diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 2 | ||||
| -rw-r--r-- | src/H5Dchunk.c | 518 | ||||
| -rw-r--r-- | src/H5Dmpio.c | 18 | ||||
| -rw-r--r-- | src/H5Dpkg.h | 3 | ||||
| -rw-r--r-- | test/set_extent.c | 67 |
5 files changed, 362 insertions, 246 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 1476952..33dc13d 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -142,6 +142,8 @@ Bug Fixes since HDF5-1.8.0 release Library ------- + - Fixed various bugs that could prevent the fill value from being written + in certain rare cases. (NAF - 2009/02/26) - Fixed a bug that prevented more than one dataset chunk from being cached at a time. (NAF - 2009/02/12) - Fixed an assertion failure caused by opening an attribute multiple times diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 87aed7b..bbe57a0 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -75,14 +75,21 @@ /* Local Typedefs */ /******************/ +/* Stack of chunks to remove during a "prune" iteration */ +typedef struct H5D_chunk_prune_stack_t { + H5D_chunk_rec_t rec; /* Chunk record */ + struct H5D_chunk_prune_stack_t *next; /* Next chunk in stack */ +} H5D_chunk_prune_stack_t; + /* Callback info for iteration to prune chunks */ typedef struct H5D_chunk_it_ud1_t { H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ const H5D_chk_idx_info_t *idx_info; /* Chunked index info */ const H5D_io_info_t *io_info; /* I/O info for dataset operation */ const hsize_t *dims; /* New dataset dimensions */ + const hbool_t *shrunk_dims; /* Dimensions which have been shrunk */ const hsize_t *down_chunks; /* "down" size of number of chunks in each dimension */ - H5SL_t *outside; /* Skip list to hold chunks outside the new dimensions */ + H5D_chunk_prune_stack_t *rm_stack; /* Stack of chunks outside the new dimensions */ H5S_t *chunk_space; /* Dataspace for a chunk */ uint32_t elmts_per_chunk;/* Elements in chunk */ hsize_t *hyper_start; /* Starting location of hyperslab */ @@ -90,18 +97,6 @@ typedef struct H5D_chunk_it_ud1_t { hbool_t fb_info_init; /* Whether the fill value buffer has been initialized */ } H5D_chunk_it_ud1_t; -/* Skip list node for storing chunks to remove during a "prune" iteration */ -typedef struct H5D_chunk_sl_ck_t { - hsize_t index; /* Index of chunk to remove (must be first) */ - H5D_chunk_rec_t rec; /* Chunk record */ -} H5D_chunk_sl_ck_t; - -/* Skip list callback info when destroying list & removing chunks during "prune" */ -typedef struct H5D_chunk_sl_rm_t { - const H5D_chk_idx_info_t *idx_info; /* I/O info for dataset operation */ - const H5O_layout_t *mesg; /* Layout message */ -} H5D_chunk_sl_rm_t; - /* Callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */ typedef struct H5D_chunk_id_ud2_t { /* down */ @@ -245,7 +240,7 @@ H5FL_DEFINE(H5D_chunk_info_t); H5FL_BLK_DEFINE_STATIC(chunk); /* Declare a free list to manage H5D_chunk_sl_ck_t objects */ -H5FL_DEFINE_STATIC(H5D_chunk_sl_ck_t); +H5FL_DEFINE_STATIC(H5D_chunk_prune_stack_t); @@ -1340,13 +1335,13 @@ done: * *------------------------------------------------------------------------- */ -hbool_t -H5D_chunk_cacheable(const H5D_io_info_t *io_info) +htri_t +H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_op) { const H5D_t *dataset = io_info->dset; - hbool_t ret_value; + htri_t ret_value = FAIL; - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cacheable) + FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cacheable) HDassert(io_info); HDassert(dataset); @@ -1365,20 +1360,38 @@ H5D_chunk_cacheable(const H5D_io_info_t *io_info) ret_value = FALSE; else { #endif /* H5_HAVE_PARALLEL */ - /* If the chunk is too large to keep in the cache and if the address - * for the chunk has been defined, then don't load the chunk into the + /* If the chunk is too large to keep in the cache and if we don't + * need to write the fill value, then don't load the chunk into the * cache, just write the data to it directly. */ H5_CHECK_OVERFLOW(dataset->shared->layout.u.chunk.size, uint32_t, size_t); - if((size_t)dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes_max) - ret_value = FALSE; - else + if((size_t)dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes_max) { + if(write_op && !H5F_addr_defined(caddr)) { + const H5O_fill_t *fill = &(dataset->shared->dcpl_cache.fill); /* Fill value info */ + H5D_fill_value_t fill_status; /* Fill value status */ + + /* Revtrieve the fill value status */ + if(H5P_is_fill_value_defined(fill, &fill_status) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") + + /* If the fill value needs to be written then we will need + * to use the cache to write the fill value */ + if(fill->fill_time == H5D_FILL_TIME_ALLOC || + (fill->fill_time == H5D_FILL_TIME_IFSET + && fill_status == H5D_FILL_VALUE_USER_DEFINED)) + ret_value = TRUE; + else + ret_value = FALSE; + } else + ret_value = FALSE; + } else ret_value = TRUE; #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ } /* end else */ +done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_cacheable() */ @@ -1510,6 +1523,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */ void *chunk; /* Pointer to locked chunk buffer */ H5D_chunk_ud_t udata; /* B-tree pass-through */ + htri_t cacheable; /* Whether the chunk is cacheable */ /* Get the actual chunk information from the skip list node */ chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); @@ -1522,7 +1536,9 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, if(H5F_addr_defined(udata.addr) || H5D_chunk_in_cache(io_info->dset, chunk_info->coords, chunk_info->index) || !skip_missing_chunks) { /* Load the chunk into cache and lock it. */ - if(H5D_chunk_cacheable(io_info)) { + if((cacheable = H5D_chunk_cacheable(io_info, udata.addr, FALSE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") + if(cacheable) { /* Pass in chunk's coordinates in a union. */ io_info->store->chunk.offset = chunk_info->coords; io_info->store->chunk.index = chunk_info->index; @@ -1641,6 +1657,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */ void *chunk; /* Pointer to locked chunk buffer */ H5D_chunk_ud_t udata; /* B-tree pass-through */ + htri_t cacheable; /* Whether the chunk is cacheable */ /* Get the actual chunk information from the skip list node */ chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); @@ -1649,7 +1666,9 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, * simply allocate space instead of load the chunk. */ if(H5D_chunk_get_info(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") - if(H5D_chunk_cacheable(io_info)) { + if((cacheable = H5D_chunk_cacheable(io_info, udata.addr, TRUE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") + if(cacheable) { hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Pass in chunk's coordinates in a union. */ @@ -3195,10 +3214,10 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_chunk_prune_cb + * Function: H5D_chunk_prune_fill * - * Purpose: Search for chunks that are no longer inside the pruned - * dataset's extent + * Purpose: Write the fill value to the parts of the chunk that are no + * longer part of the dataspace * * Return: Non-negative on success/Negative on failure * @@ -3207,201 +3226,186 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ -static int -H5D_chunk_prune_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) +static herr_t +H5D_chunk_prune_fill(const H5D_chunk_rec_t *chunk_rec, H5D_chunk_it_ud1_t *udata) { - H5D_chunk_it_ud1_t *udata = (H5D_chunk_it_ud1_t *)_udata; /* User data */ - H5D_chunk_sl_ck_t *sl_node = NULL; /* Skip list node for chunk to remove */ - unsigned rank; /* Current # of dimensions */ - hbool_t should_delete = FALSE; /* Whether the chunk should be deleted */ - hbool_t needs_fill = FALSE; /* Whether the chunk overlaps the new extent and needs fill valiues */ - unsigned u; /* Local index variable */ - int ret_value = H5_ITER_CONT; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_cb) - - /* Figure out what chunks are no longer in use for the specified extent and release them */ - rank = udata->common.mesg->u.chunk.ndims - 1; - for(u = 0; u < rank; u++) - /* The chunk record points to a chunk of storage that contains the - * beginning of the logical address space represented by UDATA. - */ - if(chunk_rec->offset[u] >= udata->dims[u]) { - /* Indicate that the chunk will be deleted */ - should_delete = TRUE; - - /* Break out of loop, we know the chunk is outside the current dimensions */ - break; - } /* end if */ - /* Check for chunk that overlaps new extent and will need fill values */ - else if((chunk_rec->offset[u] + udata->common.mesg->u.chunk.dim[u]) > udata->dims[u]) - /* Indicate that the chunk needs filling */ - /* (but continue in loop, since it could be outside the extent in - * another dimension -QAK) - */ - needs_fill = TRUE; - - /* Check for chunk to delete */ - if(should_delete) { - /* Allocate space for the shared structure */ - if(NULL == (sl_node = H5FL_MALLOC(H5D_chunk_sl_ck_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for shared B-tree info") - - /* Calculate the index of this chunk */ - if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &sl_node->index) < 0) - HGOTO_ERROR(H5E_IO, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index") + const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */ + H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ + const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ + unsigned rank = udata->common.mesg->u.chunk.ndims - 1; /* Dataset rank */ + H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */ + hssize_t sel_nelmts; /* Number of elements in selection */ + hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */ + void *chunk; /* The file chunk */ + unsigned idx_hint; /* Which chunk we're dealing with */ + H5D_chunk_ud_t chk_udata; /* User data for locking chunk */ + uint32_t bytes_accessed; /* Bytes accessed in chunk */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ - /* Store the key for the chunk */ - sl_node->rec = *chunk_rec; + FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_fill) - /* Insert the chunk description in the skip list */ - if(H5SL_insert(udata->outside, sl_node, &sl_node->index) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTINSERT, H5_ITER_ERROR, "can't insert chunk into skip list") + /* Initialize the fill value buffer, if necessary */ + if(!udata->fb_info_init) { + H5_CHECK_OVERFLOW(udata->elmts_per_chunk, uint32_t, size_t); + if(H5D_fill_init(&udata->fb_info, NULL, FALSE, NULL, NULL, NULL, NULL, + &dset->shared->dcpl_cache.fill, + dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk, + 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") + udata->fb_info_init = TRUE; } /* end if */ - /* Check for chunk that overlaps the new dataset dimensions and needs filling */ - else if(needs_fill) { - const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */ - H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ - const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ - H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */ - hssize_t sel_nelmts; /* Number of elements in selection */ - hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */ - void *chunk; /* The file chunk */ - unsigned idx_hint; /* Which chunk we're dealing with */ - H5D_chunk_ud_t chk_udata; /* User data for locking chunk */ - uint32_t bytes_accessed; /* Bytes accessed in chunk */ - - /* Initialize the fill value buffer, if necessary */ - if(!udata->fb_info_init) { - H5_CHECK_OVERFLOW(udata->elmts_per_chunk, uint32_t, size_t); - if(H5D_fill_init(&udata->fb_info, NULL, FALSE, NULL, NULL, NULL, NULL, - &dset->shared->dcpl_cache.fill, - dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk, - io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't initialize fill buffer info") - udata->fb_info_init = TRUE; - } /* end if */ - /* Compute the # of elements to leave with existing value, in each dimension */ - for(u = 0; u < rank; u++) { - count[u] = MIN(layout->u.chunk.dim[u], (udata->dims[u] - chunk_rec->offset[u])); - HDassert(count[u] > 0); - } /* end for */ + /* Compute the # of elements to leave with existing value, in each dimension */ + for(u = 0; u < rank; u++) { + count[u] = MIN(layout->u.chunk.dim[u], (udata->dims[u] - chunk_rec->offset[u])); + HDassert(count[u] > 0); + } /* end for */ - /* Select all elements in chunk, to begin with */ - if(H5S_select_all(udata->chunk_space, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select space") + /* Select all elements in chunk, to begin with */ + if(H5S_select_all(udata->chunk_space, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to select space") - /* "Subtract out" the elements to keep */ - if(H5S_select_hyperslab(udata->chunk_space, H5S_SELECT_NOTB, udata->hyper_start, NULL, count, NULL) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select hyperslab") + /* "Subtract out" the elements to keep */ + if(H5S_select_hyperslab(udata->chunk_space, H5S_SELECT_NOTB, udata->hyper_start, NULL, count, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to select hyperslab") - /* Calculate the index of this chunk */ - if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, udata->down_chunks, &io_info->store->chunk.index) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't get chunk index") + /* Calculate the index of this chunk */ + if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, udata->down_chunks, + &io_info->store->chunk.index) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't get chunk index") - /* Lock the chunk into the cache, to get a pointer to the chunk buffer */ - /* (Casting away const OK -QAK) */ - io_info->store->chunk.offset = (hsize_t *)chunk_rec->offset; - chk_udata.common.mesg = layout; - chk_udata.common.offset = chunk_rec->offset; - chk_udata.nbytes = chunk_rec->nbytes; - chk_udata.filter_mask = chunk_rec->filter_mask; - chk_udata.addr = chunk_rec->chunk_addr; - if(NULL == (chunk = (void *)H5D_chunk_lock(udata->io_info, &chk_udata, FALSE, &idx_hint))) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "unable to lock 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 */ - - /* Get the number of elements in the selection */ - sel_nelmts = H5S_GET_SELECT_NPOINTS(udata->chunk_space); - HDassert(sel_nelmts >= 0); - H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, size_t); - - /* Check for VL datatype & non-default fill value */ - if(udata->fb_info.has_vlen_fill_type) - /* Re-fill the buffer to use for this I/O operation */ - if(H5D_fill_refill_vl(&udata->fb_info, (size_t)sel_nelmts, io_info->dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, H5_ITER_ERROR, "can't refill fill value buffer") - - /* Create a selection iterator for scattering the elements to memory buffer */ - if(H5S_select_iter_init(&chunk_iter, udata->chunk_space, layout->u.chunk.dim[rank]) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "unable to initialize chunk selection information") - - /* Scatter the data into memory */ - if(H5D_scatter_mem(udata->fb_info.fill_buf, udata->chunk_space, &chunk_iter, (size_t)sel_nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) { - H5S_SELECT_ITER_RELEASE(&chunk_iter); - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "scatter failed") - } /* end if */ + /* Lock the chunk into the cache, to get a pointer to the chunk buffer */ + /* (Casting away const OK -QAK) */ + io_info->store->chunk.offset = (hsize_t *)chunk_rec->offset; + chk_udata.common.mesg = layout; + chk_udata.common.offset = chunk_rec->offset; + chk_udata.nbytes = chunk_rec->nbytes; + chk_udata.filter_mask = chunk_rec->filter_mask; + chk_udata.addr = chunk_rec->chunk_addr; + if(NULL == (chunk = (void *)H5D_chunk_lock(udata->io_info, &chk_udata, FALSE, &idx_hint))) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to lock 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 */ + + /* Get the number of elements in the selection */ + sel_nelmts = H5S_GET_SELECT_NPOINTS(udata->chunk_space); + HDassert(sel_nelmts >= 0); + H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, size_t); + + /* Check for VL datatype & non-default fill value */ + if(udata->fb_info.has_vlen_fill_type) + /* Re-fill the buffer to use for this I/O operation */ + if(H5D_fill_refill_vl(&udata->fb_info, (size_t)sel_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, udata->chunk_space, 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_scatter_mem(udata->fb_info.fill_buf, udata->chunk_space, &chunk_iter, (size_t)sel_nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) { + H5S_SELECT_ITER_RELEASE(&chunk_iter); + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed") + } /* end if */ - /* Release the selection iterator */ - if(H5S_SELECT_ITER_RELEASE(&chunk_iter) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "Can't release selection iterator") + /* 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) */ - H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, uint32_t); - bytes_accessed = (uint32_t)sel_nelmts * layout->u.chunk.dim[rank]; + /* The number of bytes accessed in the chunk */ + /* (i.e. the bytes replaced with fill values) */ + H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, uint32_t); + bytes_accessed = (uint32_t)sel_nelmts * layout->u.chunk.dim[rank]; - /* Release lock on chunk */ - if(H5D_chunk_unlock(io_info, TRUE, idx_hint, chunk, bytes_accessed) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5_ITER_ERROR, "unable to unlock raw data chunk") - } /* end else-if */ + /* Release lock on chunk */ + if(H5D_chunk_unlock(io_info, TRUE, idx_hint, chunk, bytes_accessed) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk") done: - if(ret_value != H5_ITER_CONT && sl_node) - (void)H5FL_FREE(H5D_chunk_sl_ck_t, sl_node); - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_chunk_prune_cb() */ +} /* H5D_chunk_prune_fill */ /*------------------------------------------------------------------------- - * Function: H5D_chunk_prune_sl_rm_cb + * Function: H5D_chunk_prune_cb * - * Purpose: Destroy a skip list node for "pruning" chunks, also removes - * the chunk from the index. + * Purpose: Search for chunks that are no longer inside the pruned + * dataset's extent * * Return: Non-negative on success/Negative on failure * - * Programmer: Quincey Koziol, koziol@hdfgroup.org - * May 3, 2007 + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * March 26, 2002 * *------------------------------------------------------------------------- */ -static herr_t -H5D_chunk_prune_sl_rm_cb(void *item, void UNUSED *key, void *op_data) +/* ARGSUSED */ +static int +H5D_chunk_prune_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { - H5D_chunk_sl_ck_t *sl_node = (H5D_chunk_sl_ck_t *)item; /* Temporary pointer to chunk to remove */ - H5D_chunk_sl_rm_t *rm_info = (H5D_chunk_sl_rm_t *)op_data; /* Information needed for removing chunk from B-tree */ - H5D_chunk_common_ud_t idx_udata; /* User data for index removal routine */ - herr_t ret_value = H5_ITER_CONT; /* Return value */ + H5D_chunk_it_ud1_t *udata = (H5D_chunk_it_ud1_t *)_udata; /* User data */ + H5D_chunk_prune_stack_t *stack_node = NULL; /* Stack node for chunk to remove */ + unsigned rank; /* Current # of dimensions */ + hbool_t should_delete = FALSE; /* Whether the chunk should be deleted */ + hbool_t needs_fill = FALSE; /* Whether the chunk overlaps the new extent and needs fill valiues */ + unsigned u; /* Local index variable */ + int ret_value = H5_ITER_CONT; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_sl_rm_cb) + FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_cb) - /* Sanity checks */ - HDassert(sl_node); - HDassert(rm_info); + /* Figure out what chunks are no longer in use for the specified extent and release them */ + rank = udata->common.mesg->u.chunk.ndims - 1; + for(u = 0; u < rank; u++) + /* The chunk record points to a chunk of storage that contains the + * beginning of the logical address space represented by UDATA. + */ + if(udata->shrunk_dims[u]) { + if(chunk_rec->offset[u] >= udata->dims[u]) { + /* Indicate that the chunk will be deleted */ + should_delete = TRUE; - /* Initialize the user data for the index callback */ - idx_udata.mesg = rm_info->mesg; - idx_udata.offset = sl_node->rec.offset; + /* Break out of loop, we know the chunk is outside the current dimensions */ + break; + } /* end if */ + /* Check for chunk that overlaps new extent and will need fill values */ + else if((chunk_rec->offset[u] + udata->common.mesg->u.chunk.dim[u]) > udata->dims[u]) + /* Indicate that the chunk needs filling */ + /* (but continue in loop, since it could be outside the extent in + * another dimension -QAK) + */ + needs_fill = TRUE; + } /* end if */ - /* Remove */ - if((rm_info->idx_info->layout->u.chunk.ops->remove)(rm_info->idx_info, &idx_udata) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, H5_ITER_ERROR, "unable to remove chunk entry from index") + /* Check for chunk to delete */ + if(should_delete) { + /* Allocate space for the removal stack node */ + if(NULL == (stack_node = H5FL_MALLOC(H5D_chunk_prune_stack_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for removal stack node") -done: - (void)H5FL_FREE(H5D_chunk_sl_ck_t, sl_node); + /* Store the record for the chunk */ + stack_node->rec = *chunk_rec; + /* Push the chunk description onto the stack */ + stack_node->next = udata->rm_stack; + udata->rm_stack = stack_node; + } /* end if */ + /* Check for chunk that overlaps the new dataset dimensions and needs filling */ + else if(needs_fill) + /* Write the fill value */ + if(H5D_chunk_prune_fill(chunk_rec, udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write fill value") + +done: + /* It is currently impossible to fail after the stack node has been + * malloc'ed. No need to free it here on failure. */ FUNC_LEAVE_NOAPI(ret_value) -} /* H5D_chunk_prune_sl_rm_cb() */ +} /* end H5D_chunk_prune_cb() */ /*------------------------------------------------------------------------- @@ -3515,9 +3519,13 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Cache entries */ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dataspace dimensions */ + hbool_t shrunk_dims[H5O_LAYOUT_NDIMS]; /* Dimensions which have shrunk */ H5D_chunk_it_ud1_t udata; /* Chunk index iterator user data */ hbool_t udata_init = FALSE; /* Whether the chunk index iterator user data has been initialized */ - H5D_chunk_sl_rm_t rm_info; /* User data for skip list destroy callback */ + hbool_t needs_fill; /* Whether we need to write the fill value */ + H5D_chunk_prune_stack_t *fill_stack = NULL; /* Stack of chunks to fill */ + H5D_chunk_prune_stack_t *tmp_stack; /* Temporary stack node pointer */ + H5D_chunk_common_ud_t idx_udata; /* User data for index removal routine */ H5S_t *chunk_space = NULL; /* Dataspace for a chunk */ hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Current number of chunks in each dimension */ @@ -3535,6 +3543,10 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); HDassert(dxpl_cache); + /* set the removal stack pointer in udata to NULL, so if the function fails + * early it will not try to free the nonexistent stack */ + udata.rm_stack = NULL; + /* 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") @@ -3545,35 +3557,17 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") curr_dims[rank] = layout->u.chunk.dim[rank]; - /*------------------------------------------------------------------------- - * Figure out what chunks are no longer in use for the specified extent - * and release them from the linked list raw data cache - *------------------------------------------------------------------------- - */ - for(ent = rdcc->head; ent; ent = next) { - /* Get pointer to next extry in cache, in case this one is evicted */ - next = ent->next; - - /* Check for chunk offset outside of new dimensions */ - for(u = 0; u < rank; u++) - if((hsize_t)ent->offset[u] >= curr_dims[u]) { - /* Evict the entry from the cache, but do not flush it to disk */ - if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") - - /* Break out of loop, chunk is evicted */ - break; - } /* end if */ - } /* end for */ - /* Round up to the next integer # of chunks, to accomodate partial chunks */ + /* Use current dims because the indices have already been updated! -NAF */ /* (also compute the number of elements per chunk) */ /* (also copy the chunk dimensions into 'hsize_t' array for creating dataspace) */ + /* (also compute the dimensions which have been shrunk) */ elmts_per_chunk = 1; for(u = 0; u < rank; u++) { - chunks[u] = ((old_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u]; + chunks[u] = ((curr_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u]; elmts_per_chunk *= layout->u.chunk.dim[u]; chunk_dims[u] = layout->u.chunk.dim[u]; + shrunk_dims[u] = curr_dims[u] < old_dims[u]; } /* end for */ /* Get the "down" sizes for each dimension */ @@ -3603,26 +3597,90 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) udata.io_info = &chk_io_info; udata.idx_info = &idx_info; udata.dims = curr_dims; + udata.shrunk_dims = shrunk_dims; udata.down_chunks = down_chunks; udata.elmts_per_chunk = elmts_per_chunk; udata.chunk_space = chunk_space; udata.hyper_start = hyper_start; udata_init = TRUE; - /* Initialize the skip list that will hold the chunks outside the dimensions */ - if(NULL == (udata.outside = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT))) - HGOTO_ERROR(H5E_IO, H5E_CANTCREATE, FAIL, "can't create skip list for chunks outside new dimensions") + /*------------------------------------------------------------------------- + * Figure out what chunks are no longer in use for the specified extent + * and release them from the linked list raw data cache + *------------------------------------------------------------------------- + */ + for(ent = rdcc->head; ent; ent = next) { + /* Get pointer to next extry in cache, in case this one is evicted */ + next = ent->next; + + needs_fill = FALSE; + + /* Check for chunk offset outside of new dimensions */ + for(u = 0; u < rank; u++) { + if((hsize_t)ent->offset[u] >= curr_dims[u]) { + /* Evict the entry from the cache, but do not flush it to disk */ + if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") + + /* We don't need to write the fill value */ + needs_fill = FALSE; + + /* Break out of loop, chunk is evicted */ + break; + } else if(!H5F_addr_defined(ent->chunk_addr) && shrunk_dims[u] + && (ent->offset[u] + chunk_dims[u]) > curr_dims[u]) + /* We need to write the fill value to the unused parts of chunk */ + needs_fill = TRUE; + } /* end for */ + + if(needs_fill) { + /* Allocate space for the stack node */ + if(NULL == (tmp_stack = H5FL_MALLOC(H5D_chunk_prune_stack_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for stack node") + + /* Set up chunk record for fill routine */ + tmp_stack->rec.nbytes = ent->chunk_size; + HDmemcpy(tmp_stack->rec.offset, ent->offset, sizeof(tmp_stack->rec.offset)); + tmp_stack->rec.filter_mask = 0; /* Since the chunk is already in cache this doesn't matter */ + tmp_stack->rec.chunk_addr = ent->chunk_addr; + + /* Push the chunk description onto the stack */ + tmp_stack->next = fill_stack; + fill_stack = tmp_stack; + } /* end if */ + } /* end for */ + + /* Traverse the stack of chunks to be filled, filling each. We will free + * the nodes later in the "done" section. */ + tmp_stack = fill_stack; + while(tmp_stack) { + /* Write the fill value */ + if(H5D_chunk_prune_fill(&(tmp_stack->rec), &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write fill value") + + /* Advance the stack pointer */ + tmp_stack = tmp_stack->next; + } /* end while */ /* Iterate over the chunks */ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_prune_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve prune chunks from index") - /* Set up user data for skip list callback */ - rm_info.idx_info = &idx_info; - rm_info.mesg = layout; + /* Traverse the stack of chunks to be deleted, removing each. We will free + * the nodes later in the "done" section. */ + idx_udata.mesg = layout; + tmp_stack = udata.rm_stack; + while(tmp_stack) { + /* Update the offset in idx_udata */ + idx_udata.offset = tmp_stack->rec.offset; - /* Destroy the skip list, deleting the chunks in the callback */ - H5SL_destroy(udata.outside, H5D_chunk_prune_sl_rm_cb, &rm_info); + /* Remove the chunk from disk */ + if((layout->u.chunk.ops->remove)(&idx_info, &idx_udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, H5_ITER_ERROR, "unable to remove chunk entry from index") + + /* Advance the stack pointer */ + tmp_stack = tmp_stack->next; + } /* end while */ /* Reset any cached chunk info for this dataset */ H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); @@ -3636,6 +3694,24 @@ done: HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") } /* end if */ + /* Free stack of filled chunks */ + tmp_stack = fill_stack; + while(tmp_stack) { + /* Free the stack node and advance the stack pointer */ + tmp_stack = tmp_stack->next; + (void)H5FL_FREE(H5D_chunk_prune_stack_t, fill_stack); + fill_stack = tmp_stack; + } /* end while */ + + /* Free stack of removed chunks */ + tmp_stack = udata.rm_stack; + while(tmp_stack) { + /* Free the stack node and advance the stack pointer */ + tmp_stack = tmp_stack->next; + (void)H5FL_FREE(H5D_chunk_prune_stack_t, udata.rm_stack); + udata.rm_stack = tmp_stack; + } /* end while */ + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_prune_by_extent() */ @@ -4563,7 +4639,7 @@ H5D_nonexistent_readvv(const H5D_io_info_t *io_info, size = mem_len_arr[u]; /* Compute offset in memory */ - buf = (unsigned char *)io_info->u.rbuf + mem_offset_arr[v]; + buf = (unsigned char *)io_info->u.rbuf + mem_offset_arr[u]; /* Initialize the fill value buffer */ if(H5D_fill_init(&fb_info, buf, FALSE, diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 19be413..8757ba7 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -1209,6 +1209,7 @@ if(H5DEBUG(D)) void *chunk; /* Pointer to the data chunk in cache */ uint32_t accessed_bytes; /* Total accessed size in a chunk */ unsigned idx_hint = 0; /* Cache index hint */ + htri_t cacheable; /* Whether the chunk is cacheable */ /* Switch to independent I/O */ if(last_xfer_mode != H5FD_MPIO_INDEPENDENT) { @@ -1224,7 +1225,10 @@ if(H5DEBUG(D)) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list") /* Load the chunk into cache and lock it. */ - if(H5D_chunk_cacheable(io_info)) { + if((cacheable = H5D_chunk_cacheable(io_info, udata.addr, + io_info->op_type == H5D_IO_OP_WRITE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") + if(cacheable) { hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Compute # of bytes accessed in chunk */ @@ -1439,17 +1443,21 @@ if(H5DEBUG(D)) { /* Independent I/O */ if(make_ind) { - void *chunk; /* Pointer to the data chunk in cache */ + void *chunk; /* Pointer to the data chunk in cache */ H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */ - uint32_t accessed_bytes = 0; /* Total accessed size in a chunk */ - unsigned idx_hint = 0; /* Cache index hint */ + uint32_t accessed_bytes = 0; /* Total accessed size in a chunk */ + unsigned idx_hint = 0; /* Cache index hint */ + htri_t cacheable; /* Whether the chunk is cacheable */ /* Switch to independent I/O */ if(H5D_ioinfo_xfer_mode(io_info, dx_plist, H5FD_MPIO_INDEPENDENT) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O") /* Load the chunk into cache and lock it. */ - if(H5D_chunk_cacheable(io_info)) { + if((cacheable = H5D_chunk_cacheable(io_info, udata.addr, + io_info->op_type == H5D_IO_OP_WRITE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") + if(cacheable) { hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Compute # of bytes accessed in chunk */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 3aa425b..7c94906 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -572,7 +572,8 @@ H5_DLL herr_t H5D_contig_copy(H5F_t *f_src, const H5O_layout_t *layout_src, H5F_ H5O_layout_t *layout_dst, H5T_t *src_dtype, H5O_copy_t *cpy_info, hid_t dxpl_id); /* Functions that operate on chunked dataset storage */ -H5_DLL hbool_t H5D_chunk_cacheable(const H5D_io_info_t *io_info); +H5_DLL htri_t H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, + hbool_t write_op); H5_DLL herr_t H5D_chunk_cinfo_cache_reset(H5D_chunk_cached_t *last); H5_DLL herr_t H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id); H5_DLL herr_t H5D_chunk_init(H5F_t *f, hid_t dapl_id, hid_t dxpl_id, const H5D_t *dset); diff --git a/test/set_extent.c b/test/set_extent.c index 1b6918a..b4e61b4 100644 --- a/test/set_extent.c +++ b/test/set_extent.c @@ -46,12 +46,12 @@ const char *FILENAME[] = { #define RANK1 1 #define RANK2 2 #define RANK3 3 -#define DIM0 4 -#define DIM1 4 -#define DIM2 4 -#define DIMS0 2 -#define DIMS1 2 -#define DIMS2 2 +#define DIM0 5 +#define DIM1 5 +#define DIM2 5 +#define DIMS0 3 +#define DIMS1 3 +#define DIMS2 3 #define DIME0 7 #define DIME1 7 #define DIME2 7 @@ -89,6 +89,7 @@ int main( void ) hid_t fapl; /* file access property list */ hid_t fapl2; /* file access property list w/latest format set */ hbool_t new_format; /* Whether to use the latest file format */ + hbool_t chunk_cache; /* Whether to enable chunk caching */ int nerrors = 0; h5_reset(); @@ -97,6 +98,9 @@ int main( void ) /* Copy the file access property list */ if((fapl2 = H5Pcopy(fapl)) < 0) TEST_ERROR + /* Disable chunk caching on fapl2 */ + if(H5Pset_cache(fapl2, 521, 0, 0, 0.) < 0) TEST_ERROR + /* Set the "use the latest version of the format" bounds for creating objects in the file */ if(H5Pset_libver_bounds(fapl2, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) TEST_ERROR @@ -104,19 +108,44 @@ int main( void ) for(new_format = FALSE; new_format <= TRUE; new_format++) { hid_t my_fapl; - /* Set the FAPL for the type of format */ - if(new_format) { - puts("Testing with new file format:"); - my_fapl = fapl2; - } /* end if */ - else { - puts("Testing with old file format:"); - my_fapl = fapl; - } /* end else */ - - nerrors += do_ranks( my_fapl ) < 0 ? 1 : 0; - nerrors += test_external( my_fapl ) < 0 ? 1 : 0; - nerrors += do_layouts( my_fapl ) < 0 ? 1 : 0; + /* Test chunked datasets with and without chunk cache */ + for(chunk_cache = FALSE; chunk_cache <= TRUE; chunk_cache++) { + /* Output message about the type of format */ + if(new_format) + printf("Testing with new file format"); + else + printf("Testing with old file format"); + + /* Set the FAPL for the chunk cache settings */ + if(chunk_cache) { + puts(" and chunk cache enabled:"); + my_fapl = fapl; + } /* end if */ + else { + puts(" and chunk cache disabled:"); + my_fapl = fapl2; + } /* end else */ + + /* Set the FAPL for the type of format */ + if(new_format) { + /* Set the "use the latest version of the format" bounds for + * creating objects in the file */ + if(H5Pset_libver_bounds(my_fapl, H5F_LIBVER_LATEST, + H5F_LIBVER_LATEST) < 0) TEST_ERROR + } /* end if */ + else + /* Set the "use the earliest version of the format" bounds for + * creating objects in the file */ + if(H5Pset_libver_bounds(my_fapl, H5F_LIBVER_EARLIEST, + H5F_LIBVER_LATEST) < 0) TEST_ERROR + + /* Tests which use chunked datasets */ + nerrors += do_ranks( my_fapl ) < 0 ? 1 : 0; + } /* end for */ + + /* Tests which do not use chunked datasets */ + nerrors += test_external( fapl ) < 0 ? 1 : 0; + nerrors += do_layouts( fapl ) < 0 ? 1 : 0; } /* end for */ /* Close 2nd FAPL */ |