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-rw-r--r--src/H5Dchunk.c123
1 files changed, 53 insertions, 70 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index debdbde..dcd3a8d 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -1073,21 +1073,19 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
if((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to normalize selection")
- /* Decide the number of chunks in each dimension*/
- for(u = 0; u < f_ndims; u++) {
+ /* Decide the number of chunks in each dimension */
+ 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];
- } /* end for */
#ifdef H5_HAVE_PARALLEL
/* Calculate total chunk in file map*/
fm->select_chunk = NULL;
if(io_info->using_mpi_vfd) {
H5_CHECK_OVERFLOW(fm->layout->u.chunk.nchunks, hsize_t, size_t);
- if(fm->layout->u.chunk.nchunks) {
+ if(fm->layout->u.chunk.nchunks)
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 */
@@ -1129,10 +1127,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
HDassert(fm->single_space);
/* Allocate the single chunk information */
- if(NULL == dataset->shared->cache.chunk.single_chunk_info) {
+ if(NULL == dataset->shared->cache.chunk.single_chunk_info)
if(NULL == (dataset->shared->cache.chunk.single_chunk_info = H5FL_MALLOC(H5D_chunk_info_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
- } /* end if */
fm->single_chunk_info = dataset->shared->cache.chunk.single_chunk_info;
HDassert(fm->single_chunk_info);
@@ -1147,10 +1144,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
hbool_t sel_hyper_flag; /* Whether file selection is a hyperslab */
/* Initialize skip list for chunk selections */
- if(NULL == dataset->shared->cache.chunk.sel_chunks) {
+ if(NULL == dataset->shared->cache.chunk.sel_chunks)
if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, NULL)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections")
- } /* end if */
fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks;
HDassert(fm->sel_chunks);
@@ -1245,10 +1241,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
fm->mchunk_tmpl = tmp_mspace;
/* Create temporary datatypes for selection iteration */
- if(!file_type) {
+ if(!file_type)
if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype")
- } /* end if */
/* Create selection iterator for memory selection */
if(0 == (elmt_size = H5T_get_size(mem_type)))
@@ -1540,7 +1535,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5D__create_chunk_file_map_hyper
*
- * Purpose: Create all chunk selections in file.
+ * Purpose: Create all chunk selections in file, for a hyperslab selection.
*
* Return: Non-negative on success/Negative on failure
*
@@ -1556,8 +1551,8 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
- hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
- hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
+ hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
+ hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hsize_t sel_points; /* Number of elements in file selection */
hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
@@ -1572,7 +1567,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
FUNC_ENTER_STATIC
/* Sanity check */
- HDassert(fm->f_ndims>0);
+ HDassert(fm->f_ndims > 0);
/* Get number of elements selected in file */
sel_points = fm->nelmts;
@@ -1596,7 +1591,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
/* Iterate through each chunk in the dataset */
while(sel_points) {
- /* Check for intersection of temporary chunk and file selection */
+ /* Check for intersection of current chunk and file selection */
/* (Casting away const OK - QAK) */
if(TRUE == H5S_hyper_intersect_block((H5S_t *)fm->file_space, coords, end)) {
H5S_t *tmp_fchunk; /* Temporary file dataspace */
@@ -1634,7 +1629,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
/* Add temporary chunk to the list of chunks */
/* Allocate the file & memory chunk information */
- if (NULL==(new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) {
+ if(NULL == (new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
@@ -1642,7 +1637,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
/* Initialize the chunk information */
/* Set the chunk index */
- new_chunk_info->index=chunk_index;
+ new_chunk_info->index = chunk_index;
#ifdef H5_HAVE_PARALLEL
/* Store chunk selection information, for multi-chunk I/O */
@@ -1655,16 +1650,13 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
new_chunk_info->fspace_shared = FALSE;
/* Set the memory chunk dataspace */
- new_chunk_info->mspace=NULL;
+ new_chunk_info->mspace = NULL;
new_chunk_info->mspace_shared = FALSE;
/* Copy the chunk's scaled coordinates */
HDmemcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
new_chunk_info->scaled[fm->f_ndims] = 0;
- /* Copy the chunk's scaled coordinates */
- HDmemcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
-
/* Insert the new chunk into the skip list */
if(H5SL_insert(fm->sel_chunks, new_chunk_info, &new_chunk_info->index) < 0) {
H5D__free_chunk_info(new_chunk_info, NULL, NULL);
@@ -1688,12 +1680,11 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
chunk_index++;
/* Set current increment dimension */
- curr_dim=(int)fm->f_ndims-1;
+ curr_dim = (int)fm->f_ndims - 1;
/* Increment chunk location in fastest changing dimension */
- H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t);
- coords[curr_dim]+=fm->chunk_dim[curr_dim];
- end[curr_dim]+=fm->chunk_dim[curr_dim];
+ coords[curr_dim] += fm->chunk_dim[curr_dim];
+ end[curr_dim] += fm->chunk_dim[curr_dim];
scaled[curr_dim]++;
/* Bring chunk location back into bounds, if necessary */
@@ -1707,11 +1698,14 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
/* Decrement current dimension */
curr_dim--;
- /* Increment chunk location in current dimension */
- scaled[curr_dim]++;
- coords[curr_dim] += fm->chunk_dim[curr_dim];
- end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1;
- } while(coords[curr_dim] > sel_end[curr_dim]);
+ /* Check for valid current dim */
+ if(curr_dim >= 0) {
+ /* Increment chunk location in current dimension */
+ scaled[curr_dim]++;
+ coords[curr_dim] += fm->chunk_dim[curr_dim];
+ end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1;
+ } /* end if */
+ } while(curr_dim >= 0 && (coords[curr_dim] > sel_end[curr_dim]));
/* Re-calculate the index of this chunk */
chunk_index = H5VM_array_offset_pre(fm->f_ndims, fm->layout->u.chunk.down_chunks, scaled);
@@ -1743,12 +1737,12 @@ static herr_t
H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
{
H5SL_node_t *curr_node; /* Current node in skip list */
- hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
- hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
- hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
- hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
- hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */
- hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */
+ hsize_t file_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */
+ hsize_t file_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */
+ hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */
+ hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */
+ hssize_t adjust[H5S_MAX_RANK]; /* Adjustment to make to all file chunks */
+ hssize_t chunk_adjust[H5S_MAX_RANK]; /* Adjustment to make to a particular chunk */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
@@ -1762,7 +1756,7 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get the node */
- curr_node=H5SL_first(fm->sel_chunks);
+ curr_node = H5SL_first(fm->sel_chunks);
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
@@ -1785,15 +1779,15 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Calculate the adjustment for memory selection from file selection */
- HDassert(fm->m_ndims==fm->f_ndims);
- for(u=0; u<fm->f_ndims; u++) {
- H5_CHECK_OVERFLOW(file_sel_start[u],hsize_t,hssize_t);
- H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t);
- adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u];
+ HDassert(fm->m_ndims == fm->f_ndims);
+ for(u = 0; u < fm->f_ndims; u++) {
+ H5_CHECK_OVERFLOW(file_sel_start[u], hsize_t, hssize_t);
+ H5_CHECK_OVERFLOW(mem_sel_start[u], hsize_t, hssize_t);
+ adjust[u] = (hssize_t)file_sel_start[u] - (hssize_t)mem_sel_start[u];
} /* end for */
/* Iterate over each chunk in the chunk list */
- curr_node=H5SL_first(fm->sel_chunks);
+ curr_node = H5SL_first(fm->sel_chunks);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
@@ -1832,7 +1826,7 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to adjust selection")
/* Get the next chunk node in the skip list */
- curr_node=H5SL_next(curr_node);
+ curr_node = H5SL_next(curr_node);
} /* end while */
} /* end else */
@@ -1976,7 +1970,7 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u
{
H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */
H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */
- hsize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */
+ hsize_t coords_in_mem[H5S_MAX_RANK]; /* Coordinates of element in memory */
hsize_t chunk_index; /* Chunk index */
herr_t ret_value = SUCCEED; /* Return value */
@@ -1998,14 +1992,13 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u
*/
/* Get the chunk node from the skip list */
if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index)))
- HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list")
+ HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, H5_ITER_ERROR, "can't locate chunk in skip list")
/* Check if the chunk already has a memory space */
- if(NULL == chunk_info->mspace) {
+ if(NULL == chunk_info->mspace)
/* Copy the template memory chunk dataspace */
if(NULL == (chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE)))
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
- } /* end else */
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, H5_ITER_ERROR, "unable to copy file space")
/* Update the "last chunk seen" information */
fm->last_index = chunk_index;
@@ -2014,21 +2007,21 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u
/* Get coordinates of selection iterator for memory */
if(H5S_SELECT_ITER_COORDS(&fm->mem_iter, coords_in_mem) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates")
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, H5_ITER_ERROR, "unable to get iterator coordinates")
/* Add point to memory selection for chunk */
if(fm->msel_type == H5S_SEL_POINTS) {
if(H5S_select_elements(chunk_info->mspace, H5S_SELECT_APPEND, (size_t)1, coords_in_mem) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select element")
} /* end if */
else {
if(H5S_hyper_add_span_element(chunk_info->mspace, fm->m_ndims, coords_in_mem) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select element")
} /* end else */
/* Move memory selection iterator to next element in selection */
if(H5S_SELECT_ITER_NEXT(&fm->mem_iter, (size_t)1) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL, "unable to move to next iterator location")
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, H5_ITER_ERROR, "unable to move to next iterator location")
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -2914,9 +2907,6 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled,
/* Check for cached information */
if(!H5D__chunk_cinfo_cache_found(&dset->shared->cache.chunk.last, udata)) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
-#ifdef H5_HAVE_PARALLEL
- H5P_coll_md_read_flag_t temp_cmr; /* Temp value to hold the coll metadata read setting */
-#endif /* H5_HAVE_PARALLEL */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
@@ -2925,25 +2915,18 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled,
idx_info.storage = &dset->shared->layout.storage.u.chunk;
#ifdef H5_HAVE_PARALLEL
- if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) {
- /* disable collective metadata read for chunk indexes
- as it is highly unlikely that users would read the
- same chunks from all processes. MSC - might turn on
- for root node? */
- temp_cmr = H5F_COLL_MD_READ(idx_info.f);
- H5F_set_coll_md_read(idx_info.f, H5P_FORCE_FALSE);
- } /* end if */
+ /* Disable collective metadata read for chunk indexes as it is
+ * highly unlikely that users would read the same chunks from all
+ * processes.
+ */
+ if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI))
+ H5CX_set_coll_metadata_read(FALSE);
#endif /* H5_HAVE_PARALLEL */
/* Go get the chunk information */
if((dset->shared->layout.storage.u.chunk.ops->get_addr)(&idx_info, udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address")
-#ifdef H5_HAVE_PARALLEL
- if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI))
- H5F_set_coll_md_read(idx_info.f, temp_cmr);
-#endif /* H5_HAVE_PARALLEL */
-
/*
* Cache the information retrieved.
*
generated by cgit v0.12 at 2024-11-01 15:14:29 (GMT)