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-rw-r--r--src/H5Dchunk.c136
1 files changed, 99 insertions, 37 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 5c99c90..ba80de2 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -112,7 +112,6 @@ typedef struct H5D_chunk_it_ud1_t {
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 */
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 */
@@ -122,10 +121,9 @@ typedef struct H5D_chunk_it_ud1_t {
} H5D_chunk_it_ud1_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 {
+typedef struct H5D_chunk_it_ud2_t {
/* down */
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
- const hsize_t *down_chunks; /* "down chunk" element counts for chunks */
/* up */
haddr_t *chunk_addr; /* Array of chunk addresses to fill in */
@@ -270,6 +268,88 @@ H5FL_DEFINE_STATIC(H5D_chunk_prune_stack_t);
/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_set_info_real
+ *
+ * Purpose: Internal routine to set the information about chunks for a dataset
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, June 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_set_info_real(H5O_layout_t *layout, unsigned ndims, const hsize_t *curr_dims)
+{
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_set_info_real, FAIL)
+
+ /* Sanity checks */
+ HDassert(layout);
+ HDassert(ndims > 0);
+ HDassert(curr_dims);
+
+ /* Compute the # of chunks in dataset dimensions */
+ for(u = 0, layout->u.chunk.nchunks = 1; u < ndims; u++) {
+ /* Round up to the next integer # of chunks, to accomodate partial chunks */
+ layout->u.chunk.chunks[u] = ((curr_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u];
+
+ /* Accumulate the # of chunks */
+ layout->u.chunk.nchunks *= layout->u.chunk.chunks[u];
+ } /* end for */
+
+ /* Get the "down" sizes for each dimension */
+ if(H5V_array_down(ndims, layout->u.chunk.chunks, layout->u.chunk.down_chunks) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_set_info_real() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_set_info
+ *
+ * Purpose: Sets the information about chunks for a dataset
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, June 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_set_info(const H5D_t *dset)
+{
+ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Curr. size of dataset dimensions */
+ int sndims; /* Rank of dataspace */
+ unsigned ndims; /* Rank of dataspace */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_set_info, FAIL)
+
+ /* Sanity checks */
+ HDassert(dset);
+
+ /* Get the dim info for dataset */
+ if((sndims = H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace dimensions")
+ H5_ASSIGN_OVERFLOW(ndims, sndims, int, unsigned);
+
+ /* Set the layout information */
+ if(H5D_chunk_set_info_real(&dset->shared->layout, ndims, curr_dims) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout's chunk info")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_set_info() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D_chunk_construct
*
* Purpose: Constructs new chunked layout information for dataset
@@ -407,6 +487,10 @@ H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id)
H5D_chunk_cinfo_cache_reset(&(rdcc->last));
} /* end else */
+ /* Set the number of chunks in dataset */
+ if(H5D_chunk_set_info(dset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set # of chunks for dataset")
+
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
@@ -514,24 +598,14 @@ H5D_chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info
for(u = 0; u < f_ndims; u++) {
/* Keep the size of the chunk dimensions as hsize_t for various routines */
fm->chunk_dim[u] = fm->layout->u.chunk.dim[u];
-
- /* Round up to the next integer # of chunks, to accomodate partial chunks */
- fm->chunks[u] = ((fm->f_dims[u] + dataset->shared->layout.u.chunk.dim[u]) - 1) / dataset->shared->layout.u.chunk.dim[u];
} /* 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")
-
#ifdef H5_HAVE_PARALLEL
/* Calculate total chunk in file map*/
fm->select_chunk = NULL;
- fm->total_chunks = 1;
- for(u = 0; u < fm->f_ndims; u++)
- fm->total_chunks = fm->total_chunks * fm->chunks[u];
if(io_info->using_mpi_vfd) {
- H5_CHECK_OVERFLOW(fm->total_chunks, hsize_t, size_t);
- if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->total_chunks * sizeof(H5D_chunk_info_t *))))
+ H5_CHECK_OVERFLOW(fm->layout->u.chunk.nchunks, hsize_t, size_t);
+ if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->layout->u.chunk.nchunks * sizeof(H5D_chunk_info_t *))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
#endif /* H5_HAVE_PARALLEL */
@@ -901,7 +975,7 @@ H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t
chunk_info->coords[fm->f_ndims] = 0;
/* Calculate the index of this chunk */
- if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_info->index) < 0)
+ if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_info->index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Copy selection for file's dataspace into chunk dataspace */
@@ -985,9 +1059,8 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
end[u] = (coords[u] + fm->chunk_dim[u]) - 1;
} /* end for */
-
/* Calculate the index of this chunk */
- if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
+ if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Iterate through each chunk in the dataset */
@@ -1104,8 +1177,8 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1;
} while(coords[curr_dim] > sel_end[curr_dim]);
- /* Re-Calculate the index of this chunk */
- if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
+ /* Re-calculate the index of this chunk */
+ if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
} /* end if */
} /* end while */
@@ -1253,7 +1326,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb)
/* Calculate the index of this chunk */
- if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
+ if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory skip list */
@@ -1365,7 +1438,7 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb)
/* Calculate the index of this chunk */
- if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
+ if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory skip list */
@@ -3318,8 +3391,7 @@ H5D_chunk_prune_fill(const H5D_chunk_rec_t *chunk_rec, H5D_chunk_it_ud1_t *udata
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)
+ if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, layout->u.chunk.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 */
@@ -3575,8 +3647,6 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims)
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 */
- hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */
uint32_t elmts_per_chunk; /* Elements in chunk */
unsigned rank; /* Current # of dimensions */
@@ -3611,16 +3681,11 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims)
/* (also compute the dimensions which have been shrunk) */
elmts_per_chunk = 1;
for(u = 0; u < rank; 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 */
- if(H5V_array_down(rank, chunks, down_chunks) < 0)
- HGOTO_ERROR(H5E_IO, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
-
/* Create a dataspace for a chunk & set the extent */
if(NULL == (chunk_space = H5S_create_simple(rank, chunk_dims, NULL)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
@@ -3646,7 +3711,6 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims)
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;
@@ -3789,7 +3853,7 @@ H5D_chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_addrmap_cb)
/* Compute the index for this chunk */
- if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0)
+ if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->common.mesg->u.chunk.down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index")
/* Set it in the userdata to return */
@@ -3814,12 +3878,11 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],
- const hsize_t down_chunks[])
+H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[])
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_t *dset = io_info->dset; /* Local pointer to dataset info */
- H5D_chunk_it_ud2_t udata; /* User data for iteration callback */
+ H5D_chunk_it_ud2_t udata; /* User data for iteration callback */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_addrmap, FAIL)
@@ -3832,7 +3895,6 @@ H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],
/* 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;
/* Compose chunked index info struct */