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authorQuincey Koziol <koziol@hdfgroup.org>2003-07-23 21:18:40 (GMT)
committerQuincey Koziol <koziol@hdfgroup.org>2003-07-23 21:18:40 (GMT)
commitb0e350c2d6330ab7156c600013e224149b4b711f (patch)
tree5120dfcbb10ac87935fba22d0896ddc9ef364122 /src/H5Dio.c
parent77f6e46b81d5f6583242fcbbc87c4b2f44bc9b3e (diff)
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[svn-r7259] Purpose:
Bug fix Description: I/O on chunked datasets with point selections was not working correctly. Solution: Re-wrote some parts of raw data I/O routines that build the selections for each chunk to correctly handle point selections. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
Diffstat (limited to 'src/H5Dio.c')
-rw-r--r--src/H5Dio.c708
1 files changed, 345 insertions, 363 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c
index c2a61f3..4c026b6 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -40,28 +40,22 @@
/* Information for mapping between file space and memory space */
-/* Structure holding information about a file chunk's selection for mapping */
-typedef struct H5D_fchunk_info_t {
+/* 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) */
- H5S_t *space; /* Dataspace describing chunk & selection in it */
+ H5S_t *fspace; /* Dataspace describing chunk & selection in it */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */
-} H5D_fchunk_info_t;
-
-/* Structure holding information about a memory chunk's selection for mapping */
-typedef struct H5D_mchunk_info_t {
- hsize_t index; /* "Index" of chunk in dataset (must be first for TBBT routines) */
- H5S_t *space; /* Dataspace describing chunk & selection in it */
-} H5D_mchunk_info_t;
+ H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */
+} H5D_chunk_info_t;
/* Main structure holding the mapping between file chunks and memory */
typedef struct fm_map {
H5TB_TREE *fsel; /* TBBT containing file dataspaces for all chunks */
- H5TB_TREE *msel; /* TBBT containing memory dataspaces for all chunks */
hsize_t last_index; /* Index of last chunk operated on */
H5S_t *file_space; /* Pointer to the file dataspace */
H5S_t *mem_space; /* Pointer to the memory dataspace */
hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */
- H5S_t *last_mchunk; /* Pointer to last memory chunk's dataspace */
+ H5S_t *last_chunk; /* Pointer to last memory chunk's dataspace */
H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */
unsigned f_ndims; /* Number of dimensions for file dataspace */
H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
@@ -69,6 +63,7 @@ typedef struct fm_map {
hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks 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 */
} fm_map;
/* Interface initialization */
@@ -110,12 +105,13 @@ H5D_io_assist_mpio(H5P_genplist_t *dx_plist, hbool_t doing_mpio, H5FD_mpio_xfer_
static herr_t H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm);
static herr_t H5D_destroy_chunk_map(const fm_map *fm);
-static void H5D_free_fchunk_info(void *fchunk_info);
-static void H5D_free_mchunk_info(void *mchunk_info);
+static void H5D_free_chunk_info(void *chunk_info);
static herr_t H5D_chunk_coords_assist(hssize_t *coords, size_t ndims,
const hsize_t chunks[], hsize_t chunk_idx);
-static herr_t H5D_create_chunk_file_map(const fm_map *fm);
-static herr_t H5D_create_chunk_mem_map(const fm_map *fm);
+static herr_t H5D_create_chunk_file_map_hyper(const fm_map *fm);
+static herr_t H5D_create_chunk_mem_map_hyper(const fm_map *fm);
+static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, hsize_t ndims,
+ hssize_t *coords, void *fm);
static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, hsize_t ndims,
hssize_t *coords, void *fm);
static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf,
@@ -128,11 +124,8 @@ H5FL_BLK_DEFINE(type_elem);
/* Declare a free list to manage blocks of type conversion data */
H5FL_BLK_DEFINE(type_conv);
-/* Declare a free list to manage the H5D_fchunk_info_t struct */
-H5FL_DEFINE_STATIC(H5D_fchunk_info_t);
-
-/* Declare a free list to manage the H5D_mchunk_info_t struct */
-H5FL_DEFINE_STATIC(H5D_mchunk_info_t);
+/* Declare a free list to manage the H5D_chunk_info_t struct */
+H5FL_DEFINE_STATIC(H5D_chunk_info_t);
/*--------------------------------------------------------------------------
@@ -525,8 +518,6 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */
H5P_genplist_t *dc_plist; /* Dataset creation roperty list */
unsigned sconv_flags=0; /* Flags for the space conversion */
- H5S_sel_type fsel_type; /* Selection type on disk */
- H5S_sel_type msel_type; /* Selection type in memory */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_read)
@@ -654,19 +645,8 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space")
- /* Get type of selection on disk & in memory */
- if((fsel_type=H5S_get_select_type(file_space))<0)
- HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
- if((msel_type=H5S_get_select_type(mem_space))<0)
- HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
-
/* Determine correct I/O routine to invoke */
- if((fsel_type==H5S_SEL_POINTS || msel_type==H5S_SEL_POINTS) ||
- dataset->layout.type!=H5D_CHUNKED) {
- /* Must use "contiguous" code for point selections,
- * since order of I/O accesses can be different from that of the
- * other kinds of selections
- */
+ if(dataset->layout.type!=H5D_CHUNKED) {
if(H5D_contig_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist,
dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
@@ -749,8 +729,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */
H5P_genplist_t *dc_plist; /* Dataset creation roperty list */
unsigned sconv_flags=0; /* Flags for the space conversion */
- H5S_sel_type fsel_type; /* Selection type on disk */
- H5S_sel_type msel_type; /* Selection type in memory */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_write)
@@ -882,19 +860,8 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space")
- /* Get type of selection on disk & in memory */
- if((fsel_type=H5S_get_select_type(file_space))<0)
- HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
- if((msel_type=H5S_get_select_type(mem_space))<0)
- HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
-
/* Determine correct I/O routine to invoke */
- if((fsel_type==H5S_SEL_POINTS || msel_type==H5S_SEL_POINTS) ||
- dataset->layout.type!=H5D_CHUNKED) {
- /* Must use "contiguous" code for point selections,
- * since order of I/O accesses can be different from that of the
- * other kinds of selections
- */
+ if(dataset->layout.type!=H5D_CHUNKED) {
if(H5D_contig_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist,
dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
@@ -1478,8 +1445,7 @@ UNUSED
xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/)
{
fm_map fm; /* File<->memory mapping */
- H5TB_NODE *fchunk_node; /* Current node in file chunk TBBT */
- H5TB_NODE *mchunk_node; /* Current node in memory chunk TBBT */
+ H5TB_NODE *chunk_node; /* Current node in chunk TBBT */
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
@@ -1529,54 +1495,38 @@ UNUSED
assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
- /* Get first node in chunk trees */
- fchunk_node=H5TB_first(fm.fsel->root);
- mchunk_node=H5TB_first(fm.msel->root);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get first node in chunk tree */
+ chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
- while(fchunk_node && mchunk_node) {
- H5D_fchunk_info_t *fchunk_info; /* File chunk information */
- H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */
+ while(chunk_node) {
+ H5D_chunk_info_t *chunk_info; /* chunk information */
- /* Get the actual chunk information from the tree nodes */
- fchunk_info=fchunk_node->data;
- mchunk_info=mchunk_node->data;
+ /* Get the actual chunk information from the tree node */
+ chunk_info=chunk_node->data;
#ifdef H5S_DEBUG
/* Get the number of elements selected in this chunk */
- if((schunk_nelmts=H5S_get_select_npoints(fchunk_info->space))<0)
+ if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
#endif /* H5S_DEBUG */
/* Pass in chunk's coordinates in a union. */
- store.chunk_coords = fchunk_info->coords;
+ store.chunk_coords = chunk_info->coords;
/* Perform the actual read operation */
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
dc_plist, &store, H5T_get_size(dataset->type),
- fchunk_info->space, mchunk_info->space, dxpl_id, buf);
+ chunk_info->fspace, chunk_info->mspace, dxpl_id, buf);
/* Check return value from optimized read */
if (status<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
- /* Get the next chunk nodes in the trees */
- fchunk_node=H5TB_next(fchunk_node);
- mchunk_node=H5TB_next(mchunk_node);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get the next chunk node in the tree */
+ chunk_node=H5TB_next(chunk_node);
} /* end while */
#ifdef H5S_DEBUG
@@ -1642,44 +1592,35 @@ UNUSED
/* Loop over all the chunks, performing I/O on each */
- /* Get first node in chunk trees */
- fchunk_node=H5TB_first(fm.fsel->root);
- mchunk_node=H5TB_first(fm.msel->root);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get first node in chunk tree */
+ chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
- while(fchunk_node && mchunk_node) {
- H5D_fchunk_info_t *fchunk_info; /* File chunk information */
- H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */
+ while(chunk_node) {
+ H5D_chunk_info_t *chunk_info; /* chunk information */
/* Get the actual chunk information from the tree nodes */
- fchunk_info=fchunk_node->data;
- mchunk_info=mchunk_node->data;
+ chunk_info=chunk_node->data;
/* Get the number of elements selected in this chunk */
- if((schunk_nelmts=H5S_get_select_npoints(fchunk_info->space))<0)
+ if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
/* initialize selection iterator */
- if (H5S_select_iter_init(&file_iter, fchunk_info->space, src_type_size)<0)
+ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, src_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
file_iter_init=1; /*file selection iteration info has been initialized */
- if (H5S_select_iter_init(&mem_iter, mchunk_info->space, dst_type_size)<0)
+ if (H5S_select_iter_init(&mem_iter, chunk_info->mspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init=1; /*file selection iteration info has been initialized */
- if (H5S_select_iter_init(&bkg_iter, mchunk_info->space, dst_type_size)<0)
+ if (H5S_select_iter_init(&bkg_iter, chunk_info->mspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information")
bkg_iter_init=1; /*file selection iteration info has been initialized */
/* Pass in chunk's coordinates in a union*/
- store.chunk_coords = fchunk_info->coords;
+ store.chunk_coords = chunk_info->coords;
for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
@@ -1698,7 +1639,7 @@ UNUSED
assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
- dc_plist, &store, src_type_size, fchunk_info->space,
+ dc_plist, &store, src_type_size, chunk_info->fspace,
&file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
@@ -1713,7 +1654,7 @@ UNUSED
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
- n = H5S_select_mgath(buf, dst_type_size, mchunk_info->space, &bkg_iter,
+ n = H5S_select_mgath(buf, dst_type_size, chunk_info->mspace, &bkg_iter,
smine_nelmts, dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].bkg_timer), &timer);
@@ -1737,7 +1678,7 @@ UNUSED
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
- status = H5S_select_mscat(tconv_buf, dst_type_size, mchunk_info->space,
+ status = H5S_select_mscat(tconv_buf, dst_type_size, chunk_info->mspace,
&mem_iter, smine_nelmts, dxpl_id, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].scat_timer), &timer);
@@ -1765,15 +1706,8 @@ UNUSED
bkg_iter_init=0;
} /* end if */
- /* Get the next chunk nodes in the trees */
- fchunk_node=H5TB_next(fchunk_node);
- mchunk_node=H5TB_next(mchunk_node);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get the next chunk node in the tree */
+ chunk_node=H5TB_next(chunk_node);
} /* end while */
done:
@@ -1852,8 +1786,7 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
xfer_mode, hid_t src_id, hid_t dst_id, const void *buf)
{
fm_map fm; /* File<->memory mapping */
- H5TB_NODE *fchunk_node; /* Current node in file chunk TBBT */
- H5TB_NODE *mchunk_node; /* Current node in memory chunk TBBT */
+ H5TB_NODE *chunk_node; /* Current node in chunk TBBT */
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
@@ -1926,54 +1859,38 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
HDfprintf(stderr,"%s: rank=%d - Performing optimized I/O, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
- /* Get first node in chunk trees */
- fchunk_node=H5TB_first(fm.fsel->root);
- mchunk_node=H5TB_first(fm.msel->root);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get first node in chunk tree */
+ chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
- while(fchunk_node && mchunk_node) {
- H5D_fchunk_info_t *fchunk_info; /* File chunk information */
- H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */
+ while(chunk_node) {
+ H5D_chunk_info_t *chunk_info; /* chunk information */
- /* Get the actual chunk information from the tree nodes */
- fchunk_info=fchunk_node->data;
- mchunk_info=mchunk_node->data;
+ /* Get the actual chunk information from the tree node */
+ chunk_info=chunk_node->data;
#ifdef H5S_DEBUG
/* Get the number of elements selected in this chunk */
- if((schunk_nelmts=H5S_get_select_npoints(fchunk_info->space))<0)
+ if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
#endif /* H5S_DEBUG */
/* Pass in chunk's coordinates in a union. */
- store.chunk_coords = fchunk_info->coords;
+ store.chunk_coords = chunk_info->coords;
/* Perform the actual write operation */
status = (sconv->write)(dataset->ent.file, &(dataset->layout),
dc_plist, &store, H5T_get_size(dataset->type),
- fchunk_info->space, mchunk_info->space, dxpl_id, buf);
+ chunk_info->fspace, chunk_info->mspace, dxpl_id, buf);
/* Check return value from optimized write */
if (status<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
- /* Get the next chunk nodes in the trees */
- fchunk_node=H5TB_next(fchunk_node);
- mchunk_node=H5TB_next(mchunk_node);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get the next chunk node in the tree */
+ chunk_node=H5TB_next(chunk_node);
} /* end while */
#ifdef QAK
{
@@ -2059,44 +1976,35 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
/* Loop over all the chunks, performing I/O on each */
- /* Get first node in chunk trees */
- fchunk_node=H5TB_first(fm.fsel->root);
- mchunk_node=H5TB_first(fm.msel->root);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get first node in chunk tree */
+ chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
- while(fchunk_node && mchunk_node) {
- H5D_fchunk_info_t *fchunk_info; /* File chunk information */
- H5D_mchunk_info_t *mchunk_info; /* Memory chunk information */
+ while(chunk_node) {
+ H5D_chunk_info_t *chunk_info; /* chunk information */
- /* Get the actual chunk information from the tree nodes */
- fchunk_info=fchunk_node->data;
- mchunk_info=mchunk_node->data;
+ /* Get the actual chunk information from the tree node */
+ chunk_info=chunk_node->data;
/* Get the number of elements selected in this chunk */
- if((schunk_nelmts=H5S_get_select_npoints(fchunk_info->space))<0)
+ if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
/* initialize selection iterator */
- if (H5S_select_iter_init(&file_iter, fchunk_info->space, dst_type_size)<0)
+ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
file_iter_init=1; /*file selection iteration info has been initialized */
- if (H5S_select_iter_init(&mem_iter, mchunk_info->space, src_type_size)<0)
+ if (H5S_select_iter_init(&mem_iter, chunk_info->mspace, src_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init=1; /*file selection iteration info has been initialized */
- if (H5S_select_iter_init(&bkg_iter, fchunk_info->space, dst_type_size)<0)
+ if (H5S_select_iter_init(&bkg_iter, chunk_info->fspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information")
bkg_iter_init=1; /*file selection iteration info has been initialized */
/*pass in chunk's coordinates in a union*/
- store.chunk_coords = fchunk_info->coords;
+ store.chunk_coords = chunk_info->coords;
for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
@@ -2111,7 +2019,7 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
- n = H5S_select_mgath(buf, src_type_size, mchunk_info->space, &mem_iter,
+ n = H5S_select_mgath(buf, src_type_size, chunk_info->mspace, &mem_iter,
smine_nelmts, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
@@ -2127,7 +2035,7 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5_timer_begin(&timer);
#endif
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
- dc_plist, &store, dst_type_size, fchunk_info->space,
+ dc_plist, &store, dst_type_size, chunk_info->fspace,
&bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
@@ -2153,7 +2061,7 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5_timer_begin(&timer);
#endif
status = H5S_select_fscat(dataset->ent.file, &(dataset->layout),
- dc_plist, &store, dst_type_size, fchunk_info->space,
+ dc_plist, &store, dst_type_size, chunk_info->fspace,
&file_iter, smine_nelmts, dxpl_id, tconv_buf);
#ifdef H5S_DEBUG
@@ -2182,15 +2090,8 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
bkg_iter_init=0;
} /* end if */
- /* Get the next chunk nodes in the trees */
- fchunk_node=H5TB_next(fchunk_node);
- mchunk_node=H5TB_next(mchunk_node);
-
- /* Sanity check that we either have both file & memory chunk information
- * or _don't_ have both file & memory chunk information
- * (i.e. don't run out of one kind of chunk before the other)
- */
- assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node));
+ /* Get the next chunk node in the tree */
+ chunk_node=H5TB_next(chunk_node);
} /* end while */
done:
@@ -2349,15 +2250,15 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
{
H5S_t *tmp_mspace=NULL; /* Temporary memory dataspace */
hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */
- size_t elmt_size; /* Memory datatype size */
hbool_t iter_init=0; /* 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) */
hsize_t nchunks, last_nchunks; /* Number of chunks in dataset */
H5TB_NODE *curr_node; /* Current node in TBBT */
- char bogus; /* "bogus" buffer to pass to selection iterator */
- unsigned u; /* Local index variable */
- herr_t ret_value = SUCCEED; /*return value */
+ H5S_sel_type fsel_type; /* Selection type on disk */
+ char bogus; /* "bogus" buffer to pass to selection iterator */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_create_chunk_map)
#ifdef QAK
@@ -2413,83 +2314,108 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
if(H5V_array_down(f_ndims,fm->chunks,fm->down_chunks)<0)
HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
- /* Initialize TBBT's for file & memory chunk selections */
+ /* Initialize TBBT for chunk selections */
if((fm->fsel=H5TB_fast_dmake(H5TB_FAST_HSIZE_COMPARE))==NULL)
- HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create TBBT for file chunk selections")
- if((fm->msel=H5TB_fast_dmake(H5TB_FAST_HSIZE_COMPARE))==NULL)
- HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create TBBT for memory chunk selections")
+ HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create TBBT for chunk selections")
/* Save chunk template information */
fm->mchunk_tmpl=tmp_mspace;
/* Initialize "last chunk" information */
fm->last_index=(hsize_t)-1;
- fm->last_mchunk=NULL;
+ fm->last_chunk=NULL;
- /* Copy the file dataspace */
+ /* Copy the dataspaces */
if((fm->file_space = H5S_copy(file_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file dataspace")
- if(H5S_hyper_convert(fm->file_space)<0)
- HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
-
- /* Copy the memory dataspace */
if((fm->mem_space = H5S_copy(mem_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory dataspace")
- if(H5S_hyper_convert(fm->mem_space)<0)
- HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
-
+
+ /* Get type of selection on disk & in memory */
+ if((fsel_type=H5S_get_select_type(file_space))<0)
+ HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
+ if((fm->msel_type=H5S_get_select_type(mem_space))<0)
+ HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
+
+ /* Check if file selection is a point selection */
+ if(fsel_type==H5S_SEL_POINTS) {
+ /* Create temporary datatypes for selection iteration */
+ if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0)
+ HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
+
+ /* Spaces aren't the same shape, iterate over the memory selection directly */
+ if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_file_cb, fm)<0)
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+
+ /* Reset "last chunk" info */
+ fm->last_index=(hsize_t)-1;
+ fm->last_chunk=NULL;
+ } /* end if */
+ else {
+ /* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */
+ if(H5S_hyper_convert(fm->file_space)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
+
#ifdef QAK
-{
- int mpi_rank;
- double time;
- MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
- time = MPI_Wtime();
- HDfprintf(stderr,"%s: rank=%d - Before creating chunk selections, time=%f\n",FUNC,mpi_rank,time);
-}
+ {
+ int mpi_rank;
+ double time;
+ MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+ time = MPI_Wtime();
+ HDfprintf(stderr,"%s: rank=%d - Before creating chunk selections, time=%f\n",FUNC,mpi_rank,time);
+ }
#endif /* QAK */
- /* Build the file selection for each chunk */
- if(H5D_create_chunk_file_map(fm)<0)
- HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+ /* Build the file selection for each chunk */
+ if(H5D_create_chunk_file_map_hyper(fm)<0)
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
#ifdef QAK
-{
- int mpi_rank;
- double time;
- MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
- time = MPI_Wtime();
- HDfprintf(stderr,"%s: rank=%d - After creating file chunk selections, time=%f\n",FUNC,mpi_rank,time);
- HDfprintf(stderr,"%s: rank=%d - H5S_select_shape_same=%d\n",FUNC,mpi_rank,H5S_select_shape_same(file_space,mem_space));
-}
+ {
+ int mpi_rank;
+ double time;
+ MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+ time = MPI_Wtime();
+ HDfprintf(stderr,"%s: rank=%d - After creating file chunk selections, time=%f\n",FUNC,mpi_rank,time);
+ HDfprintf(stderr,"%s: rank=%d - H5S_select_shape_same=%d\n",FUNC,mpi_rank,H5S_select_shape_same(file_space,mem_space));
+ }
#endif /* QAK */
- /* Clean file chunks' hyperslab span "scratch" information */
- curr_node=H5TB_first(fm->fsel->root);
- while(curr_node) {
- H5D_fchunk_info_t *chunk_info; /* Pointer chunk information */
+ /* Clean file chunks' hyperslab span "scratch" information */
+ curr_node=H5TB_first(fm->fsel->root);
+ while(curr_node) {
+ H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
- /* Get pointer to chunk's information */
- chunk_info=curr_node->data;
- assert(chunk_info);
+ /* Get pointer to chunk's information */
+ chunk_info=curr_node->data;
+ assert(chunk_info);
- /* Clean hyperslab span's "scratch" information */
- if(H5S_hyper_reset_scratch(chunk_info->space)<0)
- HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
+ /* Clean hyperslab span's "scratch" information */
+ if(H5S_hyper_reset_scratch(chunk_info->fspace)<0)
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
- /* Get the next chunk node in the TBBT */
- curr_node=H5TB_next(curr_node);
- } /* end while */
+ /* Get the next chunk node in the TBBT */
+ curr_node=H5TB_next(curr_node);
+ } /* end while */
+ } /* end else */
/* Build the memory selection for each chunk */
- if(H5S_select_shape_same(file_space,mem_space)==TRUE) {
+ if(fsel_type!=H5S_SEL_POINTS && H5S_select_shape_same(file_space,mem_space)==TRUE) {
+ if(H5S_hyper_convert(fm->mem_space)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
+
/* If the selections are the same shape, use the file chunk information
* to generate the memory chunk information quickly.
*/
- if(H5D_create_chunk_mem_map(fm)<0)
+ 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 {
+ size_t elmt_size; /* Memory datatype size */
+
/* Create temporary datatypes for selection iteration */
- if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0)
- HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
+ if(f_tid<0) {
+ if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0)
+ HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
+ } /* end if */
/* Create selection iterator for memory selection */
if((elmt_size=H5T_get_size(mem_type))==0)
@@ -2502,22 +2428,25 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
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")
- /* Clean memory chunks' hyperslab span "scratch" information */
- curr_node=H5TB_first(fm->msel->root);
- while(curr_node) {
- H5D_mchunk_info_t *chunk_info; /* Pointer chunk 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);
+ while(curr_node) {
+ H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
- /* Get pointer to chunk's information */
- chunk_info=curr_node->data;
- assert(chunk_info);
+ /* Get pointer to chunk's information */
+ chunk_info=curr_node->data;
+ assert(chunk_info);
- /* Clean hyperslab span's "scratch" information */
- if(H5S_hyper_reset_scratch(chunk_info->space)<0)
- HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
+ /* Clean hyperslab span's "scratch" information */
+ if(H5S_hyper_reset_scratch(chunk_info->mspace)<0)
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
- /* Get the next chunk node in the TBBT */
- curr_node=H5TB_next(curr_node);
- } /* end while */
+ /* Get the next chunk node in the TBBT */
+ curr_node=H5TB_next(curr_node);
+ } /* end while */
+ } /* end if */
} /* end else */
#ifdef QAK
@@ -2566,76 +2495,42 @@ done:
/*--------------------------------------------------------------------------
NAME
- H5D_free_fchunk_info
+ H5D_free_chunk_info
PURPOSE
- Internal routine to destroy a file chunk info node (Wrapper for compatibility
+ Internal routine to destroy a chunk info node (Wrapper for compatibility
with H5TB_dfree)
USAGE
- void H5D_free_fchunk_info(fchunk_info)
- void *fchunk_info; IN: Pointer to file chunk info to destroy
+ void H5D_free_chunk_info(chunk_info)
+ void *chunk_info; IN: Pointer to chunk info to destroy
RETURNS
No return value
DESCRIPTION
- Releases all the memory for a file chunk info node.
+ Releases all the memory for a chunk info node.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static void
-H5D_free_fchunk_info(void *_fchunk_info)
+H5D_free_chunk_info(void *_chunk_info)
{
- H5D_fchunk_info_t *fchunk_info=(H5D_fchunk_info_t *)_fchunk_info;
-
- FUNC_ENTER_NOINIT(H5D_free_fchunk_info)
-
- assert(fchunk_info);
-
- /* Close the chunk's dataspace */
- (void)H5S_close(fchunk_info->space);
-
- /* Free the actual chunk info */
- H5FL_FREE(H5D_fchunk_info_t,fchunk_info);
-
- FUNC_LEAVE_NOAPI_VOID
-} /* H5D_free_fchunk_info() */
+ H5D_chunk_info_t *chunk_info=(H5D_chunk_info_t *)_chunk_info;
-
-/*--------------------------------------------------------------------------
- NAME
- H5D_free_mchunk_info
- PURPOSE
- Internal routine to destroy a file chunk info node (Wrapper for compatibility
- with H5TB_dfree)
- USAGE
- void H5D_free_mchunk_info(mchunk_info)
- void *mchunk_info; IN: Pointer to memory chunk info to destroy
- RETURNS
- No return value
- DESCRIPTION
- Releases all the memory for a memory chunk info node.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-static void
-H5D_free_mchunk_info(void *_mchunk_info)
-{
- H5D_mchunk_info_t *mchunk_info=(H5D_mchunk_info_t *)_mchunk_info;
+ FUNC_ENTER_NOINIT(H5D_free_chunk_info)
- FUNC_ENTER_NOINIT(H5D_free_mchunk_info)
+ assert(chunk_info);
- assert(mchunk_info);
+ /* Close the chunk's file dataspace */
+ (void)H5S_close(chunk_info->fspace);
- /* Close the chunk's dataspace */
- (void)H5S_close(mchunk_info->space);
+ /* Close the chunk's memory dataspace */
+ (void)H5S_close(chunk_info->mspace);
/* Free the actual chunk info */
- H5FL_FREE(H5D_mchunk_info_t,mchunk_info);
+ H5FL_FREE(H5D_chunk_info_t,chunk_info);
FUNC_LEAVE_NOAPI_VOID
-} /* H5D_free_mchunk_info() */
+} /* H5D_free_chunk_info() */
/*-------------------------------------------------------------------------
@@ -2659,13 +2554,9 @@ H5D_destroy_chunk_map(const fm_map *fm)
FUNC_ENTER_NOINIT(H5D_destroy_chunk_map)
- /* Free the file chunk info tree */
+ /* Free the chunk info tree */
if(fm->fsel)
- H5TB_dfree(fm->fsel,H5D_free_fchunk_info,NULL);
-
- /* Free the memory chunk info tree */
- if(fm->msel)
- H5TB_dfree(fm->msel,H5D_free_mchunk_info,NULL);
+ H5TB_dfree(fm->fsel,H5D_free_chunk_info,NULL);
/* Free the file dataspace */
if(fm->file_space)
@@ -2688,7 +2579,7 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5D_create_chunk_file_map
+ * Function: H5D_create_chunk_file_map_hyper
*
* Purpose: Create all chunk selections in file.
*
@@ -2702,7 +2593,7 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_create_chunk_file_map(const fm_map *fm)
+H5D_create_chunk_file_map_hyper(const fm_map *fm)
{
H5S_t *tmp_fspace=NULL; /* Temporary file dataspace */
hssize_t sel_points; /* Number of elements in file selection */
@@ -2716,7 +2607,7 @@ H5D_create_chunk_file_map(const fm_map *fm)
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOINIT(H5D_create_chunk_file_map)
+ FUNC_ENTER_NOINIT(H5D_create_chunk_file_map_hyper)
/* Sanity check */
assert(fm->f_ndims>0);
@@ -2754,7 +2645,7 @@ H5D_create_chunk_file_map(const fm_map *fm)
/* Check for intersection of temporary chunk and file selection */
if(H5S_hyper_intersect(tmp_fspace,fm->file_space)==TRUE) {
H5S_t *tmp_fchunk; /* Temporary file dataspace */
- H5D_fchunk_info_t *new_fchunk_info; /* File chunk information to insert into tree */
+ H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */
hssize_t chunk_points; /* Number of elements in chunk selection */
/* Create "temporary" chunk for selection operations (copy file space) */
@@ -2779,32 +2670,35 @@ H5D_create_chunk_file_map(const fm_map *fm)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
} /* end if */
- /* Add temporary chunk to the list of file chunks */
+ /* Add temporary chunk to the list of chunks */
/* Allocate the file & memory chunk information */
- if (NULL==(new_fchunk_info = H5FL_MALLOC (H5D_fchunk_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 file chunk info")
+ HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
- /* Initialize the file chunk information */
+ /* Initialize the chunk information */
/* Set the chunk index */
- new_fchunk_info->index=chunk_index;
+ new_chunk_info->index=chunk_index;
/* Set the file chunk dataspace */
- new_fchunk_info->space=tmp_fchunk;
+ new_chunk_info->fspace=tmp_fchunk;
+
+ /* Set the memory chunk dataspace */
+ new_chunk_info->mspace=NULL;
/* Compute the chunk's coordinates */
- if(H5D_chunk_coords_assist(new_fchunk_info->coords, fm->f_ndims, fm->chunks, chunk_index)<0) {
- H5D_free_fchunk_info(new_fchunk_info);
+ if(H5D_chunk_coords_assist(new_chunk_info->coords, fm->f_ndims, fm->chunks, chunk_index)<0) {
+ H5D_free_chunk_info(new_chunk_info);
HGOTO_ERROR(H5E_DATASPACE,H5E_CANTCOUNT,FAIL,"can't compute chunk info")
} /* end if */
- /* Insert the new file chunk into the TBBT tree */
- if(H5TB_dins(fm->fsel,new_fchunk_info,new_fchunk_info)==NULL) {
- H5D_free_fchunk_info(new_fchunk_info);
- HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert file chunk into TBBT")
+ /* Insert the new chunk into the TBBT tree */
+ if(H5TB_dins(fm->fsel,new_chunk_info,new_chunk_info)==NULL) {
+ H5D_free_chunk_info(new_chunk_info);
+ HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into TBBT")
} /* end if */
/* Get number of elements selected in chunk */
@@ -2858,11 +2752,11 @@ done:
if(H5S_close(tmp_fspace)<0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file dataspace copy");
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_create_chunk_file_map() */
+} /* end H5D_create_chunk_file_map_hyper() */
/*-------------------------------------------------------------------------
- * Function: H5D_create_chunk_mem_map
+ * Function: H5D_create_chunk_mem_map_hyper
*
* Purpose: Create all chunk selections in memory by copying the file
* chunk selections and adjusting their offsets to be correct
@@ -2880,7 +2774,7 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_create_chunk_mem_map(const fm_map *fm)
+H5D_create_chunk_mem_map_hyper(const fm_map *fm)
{
H5TB_NODE *curr_node; /* Current node in TBBT */
hsize_t file_off[H5O_LAYOUT_NDIMS*2]; /* Offset of first block in file selection */
@@ -2890,7 +2784,7 @@ H5D_create_chunk_mem_map(const fm_map *fm)
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOINIT(H5D_create_chunk_mem_map)
+ FUNC_ENTER_NOINIT(H5D_create_chunk_mem_map_hyper)
#ifdef QAK
{
hsize_t mem_dims[H5O_LAYOUT_NDIMS]; /* Dimensions of memory space */
@@ -2939,41 +2833,33 @@ for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
#endif /* QAK */
- /* Iterate over each chunk in the file chunk list */
+ /* Iterate over each chunk in the chunk list */
curr_node=H5TB_first(fm->fsel->root);
while(curr_node) {
- H5D_fchunk_info_t *fchunk_info; /* Pointer to file chunk information */
- H5D_mchunk_info_t *mchunk_info; /* Pointer to memory chunk information */
+ H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get pointer to chunk's information */
- fchunk_info=curr_node->data;
- assert(fchunk_info);
-
- /* Allocate space for the memory chunk information */
- if (NULL==(mchunk_info = H5FL_MALLOC (H5D_mchunk_info_t)))
- HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate memory chunk info")
+ chunk_info=curr_node->data;
+ assert(chunk_info);
/* Copy the information */
- /* Set the chunk index */
- mchunk_info->index=fchunk_info->index;
-
/* Copy the memory dataspace */
- if((mchunk_info->space = H5S_copy(fm->mem_space))==NULL)
+ if((chunk_info->mspace = H5S_copy(fm->mem_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Release the current selection */
- if(H5S_select_release(mchunk_info->space)<0)
+ if(H5S_select_release(chunk_info->mspace)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection")
/* Copy the file chunk's selection */
- if(H5S_select_copy(mchunk_info->space,fchunk_info->space)<0)
+ if(H5S_select_copy(chunk_info->mspace,chunk_info->fspace)<0)
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);
- chunk_adjust[u]=adjust[u]-(fchunk_info->coords[u]*(hssize_t)fm->layout->dim[u]); /*lint !e771 The adjust array will always be initialized */
+ chunk_adjust[u]=adjust[u]-(chunk_info->coords[u]*(hssize_t)fm->layout->dim[u]); /*lint !e771 The adjust array will always be initialized */
} /* end for */
#ifdef QAK
{
@@ -2994,7 +2880,7 @@ for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",chunk_adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
#endif /* QAK */
/* Adjust the selection */
- if(H5S_hyper_adjust(mchunk_info->space,chunk_adjust)<0) /*lint !e772 The chunk_adjust array will always be initialized */
+ if(H5S_hyper_adjust(chunk_info->mspace,chunk_adjust)<0) /*lint !e772 The chunk_adjust array will always be initialized */
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
#ifdef QAK
{
@@ -3010,7 +2896,7 @@ HDfprintf(stderr,"%s: After adjusting memory selection\n",FUNC);
{
hsize_t mem_dims[H5O_LAYOUT_NDIMS]; /* Dimensions of memory space */
- if(H5S_get_simple_extent_dims(mchunk_info->space, mem_dims, NULL)<0)
+ if(H5S_get_simple_extent_dims(chunk_info->mspace, mem_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
HDfprintf(stderr,"%s: mem_dims={",FUNC);
@@ -3018,17 +2904,123 @@ HDfprintf(stderr,"%s: After adjusting memory selection\n",FUNC);
HDfprintf(stderr,"%Hd%s",mem_dims[u],(u<(fm->m_ndims-1) ? ", " : "}\n"));
}
#endif /* QAK */
- /* Insert the new memory chunk into the TBBT tree */
- if(H5TB_dins(fm->msel,mchunk_info,mchunk_info)==NULL)
- HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert memory chunk into TBBT")
-
/* Get the next chunk node in the TBBT */
curr_node=H5TB_next(curr_node);
} /* end while */
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_create_chunk_mem_map() */
+} /* end H5D_create_chunk_mem_map_hyper() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_file_cb
+ *
+ * Purpose: Callback routine for file selection iterator. Used when
+ * creating selections in file for each point selected.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Wednesday, July 23, 2003
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm)
+{
+ fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */
+ H5S_t *fspace; /* Memory chunk's dataspace */
+ hssize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */
+ hsize_t chunk_index; /* Chunk index */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOINIT(H5D_chunk_file_cb)
+
+ /* Calculate the index of this chunk */
+ if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->chunks,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) {
+ /* If the chunk index is the same as the last chunk index we used,
+ * get the cached spaces to operate on.
+ */
+ fspace=fm->last_chunk;
+ } /* end if */
+ else {
+ H5TB_NODE *chunk_node; /* TBBT node holding chunk information */
+
+ /* If the chunk index is not the same as the last chunk index we used,
+ * find the chunk in the tree.
+ */
+ /* Get the chunk node from the TBBT */
+ if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))==NULL) {
+ H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */
+
+ /* Allocate the file & memory chunk information */
+ if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t)))
+ HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
+
+ /* Initialize the chunk information */
+
+ /* Set the chunk index */
+ 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) {
+ H5FL_FREE(H5D_chunk_info_t,new_chunk_info);
+ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk")
+ } /* end if */
+
+ /* De-select the chunk space */
+ if(H5S_select_none(fspace)<0) {
+ (void)H5S_close(fspace);
+ H5FL_FREE(H5D_chunk_info_t,new_chunk_info);
+ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select dataspace")
+ } /* end if */
+
+ /* Set the file chunk dataspace */
+ new_chunk_info->fspace=fspace;
+
+ /* Set the memory chunk dataspace */
+ new_chunk_info->mspace=NULL;
+
+ /* Compute the chunk's coordinates */
+ if(H5D_chunk_coords_assist(new_chunk_info->coords, fm->f_ndims, fm->chunks, chunk_index)<0) {
+ H5D_free_chunk_info(new_chunk_info);
+ HGOTO_ERROR(H5E_DATASPACE,H5E_CANTCOUNT,FAIL,"can't compute chunk info")
+ } /* end if */
+
+ /* Insert the new chunk into the TBBT tree */
+ if(H5TB_dins(fm->fsel,new_chunk_info,new_chunk_info)==NULL) {
+ H5D_free_chunk_info(new_chunk_info);
+ HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into TBBT")
+ } /* end if */
+ } /* end if */
+ else
+ /* Get the memory space information from the node */
+ fspace=((H5D_chunk_info_t *)(chunk_node->data))->fspace;
+
+ /* Update the "last chunk seen" information */
+ fm->last_index=chunk_index;
+ fm->last_chunk=fspace;
+ } /* end else */
+
+ /* 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];
+
+ /* Add point to file selection for chunk */
+ if(H5S_select_elements(fspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_chunk)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_file_cb() */
/*-------------------------------------------------------------------------
@@ -3068,50 +3060,34 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_
/* If the chunk index is the same as the last chunk index we used,
* get the cached spaces to operate on.
*/
- mspace=fm->last_mchunk;
+ mspace=fm->last_chunk;
} /* end if */
else {
H5TB_NODE *chunk_node; /* TBBT node holding chunk information */
+
/* If the chunk index is not the same as the last chunk index we used,
* find the chunk in the tree.
*/
/* Get the chunk node from the TBBT */
- if((chunk_node=H5TB_dfind(fm->msel,&chunk_index,NULL))!=NULL) {
- /* We found the correct chunk already in the tree */
-
- /* Get the memory space information from the node */
- mspace=((H5D_mchunk_info_t *)(chunk_node->data))->space;
- } /* end if */
- else {
- H5D_mchunk_info_t *new_mchunk_info; /* Memory chunk information to insert into tree */
+ if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))==NULL)
+ HGOTO_ERROR(H5E_DATASPACE,H5E_NOTFOUND,FAIL,"can't locate chunk in TBBT")
- /* The correct chunk is not already in the tree, create a new node */
- /* in both the file and memory chunk trees */
-
- /* Allocate the memory chunk information */
- if (NULL==(new_mchunk_info = H5FL_MALLOC (H5D_mchunk_info_t)))
- HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate memory chunk info")
-
- /* Initialize the memory chunk information */
-
- /* Set the chunk index */
- new_mchunk_info->index=chunk_index;
+ /* Get the memory space information from the node */
+ mspace=((H5D_chunk_info_t *)(chunk_node->data))->mspace;
+ /* Check if the chunk already has a memory space */
+ if(mspace==NULL) {
/* Copy the template memory chunk dataspace */
- if((new_mchunk_info->space = H5S_copy(fm->mchunk_tmpl))==NULL)
+ if((mspace = H5S_copy(fm->mchunk_tmpl))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
- /* Insert the new memory chunk into the TBBT tree */
- if(H5TB_dins(fm->msel,new_mchunk_info,new_mchunk_info)==NULL)
- HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert memory chunk into TBBT")
-
- /* Get the dataspaces for use in this routine */
- mspace=new_mchunk_info->space;
+ /* Set the chunk's memory dataspace for later use */
+ ((H5D_chunk_info_t *)(chunk_node->data))->mspace=mspace;
} /* end else */
/* Update the "last chunk seen" information */
fm->last_index=chunk_index;
- fm->last_mchunk=mspace;
+ fm->last_chunk=mspace;
} /* end else */
/* Get coordinates of selection iterator for memory */
@@ -3119,8 +3095,14 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates")
/* Add point to memory selection for chunk */
- if(H5S_hyper_add_span_element(mspace, fm->m_ndims, coords_in_mem)<0)
- HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
+ if(fm->msel_type==H5S_SEL_POINTS) {
+ if(H5S_select_elements(mspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_mem)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
+ } /* end if */
+ else {
+ if(H5S_hyper_add_span_element(mspace, fm->m_ndims, coords_in_mem)<0)
+ HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
+ } /* end else */
/* Move memory selection iterator to next element in selection */
if(H5S_select_iter_next(&fm->mem_iter,1)<0)