */ - if(nbytes > ((size_t)0xffffffff)) - HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") + /* Check for the chunk expanding too much to encode in a 32-bit value */ + if(nbytes > ((size_t)0xffffffff)) + HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") #endif /* H5_SIZEOF_SIZE_T > 4 */ - /* Keep the number of bytes the chunk turned in to */ - chunk_size = nbytes; - } /* end if */ - else - H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t); + /* Keep the number of bytes the chunk turned in to */ + chunk_size = nbytes; } /* end if */ else - chunk_size = orig_chunk_size; - - /* Initialize the chunk information */ - udata.common.layout = &layout->u.chunk; - udata.common.storage = &layout->storage.u.chunk; - udata.common.offset = chunk_offset; - H5_ASSIGN_OVERFLOW(udata.nbytes, chunk_size, size_t, uint32_t); - udata.filter_mask = filter_mask; - udata.addr = HADDR_UNDEF; - - /* Allocate the chunk with all processes */ - if((ops->insert)(&idx_info, &udata) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert record into chunk index") - HDassert(H5F_addr_defined(udata.addr)); - - /* Check if fill values should be written to chunks */ - if(should_fill) { - /* Sanity check */ - HDassert(fb_info_init); - HDassert(udata.nbytes == chunk_size); + H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t); + } /* end if */ + else + chunk_size = orig_chunk_size; + + /* Initialize the chunk information */ + udata.common.layout = &layout->u.chunk; + udata.common.storage = &layout->storage.u.chunk; + udata.common.offset = chunk_offset; + H5_ASSIGN_OVERFLOW(udata.nbytes, chunk_size, size_t, uint32_t); + udata.filter_mask = filter_mask; + udata.addr = HADDR_UNDEF; + + /* Allocate the chunk with all processes */ + if((ops->insert)(&idx_info, &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert record into chunk index") + HDassert(H5F_addr_defined(udata.addr)); + + /* Check if fill values should be written to chunks */ + if(should_fill) { + /* Sanity check */ + HDassert(fb_info_init); + HDassert(udata.nbytes == chunk_size); #ifdef H5_HAVE_PARALLEL - /* Check if this file is accessed with an MPI-capable file driver */ - if(using_mpi) { - /* Write the chunks out from only one process */ - /* !! Use the internal "independent" DXPL!! -QAK */ - if(H5_PAR_META_WRITE == mpi_rank) - if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") - - /* Indicate that blocks are being written */ - blocks_written = TRUE; - } /* end if */ - else { -#endif /* H5_HAVE_PARALLEL */ + /* Check if this file is accessed with an MPI-capable file driver */ + if(using_mpi) { + /* Write the chunks out from only one process */ + /* !! Use the internal "independent" DXPL!! -QAK */ + if(H5_PAR_META_WRITE == mpi_rank) if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") + + /* Indicate that blocks are being written */ + blocks_written = TRUE; + } /* end if */ + else { +#endif /* H5_HAVE_PARALLEL */ + if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") #ifdef H5_HAVE_PARALLEL - } /* end else */ + } /* end else */ #endif /* H5_HAVE_PARALLEL */ - } /* end if */ - - /* 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 */ - } /* end if */ - /* Increment indices */ - carry = TRUE; - for(i = (int)(space_ndims - 1); i >= 0; --i) { - chunk_offset[i] += layout->u.chunk.dim[i]; - if(chunk_offset[i] >= space_dim[i]) - chunk_offset[i] = 0; - else { - carry = FALSE; - break; - } /* end else */ - } /* end for */ - } /* end while */ + /* 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); + + /* Increment indices */ + carry = TRUE; + for(i = (int)(space_ndims - 1); i >= 0; --i) { + chunk_offset[i] += chunk_dim[i]; + if(chunk_offset[i] > max_unalloc[i]) + if(i == op_dim) + chunk_offset[i] = min_unalloc[i]; + else + chunk_offset[i] = 0; + else { + carry = FALSE; + break; + } /* end else */ + } /* end for */ + } /* end while(!carry) */ + + /* Adjust max_unalloc_dim_idx so we don't allocate the same chunk twice. + * Also check if this dimension started from 0 (and hence allocated all + * of the chunks. */ + if(min_unalloc[op_dim] == 0) + break; + else + max_unalloc[op_dim] = min_unalloc[op_dim] - chunk_dim[op_dim]; + } /* end for(op_dim=0...) */ #ifdef H5_HAVE_PARALLEL /* Only need to block at the barrier if we actually initialized a chunk */ diff --git a/src/H5Ddeprec.c b/src/H5Ddeprec.c index de7f48a..e208910 100644 --- a/src/H5Ddeprec.c +++ b/src/H5Ddeprec.c @@ -320,6 +320,8 @@ H5D_extend(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id) { htri_t changed; /* Flag to indicate that the dataspace was successfully extended */ H5S_t *space; /* Dataset's dataspace */ + int rank; /* Dataspace # of dimensions */ + hsize_t curr_dims[H5O_LAYOUT_NDIMS];/* Current dimension sizes */ H5O_fill_t *fill; /* Dataset's fill value */ herr_t ret_value = SUCCEED; /* Return value */ @@ -339,8 +341,12 @@ H5D_extend(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id) * able to muck things up. */ - /* Increase the size of the data space */ + /* Retrieve the current dimensions */ space = dataset->shared->space; + if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") + + /* Increase the size of the data space */ if((changed = H5S_extend(space, size)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to increase size of data space") @@ -357,7 +363,8 @@ H5D_extend(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id) /* Allocate space for the new parts of the dataset, if appropriate */ fill = &dataset->shared->dcpl_cache.fill; if(fill->alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_EXTEND, FALSE) < 0) + if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_EXTEND, FALSE, + curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") /* Mark the dataspace as dirty, for later writing to the file */ diff --git a/src/H5Dint.c b/src/H5Dint.c index 5a9c0ea..d3800e8 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -58,7 +58,8 @@ typedef struct { /********************/ /* General stuff */ -static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id); +static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, + hsize_t old_dim[], hid_t dxpl_id); static herr_t H5D_get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache); static H5D_shared_t *H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type); @@ -1303,7 +1304,7 @@ H5D_open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id) if((H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR) && !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) && IS_H5FD_MPI(dataset->oloc.file)) { - if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_OPEN, FALSE) < 0) + if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_OPEN, FALSE, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage") } /* end if */ @@ -1560,7 +1561,7 @@ H5D_typeof(const H5D_t *dset) */ herr_t H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_alloc, - hbool_t full_overwrite) + hbool_t full_overwrite, hsize_t old_dim[]) { H5F_t *f = dset->oloc.file; /* The dataset's file pointer */ H5O_layout_t *layout; /* The dataset's layout information */ @@ -1655,7 +1656,7 @@ H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_al * this is icky. -QAK */ if(!(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR && time_alloc == H5D_ALLOC_WRITE)) - if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) + if(H5D_init_storage(dset, full_overwrite, old_dim, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end if */ else { @@ -1669,7 +1670,7 @@ H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_al * the fill value _is_ set, do that now */ if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { - if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) + if(H5D_init_storage(dset, full_overwrite, old_dim, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end if */ } /* end else */ @@ -1706,7 +1707,8 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) +H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hsize_t old_dim[], + hid_t dxpl_id) { herr_t ret_value = SUCCEED; /* Return value */ @@ -1737,9 +1739,17 @@ H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) * Allocate file space * for all chunks now and initialize each chunk with the fill value. */ - if(H5D_chunk_allocate(dset, dxpl_id, full_overwrite) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") - break; + { + hsize_t zero_dim[H5O_LAYOUT_NDIMS] = {0}; + + /* Use zeros for old dimensions if not specified */ + if(old_dim == NULL) + old_dim = zero_dim; + + if(H5D_chunk_allocate(dset, dxpl_id, full_overwrite, old_dim) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") + break; + } /* end block */ default: HDassert("not implemented yet" && 0); @@ -2157,9 +2167,8 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) /* Allocate space for the new parts of the dataset, if appropriate */ if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_EXTEND, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage") - + if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_EXTEND, FALSE, curr_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset storage") /*------------------------------------------------------------------------- * Remove chunk information in the case of chunked datasets diff --git a/src/H5Dio.c b/src/H5Dio.c index 5723847..d3120b1 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -549,7 +549,7 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, full_overwrite = (hbool_t)((hsize_t)file_nelmts == nelmts ? TRUE : FALSE); /* Allocate storage */ - if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_WRITE, full_overwrite) < 0) + if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_WRITE, full_overwrite, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") } /* end if */ diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c index d2ad2ac..b6382df 100644 --- a/src/H5Dlayout.c +++ b/src/H5Dlayout.c @@ -230,7 +230,7 @@ H5D_layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset, * allocation until later. */ if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE) < 0) + if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") /* Update external storage message, if it's used */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 9fde879..38f1ab4 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -526,7 +526,7 @@ H5_DLL H5D_t *H5D_create_named(const H5G_loc_t *loc, const char *name, H5_DLL herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id); H5_DLL herr_t H5D_alloc_storage(H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc, - hbool_t full_overwrite); + hbool_t full_overwrite, hsize_t old_dim[]); H5_DLL hsize_t H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id); H5_DLL haddr_t H5D_get_offset(const H5D_t *dset); H5_DLL herr_t H5D_iterate(void *buf, hid_t type_id, const H5S_t *space, @@ -608,7 +608,8 @@ H5_DLL herr_t H5D_chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty, unsigned idx_hint, void *chunk, uint32_t naccessed); H5_DLL herr_t H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes); -H5_DLL herr_t H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite); +H5_DLL herr_t H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, + hbool_t full_overwrite, hsize_t old_dim[]); H5_DLL herr_t H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims); #ifdef H5_HAVE_PARALLEL diff --git a/src/H5private.h b/src/H5private.h index 5be50bc..277fe70 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -1143,7 +1143,7 @@ H5_DLL int HDfprintf (FILE *stream, const char *fmt, ...); #ifndef HDsrandom #define HDsrandom(S) HDsrand(S) #endif /* HDsrandom */ - #elif H5_HAVE_RANDOM +#elif H5_HAVE_RANDOM #ifndef HDsrand #define HDsrand(S) srandom(S) #endif /* HDsrand */ |