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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
/* Pablo information */
/* (Put before include files to avoid problems with inline functions) */
#define PABLO_MASK H5Dio_mask
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FDprivate.h" /* File drivers */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Sprivate.h" /* Dataspace functions */
#include "H5TBprivate.h" /* Threaded, balanced, binary trees (TBBTs) */
#include "H5Vprivate.h" /* Vector and array functions */
/*#define H5D_DEBUG*/
#ifdef H5_HAVE_PARALLEL
/* Remove this if H5R_DATASET_REGION is no longer used in this file */
# include "H5Rpublic.h"
#endif /*H5_HAVE_PARALLEL*/
/* Local typedefs */
/* Information for mapping between file space and memory space */
/* 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 *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 */
} 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 */
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_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 */
unsigned m_ndims; /* Number of dimensions for memory dataspace */
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 */
static int interface_initialize_g = 0;
#define INTERFACE_INIT NULL
/* Local functions */
static herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space,
hid_t dset_xfer_plist, void *buf/*out*/);
static herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space,
hid_t dset_xfer_plist, const void *buf);
static herr_t
H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist,
H5P_genplist_t *dx_plist, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, void *buf/*out*/);
static herr_t
H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist,
H5P_genplist_t *dx_plist, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf);
static herr_t
H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist,
H5P_genplist_t *dx_plist, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, void *buf/*out*/);
static herr_t
H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist,
H5P_genplist_t *dx_plist, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf);
#ifdef H5_HAVE_PARALLEL
static herr_t
H5D_io_assist_mpio(H5P_genplist_t *dx_plist, H5FD_mpio_xfer_t xfer_mode,
hbool_t *xfer_mode_changed);
#endif /*H5_HAVE_PARALLEL*/
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_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_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,
const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id);
/* Declare a free list to manage blocks of single datatype element data */
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_chunk_info_t struct */
H5FL_DEFINE_STATIC(H5D_chunk_info_t);
/*--------------------------------------------------------------------------
NAME
H5Dfill
PURPOSE
Fill a selection in memory with a value
USAGE
herr_t H5Dfill(fill, fill_type, space, buf, buf_type)
const void *fill; IN: Pointer to fill value to use
hid_t fill_type_id; IN: Datatype of the fill value
void *buf; IN/OUT: Memory buffer to fill selection within
hid_t buf_type_id; IN: Datatype of the elements in buffer
hid_t space_id; IN: Dataspace describing memory buffer &
containing selection to use.
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Use the selection in the dataspace to fill elements in a memory buffer.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
If "fill" parameter is NULL, use all zeros as fill value
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id)
{
H5S_t *space; /* Dataspace */
H5T_t *fill_type; /* Fill-value datatype */
H5T_t *buf_type; /* Buffer datatype */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_API(H5Dfill, FAIL)
H5TRACE5("e","xixii",fill,fill_type_id,buf,buf_type_id,space_id);
/* Check args */
if (buf==NULL)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer")
if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataspace")
if (NULL == (fill_type=H5I_object_verify(fill_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype")
if (NULL == (buf_type=H5I_object_verify(buf_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype")
/* Fill the selection in the memory buffer */
if(H5D_fill(fill,fill_type,buf,buf_type,space, H5AC_dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed")
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dfill() */
/*--------------------------------------------------------------------------
NAME
H5D_fill
PURPOSE
Fill a selection in memory with a value (internal version)
USAGE
herr_t H5D_fill(fill, fill_type, buf, buf_type, space)
const void *fill; IN: Pointer to fill value to use
H5T_t *fill_type; IN: Datatype of the fill value
void *buf; IN/OUT: Memory buffer to fill selection within
H5T_t *buf_type; IN: Datatype of the elements in buffer
H5S_t *space; IN: Dataspace describing memory buffer &
containing selection to use.
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Use the selection in the dataspace to fill elements in a memory buffer.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
If "fill" parameter is NULL, use all zeros as fill value. If "fill_type"
parameter is NULL, use "buf_type" for the fill value datatype.
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id)
{
H5T_path_t *tpath = NULL; /* Conversion information*/
uint8_t *tconv_buf = NULL; /* Data type conv buffer */
uint8_t *bkg_buf = NULL; /* Temp conversion buffer */
hid_t src_id = -1, dst_id = -1; /* Temporary type IDs */
size_t src_type_size; /* Size of source type */
size_t dst_type_size; /* Size of destination type*/
size_t buf_size; /* Desired buffer size */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_fill)
/* Check args */
assert(buf);
assert(buf_type);
assert(space);
/* Check for "default" fill value */
if(fill_type==NULL)
fill_type=buf_type;
/* Get the memory and file datatype sizes */
src_type_size = H5T_get_size(fill_type);
dst_type_size = H5T_get_size(buf_type);
/* Get the maximum buffer size needed and allocate it */
buf_size=MAX(src_type_size,dst_type_size);
if (NULL==(tconv_buf = H5FL_BLK_MALLOC(type_elem,buf_size)) || NULL==(bkg_buf = H5FL_BLK_CALLOC(type_elem,buf_size)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Check for actual fill value to replicate */
if(fill==NULL)
/* If there's no fill value, just use zeros */
HDmemset(tconv_buf,0,dst_type_size);
else {
/* Copy the user's data into the buffer for conversion */
HDmemcpy(tconv_buf,fill,src_type_size);
/* Convert memory buffer into disk buffer */
/* Set up type conversion function */
if (NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL, dxpl_id))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types")
} else if (!H5T_path_noop(tpath)) {
if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill_type, H5T_COPY_ALL)))<0 ||
(dst_id = H5I_register(H5I_DATATYPE, H5T_copy(buf_type, H5T_COPY_ALL)))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion")
}
/* Perform data type conversion */
if (H5T_convert(tpath, src_id, dst_id, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
} /* end if */
/* Fill the selection in the memory buffer */
if(H5S_select_fill(tconv_buf, dst_type_size, space, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed")
done:
if (tconv_buf)
H5FL_BLK_FREE(type_elem,tconv_buf);
if (bkg_buf)
H5FL_BLK_FREE(type_elem,bkg_buf);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_fill() */
/*-------------------------------------------------------------------------
* Function: H5Dread
*
* Purpose: Reads (part of) a DSET from the file into application
* memory BUF. The part of the dataset to read is defined with
* MEM_SPACE_ID and FILE_SPACE_ID. The data points are
* converted from their file type to the MEM_TYPE_ID specified.
* Additional miscellaneous data transfer properties can be
* passed to this function with the PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Non-negative on success/Negative on failure
*
* Errors:
* ARGS BADTYPE Not a data space.
* ARGS BADTYPE Not a data type.
* ARGS BADTYPE Not a dataset.
* ARGS BADTYPE Not xfer parms.
* ARGS BADVALUE No output buffer.
* DATASET READERROR Can't read data.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_API(H5Dread, FAIL)
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == dset->ent.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type")
if (H5S_ALL != mem_space_id) {
if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if(H5S_select_valid(mem_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
if (H5S_ALL != file_space_id) {
if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if(H5S_select_valid(file_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == plist_id)
plist_id= H5P_DATASET_XFER_DEFAULT;
else
if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
if (!buf)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
/* read raw data */
if (H5D_read(dset, mem_type, mem_space, file_space, plist_id, buf/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
done:
FUNC_LEAVE_API(ret_value)
}
/*-------------------------------------------------------------------------
* Function: H5Dwrite
*
* Purpose: Writes (part of) a DSET from application memory BUF to the
* file. The part of the dataset to write is defined with the
* MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
* are converted from their current type (MEM_TYPE_ID) to their
* file data type. Additional miscellaneous data transfer
* properties can be passed to this function with the
* PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Non-negative on success/Negative on failure
*
* Errors:
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, const void *buf)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_API(H5Dwrite, FAIL)
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == dset->ent.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type")
if (H5S_ALL != mem_space_id) {
if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if (H5S_select_valid(mem_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
if (H5S_ALL != file_space_id) {
if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if (H5S_select_valid(file_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == plist_id)
plist_id= H5P_DATASET_XFER_DEFAULT;
else
if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
if (!buf)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
/* write raw data */
if (H5D_write(dset, mem_type, mem_space, file_space, plist_id, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
done:
FUNC_LEAVE_API(ret_value)
}
/*-------------------------------------------------------------------------
* Function: H5D_read
*
* Purpose: Reads (part of) a DATASET into application memory BUF. See
* H5Dread() for complete details.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 1998-06-09
* The data space is no longer cached in the dataset struct.
*
* Robb Matzke, 1998-08-11
* Added timing calls around all the data space I/O functions.
*
* rky, 1998-09-18
* Added must_convert to do non-optimized read when necessary.
*
* Quincey Koziol, 1999-07-02
* Changed xfer_parms parameter to xfer plist parameter, so it
* could be passed to H5T_convert.
*
* Albert Cheng, 2000-11-21
* Added the code that when it detects it is not safe to process a
* COLLECTIVE read request without hanging, it changes it to
* INDEPENDENT calls.
*
* Albert Cheng, 2000-11-27
* Changed to use the optimized MPIO transfer for Collective calls only.
*
* Raymond Lu, 2001-10-2
* Changed the way to retrieve property for generic property list.
*
* Raymond Lu, 2002-2-26
* For the new fill value design, data space can either be allocated
* or not allocated at this stage. Fill value or data from space is
* returned to outgoing buffer.
*
* QAK - 2002/04/02
* Removed the must_convert parameter and move preconditions to
* H5S_<foo>_opt_possible() routine
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/)
{
hssize_t snelmts; /*total number of elmts (signed) */
hsize_t nelmts; /*total number of elmts */
H5T_path_t *tpath = NULL; /*type conversion info */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode; /*xfer_mode for this request */
hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */
#endif /*H5_HAVE_PARALLEL*/
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 */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_read)
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(buf);
/* Get the dataset's creation property list */
if (NULL == (dc_plist = H5I_object(dataset->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Get the dataset transfer property list */
if (NULL == (dx_plist = H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
if (!file_space)
file_space = dataset->space;
if (!mem_space)
mem_space = file_space;
if((snelmts = H5S_get_select_npoints(mem_space))<0)
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection")
H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t);
#ifdef H5_HAVE_PARALLEL
/* Collect Parallel I/O information for possible later use */
xfer_mode=(H5FD_mpio_xfer_t)H5P_peek_unsigned(dx_plist, H5D_XFER_IO_XFER_MODE_NAME);
/* Collective access is not permissible without a MPI based VFD */
if (xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->ent.file))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only")
/* Set the "parallel I/O possible" flag, for H5S_find(), if we are doing collective I/O */
/* (Don't set the parallel I/O possible flag for the MPI-posix driver, since it doesn't do real collective I/O) */
if (H5S_mpi_opt_types_g && xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPIPOSIX(dataset->ent.file))
sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE;
#endif /*H5_HAVE_PARALLEL*/
/* Make certain that the number of elements in each selection is the same */
if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space))
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes")
/* Retrieve dataset properties */
/* <none needed in the general case> */
/* If space hasn't been allocated and not using external storage,
* return fill value to buffer if fill time is upon allocation, or
* do nothing if fill time is never. If the dataset is compact and
* 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) {
H5O_fill_t fill={NULL,0,NULL}; /* Fill value info */
H5D_fill_time_t fill_time; /* When to write the fill values */
H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */
/* Retrieve dataset's fill-value properties */
if(H5P_fill_value_defined(dc_plist, &fill_status)<0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
if((fill_status==H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED)
&& H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill value")
if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill time")
/* Should be impossible, but check anyway... */
if(fill_status == H5D_FILL_VALUE_UNDEFINED && (fill_time == H5D_FILL_TIME_ALLOC || fill_time == H5D_FILL_TIME_IFSET))
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read")
/* If we're never going to fill this dataset, just leave the junk in the user's buffer */
if(fill_time == H5D_FILL_TIME_NEVER)
HGOTO_DONE(SUCCEED)
/* Go fill the user's selection with the dataset's fill value */
if(H5D_fill(fill.buf,fill.type,buf,mem_type,mem_space, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed")
else
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type atoms. Data type
* conversion is necessary if the user has set the `need_bkg' to a high
* enough value in xfer_parms since turning off data type conversion also
* turns off background preservation.
*/
if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL, dxpl_id))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types")
} else if (!H5T_path_noop(tpath)) {
if ((src_id=H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 ||
(dst_id=H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion")
} /* end if */
/* Set the storage flags for the space conversion check */
switch(dataset->layout.type) {
case H5D_COMPACT:
sconv_flags |= H5S_CONV_STORAGE_COMPACT;
break;
case H5D_CONTIGUOUS:
sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS;
break;
case H5D_CHUNKED:
sconv_flags |= H5S_CONV_STORAGE_CHUNKED;
break;
default:
assert(0 && "Unhandled layout type!");
} /* end switch */
/* Get dataspace functions */
if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags, &use_par_opt_io)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space")
#ifdef H5_HAVE_PARALLEL
/* Don't reset the transfer mode if we can't or won't use it */
if(!use_par_opt_io || !H5T_path_noop(tpath))
H5D_io_assist_mpio(dx_plist, xfer_mode, &xfer_mode_changed);
#endif /*H5_HAVE_PARALLEL*/
/* Determine correct I/O routine to invoke */
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, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
} /* end if */
else {
if(H5D_chunk_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist,
dx_plist, dxpl_id, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
} /* end else */
done:
#ifdef H5_HAVE_PARALLEL
/* restore xfer_mode due to the kludge */
if (xfer_mode_changed) {
#ifdef H5D_DEBUG
if (H5DEBUG(D))
fprintf (H5DEBUG(D), "H5D: xfer_mode was COLLECTIVE, restored to INDEPENDENT\n");
#endif
xfer_mode = H5FD_MPIO_COLLECTIVE;
if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0)
HDONE_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
} /* end if */
#endif /*H5_HAVE_PARALLEL*/
if (src_id >= 0) {
if(H5I_dec_ref(src_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
if (dst_id >= 0) {
if(H5I_dec_ref(dst_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_read() */
/*-------------------------------------------------------------------------
* Function: H5D_write
*
* Purpose: Writes (part of) a DATASET to a file from application memory
* BUF. See H5Dwrite() for complete details.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space is no longer cached in the dataset struct.
*
* rky 980918
* Added must_convert to do non-optimized read when necessary.
*
* Quincey Koziol, 2 July 1999
* Changed xfer_parms parameter to xfer plist parameter, so it could
* be passed to H5T_convert
*
* Albert Cheng, 2000-11-21
* Added the code that when it detects it is not safe to process a
* COLLECTIVE write request without hanging, it changes it to
* INDEPENDENT calls.
*
* Albert Cheng, 2000-11-27
* Changed to use the optimized MPIO transfer for Collective calls only.
*
* Raymond Lu, 2001-10-2
* Changed the way to retrieve property for generic property list.
*
* Raymond Lu, 2002-2-26
* For the new fill value design, space may not be allocated until
* this function is called. Allocate and initialize space if it
* hasn't been.
*
* QAK - 2002/04/02
* Removed the must_convert parameter and move preconditions to
* H5S_<foo>_opt_possible() routine
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, const void *buf)
{
hssize_t snelmts; /*total number of elmts (signed) */
hsize_t nelmts; /*total number of elmts */
H5T_path_t *tpath = NULL; /*type conversion info */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode; /*xfer_mode for this request */
hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */
#endif /*H5_HAVE_PARALLEL*/
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 */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_write)
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(buf);
/* If MPI based VFD is used, no VL datatype support yet. */
/* This is because they use the global heap in the file and we don't */
/* support parallel access of that yet */
if (IS_H5FD_MPI(dataset->ent.file) && H5T_detect_class(mem_type, H5T_VLEN)>0)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet")
/* If MPI based VFD is used, no VL datatype support yet. */
/* This is because they use the global heap in the file and we don't */
/* support parallel access of that yet */
/* We should really use H5T_detect_class() here, but it will be difficult
* to detect the type of the reference if it is nested... -QAK
*/
if (IS_H5FD_MPI(dataset->ent.file) &&
H5T_get_class(mem_type)==H5T_REFERENCE &&
H5T_get_ref_type(mem_type)==H5R_DATASET_REGION)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet")
/* Check if we are allowed to write to this file */
if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR))
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file")
/* Get the dataset's creation property list */
if (NULL == (dc_plist = H5I_object(dataset->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Get the dataset transfer property list */
if (NULL == (dx_plist = H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
if (!file_space)
file_space = dataset->space;
if (!mem_space)
mem_space = file_space;
if((snelmts = H5S_get_select_npoints(mem_space))<0)
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection")
H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t);
#ifdef H5_HAVE_PARALLEL
/* Collect Parallel I/O information for possible later use */
xfer_mode=(H5FD_mpio_xfer_t)H5P_peek_unsigned(dx_plist, H5D_XFER_IO_XFER_MODE_NAME);
/* Collective access is not permissible without a MPI based VFD */
if (xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->ent.file))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only")
/* Set the "parallel I/O possible" flag, for H5S_find(), if we are doing collective I/O */
/* (Don't set the parallel I/O possible flag for the MPI-posix driver, since it doesn't do real collective I/O) */
if (H5S_mpi_opt_types_g && xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPIPOSIX(dataset->ent.file))
sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE;
#endif /*H5_HAVE_PARALLEL*/
/* Make certain that the number of elements in each selection is the same */
if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space))
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes")
/* Retrieve dataset properties */
/* <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) {
hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */
/* 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")
/* Allocate storage */
if(H5D_alloc_storage(dataset->ent.file,dxpl_id,dataset,H5D_ALLOC_WRITE, TRUE, (hbool_t)((hsize_t)file_nelmts==nelmts ? TRUE : FALSE))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
} /* end if */
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type atoms. Data type
* conversion is necessary if the user has set the `need_bkg' to a high
* enough value in xfer_parms since turning off data type conversion also
* turns off background preservation.
*/
if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL, dxpl_id))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types")
} else if (!H5T_path_noop(tpath)) {
if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 ||
(dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion")
} /* end if */
/* Set the storage flags for the space conversion check */
switch(dataset->layout.type) {
case H5D_COMPACT:
sconv_flags |= H5S_CONV_STORAGE_COMPACT;
break;
case H5D_CONTIGUOUS:
sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS;
break;
case H5D_CHUNKED:
sconv_flags |= H5S_CONV_STORAGE_CHUNKED;
break;
default:
assert(0 && "Unhandled layout type!");
} /* end switch */
/* Get dataspace functions */
if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags, &use_par_opt_io)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space")
#ifdef H5_HAVE_PARALLEL
/* Don't reset the transfer mode if we can't or won't use it */
if(!use_par_opt_io || !H5T_path_noop(tpath))
H5D_io_assist_mpio(dx_plist, xfer_mode, &xfer_mode_changed);
#endif /*H5_HAVE_PARALLEL*/
/* Determine correct I/O routine to invoke */
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, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
} /* end if */
else {
if(H5D_chunk_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist,
dx_plist, dxpl_id, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
} /* end else */
#ifdef OLD_WAY
/*
* This was taken out because it can be called in a parallel program with
* independent access, causing the metadata cache to get corrupted. Its been
* disabled for all types of access (serial as well as parallel) to make the
* modification time consistent for all programs. -QAK
*/
/*
* Update modification time. We have to do this explicitly because
* writing to a dataset doesn't necessarily change the object header.
*/
if (H5O_touch(&(dataset->ent), FALSE, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time")
#endif /* OLD_WAY */
done:
#ifdef H5_HAVE_PARALLEL
/* restore xfer_mode due to the kludge */
if (xfer_mode_changed) {
#ifdef H5D_DEBUG
if (H5DEBUG(D))
fprintf (H5DEBUG(D), "H5D: xfer_mode was COLLECTIVE, restored to INDEPENDENT\n");
#endif
xfer_mode = H5FD_MPIO_COLLECTIVE;
if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0)
HDONE_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
} /* end if */
#endif /*H5_HAVE_PARALLEL*/
if (src_id >= 0) {
if(H5I_dec_ref(src_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
if (dst_id >= 0) {
if(H5I_dec_ref(dst_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_write() */
/*-------------------------------------------------------------------------
* Function: H5D_contig_read
*
* Purpose: Read from a contiguous dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath,
H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist,
hid_t dxpl_id, hid_t src_id, hid_t dst_id, void *buf/*out*/)
{
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOINIT(H5D_contig_read)
/*
* If there is no type conversion then read directly into the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
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);
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
dc_plist, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type),
file_space, mem_space, dxpl_id, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].read_timer), &timer);
sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type);
sconv->stats[1].read_ncalls++;
#endif
/* Check return value from optimized read */
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
} else
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* This is the general case(type conversion).
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(dataset->type);
dst_type_size = H5T_get_size(mem_type);
target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME);
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX(src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/* Figure out the strip mine size. */
if (H5S_select_iter_init(&file_iter, file_space, 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, mem_space, 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, mem_space, 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 */
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX(path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Start strip mining... */
for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
assert(H5S_select_iter_nelmts(&file_iter)==(nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (nelmts-smine_start));
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
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);
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dc_plist, (H5D_storage_t *)&(dataset->efl), src_type_size, file_space,
&file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_mgath(buf, dst_type_size, mem_space, &bkg_iter,
smine_nelmts, dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].bkg_timer), &timer);
sconv->stats[1].bkg_nbytes += n * dst_type_size;
sconv->stats[1].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data into memory.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5S_select_mscat(tconv_buf, dst_type_size, mem_space,
&mem_iter, smine_nelmts, dxpl_id, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].scat_timer), &timer);
sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[1].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
} /* end for */
done:
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
assert(dx_plist);
if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))
H5FL_BLK_FREE(type_conv,bkg_buf);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_contig_read() */
/*-------------------------------------------------------------------------
* Function: H5D_contig_write
*
* Purpose: Write to a contiguous dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist,
H5P_genplist_t *dx_plist, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf)
{
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOINIT(H5D_contig_write)
/*
* If there is no type conversion then write directly from the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->write)(dataset->ent.file, &(dataset->layout),
dc_plist, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type),
file_space, mem_space, dxpl_id, buf);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].write_timer), &timer);
sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type);
sconv->stats[0].write_ncalls++;
#endif
/* Check return value from optimized write */
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
} else
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* This is the general case.
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(mem_type);
dst_type_size = H5T_get_size(dataset->type);
target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME);
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/* Figure out the strip mine size. */
if (H5S_select_iter_init(&file_iter, file_space, 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, mem_space, 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, file_space, 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 */
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if(H5T_detect_class(dataset->type, H5T_VLEN)) {
/* Old data is retrieved into background buffer for VL datatype. The
* data is used later for freeing heap objects. */
need_bkg = H5T_BKG_YES;
} else if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX (path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Start strip mining... */
for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
assert(H5S_select_iter_nelmts(&file_iter)==(nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (nelmts-smine_start));
/*
* Gather data from application buffer into the data type conversion
* buffer. Also gather data from the file into the background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_mgath(buf, src_type_size, mem_space, &mem_iter,
smine_nelmts, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].gath_timer), &timer);
sconv->stats[0].gath_nbytes += n * src_type_size;
sconv->stats[0].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dc_plist, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space,
&bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].bkg_timer), &timer);
sconv->stats[0].bkg_nbytes += n * dst_type_size;
sconv->stats[0].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data out to the file.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5S_select_fscat(dataset->ent.file, &(dataset->layout),
dc_plist, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space, &file_iter,
smine_nelmts, dxpl_id, tconv_buf);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].scat_timer), &timer);
sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[0].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed")
} /* end for */
done:
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
assert(dx_plist);
if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))
H5FL_BLK_FREE(type_conv,bkg_buf);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_contig_write() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_read
*
* Purpose: Read from a chunked dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_read(hsize_t
#ifdef NDEBUG
UNUSED
#endif /* NDEBUG */
nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist,
H5P_genplist_t *dx_plist, hid_t dxpl_id, hid_t src_id, hid_t dst_id, void *buf/*out*/)
{
fm_map fm; /* File<->memory mapping */
H5TB_NODE *chunk_node; /* Current node in chunk TBBT */
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
hssize_t schunk_nelmts; /* Number of elements selected in current chunk */
hsize_t chunk_nelmts; /* Number of elements selected in current chunk */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
H5D_storage_t store; /*union of EFL and chunk pointer in file space */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOINIT(H5D_chunk_read)
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
/*
* If there is no type conversion then read directly into the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
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);
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* 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(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 = chunk_info->coords;
/* Perform the actual read operation */
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
dc_plist, &store, H5T_get_size(dataset->type),
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 node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].read_timer), &timer);
sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type);
sconv->stats[1].read_ncalls++;
#endif
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* This is the general case(type conversion).
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(dataset->type);
dst_type_size = H5T_get_size(mem_type);
target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME);
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX(path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Loop over all the chunks, performing I/O on each */
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* Get the actual chunk information from the tree nodes */
chunk_info=chunk_node->data;
/* Get the number of elements selected in this chunk */
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, 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, 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, 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 = 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 */
assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start));
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
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);
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dc_plist, &store, src_type_size, chunk_info->fspace,
&file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
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);
sconv->stats[1].bkg_nbytes += n * dst_type_size;
sconv->stats[1].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0,
tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data into memory.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
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);
sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[1].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
} /* end for */
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
file_iter_init=0;
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
mem_iter_init=0;
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
bkg_iter_init=0;
} /* end if */
/* Get the next chunk node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
done:
assert(dx_plist);
if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))
H5FL_BLK_FREE(type_conv,bkg_buf);
/* Release selection iterators, if necessary */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
/* Release chunk mapping information */
if(H5D_destroy_chunk_map(&fm) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping")
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_read() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_write
*
* Purpose: Writes to a chunked dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_write(hsize_t
#ifdef NDEBUG
UNUSED
#endif /* NDEBUG */
nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist,
H5P_genplist_t *dx_plist, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf)
{
fm_map fm; /* File<->memory mapping */
H5TB_NODE *chunk_node; /* Current node in chunk TBBT */
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
hssize_t schunk_nelmts; /* Number of elements selected in current chunk */
hsize_t chunk_nelmts; /* Number of elements selected in current chunk */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
H5D_storage_t store; /*union of EFL and chunk pointer in file space */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOINIT(H5D_chunk_write)
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Entering, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
#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 chunk map, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/*
* If there is no type conversion then write directly from the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Performing optimized I/O, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* 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(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 = chunk_info->coords;
/* Perform the actual write operation */
status = (sconv->write)(dataset->ent.file, &(dataset->layout),
dc_plist, &store, H5T_get_size(dataset->type),
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 node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Done performing optimized I/O, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].write_timer), &timer);
sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type);
sconv->stats[0].write_ncalls++;
#endif
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
#ifdef QAK
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
HDfprintf(stderr,"%s: rank=%d - Performing NON-optimized I/O\n",FUNC,mpi_rank);
}
#endif /* QAK */
/*
* This is the general case(type conversion).
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(mem_type);
dst_type_size = H5T_get_size(dataset->type);
target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME);
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if(H5T_detect_class(dataset->type, H5T_VLEN)) {
/* Old data is retrieved into background buffer for VL datatype. The
* data is used later for freeing heap objects. */
need_bkg = H5T_BKG_YES;
} else if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX (path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Loop over all the chunks, performing I/O on each */
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* 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(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, 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, 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, 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 = 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 */
assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start));
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_mgath(buf, src_type_size, chunk_info->mspace, &mem_iter,
smine_nelmts, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dc_plist, &store, dst_type_size, chunk_info->fspace,
&bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].bkg_timer), &timer);
sconv->stats[0].bkg_nbytes += n * dst_type_size;
sconv->stats[0].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0,
tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data out to the file.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5S_select_fscat(dataset->ent.file, &(dataset->layout),
dc_plist, &store, dst_type_size, chunk_info->fspace,
&file_iter, smine_nelmts, dxpl_id, tconv_buf);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].scat_timer), &timer);
sconv->stats[0].scat_nbytes += n * dst_type_size;
sconv->stats[0].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed")
} /* end for */
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
file_iter_init=0;
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
mem_iter_init=0;
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
bkg_iter_init=0;
} /* end if */
/* Get the next chunk node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
done:
assert(dx_plist);
if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))
H5FL_BLK_FREE(type_conv,bkg_buf);
/* Release selection iterators, if necessary */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
/* Release chunk mapping information */
if(H5D_destroy_chunk_map(&fm) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping")
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_write() */
#ifdef H5_HAVE_PARALLEL
/*-------------------------------------------------------------------------
* Function: H5D_io_assist_mpio
*
* Purpose: Common logic for determining if the MPI transfer mode should
* be changed.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_io_assist_mpio(H5P_genplist_t *dx_plist, H5FD_mpio_xfer_t xfer_mode,
hbool_t *xfer_mode_changed)
{
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOINIT(H5D_io_assist_mpio)
/* The following may not handle a collective call correctly
* since it does not ensure all processes can handle the write
* request according to the MPI collective specification.
* Do the collective request via independent mode.
*/
if (xfer_mode==H5FD_MPIO_COLLECTIVE) {
/* Kludge: change the xfer_mode to independent, handle the request,
* then xfer_mode before return.
* Better way is to get a temporary data_xfer property with
* INDEPENDENT xfer_mode and pass it downwards.
*/
xfer_mode = H5FD_MPIO_INDEPENDENT;
if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
*xfer_mode_changed=TRUE; /* restore it before return */
#ifdef H5D_DEBUG
if (H5DEBUG(D))
fprintf(H5DEBUG(D), "H5D: Cannot handle this COLLECTIVE write request. Do it via INDEPENDENT calls\n");
#endif
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
}
#endif /*H5_HAVE_PARALLEL*/
/*-------------------------------------------------------------------------
* Function: H5D_chunk_coords_assist
*
* Purpose: Compute the coords for a particular chunk (in CHUNK_IDX),
* based on the size of the dataset's dataspace (given in
* NDIMS and CHUNKS), putting the resulting chunk's coordinate
* offsets in the COORDS array.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, const hsize_t chunks[], hsize_t chunk_idx)
{
hsize_t tmp; /* Size of "down elements" in each dimension */
size_t i, j; /* Local index variables */
FUNC_ENTER_NOINIT(H5D_chunk_coords_assist)
for(i=0; i<ndims; i++) {
tmp=1;
for(j=i+1; j<ndims; j++)
tmp *= chunks[j];
coords[i] = (hssize_t)(chunk_idx / tmp);
chunk_idx = chunk_idx % tmp;
}
coords[ndims] = 0;
FUNC_LEAVE_NOAPI(SUCCEED)
}
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_map
*
* Purpose: Creates the mapping between elements selected in each chunk
* and the elements in the memory selection.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
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)
{
H5S_t *tmp_mspace=NULL; /* Temporary memory dataspace */
H5S_t *equiv_mspace=NULL; /* Equivalent memory dataspace */
hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */
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 */
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
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Entering, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/* Initialize fm_map structure */
HDmemset(fm, 0, sizeof(fm_map));
/* Get layout for dataset */
fm->layout = &(dataset->layout);
/* Check if the memory space is scalar & make equivalent memory space */
if((sm_ndims = H5S_get_simple_extent_ndims(mem_space))<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number")
if(sm_ndims==0) {
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++)
dims[u]=1;
if((equiv_mspace = H5S_create_simple(dataset->layout.ndims-1,dims,NULL))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create equivalent dataspace for scalar space")
} /* end else */
else {
if((equiv_mspace = H5S_copy(mem_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
} /* end else */
/* Make a copy of equivalent memory space */
if((tmp_mspace = H5S_copy(equiv_mspace))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Get dim number and dimensionality for each dataspace */
fm->f_ndims=f_ndims=dataset->layout.ndims-1;
if((sm_ndims = H5S_get_simple_extent_ndims(tmp_mspace))<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number")
H5_ASSIGN_OVERFLOW(fm->m_ndims,sm_ndims,int,unsigned);
/* 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")
if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
/* Decide the number of chunks in each dimension*/
last_nchunks=0;
nchunks=1;
for(u=0; u<f_ndims; 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];
/* Track total number of chunks in dataset */
nchunks *= fm->chunks[u];
/* Check if the chunk indices will overflow */
if(nchunks<last_nchunks)
HGOTO_ERROR (H5E_DATASET, H5E_OVERFLOW, FAIL, "too many chunks")
last_nchunks=nchunks;
} /* end for */
/* Compute the "down" size of 'chunks' information */
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 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 chunk selections")
/* Save chunk template information */
fm->mchunk_tmpl=tmp_mspace;
/* Initialize "last chunk" information */
fm->last_index=(hsize_t)-1;
fm->last_chunk=NULL;
/* 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((fm->mem_space = H5S_copy(equiv_mspace))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory dataspace")
/* 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(equiv_mspace))<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);
}
#endif /* QAK */
/* 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,equiv_mspace));
}
#endif /* QAK */
/* 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);
/* 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 */
} /* end else */
/* Build the memory selection for each chunk */
if(fsel_type!=H5S_SEL_POINTS && H5S_select_shape_same(file_space,equiv_mspace)==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_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<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)
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
if (H5S_select_iter_init(&(fm->mem_iter), equiv_mspace, elmt_size)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init=1; /* 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=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);
/* 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 */
} /* end if */
} /* end else */
#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 chunk selections, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
done:
/* Release the [potentially partially built] chunk mapping information if an error occurs */
if(ret_value<0) {
if(tmp_mspace && !fm->mchunk_tmpl) {
if(H5S_close(tmp_mspace)<0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
} /* end if */
if (H5D_destroy_chunk_map(fm)<0)
HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping")
} /* end if */
if(equiv_mspace) {
if(H5S_close(equiv_mspace)<0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
} /* end if */
if(iter_init) {
if (H5S_select_iter_release(&(fm->mem_iter))<0)
HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
}
if(f_tid!=(-1)) {
if(H5I_dec_ref(f_tid)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Leaving, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_map() */
/*--------------------------------------------------------------------------
NAME
H5D_free_chunk_info
PURPOSE
Internal routine to destroy a chunk info node (Wrapper for compatibility
with H5TB_dfree)
USAGE
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 chunk info node.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static void
H5D_free_chunk_info(void *_chunk_info)
{
H5D_chunk_info_t *chunk_info=(H5D_chunk_info_t *)_chunk_info;
FUNC_ENTER_NOINIT(H5D_free_chunk_info)
assert(chunk_info);
/* Close the chunk's file dataspace */
(void)H5S_close(chunk_info->fspace);
/* Close the chunk's memory dataspace */
(void)H5S_close(chunk_info->mspace);
/* Free the actual chunk info */
H5FL_FREE(H5D_chunk_info_t,chunk_info);
FUNC_LEAVE_NOAPI_VOID
} /* H5D_free_chunk_info() */
/*-------------------------------------------------------------------------
* Function: H5D_destroy_chunk_map
*
* Purpose: Destroy chunk mapping information.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Saturday, May 17, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_destroy_chunk_map(const fm_map *fm)
{
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOINIT(H5D_destroy_chunk_map)
/* Free the chunk info tree */
if(fm->fsel)
H5TB_dfree(fm->fsel,H5D_free_chunk_info,NULL);
/* Free the file dataspace */
if(fm->file_space)
if(H5S_close(fm->file_space)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file dataspace")
/* Free the memory dataspace */
if(fm->mem_space)
if(H5S_close(fm->mem_space)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory dataspace")
/* Free the memory chunk dataspace template */
if(fm->mchunk_tmpl)
if(H5S_close(fm->mchunk_tmpl)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_destroy_chunk_map() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_file_map_hyper
*
* Purpose: Create all chunk selections in file.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 29, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
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 */
hssize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
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 */
hsize_t chunk_index; /* Index of chunk */
int curr_dim; /* Current dimension to increment */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_create_chunk_file_map_hyper)
/* Sanity check */
assert(fm->f_ndims>0);
/* Make a copy of file dataspace */
if((tmp_fspace = H5S_copy(fm->file_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Get number of elements selected in file */
if((sel_points=H5S_get_select_npoints(tmp_fspace))<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
/* Get offset of first block in file selection */
if(H5S_get_select_bounds(tmp_fspace, sel_start, sel_end)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* 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];
coords[u]=start_coords[u];
count[u]=fm->layout->dim[u];
} /* end for */
/* Select initial chunk as hyperslab */
if(H5S_select_hyperslab(tmp_fspace,H5S_SELECT_SET,coords,NULL,count,NULL)<0) /*lint !e772 The coords and count arrays should always be initialized */
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create hyperslab selection")
/* Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_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")
/* Iterate through each chunk in the dataset */
while(sel_points) {
/* 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_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) */
if((tmp_fchunk = H5S_copy(fm->file_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* "AND" temporary chunk and current chunk */
if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,count,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) {
(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 */
if(H5S_hyper_adjust(tmp_fchunk,coords)<0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
} /* end if */
/* Add temporary chunk to the list of chunks */
/* Allocate the file & memory chunk information */
if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
/* Initialize the chunk information */
/* Set the chunk index */
new_chunk_info->index=chunk_index;
/* Set the file chunk dataspace */
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_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 */
/* Get number of elements selected in chunk */
if((chunk_points=H5S_get_select_npoints(tmp_fchunk))<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
/* Decrement # of points left in file selection */
sel_points-=chunk_points;
/* Leave if we are done */
if(sel_points==0)
HGOTO_DONE(SUCCEED)
assert(sel_points>0);
} /* end if */
/* Increment chunk index */
chunk_index++;
/* Set current increment dimension */
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];
/* Bring chunk location back into bounds, if necessary */
if(coords[curr_dim]>sel_end[curr_dim]) {
do {
/* Reset current dimension's location to 0 */
coords[curr_dim]=start_coords[curr_dim]; /*lint !e771 The start_coords will always be initialized */
/* Decrement current dimension */
curr_dim--;
/* Increment chunk location in current dimension */
coords[curr_dim]+=(hssize_t)count[curr_dim];
} 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->chunks,fm->down_chunks,&chunk_index)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
} /* end if */
/* Move template chunk's offset to current location of chunk */
if(H5S_hyper_move(tmp_fspace,coords)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't move chunk selection")
} /* end while */
done:
if(tmp_fspace)
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_hyper() */
/*-------------------------------------------------------------------------
* 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
* for the memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 29, 2003
*
* Assumptions: That the file and memory selections are the same shape.
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
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 */
hsize_t mem_off[H5O_LAYOUT_NDIMS*2]; /* Offset of first block in memory selection */
hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */
hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_create_chunk_mem_map_hyper)
#ifdef QAK
{
hsize_t mem_dims[H5O_LAYOUT_NDIMS]; /* Dimensions of memory space */
if(H5S_get_simple_extent_dims(fm->mem_space, mem_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
HDfprintf(stderr,"%s: mem_dims={",FUNC);
for(u=0; u<fm->m_ndims; u++)
HDfprintf(stderr,"%Hd%s",mem_dims[u],(u<(fm->m_ndims-1) ? ", " : "}\n"));
}
#endif /* QAK */
/* Sanity check */
assert(fm->f_ndims>0);
/* Get offset of first block in file selection */
if(H5S_get_select_hyper_blocklist(fm->file_space, (hsize_t)0, (hsize_t)1, file_off)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection block info")
/* Get offset of first block in memory selection */
if(H5S_get_select_hyper_blocklist(fm->mem_space, (hsize_t)0, (hsize_t)1, mem_off)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection block info")
/* Calculate the adjustment for memory selection from file selection */
assert(fm->m_ndims==fm->f_ndims);
for(u=0; u<fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(file_off[u],hsize_t,hssize_t);
H5_CHECK_OVERFLOW(mem_off[u],hsize_t,hssize_t);
adjust[u]=(hssize_t)file_off[u]-(hssize_t)mem_off[u];
} /* end for */
#ifdef QAK
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
if(mpi_rank==1) {
HDfprintf(stderr,"%s: rank=%d - adjust={",FUNC,mpi_rank);
for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
} /* end if */
}
#endif /* QAK */
#ifdef QAK
HDfprintf(stderr,"%s: adjust={",FUNC);
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 chunk list */
curr_node=H5TB_first(fm->fsel->root);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get pointer to chunk's information */
chunk_info=curr_node->data;
assert(chunk_info);
/* Copy the information */
/* Copy the memory dataspace */
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(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(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]-(chunk_info->coords[u]*(hssize_t)fm->layout->dim[u]); /*lint !e771 The adjust array will always be initialized */
} /* end for */
#ifdef QAK
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
if(mpi_rank==1) {
HDfprintf(stderr,"%s: rank=%d - Before adjusting memory selection\n",FUNC,mpi_rank);
HDfprintf(stderr,"%s: rank=%d - chunk_adjust={",FUNC,mpi_rank);
for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",chunk_adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
} /* end if */
}
#endif /* QAK */
#ifdef QAK
HDfprintf(stderr,"%s: Before adjusting memory selection\n",FUNC);
HDfprintf(stderr,"%s: chunk_adjust={",FUNC);
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(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
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
if(mpi_rank==1)
HDfprintf(stderr,"%s: rank=%d - After adjusting memory selection\n",FUNC,mpi_rank);
}
#endif /* QAK */
#ifdef QAK
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(chunk_info->mspace, mem_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
HDfprintf(stderr,"%s: mem_dims={",FUNC);
for(u=0; u<fm->m_ndims; u++)
HDfprintf(stderr,"%Hd%s",mem_dims[u],(u<(fm->m_ndims-1) ? ", " : "}\n"));
}
#endif /* QAK */
/* 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_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() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_mem_cb
*
* Purpose: Callback routine for file selection iterator. Used when
* creating selections in memory for each chunk.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_mem_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 *mspace; /* Memory chunk's dataspace */
hssize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */
hsize_t chunk_index; /* Chunk index */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_chunk_mem_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.
*/
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->fsel,&chunk_index,NULL))==NULL)
HGOTO_ERROR(H5E_DATASPACE,H5E_NOTFOUND,FAIL,"can't locate chunk in TBBT")
/* 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((mspace = H5S_copy(fm->mchunk_tmpl))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file 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_chunk=mspace;
} /* end else */
/* Get coordinates of selection iterator for memory */
if(H5S_select_iter_coords(&fm->mem_iter,coords_in_mem)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates")
/* Add point to memory selection for chunk */
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)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTNEXT, FAIL, "unable to move to next iterator location")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_mem_cb() */
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