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[svn-r14278] Description:

Browse Source 
- Remember # of elements in file selection, instead of querying more than
        once
    - Handle building chunk map for single element as special case

Tested on:
        FreeBSD/32 6.2 (duty) in debug mode
        FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
                                in debug mode
        Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
                                in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                                in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                                w/szip filter, in production mode
        Mac OS X/32 10.4.10 (amazon) in debug mode
        Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
This commit is contained in:
Quincey Koziol 2007-11-20 17:12:52 -05:00
parent 3d7bb85a3d
commit 3aa3af4fb6
10 changed files with 396 additions and 118 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

323
src/H5Dio.c
View File

@ -93,9 +93,12 @@ static herr_t H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache,
/* Chunk operations */
static herr_t H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
const H5T_t *mem_type, const H5S_t *file_space, const H5S_t *mem_space);
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
const H5T_t *mem_type);
static herr_t H5D_destroy_chunk_map(const H5D_chunk_map_t *fm);
static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata);
static herr_t H5D_create_chunk_map_single(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm);
@ -1368,7 +1371,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
assert (buf);
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(&fm, io_info, mem_type, file_space, mem_space) < 0)
if(H5D_create_chunk_map(&fm, io_info, nelmts, file_space, mem_space, mem_type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
/* Set dataset storage for I/O info */
@ -1759,7 +1762,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts,
assert (buf);
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(&fm, io_info, mem_type, file_space, mem_space) < 0)
if(H5D_create_chunk_map(&fm, io_info, nelmts, file_space, mem_space, mem_type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
/* Set dataset storage for I/O info */
@ -2334,7 +2337,8 @@ done:
*/
static herr_t
H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
const H5T_t *mem_type, const H5S_t *file_space, const H5S_t *mem_space)
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
const H5T_t *mem_type)
{
H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */
H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
@ -2355,7 +2359,7 @@ H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
/* Get layout for dataset */
fm->layout = &(dataset->shared->layout);
fm->nelmts = nelmts;
/* Check if the memory space is scalar & make equivalent memory space */
if((sm_ndims = H5S_GET_EXTENT_NDIMS(mem_space)) < 0)
@ -2365,7 +2369,6 @@ H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
/* Get dim number and dimensionality for each dataspace */
fm->f_ndims = f_ndims = dataset->shared->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")
@ -2411,107 +2414,43 @@ H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
HGOTO_ERROR(H5E_DATASET,H5E_CANTCREATE,FAIL,"can't create skip list for chunk selections")
/* Initialize "last chunk" information */
fm->last_index=(hsize_t)-1;
fm->last_chunk_info=NULL;
fm->last_index = (hsize_t)-1;
fm->last_chunk_info = NULL;
/* Point at the dataspaces */
fm->file_space = file_space;
fm->mem_space = mem_space;
/* Get type of selection on disk & in memory */
if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE)
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)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
/* If the selection is NONE or POINTS, set the flag to FALSE */
if(fsel_type == H5S_SEL_POINTS || fsel_type == H5S_SEL_NONE)
sel_hyper_flag = FALSE;
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(H5D_create_chunk_file_map_hyper(fm, io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
/* Clean file chunks' hyperslab span "scratch" information */
curr_node=H5SL_first(fm->fsel);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info=H5SL_item(curr_node);
assert(chunk_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 skip list */
curr_node=H5SL_next(curr_node);
} /* end while */
} /* end if */
else {
/* Create temporary datatypes for selection iteration */
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL))) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
/* Spaces might not be the same shape, iterate over the file 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_info=NULL;
} /* end else */
/* Build the memory selection for each chunk */
if(sel_hyper_flag && H5S_select_shape_same(file_space, mem_space) == TRUE) {
/* Special case for only one element in selection */
/* (usually appending a record) */
if(nelmts == 1) {
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
/* 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_hyper(fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
/* Set up chunk mapping for single element */
if(H5D_create_chunk_map_single(fm, io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element")
} /* end if */
else {
size_t elmt_size; /* Memory datatype size */
/* Get type of selection on disk & in memory */
if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
if((fm->msel_type = H5S_GET_SELECT_TYPE(mem_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
/* Make a copy of equivalent memory space */
if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* If the selection is NONE or POINTS, set the flag to FALSE */
if(fsel_type == H5S_SEL_POINTS || fsel_type == H5S_SEL_NONE)
sel_hyper_flag = FALSE;
else
sel_hyper_flag = TRUE;
/* De-select the mem space copy */
if(H5S_select_none(tmp_mspace) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space")
/* Check if file selection is a not a hyperslab selection */
if(sel_hyper_flag) {
/* Build the file selection for each chunk */
if(H5D_create_chunk_file_map_hyper(fm, io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
/* Save chunk template information */
fm->mchunk_tmpl=tmp_mspace;
/* Create temporary datatypes for selection iteration */
if(f_tid<0) {
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->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)
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init = TRUE; /* Selection iteration info has been initialized */
/* 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")
/* Clean up hyperslab stuff, if necessary */
if(fm->msel_type != H5S_SEL_POINTS) {
/* Clean memory chunks' hyperslab span "scratch" information */
/* Clean file chunks' hyperslab span "scratch" information */
curr_node=H5SL_first(fm->fsel);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
@ -2521,13 +2460,89 @@ H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
assert(chunk_info);
/* Clean hyperslab span's "scratch" information */
if(H5S_hyper_reset_scratch(chunk_info->mspace) < 0)
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 skip list */
curr_node=H5SL_next(curr_node);
} /* end while */
} /* end if */
else {
/* Create temporary datatypes for selection iteration */
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL))) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
/* Spaces might not be the same shape, iterate over the file 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_info=NULL;
} /* end else */
/* Build the memory selection for each chunk */
if(sel_hyper_flag && H5S_select_shape_same(file_space, mem_space) == TRUE) {
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
/* 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_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 */
/* Make a copy of equivalent memory space */
if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* De-select the mem space copy */
if(H5S_select_none(tmp_mspace) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space")
/* Save chunk template information */
fm->mchunk_tmpl=tmp_mspace;
/* Create temporary datatypes for selection iteration */
if(f_tid<0) {
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->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)
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init = TRUE; /* Selection iteration info has been initialized */
/* 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")
/* Clean up hyperslab stuff, if necessary */
if(fm->msel_type != H5S_SEL_POINTS) {
/* Clean memory chunks' hyperslab span "scratch" information */
curr_node=H5SL_first(fm->fsel);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info=H5SL_item(curr_node);
assert(chunk_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 skip list */
curr_node=H5SL_next(curr_node);
} /* end while */
} /* end if */
} /* end else */
} /* end else */
done:
@ -2644,6 +2659,101 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_destroy_chunk_map() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_map_single
*
* Purpose: Create chunk selections when appending a single record
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 20, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t
#ifndef H5_HAVE_PARALLEL
UNUSED
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
H5S_t *tmp_fchunk = NULL; /* Temporary file dataspace */
H5D_chunk_info_t *new_chunk_info = NULL; /* chunk information to insert into skip list */
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 */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map_single)
/* Sanity check */
HDassert(fm->f_ndims > 0);
/* Get coordinate for selection */
if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* 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")
new_chunk_info->chunk_points = 1;
/* Set chunk location & hyperslab size */
for(u = 0; u < fm->f_ndims; u++) {
HDassert(sel_start[u] == sel_end[u]);
new_chunk_info->coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u];
} /* end for */
new_chunk_info->coords[fm->f_ndims] = 0;
/* Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims, new_chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &new_chunk_info->index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Create chunk dataspace for selection operations (copy file space) */
if((tmp_fchunk = H5S_copy(fm->file_space, FALSE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Resize chunk's dataspace dimensions to size of chunk */
if(H5S_set_extent_real(tmp_fchunk, fm->chunk_dim) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions")
/* Move selection back to have correct offset in chunk */
if(H5S_SELECT_ADJUST_U(tmp_fchunk, new_chunk_info->coords) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
#ifdef H5_HAVE_PARALLEL
/* store chunk selection information */
if(io_info->using_mpi_vfd)
fm->select_chunk[new_chunk_info->index] = TRUE;
#endif /* H5_HAVE_PARALLEL */
/* Set the file chunk dataspace */
new_chunk_info->fspace = tmp_fchunk;
/* Just point at the memory dataspace & selection */
/* (Casting away const OK -QAK) */
new_chunk_info->mspace = (H5S_t *)fm->mem_space;
/* Indicate that the chunk's memory space is shared */
new_chunk_info->mspace_shared = 1;
/* Insert the new chunk into the skip list */
if(H5SL_insert(fm->fsel, new_chunk_info, &new_chunk_info->index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert chunk into skip list")
done:
if(ret_value < 0) {
if(new_chunk_info)
(void)H5D_free_chunk_info(new_chunk_info, NULL, NULL);
if(tmp_fchunk)
(void)H5S_close(tmp_fchunk);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_map_single() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_file_map_hyper
@ -2658,15 +2768,18 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info)
H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
#ifndef H5_HAVE_PARALLEL
UNUSED
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
hssize_t ssel_points; /* Number of elements in 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 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 start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t chunk_index; /* Index of chunk */
int curr_dim; /* Current dimension to increment */
unsigned u; /* Local index variable */
@ -2678,9 +2791,7 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t *io_inf
assert(fm->f_ndims>0);
/* Get number of elements selected in file */
if((ssel_points=H5S_GET_SELECT_NPOINTS(fm->file_space)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
H5_ASSIGN_OVERFLOW(sel_points,ssel_points,hssize_t,hsize_t);
sel_points = fm->nelmts;
/* Get bounding box for selection (to reduce the number of chunks to iterate over) */
if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0)
@ -2731,7 +2842,7 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t *io_inf
} /* end if */
/* Move selection back to have correct offset in chunk */
if(H5S_hyper_adjust_u(tmp_fchunk,coords) < 0) {
if(H5S_SELECT_ADJUST_U(tmp_fchunk, coords) < 0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
} /* end if */

23
src/H5Dpkg.h
View File

@ -200,21 +200,26 @@ typedef struct H5D_chunk_info_t {
/* Main structure holding the mapping between file chunks and memory */
typedef struct H5D_chunk_map_t {
H5O_layout_t *layout; /* Dataset layout information*/
hsize_t nelmts; /* Number of elements selected in file & memory dataspaces */
const H5S_t *file_space; /* Pointer to the file dataspace */
unsigned f_ndims; /* Number of dimensions for file dataspace */
hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */
const H5S_t *mem_space; /* Pointer to the memory dataspace */
H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */
H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
unsigned m_ndims; /* Number of dimensions for memory dataspace */
H5S_sel_type msel_type; /* Selection type in memory */
H5SL_t *fsel; /* Skip list containing file dataspaces for all chunks */
hsize_t last_index; /* Index of last chunk operated on */
H5D_chunk_info_t *last_chunk_info; /* Pointer to last chunk's info */
const H5S_t *file_space; /* Pointer to the file dataspace */
const H5S_t *mem_space; /* Pointer to the memory dataspace */
hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */
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 */
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 */
#ifdef H5_HAVE_PARALLEL
hsize_t total_chunks; /* Number of total chunks */
hbool_t *select_chunk; /* store the information about whether this chunk is selected or not */

2
src/H5Pdcpl.c
View File

@ -2722,8 +2722,6 @@ H5Pget_filter_by_id1(hid_t plist_id, H5Z_filter_t id, unsigned int *flags/*out*/
size_t *cd_nelmts/*in_out*/, unsigned cd_values[]/*out*/,
size_t namelen, char name[]/*out*/)
{
H5O_pline_t pline; /* Filter pipeline */
H5Z_filter_info_t *filter; /* Pointer to filter information */
H5P_genplist_t *plist; /* Property list pointer */
herr_t ret_value = SUCCEED; /* Return value */

33
src/H5Sall.c
View File

@ -45,6 +45,7 @@ static herr_t H5S_all_bounds(const H5S_t *space, hsize_t *start, hsize_t *end);
static htri_t H5S_all_is_contiguous(const H5S_t *space);
static htri_t H5S_all_is_single(const H5S_t *space);
static htri_t H5S_all_is_regular(const H5S_t *space);
static herr_t H5S_all_adjust_u(H5S_t *space, const hsize_t *offset);
static herr_t H5S_all_iter_init(H5S_sel_iter_t *iter, const H5S_t *space);
/* Selection iteration callbacks */
@ -72,6 +73,7 @@ const H5S_select_class_t H5S_sel_all[1] = {{
H5S_all_is_contiguous,
H5S_all_is_single,
H5S_all_is_regular,
H5S_all_adjust_u,
H5S_all_iter_init,
}};
@ -693,6 +695,37 @@ H5S_all_is_regular(const H5S_t UNUSED *space)
FUNC_LEAVE_NOAPI(TRUE);
} /* H5S_all_is_regular() */
/*--------------------------------------------------------------------------
NAME
H5S_all_adjust_u
PURPOSE
Adjust an "all" selection by subtracting an offset
USAGE
herr_t H5S_all_adjust_u(space, offset)
H5S_t *space; IN/OUT: Pointer to dataspace to adjust
const hsize_t *offset; IN: Offset to subtract
RETURNS
Non-negative on success, negative on failure
DESCRIPTION
Moves selection by subtracting an offset from it.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5S_all_adjust_u(H5S_t UNUSED *space, const hsize_t UNUSED *offset)
{
FUNC_ENTER_NOAPI_NOFUNC(H5S_all_adjust_u)
/* Check args */
HDassert(space);
HDassert(offset);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5S_all_adjust_u() */
/*--------------------------------------------------------------------------
NAME

2
src/H5Shyper.c
View File

@ -60,6 +60,7 @@ static herr_t H5S_hyper_bounds(const H5S_t *space, hsize_t *start, hsize_t *end)
static htri_t H5S_hyper_is_contiguous(const H5S_t *space);
static htri_t H5S_hyper_is_single(const H5S_t *space);
static htri_t H5S_hyper_is_regular(const H5S_t *space);
static herr_t H5S_hyper_adjust_u(H5S_t *space, const hsize_t *offset);
static herr_t H5S_hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space);
/* Selection iteration callbacks */
@ -92,6 +93,7 @@ const H5S_select_class_t H5S_sel_hyper[1] = {{
H5S_hyper_is_contiguous,
H5S_hyper_is_single,
H5S_hyper_is_regular,
H5S_hyper_adjust_u,
H5S_hyper_iter_init,
}};

33
src/H5Snone.c
View File

@ -46,6 +46,7 @@ static herr_t H5S_none_bounds(const H5S_t *space, hsize_t *start, hsize_t *end);
static htri_t H5S_none_is_contiguous(const H5S_t *space);
static htri_t H5S_none_is_single(const H5S_t *space);
static htri_t H5S_none_is_regular(const H5S_t *space);
static herr_t H5S_none_adjust_u(H5S_t *space, const hsize_t *offset);
static herr_t H5S_none_iter_init(H5S_sel_iter_t *iter, const H5S_t *space);
/* Selection iteration callbacks */
@ -73,6 +74,7 @@ const H5S_select_class_t H5S_sel_none[1] = {{
H5S_none_is_contiguous,
H5S_none_is_single,
H5S_none_is_regular,
H5S_none_adjust_u,
H5S_none_iter_init,
}};
@ -649,6 +651,37 @@ H5S_none_is_regular(const H5S_t UNUSED *space)
FUNC_LEAVE_NOAPI(TRUE);
} /* H5S_none_is_regular() */
/*--------------------------------------------------------------------------
NAME
H5S_none_adjust_u
PURPOSE
Adjust an "none" selection by subtracting an offset
USAGE
herr_t H5S_none_adjust_u(space, offset)
H5S_t *space; IN/OUT: Pointer to dataspace to adjust
const hsize_t *offset; IN: Offset to subtract
RETURNS
Non-negative on success, negative on failure
DESCRIPTION
Moves selection by subtracting an offset from it.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5S_none_adjust_u(H5S_t UNUSED *space, const hsize_t UNUSED *offset)
{
FUNC_ENTER_NOAPI_NOFUNC(H5S_none_adjust_u)
/* Check args */
HDassert(space);
HDassert(offset);
FUNC_LEAVE_NOAPI(FAIL)
} /* H5S_none_adjust_u() */
/*--------------------------------------------------------------------------
NAME

3
src/H5Spkg.h
View File

@ -141,6 +141,8 @@ typedef htri_t (*H5S_sel_is_contiguous_func_t)(const H5S_t *space);
typedef htri_t (*H5S_sel_is_single_func_t)(const H5S_t *space);
/* Method to determine if current selection is "regular" */
typedef htri_t (*H5S_sel_is_regular_func_t)(const H5S_t *space);
/* Method to adjust a selection by an offset */
typedef herr_t (*H5S_sel_adjust_u_func_t)(H5S_t *space, const hsize_t *offset);
/* Method to initialize iterator for current selection */
typedef herr_t (*H5S_sel_iter_init_func_t)(H5S_sel_iter_t *sel_iter, const H5S_t *space);
@ -160,6 +162,7 @@ typedef struct {
H5S_sel_is_contiguous_func_t is_contiguous; /* Method to determine if current selection is contiguous */
H5S_sel_is_single_func_t is_single; /* Method to determine if current selection is a single block */
H5S_sel_is_regular_func_t is_regular; /* Method to determine if current selection is "regular" */
H5S_sel_adjust_u_func_t adjust_u; /* Method to adjust a selection by an offset */
H5S_sel_iter_init_func_t iter_init; /* Method to initialize iterator for current selection */
} H5S_select_class_t;

54
src/H5Spoint.c
View File

@ -47,6 +47,7 @@ static herr_t H5S_point_bounds(const H5S_t *space, hsize_t *start, hsize_t *end)
static htri_t H5S_point_is_contiguous(const H5S_t *space);
static htri_t H5S_point_is_single(const H5S_t *space);
static htri_t H5S_point_is_regular(const H5S_t *space);
static herr_t H5S_point_adjust_u(H5S_t *space, const hsize_t *offset);
static herr_t H5S_point_iter_init(H5S_sel_iter_t *iter, const H5S_t *space);
/* Selection iteration callbacks */
@ -74,6 +75,7 @@ const H5S_select_class_t H5S_sel_point[1] = {{
H5S_point_is_contiguous,
H5S_point_is_single,
H5S_point_is_regular,
H5S_point_adjust_u,
H5S_point_iter_init,
}};
@ -1193,6 +1195,58 @@ H5S_point_is_regular(const H5S_t *space)
FUNC_LEAVE_NOAPI(ret_value);
} /* H5S_point_is_regular() */
/*--------------------------------------------------------------------------
NAME
H5S_point_adjust_u
PURPOSE
Adjust a "point" selection by subtracting an offset
USAGE
herr_t H5S_point_adjust_u(space, offset)
H5S_t *space; IN/OUT: Pointer to dataspace to adjust
const hsize_t *offset; IN: Offset to subtract
RETURNS
Non-negative on success, negative on failure
DESCRIPTION
Moves a point selection by subtracting an offset from it.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5S_point_adjust_u(H5S_t *space, const hsize_t *offset)
{
H5S_pnt_node_t *node; /* Point node */
unsigned rank; /* Dataspace rank */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5S_point_adjust_u)
HDassert(space);
HDassert(offset);
/* Iterate through the nodes, checking the bounds on each element */
node = space->select.sel_info.pnt_lst->head;
rank = space->extent.rank;
while(node) {
unsigned u; /* Local index variable */
/* Adjust each coordinate for point node */
for(u = 0; u < rank; u++) {
/* Check for offset moving selection negative */
HDassert(node->pnt[u] >= offset[u]);
/* Adjust node's coordinate location */
node->pnt[u] -= offset[u];
} /* end for */
/* Advance to next point node in selection */
node = node->next;
} /* end while */
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5S_point_adjust_u() */
/*--------------------------------------------------------------------------
NAME

4
src/H5Sprivate.h
View File

@ -155,6 +155,7 @@ typedef struct H5S_iostats_t {
#define H5S_SELECT_IS_CONTIGUOUS(S) ((*(S)->select.type->is_contiguous)(S))
#define H5S_SELECT_IS_SINGLE(S) ((*(S)->select.type->is_single)(S))
#define H5S_SELECT_IS_REGULAR(S) ((*(S)->select.type->is_regular)(S))
#define H5S_SELECT_ADJUST_U(S,O) ((*(S)->select.type->adjust_u)(S, O))
#define H5S_SELECT_ITER_COORDS(ITER,COORDS) ((*(ITER)->type->iter_coords)(ITER,COORDS))
#define H5S_SELECT_ITER_BLOCK(ITER,START,END) ((*(ITER)->type->iter_block)(ITER,START,END))
#define H5S_SELECT_ITER_NELMTS(ITER) ((*(ITER)->type->iter_nelmts)(ITER))
@ -177,6 +178,7 @@ typedef struct H5S_iostats_t {
#define H5S_SELECT_IS_CONTIGUOUS(S) (H5S_select_is_contiguous(S))
#define H5S_SELECT_IS_SINGLE(S) (H5S_select_is_single(S))
#define H5S_SELECT_IS_REGULAR(S) (H5S_select_is_regular(S))
#define H5S_SELECT_ADJUST_U(S,O) (H5S_select_adjust_u(S, O))
#define H5S_SELECT_ITER_COORDS(ITER,COORDS) (H5S_select_iter_coords(ITER,COORDS))
#define H5S_SELECT_ITER_BLOCK(ITER,START,END) (H5S_select_iter_block(ITER,START,END))
#define H5S_SELECT_ITER_NELMTS(ITER) (H5S_select_iter_nelmts(ITER))
@ -244,6 +246,7 @@ H5_DLL herr_t H5S_select_serialize(const H5S_t *space, uint8_t *buf);
H5_DLL htri_t H5S_select_is_contiguous(const H5S_t *space);
H5_DLL htri_t H5S_select_is_single(const H5S_t *space);
H5_DLL htri_t H5S_select_is_regular(const H5S_t *space);
H5_DLL herr_t H5S_select_adjust_u(H5S_t *space, const hsize_t *offset);
/* Operations on all selections */
H5_DLL herr_t H5S_select_all(H5S_t *space, hbool_t rel_prev);
@ -266,7 +269,6 @@ H5_DLL herr_t H5S_hyper_convert(H5S_t *space);
H5_DLL htri_t H5S_hyper_intersect (H5S_t *space1, H5S_t *space2);
#endif /* LATER */
H5_DLL htri_t H5S_hyper_intersect_block (H5S_t *space, hsize_t *start, hsize_t *end);
H5_DLL herr_t H5S_hyper_adjust_u(H5S_t *space, const hsize_t *offset);
H5_DLL herr_t H5S_hyper_adjust_s(H5S_t *space, const hssize_t *offset);
H5_DLL herr_t H5S_hyper_move(H5S_t *space, const hssize_t *offset);
H5_DLL herr_t H5S_hyper_normalize_offset(H5S_t *space, hssize_t *old_offset);

37
src/H5Sselect.c
View File

@ -687,6 +687,43 @@ H5S_select_is_regular(const H5S_t *space)
FUNC_LEAVE_NOAPI(ret_value);
} /* H5S_select_is_regular() */
/*--------------------------------------------------------------------------
NAME
H5S_select_adjust_u
PURPOSE
Adjust a selection by subtracting an offset
USAGE
herr_t H5S_select_adjust_u(space, offset)
H5S_t *space; IN/OUT: Pointer to dataspace to adjust
const hsize_t *offset; IN: Offset to subtract
RETURNS
Non-negative on success, negative on failure
DESCRIPTION
Moves a selection by subtracting an offset from it.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
This routine participates in the "Inlining C function pointers"
pattern, don't call it directly, use the appropriate macro
defined in H5Sprivate.h.
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5S_select_adjust_u(H5S_t *space, const hsize_t *offset)
{
herr_t ret_value; /* return value */
FUNC_ENTER_NOAPI_NOFUNC(H5S_select_adjust_u)
/* Check args */
HDassert(space);
ret_value = (*space->select.type->adjust_u)(space, offset);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5S_select_adjust_u() */
/*--------------------------------------------------------------------------
NAME