summaryrefslogtreecommitdiffstats
path: root/src/H5Dchunk.c
diff options
context:
space:
mode:
authorkmu <kmu@hdfgroup.org>2020-01-14 17:25:49 (GMT)
committerkmu <kmu@hdfgroup.org>2020-01-14 17:25:49 (GMT)
commit71b817038d8cd82163cf71119873b2ba65a2c81b (patch)
treeff2e04387a658c1d4188f402bc332825710577b8 /src/H5Dchunk.c
parent7366709e4000a96a9942934da0d13474213567f3 (diff)
parentc3c60dc7b5d5104475748f9967135903e3974cc3 (diff)
downloadhdf5-71b817038d8cd82163cf71119873b2ba65a2c81b.zip
hdf5-71b817038d8cd82163cf71119873b2ba65a2c81b.tar.gz
hdf5-71b817038d8cd82163cf71119873b2ba65a2c81b.tar.bz2
Merge branch 'develop' of https://git.hdfgroup.org/scm/hdffv/hdf5 into develop
Diffstat (limited to 'src/H5Dchunk.c')
-rw-r--r--src/H5Dchunk.c134
1 files changed, 58 insertions, 76 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 35773b6..17b0d16 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -1100,14 +1100,10 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
H5D_chunk_map_t *fm)
{
const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */
- H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */
htri_t file_space_normalized = FALSE; /* File dataspace was normalized */
- H5T_t *file_type = NULL; /* Temporary copy of file datatype for iteration */
- hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */
unsigned f_ndims; /* The number of dimensions of the file's dataspace */
int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */
- char bogus; /* "bogus" buffer to pass to selection iterator */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
@@ -1268,22 +1264,22 @@ H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_
else
sel_hyper_flag = TRUE;
- /* Check if file selection is a not a hyperslab selection */
- if(sel_hyper_flag) {
- /* Build the file selection for each chunk */
- if(H5S_SEL_ALL == fm->fsel_type) {
- if(H5D__create_chunk_file_map_all(fm, io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
- } /* end if */
- else {
- /* Sanity check */
- HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS);
-
- if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
- } /* end else */
+ /* Check if file selection is a not a hyperslab selection */
+ if(sel_hyper_flag) {
+ /* Build the file selection for each chunk */
+ if(H5S_SEL_ALL == fm->fsel_type) {
+ if(H5D__create_chunk_file_map_all(fm, io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
} /* end if */
else {
+ /* Sanity check */
+ HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS);
+
+ if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+ } /* end else */
+ } /* end if */
+ else {
H5S_sel_iter_op_t iter_op; /* Operator for iteration */
H5D_chunk_file_iter_ud_t udata; /* User data for iteration */
@@ -1320,14 +1316,12 @@ H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_
if(H5D__create_chunk_mem_map_hyper(fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
} /* end if */
- else if(sel_hyper_flag &&
- fm->f_ndims == 1 && fm->m_ndims == 1 &&
+ else if(sel_hyper_flag && fm->f_ndims == 1 && fm->m_ndims == 1 &&
H5S_SELECT_IS_REGULAR(fm->mem_space) && H5S_SELECT_IS_SINGLE(fm->mem_space)) {
-
if(H5D__create_chunk_mem_map_1d(fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
-
- } else {
+ } /* end else-if */
+ else {
H5S_sel_iter_op_t iter_op; /* Operator for iteration */
size_t elmt_size; /* Memory datatype size */
@@ -1343,8 +1337,8 @@ H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_
fm->mchunk_tmpl = tmp_mspace;
/* Create temporary datatypes for selection iteration */
- if(!file_type)
- if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL)))
+ 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")
/* Create selection iterator for memory selection */
@@ -1366,11 +1360,9 @@ H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_
done:
/* Release the [potentially partially built] chunk mapping information if an error occurs */
if(ret_value < 0) {
- if(tmp_mspace && !fm->mchunk_tmpl) {
+ if(tmp_mspace && !fm->mchunk_tmpl)
if(H5S_close(tmp_mspace) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
- } /* end if */
-
if(H5D__chunk_io_term(fm) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping")
} /* end if */
@@ -2139,13 +2131,7 @@ H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm)
{
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
H5SL_node_t *curr_node; /* Current node in skip list */
- 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 */
- unsigned u; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
@@ -2171,6 +2157,7 @@ H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm)
else {
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 */
+
HDassert(fm->m_ndims == 1);
if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end) < 0)
@@ -2179,7 +2166,7 @@ H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm)
/* Iterate over each chunk in the chunk list */
curr_node = H5SL_first(fm->sel_chunks);
while(curr_node) {
- hssize_t schunk_points; /* Number of elements in chunk selection */
+ hsize_t chunk_points; /* Number of elements in chunk selection */
hsize_t tmp_count = 1;
/* Get pointer to chunk's information */
@@ -2190,12 +2177,12 @@ H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm)
if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
- schunk_points = H5S_GET_SELECT_NPOINTS(chunk_info->fspace);
+ chunk_points = H5S_GET_SELECT_NPOINTS(chunk_info->fspace);
- if(H5S_select_hyperslab(chunk_info->mspace, H5S_SELECT_SET, mem_sel_start, NULL, &tmp_count, &schunk_points) < 0)
+ if(H5S_select_hyperslab(chunk_info->mspace, H5S_SELECT_SET, mem_sel_start, NULL, &tmp_count, &chunk_points) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk memory selection")
- mem_sel_start[0] += schunk_points;
+ mem_sel_start[0] += chunk_points;
/* Get the next chunk node in the skip list */
curr_node = H5SL_next(curr_node);
@@ -5037,8 +5024,7 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
blocks++;
}
- /* MSC
- * should use this if MPI_type_create_hindexed block is working
+ /* MSC - should use this if MPI_type_create_hindexed block is working:
* mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, &file_type);
*/
mpi_code = MPI_Type_create_hindexed(blocks, block_lens, chunk_disp_array, MPI_BYTE, &file_type);
@@ -5512,7 +5498,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, const hsize_t *old_dim)
} /* end if */
else
dims_outside_fill[u] = FALSE;
- } /* end if */
+ } /* end else */
carry = FALSE;
while(!carry) {
@@ -5665,9 +5651,8 @@ H5D__chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
H5D_chunk_it_ud2_t *udata = (H5D_chunk_it_ud2_t *)_udata; /* User data for callback */
unsigned rank = udata->common.layout->ndims - 1; /* # of dimensions of dataset */
hsize_t chunk_index;
- int ret_value = H5_ITER_CONT; /* Return value */
- FUNC_ENTER_STATIC
+ FUNC_ENTER_STATIC_NOERR
/* Compute the index for this chunk */
chunk_index = H5VM_array_offset_pre(rank, udata->common.layout->down_chunks, chunk_rec->scaled);
@@ -5675,8 +5660,7 @@ H5D__chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
/* Set it in the userdata to return */
udata->chunk_addr[chunk_index] = chunk_rec->chunk_addr;
-done:
- FUNC_LEAVE_NOAPI(ret_value)
+ FUNC_LEAVE_NOAPI(H5_ITER_CONT)
} /* H5D__chunk_addrmap_cb() */
@@ -5969,11 +5953,10 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
/* Check for an edge chunk that is not filtered */
if(pline && pline->nused) {
must_filter = TRUE;
- if( (udata->common.layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) &&
- (H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, udata->common.layout->dim,
- chunk_rec->scaled, udata->dset_dims)) )
+ if((udata->common.layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) &&
+ H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, udata->common.layout->dim, chunk_rec->scaled, udata->dset_dims))
must_filter = FALSE;
- }
+ } /* end if */
/* Check parameter for type conversion */
if(udata->do_convert) {
@@ -6011,7 +5994,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HDassert(!H5F_addr_defined(chunk_rec->chunk_addr));
H5MM_memcpy(buf, udata->chunk, nbytes);
udata->chunk = NULL;
- }
+ } /* end if */
else {
H5D_rdcc_ent_t *ent = NULL; /* Cache entry */
unsigned idx; /* Index of chunk in cache, if present */
@@ -6044,13 +6027,13 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t);
H5MM_memcpy(buf, ent->chunk, nbytes);
- }
+ } /* end if */
else {
/* read chunk data from the source file */
if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
- }
- }
+ } /* end else */
+ } /* end else */
/* Need to uncompress filtered variable-length & reference data elements that are not found in chunk cache */
if(must_filter && (is_vlen || fix_ref) && !udata->chunk_in_cache) {
@@ -7088,7 +7071,7 @@ H5D__chunk_format_convert(H5D_t *dset, H5D_chk_idx_info_t *idx_info, H5D_chk_idx
udata.dset_ndims = dset->shared->ndims;
udata.dset_dims = dset->shared->curr_dims;
- /* terate over the chunks in the current index and insert the chunk addresses into version 1 B-tree index */
+ /* Iterate over the chunks in the current index and insert the chunk addresses into version 1 B-tree index */
if((idx_info->storage->ops->iterate)(idx_info, H5D__chunk_format_convert_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to chunk info")
@@ -7152,7 +7135,6 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
hsize_t num_chunks = 0; /* Number of written chunks */
H5D_rdcc_ent_t *ent; /* Cache entry */
const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
- const H5O_layout_t *layout; /* Dataset layout */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
@@ -7162,7 +7144,6 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
HDassert(space);
HDassert(nchunks);
- layout = &(dset->shared->layout); /* Dataset layout */
rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
HDassert(rdcc);
@@ -7179,15 +7160,14 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
idx_info.storage = &dset->shared->layout.storage.u.chunk;
/* If the dataset is not written, number of chunks will be 0 */
- if(!H5F_addr_defined(idx_info.storage->idx_addr)) {
+ if(!H5F_addr_defined(idx_info.storage->idx_addr))
*nchunks = 0;
- }
else {
/* Iterate over the allocated chunks */
if((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_num_chunks_cb, &num_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
*nchunks = num_chunks;
- }
+ } /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -7212,7 +7192,6 @@ static int
H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_info_iter_ud_t *chunk_info = (H5D_chunk_info_iter_ud_t *)_udata;
- hsize_t ii = 0; /* Dimension index */
int ret_value = H5_ITER_CONT; /* Callback return value */
FUNC_ENTER_STATIC_NOERR
@@ -7222,17 +7201,20 @@ H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HDassert(chunk_info);
/* If this is the queried chunk, retrieve its info and stop iterating */
- if (chunk_info->curr_idx == chunk_info->chunk_idx) {
+ if(chunk_info->curr_idx == chunk_info->chunk_idx) {
+ hsize_t ii = 0; /* Dimension index */
+
+ /* Copy info */
chunk_info->filter_mask = chunk_rec->filter_mask;
chunk_info->chunk_addr = chunk_rec->chunk_addr;
chunk_info->nbytes = chunk_rec->nbytes;
- for (ii = 0; ii < chunk_info->ndims; ii++)
+ for(ii = 0; ii < chunk_info->ndims; ii++)
chunk_info->scaled[ii] = chunk_rec->scaled[ii];
chunk_info->found = TRUE;
/* Stop iterating */
ret_value = H5_ITER_STOP;
- }
+ } /* end if */
/* Go to the next chunk */
else
chunk_info->curr_idx++;
@@ -7291,9 +7273,9 @@ H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
idx_info.storage = &dset->shared->layout.storage.u.chunk;
/* Set addr & size for when dset is not written or queried chunk is not found */
- if (addr)
+ if(addr)
*addr = HADDR_UNDEF;
- if (size)
+ if(size)
*size = 0;
/* If the chunk is written, get its info, otherwise, return without error */
@@ -7322,7 +7304,7 @@ H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
if(offset)
for(ii = 0; ii < udata.ndims; ii++)
offset[ii] = udata.scaled[ii] * dset->shared->layout.u.chunk.dim[ii];
- }
+ } /* end if */
} /* end if H5F_addr_defined */
done:
@@ -7347,9 +7329,9 @@ done:
static int
H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
- hsize_t ii;
H5D_chunk_info_iter_ud_t *chunk_info = (H5D_chunk_info_iter_ud_t *)_udata;
hbool_t different = FALSE; /* TRUE when a scaled value pair mismatch */
+ hsize_t ii; /* Local index value */
int ret_value = H5_ITER_CONT; /* Callback return value */
FUNC_ENTER_STATIC_NOERR
@@ -7359,12 +7341,12 @@ H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HDassert(chunk_info);
/* Going through the scaled, stop when a mismatch is found */
- for (ii = 0; ii < chunk_info->ndims && !different; ii++)
- if (chunk_info->scaled[ii] != chunk_rec->scaled[ii])
+ for(ii = 0; ii < chunk_info->ndims && !different; ii++)
+ if(chunk_info->scaled[ii] != chunk_rec->scaled[ii])
different = TRUE;
/* Same scaled coords means the chunk is found, copy the chunk info */
- if (!different) {
+ if(!different) {
chunk_info->nbytes = chunk_rec->nbytes;
chunk_info->filter_mask = chunk_rec->filter_mask;
chunk_info->chunk_addr = chunk_rec->chunk_addr;
@@ -7372,7 +7354,7 @@ H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
/* Stop iterating */
ret_value = H5_ITER_STOP;
- }
+ } /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D__get_chunk_info_by_coord_cb() */
@@ -7423,9 +7405,9 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned*
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
/* Set addr & size for when dset is not written or queried chunk is not found */
- if (addr)
+ if(addr)
*addr = HADDR_UNDEF;
- if (size)
+ if(size)
*size = 0;
/* Compose chunked index info struct */
@@ -7452,14 +7434,14 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned*
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve information of the chunk by its scaled coordinates")
/* Obtain requested info if the chunk is found */
- if (udata.found) {
+ if(udata.found) {
if(filter_mask)
*filter_mask = udata.filter_mask;
if(addr)
*addr = udata.chunk_addr;
if(size)
*size = udata.nbytes;
- }
+ } /* end if */
} /* end if H5F_addr_defined */
done: