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-rw-r--r--src/H5Dio.c116
1 files changed, 63 insertions, 53 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c
index d39112d..d8a8f3c 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -43,7 +43,7 @@
/* Structure holding information about a chunk's selection for mapping */
typedef struct H5D_chunk_info_t {
hsize_t index; /* "Index" of chunk in dataset (must be first for TBBT routines) */
- hsize_t chunk_points; /* Number of elements selected in chunk */
+ size_t chunk_points; /* Number of elements selected in chunk */
H5S_t *fspace; /* Dataspace describing chunk & selection in it */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */
H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */
@@ -64,6 +64,7 @@ typedef struct fm_map {
H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
unsigned m_ndims; /* Number of dimensions for memory dataspace */
hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */
+ hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */
H5O_layout_t *layout; /* Dataset layout information*/
H5S_sel_type msel_type; /* Selection type in memory */
@@ -690,8 +691,9 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
* fill time is NEVER, there is no way to tell whether part of data
* has been overwritten. So just proceed in reading.
*/
- if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT
- && dataset->layout.addr==HADDR_UNDEF) {
+ if(nelmts > 0 && dataset->efl.nused==0 &&
+ ((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr))
+ || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr)))) {
H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */
/* Retrieve dataset's fill-value properties */
@@ -908,14 +910,15 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
/* <none needed currently> */
/* Allocate data space and initialize it if it hasn't been. */
- if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT
- && dataset->layout.addr==HADDR_UNDEF) {
+ if(nelmts > 0 && dataset->efl.nused==0 &&
+ ((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr))
+ || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr)))) {
hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */
hbool_t full_overwrite; /* Whether we are over-writing all the elements */
/* Get the number of elements in file dataset's dataspace */
- if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0)
- HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset");
+ if((file_nelmts=H5S_GET_SIMPLE_EXTENT_NPOINTS(file_space))<0)
+ HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset")
/* Always allow fill values to be written if the dataset has a VL datatype */
if(H5T_detect_class(dataset->type, H5T_VLEN))
@@ -1073,7 +1076,9 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
H5_timer_begin(&timer);
#endif
/* Sanity check dataset, then read it */
- assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
+ assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr))
+ || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr)))
+ || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t);
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
@@ -1169,7 +1174,9 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
H5_timer_begin(&timer);
#endif
/* Sanity check that space is allocated, then read data from it */
- assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
+ assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr))
+ || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr)))
+ || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
&dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), file_space,
@@ -1537,8 +1544,9 @@ UNUSED
H5_timer_begin(&timer);
#endif
/* Sanity check dataset, then read it */
- assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
- dataset->layout.type==H5D_COMPACT);
+ assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr))
+ || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr)))
+ || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT);
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
@@ -1666,8 +1674,9 @@ UNUSED
H5_timer_begin(&timer);
#endif
/* Sanity check that space is allocated, then read data from it */
- assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
- dataset->layout.type==H5D_COMPACT);
+ assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr))
+ || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr)))
+ || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT);
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
&dataset->dcpl_cache, &store, chunk_info->fspace,
&file_iter, smine_nelmts, dxpl_cache, dxpl_id, tconv_buf/*out*/);
@@ -2262,16 +2271,16 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
hsize_t dims[H5O_LAYOUT_NDIMS]; /* Temporary dimension information */
/* Set up "equivalent" n-dimensional dataspace with size '1' in each dimension */
- for(u=0; u<dataset->layout.ndims-1; u++)
+ for(u=0; u<dataset->layout.u.chunk.ndims-1; u++)
dims[u]=1;
- if((equiv_mspace = H5S_create_simple(dataset->layout.ndims-1,dims,NULL))==NULL)
+ if((equiv_mspace = H5S_create_simple(dataset->layout.u.chunk.ndims-1,dims,NULL))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create equivalent dataspace for scalar space")
/* Indicate that this space needs to be released */
equiv_mspace_init=1;
/* Set the number of dimensions for the memory dataspace */
- fm->m_ndims=dataset->layout.ndims-1;
+ fm->m_ndims=dataset->layout.u.chunk.ndims-1;
} /* end else */
else {
equiv_mspace=(H5S_t *)mem_space; /* Casting away 'const' OK... */
@@ -2281,7 +2290,7 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
} /* end else */
/* Get dim number and dimensionality for each dataspace */
- fm->f_ndims=f_ndims=dataset->layout.ndims-1;
+ fm->f_ndims=f_ndims=dataset->layout.u.chunk.ndims-1;
if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality");
@@ -2290,8 +2299,11 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
last_nchunks=0;
nchunks=1;
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->layout.dim[u])-1) / dataset->layout.dim[u];
+ fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.u.chunk.dim[u])-1) / dataset->layout.u.chunk.dim[u];
/* Track total number of chunks in dataset */
nchunks *= fm->chunks[u];
@@ -2418,9 +2430,9 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
/* Spaces aren't the same shape, iterate over the memory selection directly */
if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm)<0)
- HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections");
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
- /* Clean memory chunks' hyperslab span "scratch" information */
+ /* Clean up hyperslab stuff, if necessary */
if(fm->msel_type!=H5S_SEL_POINTS) {
/* Clean memory chunks' hyperslab span "scratch" information */
curr_node=H5TB_first(fm->fsel->root);
@@ -2591,7 +2603,6 @@ H5D_create_chunk_file_map_hyper(fm_map *fm)
hssize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hssize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
- hsize_t count[H5O_LAYOUT_NDIMS]; /* Hyperslab count information */
hssize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t chunk_index; /* Index of chunk */
int curr_dim; /* Current dimension to increment */
@@ -2613,21 +2624,21 @@ H5D_create_chunk_file_map_hyper(fm_map *fm)
/* Set initial chunk location & hyperslab size */
for(u=0; u<fm->f_ndims; u++) {
- H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t);
- start_coords[u]=(sel_start[u]/(hssize_t)fm->layout->dim[u])*(hssize_t)fm->layout->dim[u];
+ H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t);
+ start_coords[u]=(sel_start[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u];
coords[u]=start_coords[u];
- count[u]=fm->layout->dim[u];
- end[u]=(coords[u]+count[u])-1;
+ 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->dim,fm->down_chunks,&chunk_index)<0)
- HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index");
+ if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Iterate through each chunk in the dataset */
while(sel_points) {
/* Check for intersection of temporary chunk and file selection */
- if(H5S_hyper_intersect_block(fm->file_space,coords,end)==TRUE) {
+ /* (Casting away const OK - QAK) */
+ if(H5S_hyper_intersect_block((H5S_t *)fm->file_space,coords,end)==TRUE) {
H5S_t *tmp_fchunk; /* Temporary file dataspace */
H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */
hssize_t schunk_points; /* Number of elements in chunk selection */
@@ -2645,15 +2656,15 @@ H5D_create_chunk_file_map_hyper(fm_map *fm)
HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
/* "AND" temporary chunk and current chunk */
- if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,count,NULL)<0) {
- H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection");
+ if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL)<0) {
+ (void)H5S_close(tmp_fchunk);
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection")
} /* end if */
/* Resize chunk's dataspace dimensions to size of chunk */
- if(H5S_set_extent_real(tmp_fchunk,count)<0) {
- H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions");
+ if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim)<0) {
+ (void)H5S_close(tmp_fchunk);
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions")
} /* end if */
/* Move selection back to have correct offset in chunk */
@@ -2695,7 +2706,7 @@ H5D_create_chunk_file_map_hyper(fm_map *fm)
/* Get number of elements selected in chunk */
if((schunk_points=H5S_GET_SELECT_NPOINTS(tmp_fchunk))<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
- H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,hsize_t);
+ H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,size_t);
/* Decrement # of points left in file selection */
sel_points-=schunk_points;
@@ -2713,9 +2724,9 @@ H5D_create_chunk_file_map_hyper(fm_map *fm)
curr_dim=(int)fm->f_ndims-1;
/* Increment chunk location in fastest changing dimension */
- H5_CHECK_OVERFLOW(count[curr_dim],hsize_t,hssize_t);
- coords[curr_dim]+=(hssize_t)count[curr_dim];
- end[curr_dim]+=(hssize_t)count[curr_dim];
+ H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t);
+ coords[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim];
+ end[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim];
/* Bring chunk location back into bounds, if necessary */
if(coords[curr_dim]>sel_end[curr_dim]) {
@@ -2727,13 +2738,13 @@ H5D_create_chunk_file_map_hyper(fm_map *fm)
curr_dim--;
/* Increment chunk location in current dimension */
- coords[curr_dim]+=(hssize_t)count[curr_dim];
- end[curr_dim]=(coords[curr_dim]+(hssize_t)count[curr_dim])-1;
+ coords[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim];
+ end[curr_dim]=(coords[curr_dim]+(hssize_t)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->dim,fm->down_chunks,&chunk_index)<0)
- HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index");
+ if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
} /* end if */
} /* end while */
@@ -2809,7 +2820,8 @@ H5D_create_chunk_mem_map_hyper(const fm_map *fm)
} /* end if */
else {
/* Just point at the memory dataspace & selection */
- chunk_info->mspace=fm->mem_space;
+ /* (Casting away const OK -QAK) */
+ chunk_info->mspace=(H5S_t *)fm->mem_space;
/* Indicate that the chunk's memory space is shared */
chunk_info->mspace_shared=1;
@@ -2869,10 +2881,8 @@ H5D_create_chunk_mem_map_hyper(const fm_map *fm)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection")
/* Compensate for the chunk offset */
- for(u=0; u<fm->f_ndims; u++) {
- H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t);
+ for(u=0; u<fm->f_ndims; u++)
chunk_adjust[u]=adjust[u]-chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */
- } /* end for */
#ifdef QAK
{
int mpi_rank;
@@ -2954,7 +2964,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb)
/* Calculate the index of this chunk */
- if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0)
+ if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory TBBTs */
@@ -2985,7 +2995,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize
new_chunk_info->index=chunk_index;
/* Create a dataspace for the chunk */
- if((fspace = H5S_create_simple(fm->f_ndims,fm->layout->dim,NULL))==NULL) {
+ if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) {
H5FL_FREE(H5D_chunk_info_t,new_chunk_info);
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk")
} /* end if */
@@ -3009,8 +3019,8 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize
/* Compute the chunk's coordinates */
for(u=0; u<fm->f_ndims; u++) {
- H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t);
- new_chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->dim[u])*(hssize_t)fm->layout->dim[u];
+ H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t);
+ new_chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u];
} /* end for */
new_chunk_info->coords[fm->f_ndims]=0;
@@ -3034,7 +3044,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize
/* Get the coordinates of the element in the chunk */
for(u=0; u<fm->f_ndims; u++)
- coords_in_chunk[u]=coords[u]%fm->layout->dim[u];
+ coords_in_chunk[u]=coords[u]%fm->layout->u.chunk.dim[u];
/* Add point to file selection for chunk */
if(H5S_select_elements(chunk_info->fspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_chunk)<0)
@@ -3077,8 +3087,8 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb);
/* Calculate the index of this chunk */
- if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0)
- HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index");
+ if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory TBBTs */
if(chunk_index==fm->last_index) {
generated by cgit v0.12 at 2024-11-06 14:18:26 (GMT)