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authorScot Breitenfeld <brtnfld@hdfgroup.org>2008-04-30 19:51:13 (GMT)
committerScot Breitenfeld <brtnfld@hdfgroup.org>2008-04-30 19:51:13 (GMT)
commitaec106e324ce20e5efb725c25a6a333c7970127b (patch)
tree234df369115a46b08037c5f385061cf58823e497 /src/H5Dio.c
parent5773fd34bc5adf59b4530d95ac9f0c0585902803 (diff)
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[svn-r14903] Undoing change committed in r14902.
Diffstat (limited to 'src/H5Dio.c')
-rw-r--r--src/H5Dio.c3217
1 files changed, 379 insertions, 2838 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 8576464..17bab19 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -28,27 +28,17 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
-#include "H5MMprivate.h" /* Memory management */
-#include "H5Sprivate.h" /* Dataspace functions */
-#include "H5SLprivate.h" /* Skip lists */
-#include "H5Vprivate.h" /* Vector and array functions */
#ifdef H5_HAVE_PARALLEL
/* Remove this if H5R_DATASET_REGION is no longer used in this file */
-# include "H5Rpublic.h"
+#include "H5Rpublic.h"
#endif /*H5_HAVE_PARALLEL*/
+
/****************/
/* Local Macros */
/****************/
-#define H5D_DEFAULT_SKIPLIST_HEIGHT 8
-
-/* Macros for iterating over chunks to operate on */
-#define H5D_CHUNK_GET_FIRST_NODE(map) (map.use_single ? (H5SL_node_t *)(1) : H5SL_first(map.sel_chunks))
-#define H5D_CHUNK_GET_NODE_INFO(map, node) (map.use_single ? map.single_chunk_info : (H5D_chunk_info_t *)H5SL_item(node))
-#define H5D_CHUNK_GET_NEXT_NODE(map, node) (map.use_single ? (H5SL_node_t *)NULL : H5SL_next(node))
-
/******************/
/* Local Typedefs */
@@ -59,64 +49,36 @@
/* Local Prototypes */
/********************/
+/* Internal I/O routines */
static herr_t H5D_read(H5D_t *dataset, hid_t mem_type_id,
- const H5S_t *mem_space, const H5S_t *file_space,
- hid_t dset_xfer_plist, void *buf/*out*/);
+ 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, hid_t mem_type_id,
- const H5S_t *mem_space, const H5S_t *file_space,
- hid_t dset_xfer_plist, const void *buf);
-static herr_t H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, void *buf/*out*/);
-static herr_t H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, const void *buf);
-static herr_t H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, void *buf/*out*/);
-static herr_t H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, const void *buf);
-static herr_t H5D_compound_opt_read(size_t nelmts, const H5S_t *mem_space,
- H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache,
- hid_t src_id, hid_t dst_id, H5T_subset_t subset, void *data_buf,
- void *user_buf/*out*/);
-static herr_t H5D_compound_opt_write(size_t nelmts, hid_t src_id, hid_t dst_id,
- void *data_buf);
+ const H5S_t *mem_space, const H5S_t *file_space, hid_t dset_xfer_plist,
+ const void *buf);
+/* Setup/teardown routines */
+static herr_t H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache,
+ hid_t dxpl_id, const H5D_type_info_t *type_info, H5D_storage_t *store,
+ H5D_io_info_t *io_info);
+static herr_t H5D_typeinfo_init(const H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache,
+ hid_t dxpl_id, hid_t mem_type_id, hbool_t do_write,
+ H5D_type_info_t *type_info);
#ifdef H5_HAVE_PARALLEL
+static herr_t H5D_ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset,
+ const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm);
static herr_t H5D_ioinfo_term(H5D_io_info_t *io_info);
#endif /* H5_HAVE_PARALLEL */
+static herr_t H5D_typeinfo_term(const H5D_type_info_t *type_info);
-/* I/O info operations */
-static herr_t H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache,
- hid_t dxpl_id, const H5S_t *mem_space, const H5S_t *file_space,
- H5T_path_t *tpath, H5D_io_info_t *io_info);
-
-/* Chunk operations */
-static herr_t H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
- hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
- const H5T_t *mem_type);
-static herr_t H5D_destroy_chunk_map(const H5D_chunk_map_t *fm);
-static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata);
-static herr_t H5D_create_chunk_map_single(H5D_chunk_map_t *fm,
- const H5D_io_info_t *io_info);
-static herr_t H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm,
- const H5D_io_info_t *io_info);
-static herr_t H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm);
-static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, unsigned ndims,
- const hsize_t *coords, void *fm);
-static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims,
- const hsize_t *coords, void *fm);
/*********************/
/* Package Variables */
/*********************/
+
/*******************/
/* Local Variables */
/*******************/
@@ -124,142 +86,6 @@ static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims,
/* 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(H5D_chunk_info_t);
-
-/* Declare a free list to manage sequences of size_t */
-H5FL_SEQ_DEFINE_STATIC(size_t);
-
-/* Declare a free list to manage sequences of hsize_t */
-H5FL_SEQ_DEFINE_STATIC(hsize_t);
-
-
-
-/*--------------------------------------------------------------------------
- NAME
- H5D_get_dxpl_cache_real
- PURPOSE
- Get all the values for the DXPL cache.
- USAGE
- herr_t H5D_get_dxpl_cache_real(dxpl_id, cache)
- hid_t dxpl_id; IN: DXPL to query
- H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values
- RETURNS
- Non-negative on success/Negative on failure.
- DESCRIPTION
- Query all the values from a DXPL that are needed by internal routines
- within the library.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-herr_t
-H5D_get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache)
-{
- H5P_genplist_t *dx_plist; /* Data transfer property list */
- herr_t ret_value=SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_get_dxpl_cache_real,FAIL)
-
- /* Check args */
- assert(cache);
-
- /* Get the dataset transfer property list */
- if (NULL == (dx_plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
-
- /* Get maximum temporary buffer size */
- if(H5P_get(dx_plist, H5D_XFER_MAX_TEMP_BUF_NAME, &cache->max_temp_buf) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve maximum temporary buffer size")
-
- /* Get temporary buffer pointer */
- if(H5P_get(dx_plist, H5D_XFER_TCONV_BUF_NAME, &cache->tconv_buf) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve temporary buffer pointer")
-
- /* Get background buffer pointer */
- if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_NAME, &cache->bkgr_buf) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer pointer")
-
- /* Get background buffer type */
- if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &cache->bkgr_buf_type) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
-
- /* Get B-tree split ratios */
- if(H5P_get(dx_plist, H5D_XFER_BTREE_SPLIT_RATIO_NAME, &cache->btree_split_ratio) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve B-tree split ratios")
-
- /* Get I/O vector size */
- if(H5P_get(dx_plist, H5D_XFER_HYPER_VECTOR_SIZE_NAME, &cache->vec_size) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve I/O vector size")
-
-#ifdef H5_HAVE_PARALLEL
- /* Collect Parallel I/O information for possible later use */
- if(H5P_get(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &cache->xfer_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve parallel transfer method")
- if(H5P_get(dx_plist, H5D_XFER_IO_XFER_OPT_MODE_NAME, &cache->xfer_opt_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve parallel transfer method")
-#endif /*H5_HAVE_PARALLEL*/
-
- /* Get error detection properties */
- if(H5P_get(dx_plist, H5D_XFER_EDC_NAME, &cache->err_detect) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve error detection info")
-
- /* Get filter callback function */
- if(H5P_get(dx_plist, H5D_XFER_FILTER_CB_NAME, &cache->filter_cb) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve filter callback function")
-
- /* Get the data transform property */
- if(H5P_get(dx_plist, H5D_XFER_XFORM_NAME, &cache->data_xform_prop) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve data transform info")
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_get_dxpl_cache_real() */
-
-
-/*--------------------------------------------------------------------------
- NAME
- H5D_get_dxpl_cache
- PURPOSE
- Get all the values for the DXPL cache.
- USAGE
- herr_t H5D_get_dxpl_cache(dxpl_id, cache)
- hid_t dxpl_id; IN: DXPL to query
- H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values
- RETURNS
- Non-negative on success/Negative on failure.
- DESCRIPTION
- Query all the values from a DXPL that are needed by internal routines
- within the library.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- The CACHE pointer should point at already allocated memory to place
- non-default property list info. If a default property list is used, the
- CACHE pointer will be changed to point at the default information.
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-herr_t
-H5D_get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t **cache)
-{
- herr_t ret_value=SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_get_dxpl_cache,FAIL)
-
- /* Check args */
- assert(cache);
-
- /* Check for the default DXPL */
- if(dxpl_id==H5P_DATASET_XFER_DEFAULT)
- *cache=&H5D_def_dxpl_cache;
- else
- if(H5D_get_dxpl_cache_real(dxpl_id,*cache) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't retrieve DXPL values")
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_get_dxpl_cache() */
/*-------------------------------------------------------------------------
@@ -300,7 +126,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
char fake_char;
- herr_t ret_value=SUCCEED; /* Return value */
+ 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,
@@ -316,7 +142,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
- if(H5S_SELECT_VALID(mem_space)!=TRUE)
+ if(H5S_SELECT_VALID(mem_space) != TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
} /* end if */
if(H5S_ALL != file_space_id) {
@@ -324,33 +150,33 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
- if(H5S_SELECT_VALID(file_space)!=TRUE)
+ if(H5S_SELECT_VALID(file_space) != TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
- }
+ } /* end if */
/* 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))
+ if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
- if (!buf && H5S_GET_SELECT_NPOINTS(file_space)!=0)
+ if(!buf && H5S_GET_SELECT_NPOINTS(file_space) != 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
/* If the buffer is nil, and 0 element is selected, make a fake buffer.
* This is for some MPI package like ChaMPIon on NCSA's tungsten which
* doesn't support this feature.
*/
- if (!buf)
+ if(!buf)
buf = &fake_char;
/* read raw data */
- if (H5D_read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
+ if(H5D_read(dset, mem_type_id, 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)
-}
+} /* end H5Dread() */
/*-------------------------------------------------------------------------
@@ -392,7 +218,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
char fake_char;
- herr_t ret_value=SUCCEED; /* Return value */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(H5Dwrite, FAIL)
H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id,
@@ -408,7 +234,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
- if (H5S_SELECT_VALID(mem_space)!=TRUE)
+ if(H5S_SELECT_VALID(mem_space) != TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
} /* end if */
if(H5S_ALL != file_space_id) {
@@ -416,7 +242,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
- if(H5S_SELECT_VALID(file_space)!=TRUE)
+ if(H5S_SELECT_VALID(file_space) != TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
} /* end if */
@@ -424,16 +250,16 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
if(H5P_DEFAULT == plist_id)
plist_id= H5P_DATASET_XFER_DEFAULT;
else
- if(TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER))
+ if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
- if(!buf && H5S_GET_SELECT_NPOINTS(file_space)!=0)
+ if(!buf && H5S_GET_SELECT_NPOINTS(file_space) != 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
/* If the buffer is nil, and 0 element is selected, make a fake buffer.
* This is for some MPI package like ChaMPIon on NCSA's tungsten which
* doesn't support this feature.
*/
- if (!buf)
+ if(!buf)
buf = &fake_char;
/* write raw data */
@@ -442,7 +268,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
done:
FUNC_LEAVE_API(ret_value)
-}
+} /* end H5Dwrite() */
/*-------------------------------------------------------------------------
@@ -462,16 +288,18 @@ static herr_t
H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/)
{
+ H5D_chunk_map_t fm; /* Chunk file<->memory mapping */
+ H5D_io_info_t io_info; /* Dataset I/O info */
+ H5D_type_info_t type_info; /* Datatype info for operation */
+ H5D_storage_t store; /*union of EFL and chunk pointer in file space */
hssize_t snelmts; /*total number of elmts (signed) */
hsize_t nelmts; /*total number of elmts */
- H5T_path_t *tpath = NULL; /*type conversion info */
- const H5T_t *mem_type = NULL; /* Memory datatype */
- H5D_io_info_t io_info; /* Dataset I/O info */
#ifdef H5_HAVE_PARALLEL
hbool_t io_info_init = FALSE; /* Whether the I/O info has been initialized */
#endif /*H5_HAVE_PARALLEL*/
+ hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_read)
@@ -479,10 +307,6 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
/* check args */
HDassert(dataset && dataset->oloc.file);
- /* Get memory datatype */
- if(NULL == (mem_type = (const H5T_t *)H5I_object_verify(mem_type_id, H5I_DATATYPE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
-
if(!file_space)
file_space = dataset->shared->space;
if(!mem_space)
@@ -492,23 +316,27 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t);
/* Fill the DXPL cache values for later use */
- if(H5D_get_dxpl_cache(dxpl_id,&dxpl_cache) < 0)
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+ /* Set up datatype info for operation */
+ if(H5D_typeinfo_init(dataset, dxpl_cache, dxpl_id, mem_type_id, FALSE, &type_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info")
+
#ifdef H5_HAVE_PARALLEL
/* Collective access is not permissible without a MPI based VFD */
- if (dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->oloc.file))
+ if(dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->oloc.file))
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only")
#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))
+ 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")
/* Make sure that both selections have their extents set */
- if( !(H5S_has_extent(file_space)) )
+ if(!(H5S_has_extent(file_space)))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set")
- if( !(H5S_has_extent(mem_space)) )
+ if(!(H5S_has_extent(mem_space)))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set")
/* Retrieve dataset properties */
@@ -539,49 +367,56 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
HGOTO_DONE(SUCCEED)
/* Go fill the user's selection with the dataset's fill value */
- if(H5D_fill(dataset->shared->dcpl_cache.fill.buf, dataset->shared->type, buf, mem_type, mem_space, dxpl_id) < 0)
+ if(H5D_fill(dataset->shared->dcpl_cache.fill.buf, dataset->shared->type, buf, type_info.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 datatype 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 datatype conversion also
- * turns off background preservation.
- */
- if (NULL==(tpath=H5T_path_find(dataset->shared->type, mem_type, NULL, NULL, dxpl_id, FALSE)))
- HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype")
-
/* Set up I/O operation */
- if(H5D_ioinfo_init(dataset,dxpl_cache,dxpl_id,mem_space,file_space,tpath,&io_info) < 0)
+ io_info.op_type = H5D_IO_OP_READ;
+ io_info.u.rbuf = buf;
+ if(H5D_ioinfo_init(dataset, dxpl_cache, dxpl_id, &type_info, &store, &io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation")
#ifdef H5_HAVE_PARALLEL
io_info_init = TRUE;
#endif /*H5_HAVE_PARALLEL*/
- /* Determine correct I/O routine to invoke */
- if(dataset->shared->layout.type!=H5D_CHUNKED) {
- if(H5D_contig_read(&io_info, nelmts, mem_type, mem_space, file_space, tpath,
- dataset->shared->type_id, mem_type_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
- } /* end if */
- else {
- if(H5D_chunk_read(&io_info, nelmts, mem_type, mem_space, file_space, tpath,
- dataset->shared->type_id, mem_type_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
- } /* end else */
+ /* Sanity check that space is allocated, if there are elements */
+ if(nelmts > 0)
+ HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
+ || (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
+ || dataset->shared->dcpl_cache.efl.nused > 0
+ || dataset->shared->layout.type == H5D_COMPACT);
+
+ /* Call storage method's I/O initialization routine */
+ if(io_info.layout_ops.init && (*io_info.layout_ops.init)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info")
+ io_op_init = TRUE;
+
+#ifdef H5_HAVE_PARALLEL
+ /* Adjust I/O info for any parallel I/O */
+ if(H5D_ioinfo_adjust(&io_info, dataset, dxpl_cache, dxpl_id, file_space, mem_space, &type_info, &fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O")
+#endif /*H5_HAVE_PARALLEL*/
+
+ /* Invoke correct "high level" I/O routine */
+ if((*io_info.io_ops.multi_read)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
done:
+ /* Shut down the I/O op information */
+ if(io_op_init && io_info.layout_ops.term && (*io_info.layout_ops.term)(&fm) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info")
#ifdef H5_HAVE_PARALLEL
/* Shut down io_info struct */
- if (io_info_init)
+ if(io_info_init)
if(H5D_ioinfo_term(&io_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "can't shut down io_info")
#endif /*H5_HAVE_PARALLEL*/
+ /* Shut down datatype info for operation */
+ if(H5D_typeinfo_term(&type_info) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_read() */
@@ -604,16 +439,18 @@ static herr_t
H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, const void *buf)
{
+ H5D_chunk_map_t fm; /* Chunk file<->memory mapping */
+ H5D_io_info_t io_info; /* Dataset I/O info */
+ H5D_type_info_t type_info; /* Datatype info for operation */
+ H5D_storage_t store; /*union of EFL and chunk pointer in file space */
hssize_t snelmts; /*total number of elmts (signed) */
hsize_t nelmts; /*total number of elmts */
- H5T_path_t *tpath = NULL; /*type conversion info */
- const H5T_t *mem_type = NULL; /* Memory datatype */
- H5D_io_info_t io_info; /* Dataset I/O info */
#ifdef H5_HAVE_PARALLEL
hbool_t io_info_init = FALSE; /* Whether the I/O info has been initialized */
#endif /*H5_HAVE_PARALLEL*/
+ hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_write)
@@ -621,33 +458,33 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
/* check args */
HDassert(dataset && dataset->oloc.file);
- /* Get the memory datatype */
- if(NULL == (mem_type = (const H5T_t *)H5I_object_verify(mem_type_id, H5I_DATATYPE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
-
/* All filters in the DCPL must have encoding enabled. */
if(!dataset->shared->checked_filters) {
- if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) <0)
+ if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters")
dataset->shared->checked_filters = TRUE;
} /* end if */
/* Check if we are allowed to write to this file */
- if(0==(H5F_get_intent(dataset->oloc.file) & H5F_ACC_RDWR))
+ if(0 == (H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR))
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file")
/* Fill the DXPL cache values for later use */
- if(H5D_get_dxpl_cache(dxpl_id,&dxpl_cache) < 0)
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+ /* Set up datatype info for operation */
+ if(H5D_typeinfo_init(dataset, dxpl_cache, dxpl_id, mem_type_id, TRUE, &type_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info")
+
/* Various MPI based checks */
#ifdef H5_HAVE_PARALLEL
if(IS_H5FD_MPI(dataset->oloc.file)) {
/* 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(H5T_detect_class(mem_type, H5T_VLEN)>0)
+ if(H5T_detect_class(type_info.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. */
@@ -656,42 +493,48 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
/* 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 (H5T_get_class(mem_type, TRUE)==H5T_REFERENCE &&
- H5T_get_ref_type(mem_type)==H5R_DATASET_REGION)
+ if(H5T_get_class(type_info.mem_type, TRUE) == H5T_REFERENCE &&
+ H5T_get_ref_type(type_info.mem_type) == H5R_DATASET_REGION)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet")
+
+ /* Can't write to chunked datasets with filters, in parallel */
+ if(dataset->shared->layout.type == H5D_CHUNKED &&
+ dataset->shared->dcpl_cache.pline.nused > 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot write to chunked storage with filters in parallel")
} /* end if */
else {
/* Collective access is not permissible without a MPI based VFD */
- if (dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE)
+ if(dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only")
} /* end else */
#endif /*H5_HAVE_PARALLEL*/
- if (!file_space)
+ /* Initialize dataspace information */
+ if(!file_space)
file_space = dataset->shared->space;
- if (!mem_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);
+ H5_ASSIGN_OVERFLOW(nelmts, snelmts, hssize_t, hsize_t);
/* Make certain that the number of elements in each selection is the same */
- if (nelmts!=(hsize_t)H5S_GET_SELECT_NPOINTS(file_space))
+ 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")
/* Make sure that both selections have their extents set */
- if( !(H5S_has_extent(file_space)) )
+ if(!(H5S_has_extent(file_space)))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set")
- if( !(H5S_has_extent(mem_space)) )
+ if(!(H5S_has_extent(mem_space)))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set")
/* Retrieve dataset properties */
/* <none needed currently> */
/* Allocate data space and initialize it if it hasn't been. */
- if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused==0 &&
- ((dataset->shared->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
- || (dataset->shared->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))) {
+ if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 &&
+ ((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
+ || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))) {
hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */
hbool_t full_overwrite; /* Whether we are over-writing all the elements */
@@ -703,42 +546,36 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
if(H5T_detect_class(dataset->shared->type, H5T_VLEN))
full_overwrite = FALSE;
else
- full_overwrite = (hsize_t)file_nelmts==nelmts ? TRUE : FALSE;
+ full_overwrite = (hsize_t)file_nelmts == nelmts ? TRUE : FALSE;
/* Allocate storage */
if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_WRITE, full_overwrite) < 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 datatype 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 datatype conversion also
- * turns off background preservation.
- */
- if (NULL==(tpath=H5T_path_find(mem_type, dataset->shared->type, NULL, NULL, dxpl_id, FALSE)))
- HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype")
-
/* Set up I/O operation */
- if(H5D_ioinfo_init(dataset,dxpl_cache,dxpl_id,mem_space,file_space,tpath,&io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation")
+ io_info.op_type = H5D_IO_OP_WRITE;
+ io_info.u.wbuf = buf;
+ if(H5D_ioinfo_init(dataset, dxpl_cache, dxpl_id, &type_info, &store, &io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up I/O operation")
#ifdef H5_HAVE_PARALLEL
io_info_init = TRUE;
#endif /*H5_HAVE_PARALLEL*/
- /* Determine correct I/O routine to invoke */
- if(dataset->shared->layout.type!=H5D_CHUNKED) {
- if(H5D_contig_write(&io_info, nelmts, mem_type, mem_space, file_space, tpath,
- mem_type_id, dataset->shared->type_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
- } /* end if */
- else {
- if(H5D_chunk_write(&io_info, nelmts, mem_type, mem_space, file_space, tpath,
- mem_type_id, dataset->shared->type_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
- } /* end else */
+ /* Call storage method's I/O initialization routine */
+ if(io_info.layout_ops.init && (*io_info.layout_ops.init)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info")
+ io_op_init = TRUE;
+
+#ifdef H5_HAVE_PARALLEL
+ /* Adjust I/O info for any parallel I/O */
+ if(H5D_ioinfo_adjust(&io_info, dataset, dxpl_cache, dxpl_id, file_space, mem_space, &type_info, &fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O")
+#endif /*H5_HAVE_PARALLEL*/
+
+ /* Invoke correct "high level" I/O routine */
+ if((*io_info.io_ops.multi_write)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
#ifdef OLD_WAY
/*
@@ -756,2667 +593,325 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
#endif /* OLD_WAY */
done:
+ /* Shut down the I/O op information */
+ if(io_op_init && io_info.layout_ops.term && (*io_info.layout_ops.term)(&fm) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info")
#ifdef H5_HAVE_PARALLEL
/* Shut down io_info struct */
- if (io_info_init)
- if(H5D_ioinfo_term(&io_info) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "can't shut down io_info")
+ if(io_info_init && H5D_ioinfo_term(&io_info) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "can't shut down io_info")
#endif /*H5_HAVE_PARALLEL*/
+ /* Shut down datatype info for operation */
+ if(H5D_typeinfo_term(&type_info) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_write() */
/*-------------------------------------------------------------------------
- * Function: H5D_contig_read
+ * Function: H5D_ioinfo_init
*
- * Purpose: Read from a contiguous dataset.
+ * Purpose: Routine for determining correct I/O operations for
+ * each I/O action.
*
* Return: Non-negative on success/Negative on failure
*
- * Programmer: Raymond Lu
- * Thursday, April 10, 2003
+ * Programmer: Quincey Koziol
+ * Thursday, September 30, 2004
*
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, void *buf/*out*/)
+H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
+ const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info)
{
- H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */
- const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */
- 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 max_type_size; /* Size of largest source/destination type */
- size_t target_size; /*desired buffer size */
- size_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; /*datatype conv buffer */
- uint8_t *bkg_buf = NULL; /*background buffer */
- hsize_t smine_start; /*strip mine start loc */
- size_t n, smine_nelmts; /*elements per strip */
- H5D_storage_t store; /*union of storage info for dataset */
-
-
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read)
-
- assert (buf);
-
- /* Initialize storage info for this dataset */
- if (dataset->shared->dcpl_cache.efl.nused > 0)
- HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
- else {
- store.contig.dset_addr = dataset->shared->layout.u.contig.addr;
- store.contig.dset_size = dataset->shared->layout.u.contig.size;
- } /* end if */
-
- /* Set dataset storage for I/O info */
- io_info->store=&store;
-
- /*
- * If there is no type conversion then read directly into the
- * application's buffer. This saves at least one mem-to-mem copy.
- */
- if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- /* Sanity check dataset, then read it */
- assert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
- || (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
- || dataset->shared->dcpl_cache.efl.nused > 0 || 0 == nelmts
- || dataset->shared->layout.type==H5D_COMPACT);
- H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t);
-
-#ifdef H5_HAVE_PARALLEL
- if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
- if(H5D_contig_collective_io(io_info,file_space,mem_space,buf,FALSE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous read failed in collective mode");
- }
- else
-#endif
- {
- if((io_info->ops.read)(io_info, (size_t)nelmts,
- H5T_get_size(dataset->shared->type), file_space, mem_space,
- (haddr_t)0, NULL, buf/*out*/) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous read failed ");
- }
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].read_timer), &timer);
- io_info->stats->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->shared->type);
- io_info->stats->stats[1].read_ncalls++;
-#endif
-
- /* direct xfer accomplished successfully */
- HGOTO_DONE(SUCCEED)
- } /* end if */
-
- /*
- * This is the general case (type conversion, usually).
- */
- if(nelmts==0)
- HGOTO_DONE(SUCCEED)
-
- /* Compute element sizes and other parameters */
- src_type_size = H5T_get_size(dataset->shared->type);
- dst_type_size = H5T_get_size(mem_type);
- max_type_size = MAX(src_type_size, dst_type_size);
- target_size = dxpl_cache->max_temp_buf;
- /* 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_TEMP_BUF_SIZE) {
- /* If the buffer is too small to hold even one element, make it bigger */
- if(target_size<max_type_size)
- target_size = max_type_size;
- /* If the buffer is too large to hold all the elements, make it smaller */
- else if(target_size>(nelmts*max_type_size))
- target_size=(size_t)(nelmts*max_type_size);
- } /* end if */
- request_nelmts = target_size / max_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 */
- need_bkg=dxpl_cache->bkgr_buf_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 = (uint8_t *)dxpl_cache->tconv_buf)) {
- /* Allocate temporary buffer */
- if(NULL == (tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
- } /* end if */
- if(need_bkg && NULL == (bkg_buf = (uint8_t *)dxpl_cache->bkgr_buf)) {
- /* Allocate background buffer */
- /* (Need calloc()-like call since memory needs to be initialized) */
- if(NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, (request_nelmts * dst_type_size))))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
- } /* end if */
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_ioinfo_init)
- /* 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 = (size_t)MIN(request_nelmts, (nelmts-smine_start));
+ /* check args */
+ HDassert(dset);
+ HDassert(dset->oloc.file);
+ HDassert(type_info);
+ HDassert(type_info->tpath);
+ HDassert(io_info);
- /*
- * Gather the data from disk into the datatype 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 */
- HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
- || (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
- || dataset->shared->dcpl_cache.efl.nused > 0 ||
- dataset->shared->layout.type == H5D_COMPACT);
- n = H5D_select_fgath(io_info, file_space, &file_iter, smine_nelmts, (haddr_t)0, NULL, tconv_buf/*out*/);
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer);
- io_info->stats->stats[1].gath_nbytes += n * src_type_size;
- io_info->stats->stats[1].gath_ncalls++;
-#endif
- if (n!=smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
-
- /* If the source and destination are compound types and subset of each other
- * and no conversion is needed, copy the data directly into user's buffer and
- * bypass the rest of steps. This optimization is for Chicago company */
- if(H5T_SUBSET_SRC==H5T_path_compound_subset(tpath)) {
- if(H5D_compound_opt_read(smine_nelmts, mem_space, &mem_iter, dxpl_cache,
- src_id, dst_id, H5T_SUBSET_SRC, tconv_buf, buf /*out*/)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
-
- continue;
- } else if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) {
- if(H5D_compound_opt_read(smine_nelmts, mem_space, &mem_iter, dxpl_cache,
- src_id, dst_id, H5T_SUBSET_DST, tconv_buf, buf /*out*/)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
-
- continue;
- }
-
- if (H5T_BKG_YES==need_bkg) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- n = H5D_select_mgath(buf, mem_space, &bkg_iter,
- smine_nelmts, dxpl_cache, bkg_buf/*out*/);
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].bkg_timer), &timer);
- io_info->stats->stats[1].bkg_nbytes += n * dst_type_size;
- io_info->stats->stats[1].bkg_ncalls++;
-#endif
- if (n!=smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
- } /* end if */
+ /* Set up "normal" I/O fields */
+ io_info->dset = dset;
+ io_info->dxpl_cache = dxpl_cache;
+ io_info->dxpl_id = dxpl_id;
+ io_info->store = store;
- /*
- * Perform datatype conversion.
- */
- if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
+ /* Set I/O operations to initial values */
+ io_info->layout_ops = *dset->shared->layout_ops;
- /* Do the data transform after the conversion (since we're using type mem_type) */
- if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
- if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, mem_type) < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
+ /* Set the "high-level" I/O operations for the dataset */
+ io_info->io_ops.multi_read = dset->shared->layout_ops->ser_read;
+ io_info->io_ops.multi_write = dset->shared->layout_ops->ser_write;
+ /* Set the I/O operations for reading/writing single blocks on disk */
+ if(type_info->is_xform_noop && type_info->is_conv_noop) {
/*
- * Scatter the data into memory.
+ * If there is no data transform or type conversion then read directly into
+ * the application's buffer. This saves at least one mem-to-mem copy.
*/
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- status = H5D_select_mscat(tconv_buf, mem_space,
- &mem_iter, smine_nelmts, dxpl_cache, buf/*out*/);
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].scat_timer), &timer);
- io_info->stats->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
- io_info->stats->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")
+ io_info->io_ops.single_read = H5D_select_read;
+ io_info->io_ops.single_write = H5D_select_write;
} /* 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 */
-
- if (tconv_buf && NULL==dxpl_cache->tconv_buf)
- (void)H5FL_BLK_FREE(type_conv,tconv_buf);
- if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
- (void)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
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, const void *buf)
-{
- H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */
- const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */
- 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 max_type_size; /* Size of largest source/destination type */
- size_t target_size; /*desired buffer size */
- size_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; /*datatype conv buffer */
- uint8_t *bkg_buf = NULL; /*background buffer */
- hsize_t smine_start; /*strip mine start loc */
- size_t n, smine_nelmts; /*elements per strip */
- H5D_storage_t store; /*union of storage info for dataset */
-
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write)
-
- assert (buf);
-
- /* Initialize storage info for this dataset */
- if(dataset->shared->dcpl_cache.efl.nused > 0)
- HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
else {
- store.contig.dset_addr = dataset->shared->layout.u.contig.addr;
- store.contig.dset_size = dataset->shared->layout.u.contig.size;
- } /* end if */
-
- /* Set dataset storage for I/O info */
- io_info->store = &store;
-
- /*
- * If there is no type conversion then write directly from the
- * application's buffer. This saves at least one mem-to-mem copy.
- */
- if(H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t);
-#ifdef H5_HAVE_PARALLEL
- if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
- if(H5D_contig_collective_io(io_info, file_space, mem_space, buf, TRUE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous write failed in collective mode")
- }
- else
-#endif
- {
- if((io_info->ops.write)(io_info, (size_t)nelmts,
- H5T_get_size(dataset->shared->type), file_space, mem_space,
- (haddr_t)0, NULL, buf/*out*/) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous write failed ")
- }
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[0].write_timer), &timer);
- io_info->stats->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type);
- io_info->stats->stats[0].write_ncalls++;
-#endif
-
- /* direct xfer accomplished successfully */
- HGOTO_DONE(SUCCEED)
- } /* end if */
-
- /*
- * This is the general case.
- */
- if(nelmts==0)
- HGOTO_DONE(SUCCEED)
-
- /* Compute element sizes and other parameters */
- src_type_size = H5T_get_size(mem_type);
- dst_type_size = H5T_get_size(dataset->shared->type);
- max_type_size = MAX(src_type_size, dst_type_size);
- target_size = dxpl_cache->max_temp_buf;
- /* 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_TEMP_BUF_SIZE) {
- /* If the buffer is too small to hold even one element, make it bigger */
- if(target_size<max_type_size)
- target_size = max_type_size;
- /* If the buffer is too large to hold all the elements, make it smaller */
- else if(target_size>(nelmts*max_type_size))
- target_size=(size_t)(nelmts*max_type_size);
- } /* end if */
- request_nelmts = target_size / max_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->shared->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 */
- need_bkg=dxpl_cache->bkgr_buf_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 = (uint8_t *)dxpl_cache->tconv_buf)) {
- /* Allocate temporary buffer */
- if(NULL == (tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
- } /* end if */
- if(need_bkg && NULL == (bkg_buf = (uint8_t *)dxpl_cache->bkgr_buf)) {
- /* Allocate background buffer */
- /* (Don't need calloc()-like call since file data is already initialized) */
- if(NULL == (bkg_buf = H5FL_BLK_MALLOC(type_conv, (request_nelmts * dst_type_size))))
- 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 = (size_t)MIN(request_nelmts, (nelmts-smine_start));
-
- /*
- * Gather data from application buffer into the datatype conversion
- * buffer. Also gather data from the file into the background buffer
- * if necessary.
- */
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- n = H5D_select_mgath(buf, mem_space, &mem_iter,
- smine_nelmts, dxpl_cache, tconv_buf/*out*/);
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[0].gath_timer), &timer);
- io_info->stats->stats[0].gath_nbytes += n * src_type_size;
- io_info->stats->stats[0].gath_ncalls++;
-#endif
- if (n!=smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed")
-
- /* If the source and destination are compound types and the destination is
- * is a subset of the source and no conversion is needed, copy the data
- * directly into user's buffer and bypass the rest of steps. If the source
- * is a subset of the destination, the optimization is done in conversion
- * function H5T_conv_struct_opt to protect the background data. This
- * optimization is for Chicago company */
- if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) {
- if(H5D_compound_opt_write(smine_nelmts, src_id, dst_id, tconv_buf)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
- } else {
- if (H5T_BKG_YES==need_bkg) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- n = H5D_select_fgath(io_info, file_space, &bkg_iter, smine_nelmts,
- (haddr_t)0, NULL, bkg_buf/*out*/);
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer);
- io_info->stats->stats[0].bkg_nbytes += n * dst_type_size;
- io_info->stats->stats[0].bkg_ncalls++;
-#endif
- if (n!=smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
- } /* end if */
-
- /*
- * Perform datatype conversion.
- */
- if(H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
-
- /* Do the data transform after the type conversion (since we're using dataset->shared->type). */
- if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
- if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
- }
-
/*
- * Scatter the data out to the file.
+ * This is the general case (type conversion, usually).
*/
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- status = H5D_select_fscat(io_info, file_space, &file_iter, smine_nelmts,
- (haddr_t)0, NULL, tconv_buf);
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[0].scat_timer), &timer);
- io_info->stats->stats[0].scat_nbytes += smine_nelmts * dst_type_size;
- io_info->stats->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 */
-
- if (tconv_buf && NULL==dxpl_cache->tconv_buf)
- (void)H5FL_BLK_FREE(type_conv,tconv_buf);
- if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
- (void)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
- *
- * Modification:
- * Raymond Lu
- * 20 July 2007
- * Moved H5D_istore_lock and H5D_istore_unlock to this level
- * from H5D_istore_readvv to avoid frequent lock and unlock
- * and to improve performance.
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, void *buf/*out*/)
-{
- H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */
- const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */
- H5D_chunk_map_t fm; /* File<->memory mapping */
- H5SL_node_t *chunk_node; /* Current node in chunk skip list */
- 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 max_type_size; /* Size of largest source/destination type */
- size_t target_size; /*desired buffer size */
- size_t request_nelmts; /*requested strip mine */
- hsize_t smine_start; /*strip mine start loc */
- size_t n, smine_nelmts; /*elements per strip */
- size_t accessed_bytes = 0; /*total accessed size in a chunk */
- H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
- hbool_t mem_iter_init = FALSE; /*memory selection iteration info has been initialized */
- H5S_sel_iter_t bkg_iter; /*background iteration info*/
- hbool_t bkg_iter_init = FALSE; /*background iteration info has been initialized */
- H5S_sel_iter_t file_iter; /*file selection iteration info*/
- hbool_t file_iter_init = FALSE; /*file selection iteration info has been initialized */
- H5T_bkg_t need_bkg; /*type of background buf*/
- uint8_t *tconv_buf = NULL; /*datatype conv buffer */
- uint8_t *bkg_buf = NULL; /*background buffer */
- H5D_storage_t store; /*union of EFL and chunk pointer in file space */
- void *chunk = NULL;
- haddr_t chunk_addr; /* Chunk address on disk */
- H5D_istore_ud1_t udata; /*B-tree pass-through */
- unsigned idx_hint=0; /* Cache index hint */
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read)
-
- assert (buf);
-
- /* Map elements between file and memory for each chunk*/
- if(H5D_create_chunk_map(&fm, io_info, nelmts, file_space, mem_space, mem_type) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
-
- /* Set dataset storage for I/O info */
- io_info->store=&store;
-
- /* Compute element sizes */
- src_type_size = H5T_get_size(dataset->shared->type);
- dst_type_size = H5T_get_size(mem_type);
- max_type_size = MAX(src_type_size, dst_type_size);
-
- /*
- * If there is no type conversion then read directly into the
- * application's buffer. This saves at least one mem-to-mem copy.
- */
- if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- /* Sanity check dataset, then read it */
- HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
- || (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
- || dataset->shared->dcpl_cache.efl.nused > 0 || 0 == nelmts
- || dataset->shared->layout.type == H5D_COMPACT);
-
-#ifdef H5_HAVE_PARALLEL
- /* Check whether the collective mode can be turned off globally*/
-#ifndef H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS
- if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
- if(H5D_mpio_chunk_adjust_iomode(io_info ,&fm))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't adjust collective I/O")
- }
-#endif /* H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS */
- /* Temporarily shut down collective IO for chunking */
- if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
- if(H5D_chunk_collective_io(io_info, &fm, buf, FALSE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunked read failed in collective mode")
- }
- else {/* sequential or independent read */
-#endif
- /* Get first node in chunk skip list */
- chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
-
- while(chunk_node) {
- H5D_chunk_info_t *chunk_info; /* chunk information */
-
- /* Get the actual chunk information from the skip list node */
- chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
-
- /* Pass in chunk's coordinates in a union. */
- store.chunk.offset = chunk_info->coords;
- store.chunk.index = chunk_info->index;
-
- /* Load the chunk into cache and lock it. */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
- if(H5D_istore_if_load(io_info, chunk_addr)) {
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint)))
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
- } else
- chunk = NULL;
-
- /* Perform the actual read operation */
- if((io_info->ops.read)(io_info, chunk_info->chunk_points,
- src_type_size, chunk_info->fspace,
- chunk_info->mspace, chunk_addr, chunk, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, " chunked read failed")
-
- /* Release the cache lock on the chunk. */
- if(chunk) {
- accessed_bytes = chunk_info->chunk_points * src_type_size;
- if(H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, accessed_bytes) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
- } /* end if */
-
- /* Advance to next chunk in list */
- chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
- } /* end while */
-#ifdef H5_HAVE_PARALLEL
- }
-#endif
-
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].read_timer), &timer);
- io_info->stats->stats[1].read_nbytes += nelmts * src_type_size;
- io_info->stats->stats[1].read_ncalls++;
-#endif
-
- /* direct xfer accomplished successfully */
- HGOTO_DONE(SUCCEED)
- } /* end if */
-
- /*
- * This is the general case (type conversion, usually).
- */
- if(nelmts==0)
- HGOTO_DONE(SUCCEED)
-
- /* Compute buffer sizes and other parameters */
- target_size = dxpl_cache->max_temp_buf;
- /* 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_TEMP_BUF_SIZE) {
- /* If the buffer is too small to hold even one element, make it bigger */
- if(target_size<max_type_size)
- target_size = max_type_size;
- /* If the buffer is too large to hold all the elements, make it smaller */
- else if(target_size>(nelmts*max_type_size))
- target_size=(size_t)(nelmts*max_type_size);
- } /* end if */
- request_nelmts = target_size / max_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 */
- need_bkg=dxpl_cache->bkgr_buf_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*/
+ io_info->io_ops.single_read = H5D_scatgath_read;
+ io_info->io_ops.single_write = H5D_scatgath_write;
} /* end else */
- if(NULL == (tconv_buf = (uint8_t *)dxpl_cache->tconv_buf)) {
- /* Allocate temporary buffer */
- if(NULL == (tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
- } /* end if */
- if(need_bkg && NULL == (bkg_buf = (uint8_t *)dxpl_cache->bkgr_buf)) {
- /* Allocate background buffer */
- /* (Need calloc()-like call since memory needs to be initialized) */
- if(NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, (request_nelmts * dst_type_size))))
- 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 skip list */
- chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
-
- /* 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 skip list nodes */
- chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
-
- /* 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 = TRUE; /*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 = TRUE; /*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 = TRUE; /*file selection iteration info has been initialized */
-
- /* Pass in chunk's coordinates in a union*/
- store.chunk.offset = chunk_info->coords;
- store.chunk.index = chunk_info->index;
-
- /* Load the chunk into cache and lock it. */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
-
- if(H5D_istore_if_load(io_info, chunk_addr)) {
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint)))
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
- } else
- chunk = NULL;
-
- for(smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) {
- /* Go figure out how many elements to read from the file */
- assert(H5S_SELECT_ITER_NELMTS(&file_iter)==(chunk_info->chunk_points-smine_start));
- smine_nelmts = (size_t)MIN(request_nelmts, (chunk_info->chunk_points-smine_start));
-
- /*
- * Gather the data from disk into the datatype 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 */
- HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
- || (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
- || dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT);
-
- if(chunk) {
- n = H5D_select_mgath(chunk, chunk_info->fspace, &file_iter,
- smine_nelmts, dxpl_cache, tconv_buf/*out*/);
- } else {
- n = H5D_select_fgath(io_info, chunk_info->fspace, &file_iter, smine_nelmts,
- chunk_addr, NULL, tconv_buf/*out*/);
- }
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer);
- io_info->stats->stats[1].gath_nbytes += n * src_type_size;
- io_info->stats->stats[1].gath_ncalls++;
-#endif
- if(n != smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
-
- /* If the source and destination are compound types and subset of each other
- * and no conversion is needed, copy the data directly into user's buffer and
- * bypass the rest of steps. This optimization is for Chicago company */
- if(H5T_SUBSET_SRC==H5T_path_compound_subset(tpath)) {
- if(H5D_compound_opt_read(smine_nelmts, chunk_info->mspace, &mem_iter, dxpl_cache,
- src_id, dst_id, H5T_SUBSET_SRC, tconv_buf, buf /*out*/)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
-
- continue;
- } else if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) {
- if(H5D_compound_opt_read(smine_nelmts, chunk_info->mspace, &mem_iter, dxpl_cache,
- src_id, dst_id, H5T_SUBSET_DST, tconv_buf, buf /*out*/)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
-
- continue;
- }
-
- if(H5T_BKG_YES == need_bkg) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- n = H5D_select_mgath(buf, chunk_info->mspace, &bkg_iter, smine_nelmts, dxpl_cache, bkg_buf/*out*/);
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].bkg_timer), &timer);
- io_info->stats->stats[1].bkg_nbytes += n * dst_type_size;
- io_info->stats->stats[1].bkg_ncalls++;
-#endif
- if(n != smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
- } /* end if */
-
- /*
- * Perform datatype conversion.
- */
- if(H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
-
- /* Do the data transform after the conversion (since we're using type mem_type) */
- if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
- if(H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, mem_type) < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
-
- /*
- * Scatter the data into memory.
- */
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- status = H5D_select_mscat(tconv_buf, chunk_info->mspace, &mem_iter, smine_nelmts, dxpl_cache, buf/*out*/);
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].scat_timer), &timer);
- io_info->stats->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
- io_info->stats->stats[1].scat_ncalls++;
-#endif
- if(status < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
- } /* end for */
-
- /* Release the cache lock on the chunk. */
- if(chunk) {
- accessed_bytes = chunk_info->chunk_points * src_type_size;
- if(H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, accessed_bytes) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
- } /* end if */
-
- /* 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 = FALSE;
- } /* 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 = FALSE;
- } /* 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 = FALSE;
- } /* end if */
-
- /* Get the next chunk node in the skip list */
- chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
- } /* end while */
-
-done:
- /* 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 */
-
- if(tconv_buf && NULL == dxpl_cache->tconv_buf)
- (void)H5FL_BLK_FREE(type_conv, tconv_buf);
- if(bkg_buf && NULL == dxpl_cache->bkgr_buf)
- (void)H5FL_BLK_FREE(type_conv, bkg_buf);
-
- /* 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
- *
- * Modification:
- * Raymond Lu
- * 20 July 2007
- * Moved H5D_istore_lock and H5D_istore_unlock to this level
- * from H5D_istore_writevv to avoid frequent lock and unlock
- * and to improve performance.
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts,
- const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, H5T_path_t *tpath,
- hid_t src_id, hid_t dst_id, const void *buf)
-{
- H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */
- const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */
- H5D_chunk_map_t fm; /* File<->memory mapping */
- H5SL_node_t *chunk_node; /* Current node in chunk skip list */
- 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 max_type_size; /* Size of largest source/destination type */
- size_t target_size; /*desired buffer size */
- size_t request_nelmts; /*requested strip mine */
- size_t accessed_bytes; /*total accessed size in a chunk */
- hsize_t smine_start; /*strip mine start loc */
- size_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; /*datatype conv buffer */
- uint8_t *bkg_buf = NULL; /*background buffer */
- H5D_storage_t store; /*union of EFL and chunk pointer in file space */
- void *chunk = NULL;
- haddr_t chunk_addr; /* Chunk address on disk */
- H5D_istore_ud1_t udata; /*B-tree pass-through */
- unsigned idx_hint=0; /* Cache index hint */
- hbool_t relax=TRUE; /* Whether whole chunk is selected */
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write)
-
- assert (buf);
-
- /* Map elements between file and memory for each chunk*/
- if(H5D_create_chunk_map(&fm, io_info, nelmts, file_space, mem_space, mem_type) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
-
- /* Set dataset storage for I/O info */
- io_info->store=&store;
-
-#ifdef H5_HAVE_PARALLEL
- /* Additional sanity checks when operating in parallel */
- if(io_info->using_mpi_vfd) {
- if (chunk_addr==HADDR_UNDEF)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk")
- if (dataset->shared->dcpl_cache.pline.nused>0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot write to chunked storage with filters in parallel")
- } /* end if */
-#endif /* H5_HAVE_PARALLEL */
-
- /* Compute element sizes and other parameters */
- src_type_size = H5T_get_size(mem_type);
- dst_type_size = H5T_get_size(dataset->shared->type);
- max_type_size = MAX(src_type_size, dst_type_size);
-
- /*
- * If there is no type conversion then write directly from the
- * application's buffer. This saves at least one mem-to-mem copy.
- */
- if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
#ifdef H5_HAVE_PARALLEL
- /* Check whether the collective mode can be turned off globally*/
-#ifndef H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS
- if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
- if(H5D_mpio_chunk_adjust_iomode(io_info,&fm))
- HGOTO_ERROR(H5E_DATASET,H5E_CANTGET,FAIL,"can't adjust collective I/O")
- }
-#endif /* H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS */
- /* Temporarily shut down collective IO for chunking */
- if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
- if(H5D_chunk_collective_io(io_info,&fm,buf,TRUE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunked write failed in collective mode");
- }
- else {/* sequential or independent write */
+ /* Determine if the file was opened with an MPI VFD */
+ io_info->using_mpi_vfd = IS_H5FD_MPI(dset->oloc.file);
#endif /* H5_HAVE_PARALLEL */
- /* Get first node in chunk skip list */
- chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
-
- while(chunk_node) {
- H5D_chunk_info_t *chunk_info; /* Chunk information */
-
- /* Get the actual chunk information from the skip list node */
- chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
-
- /* Pass in chunk's coordinates in a union. */
- store.chunk.offset = chunk_info->coords;
- store.chunk.index = chunk_info->index;
-
- /* Load the chunk into cache. But if the whole chunk is written,
- * simply allocate space instead of load the chunk. */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
-
- if(H5D_istore_if_load(io_info, chunk_addr)) {
- accessed_bytes = chunk_info->chunk_points * dst_type_size;
- if(accessed_bytes != dataset->shared->layout.u.chunk.size)
- relax = FALSE;
-
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint)))
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
- } else
- chunk = NULL;
-
- /* Perform the actual read operation */
- if((io_info->ops.write)(io_info, chunk_info->chunk_points,
- dst_type_size, chunk_info->fspace,
- chunk_info->mspace, chunk_addr, chunk, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, " chunked write failed")
-
- /* Release the cache lock on the chunk. */
- if(chunk) {
- if(H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, accessed_bytes) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
- } /* end if */
- relax = TRUE;
-
- /* Advance to next chunk in list */
- chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
- } /* end while */
-#ifdef H5_HAVE_PARALLEL
- }
-#endif
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[0].write_timer), &timer);
- io_info->stats->stats[0].write_nbytes += nelmts * src_type_size;
- io_info->stats->stats[0].write_ncalls++;
-#endif
-
- /* direct xfer accomplished successfully */
- HGOTO_DONE(SUCCEED)
- } /* end if */
-
- /*
- * This is the general case (type conversion, usually).
- */
- if(nelmts==0)
- HGOTO_DONE(SUCCEED)
-
- /* Compute buffer sizes and other parameters */
- target_size = dxpl_cache->max_temp_buf;
- /* 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_TEMP_BUF_SIZE) {
- /* If the buffer is too small to hold even one element, make it bigger */
- if(target_size<max_type_size)
- target_size = max_type_size;
- /* If the buffer is too large to hold all the elements, make it smaller */
- else if(target_size>(nelmts*max_type_size))
- target_size=(size_t)(nelmts*max_type_size);
- } /* end if */
- request_nelmts = target_size / max_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->shared->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 */
- need_bkg=dxpl_cache->bkgr_buf_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 = (uint8_t *)dxpl_cache->tconv_buf)) {
- /* Allocate temporary buffer */
- if(NULL == (tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
- } /* end if */
- if(need_bkg && NULL == (bkg_buf = (uint8_t *)dxpl_cache->bkgr_buf)) {
- /* Allocate background buffer */
- /* (Don't need calloc()-like call since file data is already initialized) */
- if(NULL == (bkg_buf = H5FL_BLK_MALLOC(type_conv, (request_nelmts * dst_type_size))))
- 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 skip list */
- chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
-
- /* 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 skip list node */
- chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
-
- /* 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.offset = chunk_info->coords;
- store.chunk.index = chunk_info->index;
-
- /* Load the chunk into cache. But if the whole chunk is written,
- * simply allocate space instead of load the chunk. */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
-
- if(H5D_istore_if_load(io_info, chunk_addr)) {
- accessed_bytes = chunk_info->chunk_points * dst_type_size;
- if(accessed_bytes != dataset->shared->layout.u.chunk.size)
- relax=FALSE;
- if(relax) {
- accessed_bytes = H5S_GET_SELECT_NPOINTS(chunk_info->mspace) * src_type_size;
- if(accessed_bytes != dataset->shared->layout.u.chunk.size)
- relax = FALSE;
- }
-
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint)))
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
- } else
- chunk = NULL;
-
- for(smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) {
- /* Go figure out how many elements to read from the file */
- assert(H5S_SELECT_ITER_NELMTS(&file_iter)==(chunk_info->chunk_points-smine_start));
- smine_nelmts = (size_t)MIN(request_nelmts, (chunk_info->chunk_points-smine_start));
-
- /*
- * Gather the data from disk into the datatype conversion
- * buffer. Also gather data from application to background buffer
- * if necessary.
- */
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- n = H5D_select_mgath(buf, chunk_info->mspace, &mem_iter,
- smine_nelmts, dxpl_cache, tconv_buf/*out*/);
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer);
- io_info->stats->stats[1].gath_nbytes += n * src_type_size;
- io_info->stats->stats[1].gath_ncalls++;
-#endif
- if (n!=smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
-
- /* If the source and destination are compound types and the destination is
- * is a subset of the source and no conversion is needed, copy the data
- * directly into user's buffer and bypass the rest of steps. If the source
- * is a subset of the destination, the optimization is done in conversion
- * function H5T_conv_struct_opt to protect the background data. This
- * optimization is for Chicago company */
- if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) {
- if(H5D_compound_opt_write(smine_nelmts, src_id, dst_id, tconv_buf)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
- } else {
- if (H5T_BKG_YES==need_bkg) {
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- if(chunk) {
- n = H5D_select_mgath(chunk, chunk_info->fspace, &bkg_iter,
- smine_nelmts, dxpl_cache, bkg_buf/*out*/);
- } else {
- n = H5D_select_fgath(io_info, chunk_info->fspace, &bkg_iter, smine_nelmts,
- chunk_addr, NULL, bkg_buf/*out*/);
- }
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer);
- io_info->stats->stats[0].bkg_nbytes += n * dst_type_size;
- io_info->stats->stats[0].bkg_ncalls++;
-#endif
- if (n!=smine_nelmts)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
- } /* end if */
-
- /*
- * Perform datatype conversion.
- */
- if(H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
-
- /* Do the data transform after the type conversion (since we're using dataset->shared->type) */
- if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
- if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
- }
-
- /*
- * Scatter the data out to the file.
- */
-#ifdef H5S_DEBUG
- H5_timer_begin(&timer);
-#endif
- status = H5D_select_fscat(io_info,
- chunk_info->fspace, &file_iter, smine_nelmts,
- chunk_addr, chunk, tconv_buf);
-
-#ifdef H5S_DEBUG
- H5_timer_end(&(io_info->stats->stats[0].scat_timer), &timer);
- io_info->stats->stats[0].scat_nbytes += n * dst_type_size;
- io_info->stats->stats[0].scat_ncalls++;
-#endif
- if (status<0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed")
- } /* end for */
-
- /* Release the cache lock on the chunk. */
- if(chunk) {
- accessed_bytes = chunk_info->chunk_points * dst_type_size;
- if(H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, accessed_bytes) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
- } /* end if */
- relax = TRUE;
-
- /* 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 skip list */
- chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
- } /* end while */
-
-done:
- /* 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 */
-
- if (tconv_buf && NULL==dxpl_cache->tconv_buf)
- (void)H5FL_BLK_FREE(type_conv,tconv_buf);
- if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
- (void)H5FL_BLK_FREE(type_conv,bkg_buf);
-
- /* 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() */
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D_ioinfo_init() */
/*-------------------------------------------------------------------------
- * Function: H5D_compound_opt_read
+ * Function: H5D_typeinfo_init
*
- * Purpose: A shortcut optimization for the Chicago company for
- * a special optimization case when the source and
- * destination members are a subset of each other, and
- * the order is the same, and no conversion is needed.
- * For example:
- * struct source { struct destination {
- * TYPE1 A; --> TYPE1 A;
- * TYPE2 B; --> TYPE2 B;
- * TYPE3 C; --> TYPE3 C;
- * }; TYPE4 D;
- * TYPE5 E;
- * };
- * or
- * struct destination { struct source {
- * TYPE1 A; <-- TYPE1 A;
- * TYPE2 B; <-- TYPE2 B;
- * TYPE3 C; <-- TYPE3 C;
- * }; TYPE4 D;
- * TYPE5 E;
- * };
- * The optimization is simply moving data to the appropriate
- * places in the buffer.
+ * Purpose: Routine for determining correct datatype information for
+ * each I/O action.
*
* Return: Non-negative on success/Negative on failure
*
- * Programmer: Raymond Lu
- * 11 June 2007
+ * Programmer: Quincey Koziol
+ * Tuesday, March 4, 2008
*
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_compound_opt_read(size_t nelmts, const H5S_t *space,
- H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache,
- hid_t src_id, hid_t dst_id, H5T_subset_t subset,
- void *data_buf, void *user_buf/*out*/)
+H5D_typeinfo_init(const H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache,
+ hid_t dxpl_id, hid_t mem_type_id, hbool_t do_write,
+ H5D_type_info_t *type_info)
{
- uint8_t *dbuf = (uint8_t *)data_buf; /*cast for pointer arithmetic */
- uint8_t *ubuf = (uint8_t *)user_buf; /*cast for pointer arithmetic */
- uint8_t *xdbuf;
- uint8_t *xubuf;
-
- hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
- hsize_t *off=NULL; /* Pointer to sequence offsets */
- size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
- size_t *len=NULL; /* Pointer to sequence lengths */
- size_t nseq; /* Number of sequences generated */
- size_t curr_off; /* offset of bytes left to process in sequence */
- size_t curr_seq; /* Current sequence being processed */
- size_t curr_len; /* Length of bytes left to process in sequence */
- size_t curr_nelmts; /* number of elements to process in sequence */
- size_t i;
-
- H5T_t *src, *dst;
- size_t src_stride, dst_stride, type_size = 0;
- size_t elmtno; /*element counter */
-
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_compound_opt_read)
-
- /* Check args */
- assert (data_buf);
- assert (user_buf);
- assert (space);
- assert (iter);
- assert (nelmts>0);
-
- /* Allocate the vector I/O arrays */
- if(dxpl_cache->vec_size != H5D_IO_VECTOR_SIZE) {
- if((len = H5FL_SEQ_MALLOC(size_t,dxpl_cache->vec_size))==NULL)
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array");
- if((off = H5FL_SEQ_MALLOC(hsize_t,dxpl_cache->vec_size))==NULL)
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array");
- } /* end if */
- else {
- len=_len;
- off=_off;
- } /* end else */
-
- if (NULL == (src = (H5T_t *)H5I_object(src_id)) || NULL == (dst = (H5T_t *)H5I_object(dst_id)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
-
- src_stride = H5T_get_size(src);
- dst_stride = H5T_get_size(dst);
-
- if(H5T_SUBSET_SRC == subset)
- type_size = src_stride;
- else if(H5T_SUBSET_DST == subset)
- type_size = dst_stride;
-
- xdbuf = dbuf;
-
- /* Loop until all elements are written */
- while(nelmts>0) {
- /* Get list of sequences for selection to write */
- if(H5S_SELECT_GET_SEQ_LIST(space,0,iter,dxpl_cache->vec_size,nelmts,&nseq,&elmtno,off,len)<0)
- HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed");
-
- /* Loop, while sequences left to process */
- for(curr_seq=0; curr_seq<nseq; curr_seq++) {
- /* Get the number of bytes and offset in sequence */
- curr_len=len[curr_seq];
- curr_off=off[curr_seq];
-
- /* Decide the number of elements and position in the buffer. */
- curr_nelmts = curr_len/dst_stride;
- xubuf = ubuf + curr_off;
+ const H5T_t *src_type; /* Source datatype */
+ const H5T_t *dst_type; /* Destination datatype */
+ herr_t ret_value = SUCCEED; /* Return value */
- /* Copy the data into the right place. */
- for(i=0; i<curr_nelmts; i++) {
- HDmemmove(xubuf, xdbuf, type_size);
+ FUNC_ENTER_NOAPI_NOINIT(H5D_typeinfo_init)
- /* Update pointers */
- xdbuf += src_stride;
- xubuf += dst_stride;
- }
+ /* check args */
+ HDassert(type_info);
+ HDassert(dset);
- } /* end for */
+ /* Initialize type info safely */
+ HDmemset(type_info, 0, sizeof(H5D_type_info_t));
- /* Decrement number of elements left to process */
- nelmts -= elmtno;
- } /* end while */
+ /* Get the memory & dataset datatypes */
+ if(NULL == (type_info->mem_type = (const H5T_t *)H5I_object_verify(mem_type_id, H5I_DATATYPE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
+ type_info->dset_type = dset->shared->type;
-done:
- if(dxpl_cache->vec_size != H5D_IO_VECTOR_SIZE) {
- if(len!=NULL)
- H5FL_SEQ_FREE(size_t,len);
- if(off!=NULL)
- H5FL_SEQ_FREE(hsize_t,off);
+ if(do_write) {
+ src_type = type_info->mem_type;
+ dst_type = dset->shared->type;
+ type_info->src_type_id = mem_type_id;
+ type_info->dst_type_id = dset->shared->type_id;
} /* end if */
+ else {
+ src_type = dset->shared->type;
+ dst_type = type_info->mem_type;
+ type_info->src_type_id = dset->shared->type_id;
+ type_info->dst_type_id = mem_type_id;
+ } /* end else */
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_compound_opt_read() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_compound_opt_write
- *
- * Purpose: A shortcut optimization for the Chicago company for
- * a special optimization case when the source and
- * destination members are a subset of each other, and
- * the order is the same, and no conversion is needed.
- * For example:
- * struct source { struct destination {
- * TYPE1 A; --> TYPE1 A;
- * TYPE2 B; --> TYPE2 B;
- * TYPE3 C; --> TYPE3 C;
- * }; TYPE4 D;
- * TYPE5 E;
- * };
- * or
- * struct destination { struct source {
- * TYPE1 A; <-- TYPE1 A;
- * TYPE2 B; <-- TYPE2 B;
- * TYPE3 C; <-- TYPE3 C;
- * }; TYPE4 D;
- * TYPE5 E;
- * };
- * The optimization is simply moving data to the appropriate
- * places in the buffer.
- *
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Raymond Lu
- * 11 June 2007
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_compound_opt_write(size_t nelmts, hid_t src_id, hid_t dst_id, void *data_buf)
-{
- uint8_t *dbuf = (uint8_t *)data_buf; /*cast for pointer arithmetic */
- uint8_t *xsbuf, *xdbuf;
- size_t i;
- H5T_t *src, *dst;
- size_t src_stride, dst_stride;
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_compound_opt_write)
-
- /* Check args */
- assert (data_buf);
- assert (nelmts>0);
-
- if (NULL == (src = (H5T_t *)H5I_object(src_id)) || NULL == (dst = (H5T_t *)H5I_object(dst_id)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
-
- src_stride = H5T_get_size(src);
- dst_stride = H5T_get_size(dst);
-
- xsbuf = dbuf;
- xdbuf = dbuf;
-
- /* Loop until all elements are written */
- for(i=0; i<nelmts; i++) {
- HDmemmove(xdbuf, xsbuf, dst_stride);
-
- /* Update pointers */
- xsbuf += src_stride;
- xdbuf += dst_stride;
- }
-
-done:
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_compound_opt_write() */
-
-
-/*-------------------------------------------------------------------------
- * 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
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info,
- hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
- const H5T_t *mem_type)
-{
- H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */
- H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
- hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */
- htri_t file_space_normalized = FALSE; /* File dataspace was normalized */
- hid_t f_tid = (-1); /* Temporary copy of file datatype for iteration */
- hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */
- unsigned f_ndims; /* The number of dimensions of the file's dataspace */
- int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */
- H5SL_node_t *curr_node; /* Current node in skip list */
- H5S_sel_type fsel_type; /* Selection type on disk */
- char bogus; /* "bogus" buffer to pass to selection iterator */
- unsigned u; /* Local index variable */
- hbool_t sel_hyper_flag;
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map)
-
- /* Get layout for dataset */
- fm->layout = &(dataset->shared->layout);
- fm->nelmts = nelmts;
-
- /* Check if the memory space is scalar & make equivalent memory space */
- if((sm_ndims = H5S_GET_EXTENT_NDIMS(mem_space)) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number")
- /* Set the number of dimensions for the memory dataspace */
- H5_ASSIGN_OVERFLOW(fm->m_ndims, sm_ndims, int, unsigned);
-
- /* Get dim number and dimensionality for each dataspace */
- fm->f_ndims = f_ndims = dataset->shared->layout.u.chunk.ndims - 1;
- if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
-
- /* Normalize hyperslab selections by adjusting them by the offset */
- /* (It might be worthwhile to normalize both the file and memory dataspaces
- * before any (contiguous, chunked, etc) file I/O operation, in order to
- * speed up hyperslab calculations by removing the extra checks and/or
- * additions involving the offset and the hyperslab selection -QAK)
+ /*
+ * 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 datatype 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 datatype conversion also
+ * turns off background preservation.
*/
- if((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
-
- /* Decide the number of chunks in each dimension*/
- for(u=0; u<f_ndims; u++) {
- /* Keep the size of the chunk dimensions as hsize_t for various routines */
- fm->chunk_dim[u]=fm->layout->u.chunk.dim[u];
-
- /* Round up to the next integer # of chunks, to accomodate partial chunks */
- fm->chunks[u] = ((fm->f_dims[u]+dataset->shared->layout.u.chunk.dim[u])-1) / dataset->shared->layout.u.chunk.dim[u];
- } /* 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")
-
-#ifdef H5_HAVE_PARALLEL
- /* Calculate total chunk in file map*/
- fm->select_chunk = NULL;
- fm->total_chunks = 1;
- for(u = 0; u < fm->f_ndims; u++)
- fm->total_chunks = fm->total_chunks * fm->chunks[u];
- if(io_info->using_mpi_vfd) {
- H5_CHECK_OVERFLOW(fm->total_chunks, hsize_t, size_t);
- if(NULL == (fm->select_chunk = (hbool_t *)H5MM_calloc((size_t)fm->total_chunks * sizeof(hbool_t))))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
- } /* end if */
-#endif /* H5_HAVE_PARALLEL */
-
-
- /* Initialize "last chunk" information */
- fm->last_index = (hsize_t)-1;
- fm->last_chunk_info = NULL;
-
- /* Point at the dataspaces */
- fm->file_space = file_space;
- fm->mem_space = mem_space;
-
- /* Special case for only one element in selection */
- /* (usually appending a record) */
- if(nelmts == 1
-#ifdef H5_HAVE_PARALLEL
- && !(io_info->using_mpi_vfd)
-#endif /* H5_HAVE_PARALLEL */
- ) {
- /* Initialize skip list for chunk selections */
- fm->sel_chunks = NULL;
- fm->use_single = TRUE;
-
- /* Initialize single chunk dataspace */
- if(NULL == dataset->shared->cache.chunk.single_space) {
- /* Make a copy of the dataspace for the dataset */
- if((dataset->shared->cache.chunk.single_space = H5S_copy(file_space, TRUE, FALSE)) == NULL)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
-
- /* Resize chunk's dataspace dimensions to size of chunk */
- if(H5S_set_extent_real(dataset->shared->cache.chunk.single_space, fm->chunk_dim) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "can't adjust chunk dimensions")
-
- /* Set the single chunk dataspace to 'all' selection */
- if(H5S_select_all(dataset->shared->cache.chunk.single_space, TRUE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to set all selection")
- } /* end if */
- fm->single_space = dataset->shared->cache.chunk.single_space;
- HDassert(fm->single_space);
-
- /* Allocate the single chunk information */
- if(NULL == dataset->shared->cache.chunk.single_chunk_info) {
- if(NULL == (dataset->shared->cache.chunk.single_chunk_info = H5FL_MALLOC(H5D_chunk_info_t)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
- } /* end if */
- fm->single_chunk_info = dataset->shared->cache.chunk.single_chunk_info;
- HDassert(fm->single_chunk_info);
-
- /* Reset chunk template information */
- fm->mchunk_tmpl = NULL;
+ if(NULL == (type_info->tpath = H5T_path_find(src_type, dst_type, NULL, NULL, dxpl_id, FALSE)))
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype")
- /* Set up chunk mapping for single element */
- if(H5D_create_chunk_map_single(fm, io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element")
+ /* Precompute some useful information */
+ type_info->src_type_size = H5T_get_size(src_type);
+ type_info->dst_type_size = H5T_get_size(dst_type);
+ type_info->max_type_size = MAX(type_info->src_type_size, type_info->dst_type_size);
+ type_info->is_conv_noop = H5T_path_noop(type_info->tpath);
+ type_info->is_xform_noop = H5Z_xform_noop(dxpl_cache->data_xform_prop);
+ if(type_info->is_xform_noop && type_info->is_conv_noop) {
+ type_info->cmpd_subset = H5T_SUBSET_FALSE;
+ type_info->need_bkg = H5T_BKG_NO;
} /* end if */
else {
- /* Initialize skip list for chunk selections */
- if(NULL == dataset->shared->cache.chunk.sel_chunks) {
- if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_DEFAULT_SKIPLIST_HEIGHT)))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections")
- } /* end if */
- fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks;
- HDassert(fm->sel_chunks);
-
- /* We are not using single element mode */
- fm->use_single = FALSE;
+ size_t target_size; /* Desired buffer size */
- /* Get type of selection on disk & in memory */
- if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE)
- HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
- if((fm->msel_type = H5S_GET_SELECT_TYPE(mem_space)) < H5S_SEL_NONE)
- HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
+ /* Check if the datatypes are compound subsets of one another */
+ type_info->cmpd_subset = H5T_path_compound_subset(type_info->tpath);
- /* If the selection is NONE or POINTS, set the flag to FALSE */
- if(fsel_type == H5S_SEL_POINTS || fsel_type == H5S_SEL_NONE)
- sel_hyper_flag = FALSE;
- else
- sel_hyper_flag = TRUE;
-
- /* Check if file selection is a not a hyperslab selection */
- if(sel_hyper_flag) {
- /* Build the file selection for each chunk */
- if(H5D_create_chunk_file_map_hyper(fm, io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
-
- /* Clean file chunks' hyperslab span "scratch" information */
- curr_node=H5SL_first(fm->sel_chunks);
- while(curr_node) {
- H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
-
- /* Get pointer to chunk's information */
- chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
- assert(chunk_info);
-
- /* Clean hyperslab span's "scratch" information */
- if(H5S_hyper_reset_scratch(chunk_info->fspace) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
-
- /* Get the next chunk node in the skip list */
- curr_node=H5SL_next(curr_node);
- } /* end while */
- } /* end if */
+ /* Check if we need a background buffer */
+ if(do_write && H5T_detect_class(dset->shared->type, H5T_VLEN))
+ type_info->need_bkg = H5T_BKG_YES;
else {
- /* Create temporary datatypes for selection iteration */
- if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL))) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
-
- /* Spaces might not be the same shape, iterate over the file selection directly */
- if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_file_cb, fm) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
-
- /* Reset "last chunk" info */
- fm->last_index=(hsize_t)-1;
- fm->last_chunk_info=NULL;
- } /* end else */
-
- /* Build the memory selection for each chunk */
- if(sel_hyper_flag && H5S_select_shape_same(file_space, mem_space) == TRUE) {
- /* Reset chunk template information */
- fm->mchunk_tmpl = NULL;
-
- /* If the selections are the same shape, use the file chunk information
- * to generate the memory chunk information quickly.
- */
- if(H5D_create_chunk_mem_map_hyper(fm) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
- } /* end if */
- else {
- size_t elmt_size; /* Memory datatype size */
-
- /* Make a copy of equivalent memory space */
- if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
-
- /* De-select the mem space copy */
- if(H5S_select_none(tmp_mspace) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space")
-
- /* Save chunk template information */
- fm->mchunk_tmpl=tmp_mspace;
+ H5T_bkg_t path_bkg; /* Type conversion's background info */
- /* Create temporary datatypes for selection iteration */
- if(f_tid<0) {
- if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL))) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
- } /* end if */
-
- /* Create selection iterator for memory selection */
- if((elmt_size=H5T_get_size(mem_type))==0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
- if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
- iter_init = TRUE; /* Selection iteration info has been initialized */
-
- /* Spaces aren't the same shape, iterate over the memory selection directly */
- if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
-
- /* Clean up hyperslab stuff, if necessary */
- if(fm->msel_type != H5S_SEL_POINTS) {
- /* Clean memory chunks' hyperslab span "scratch" information */
- curr_node=H5SL_first(fm->sel_chunks);
- while(curr_node) {
- H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
-
- /* Get pointer to chunk's information */
- chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
- assert(chunk_info);
-
- /* Clean hyperslab span's "scratch" information */
- if(H5S_hyper_reset_scratch(chunk_info->mspace) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
-
- /* Get the next chunk node in the skip list */
- curr_node=H5SL_next(curr_node);
- } /* end while */
+ if((path_bkg = H5T_path_bkg(type_info->tpath))) {
+ /* Retrieve the bkgr buffer property */
+ type_info->need_bkg = dxpl_cache->bkgr_buf_type;
+ type_info->need_bkg = MAX(path_bkg, type_info->need_bkg);
} /* end if */
+ else
+ type_info->need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
- } /* end else */
-
-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 */
-
- /* Reset the global dataspace info */
- fm->file_space = NULL;
- fm->mem_space = NULL;
-
- if(iter_init) {
- if(H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0)
- HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
- } /* end if */
- 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 */
- if(file_space_normalized) {
- if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
- } /* end if */
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_create_chunk_map() */
-
-
-/*--------------------------------------------------------------------------
- NAME
- H5D_free_chunk_info
- PURPOSE
- Internal routine to destroy a chunk info node
- 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. Called by H5SL_free
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-static herr_t
-H5D_free_chunk_info(void *item, void UNUSED *key, void UNUSED *opdata)
-{
- H5D_chunk_info_t *chunk_info = (H5D_chunk_info_t *)item;
-
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_free_chunk_info)
-
- HDassert(chunk_info);
-
- /* Close the chunk's file dataspace, if it's not shared */
- if(!chunk_info->fspace_shared)
- (void)H5S_close(chunk_info->fspace);
- else
- H5S_select_all(chunk_info->fspace, TRUE);
-
- /* Close the chunk's memory dataspace, if it's not shared */
- if(!chunk_info->mspace_shared)
- (void)H5S_close(chunk_info->mspace);
-
- /* Free the actual chunk info */
- H5FL_FREE(H5D_chunk_info_t, chunk_info);
-
- FUNC_LEAVE_NOAPI(0);
-} /* 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
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_destroy_chunk_map(const H5D_chunk_map_t *fm)
-{
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_destroy_chunk_map)
-
- /* Single element I/O vs. multiple element I/O cleanup */
- if(fm->use_single) {
- /* Sanity checks */
- HDassert(fm->sel_chunks == NULL);
- HDassert(fm->single_chunk_info);
- HDassert(fm->single_chunk_info->fspace_shared);
- HDassert(fm->single_chunk_info->mspace_shared);
-
- /* Reset the selection for the single element I/O */
- H5S_select_all(fm->single_space, TRUE);
- } /* end if */
- else {
- /* Release the nodes on the list of selected chunks */
- if(fm->sel_chunks)
- if(H5SL_free(fm->sel_chunks, H5D_free_chunk_info, NULL) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTNEXT, FAIL, "can't iterate over chunks")
- } /* end else */
-
- /* 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")
-#ifdef H5_HAVE_PARALLEL
- if(fm->select_chunk)
- H5MM_xfree(fm->select_chunk);
-#endif /* H5_HAVE_PARALLEL */
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_destroy_chunk_map() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_create_chunk_map_single
- *
- * Purpose: Create chunk selections when appending a single record
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Quincey Koziol
- * Tuesday, November 20, 2007
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t
-#ifndef H5_HAVE_PARALLEL
- UNUSED
-#endif /* H5_HAVE_PARALLEL */
- *io_info)
-{
- H5D_chunk_info_t *chunk_info; /* Chunk information to insert into skip list */
- hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
- hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
- unsigned u; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map_single)
+ /* Set up datatype conversion/background buffers */
- /* Sanity check */
- HDassert(fm->f_ndims > 0);
+ /* Get buffer size from DXPL */
+ target_size = dxpl_cache->max_temp_buf;
- /* Get coordinate for selection */
- if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
+ /* If the buffer is too small to hold even one element, try to make it bigger */
+ if(target_size < type_info->max_type_size) {
+ hbool_t default_buffer_info; /* Whether the buffer information are the defaults */
- /* Initialize the 'single chunk' file & memory chunk information */
- chunk_info = fm->single_chunk_info;
- chunk_info->chunk_points = 1;
+ /* Detect if we have all default settings for buffers */
+ default_buffer_info = (H5D_TEMP_BUF_SIZE == dxpl_cache->max_temp_buf)
+ && (NULL == dxpl_cache->tconv_buf) && (NULL == dxpl_cache->bkgr_buf);
- /* Set chunk location & hyperslab size */
- for(u = 0; u < fm->f_ndims; u++) {
- HDassert(sel_start[u] == sel_end[u]);
- chunk_info->coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u];
- } /* end for */
- chunk_info->coords[fm->f_ndims] = 0;
-
- /* Calculate the index of this chunk */
- if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_info->index) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
-
- /* Copy selection for file's dataspace into chunk dataspace */
- if(H5S_select_copy(fm->single_space, fm->file_space, FALSE) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file selection")
-
- /* Move selection back to have correct offset in chunk */
- if(H5S_SELECT_ADJUST_U(fm->single_space, chunk_info->coords) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
-
-#ifdef H5_HAVE_PARALLEL
- /* store chunk selection information */
- if(io_info->using_mpi_vfd)
- fm->select_chunk[chunk_info->index] = TRUE;
-#endif /* H5_HAVE_PARALLEL */
-
- /* Set the file dataspace for the chunk to the shared 'single' dataspace */
- chunk_info->fspace = fm->single_space;
-
- /* Indicate that the chunk's file dataspace is shared */
- chunk_info->fspace_shared = TRUE;
-
- /* Just point at the memory dataspace & selection */
- /* (Casting away const OK -QAK) */
- chunk_info->mspace = (H5S_t *)fm->mem_space;
-
- /* Indicate that the chunk's memory dataspace is shared */
- chunk_info->mspace_shared = TRUE;
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_create_chunk_map_single() */
-
-
-/*-------------------------------------------------------------------------
- * 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
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
-#ifndef H5_HAVE_PARALLEL
- UNUSED
-#endif /* H5_HAVE_PARALLEL */
- *io_info)
-{
- hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
- hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
- hsize_t sel_points; /* Number of elements in file selection */
- hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
- hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
- hsize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
- hsize_t chunk_index; /* Index of chunk */
- int curr_dim; /* Current dimension to increment */
- unsigned u; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_file_map_hyper)
-
- /* Sanity check */
- assert(fm->f_ndims>0);
-
- /* Get number of elements selected in file */
- sel_points = fm->nelmts;
-
- /* Get bounding box for selection (to reduce the number of chunks to iterate over) */
- if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0)
- 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++) {
- start_coords[u]=(sel_start[u]/fm->layout->u.chunk.dim[u])*fm->layout->u.chunk.dim[u];
- coords[u]=start_coords[u];
- end[u]=(coords[u]+fm->chunk_dim[u])-1;
- } /* end for */
-
-
- /* Calculate the index of this chunk */
- if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
-
- /* Iterate through each chunk in the dataset */
- while(sel_points) {
- /* Check for intersection of temporary chunk and file selection */
- /* (Casting away const OK - QAK) */
- if(H5S_hyper_intersect_block((H5S_t *)fm->file_space,coords,end)==TRUE) {
- H5S_t *tmp_fchunk; /* Temporary file dataspace */
- H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */
- hssize_t schunk_points; /* Number of elements in chunk selection */
-
- /* Create "temporary" chunk for selection operations (copy file space) */
- if((tmp_fchunk = H5S_copy(fm->file_space, TRUE, FALSE)) == NULL)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
-
- /* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */
- if(H5S_hyper_convert(tmp_fchunk) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
- } /* end if */
-
- /* "AND" temporary chunk and current chunk */
- if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection")
- } /* end if */
-
- /* Resize chunk's dataspace dimensions to size of chunk */
- if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions")
- } /* end if */
-
- /* Move selection back to have correct offset in chunk */
- if(H5S_SELECT_ADJUST_U(tmp_fchunk, coords) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
- } /* end if */
-
- /* 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;
-
-#ifdef H5_HAVE_PARALLEL
- /* store chunk selection information */
- if(io_info->using_mpi_vfd)
- fm->select_chunk[chunk_index] = TRUE;
-#endif /* H5_HAVE_PARALLEL */
-
- /* Set the file chunk dataspace */
- new_chunk_info->fspace = tmp_fchunk;
- new_chunk_info->fspace_shared = FALSE;
-
- /* Set the memory chunk dataspace */
- new_chunk_info->mspace=NULL;
- new_chunk_info->mspace_shared = FALSE;
-
- /* Copy the chunk's coordinates */
- for(u=0; u<fm->f_ndims; u++)
- new_chunk_info->coords[u]=coords[u];
- new_chunk_info->coords[fm->f_ndims]=0;
-
- /* Insert the new chunk into the skip list */
- if(H5SL_insert(fm->sel_chunks,new_chunk_info,&new_chunk_info->index) < 0) {
- H5D_free_chunk_info(new_chunk_info,NULL,NULL);
- HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list")
- } /* end if */
-
- /* Get number of elements selected in chunk */
- if((schunk_points=H5S_GET_SELECT_NPOINTS(tmp_fchunk)) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
- H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,size_t);
-
- /* Decrement # of points left in file selection */
- sel_points-=(hsize_t)schunk_points;
-
- /* Leave if we are done */
- if(sel_points==0)
- HGOTO_DONE(SUCCEED)
- assert(sel_points>0);
+ /* Check if we are using the default buffer info */
+ if(default_buffer_info)
+ /* OK to get bigger for library default settings */
+ target_size = type_info->max_type_size;
+ else
+ /* Don't get bigger than the application has requested */
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
} /* 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(fm->chunk_dim[curr_dim],hsize_t,hssize_t);
- coords[curr_dim]+=fm->chunk_dim[curr_dim];
- end[curr_dim]+=fm->chunk_dim[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 */
- end[curr_dim]=(coords[curr_dim]+(hssize_t)fm->chunk_dim[curr_dim])-1;
-
- /* Decrement current dimension */
- curr_dim--;
-
- /* Increment chunk location in current dimension */
- coords[curr_dim]+=fm->chunk_dim[curr_dim];
- end[curr_dim]=(coords[curr_dim]+fm->chunk_dim[curr_dim])-1;
- } while(coords[curr_dim]>sel_end[curr_dim]);
-
- /* Re-Calculate the index of this chunk */
- if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
- } /* end if */
- } /* end while */
-
-done:
- 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.
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
-{
- H5SL_node_t *curr_node; /* Current node in skip list */
- hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
- hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
- hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
- hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file 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_NOAPI_NOINIT(H5D_create_chunk_mem_map_hyper)
-
- /* Sanity check */
- assert(fm->f_ndims>0);
-
- /* Check for all I/O going to a single chunk */
- if(H5SL_count(fm->sel_chunks)==1) {
- H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
-
- /* Get the node */
- curr_node=H5SL_first(fm->sel_chunks);
-
- /* Get pointer to chunk's information */
- chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
- assert(chunk_info);
-
- /* Just point at the memory dataspace & selection */
- /* (Casting away const OK -QAK) */
- chunk_info->mspace=(H5S_t *)fm->mem_space;
-
- /* Indicate that the chunk's memory space is shared */
- chunk_info->mspace_shared = TRUE;
- } /* end if */
- else {
- /* Get bounding box for file selection */
- if(H5S_SELECT_BOUNDS(fm->file_space, file_sel_start, file_sel_end) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
-
- /* Get bounding box for memory selection */
- if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound 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_sel_start[u],hsize_t,hssize_t);
- H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t);
- adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u];
- } /* end for */
-
- /* Iterate over each chunk in the chunk list */
- curr_node=H5SL_first(fm->sel_chunks);
- while(curr_node) {
- H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
-
- /* Get pointer to chunk's information */
- chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
- assert(chunk_info);
-
- /* Copy the information */
-
- /* Copy the memory dataspace */
- if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == 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,FALSE) < 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(chunk_info->coords[u],hsize_t,hssize_t);
- chunk_adjust[u]=adjust[u]-(hssize_t)chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */
- } /* end for */
-
- /* Adjust the selection */
- if(H5S_hyper_adjust_s(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")
-
- /* Get the next chunk node in the skip list */
- curr_node=H5SL_next(curr_node);
- } /* end while */
- } /* end else */
+ /* Compute the number of elements that will fit into buffer */
+ type_info->request_nelmts = target_size / type_info->max_type_size;
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_create_chunk_mem_map_hyper() */
+ /* Sanity check elements in temporary buffer */
+ if(type_info->request_nelmts == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
-
-/*-------------------------------------------------------------------------
- * 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
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm)
-{
- H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */
- H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */
- hsize_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_NOAPI_NOINIT(H5D_chunk_file_cb)
-
- /* Calculate the index of this chunk */
- if(H5V_chunk_index(ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
-
- /* Find correct chunk in file & memory skip list */
- if(chunk_index==fm->last_index) {
- /* If the chunk index is the same as the last chunk index we used,
- * get the cached info to operate on.
- */
- chunk_info=fm->last_chunk_info;
- } /* end if */
- else {
- /* If the chunk index is not the same as the last chunk index we used,
- * find the chunk in the skip list.
+ /*
+ * 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.
*/
- /* Get the chunk node from the skip list */
- if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index))) {
- H5S_t *fspace; /* Memory chunk's dataspace */
-
- /* Allocate the file & memory chunk information */
- if (NULL==(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 */
- chunk_info->index=chunk_index;
-
- /* Create a dataspace for the chunk */
- if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) {
- H5FL_FREE(H5D_chunk_info_t,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,chunk_info);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select dataspace")
- } /* end if */
-
- /* Set the file chunk dataspace */
- chunk_info->fspace = fspace;
- chunk_info->fspace_shared = FALSE;
-
- /* Set the memory chunk dataspace */
- chunk_info->mspace=NULL;
- chunk_info->mspace_shared = FALSE;
-
- /* Set the number of selected elements in chunk to zero */
- chunk_info->chunk_points=0;
-
- /* Compute the chunk's coordinates */
- for(u=0; u<fm->f_ndims; u++) {
- H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t);
- chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u];
- } /* end for */
- chunk_info->coords[fm->f_ndims]=0;
-
- /* Insert the new chunk into the skip list */
- if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) {
- H5D_free_chunk_info(chunk_info,NULL,NULL);
- HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list")
- } /* end if */
+ if(NULL == (type_info->tconv_buf = (uint8_t *)dxpl_cache->tconv_buf)) {
+ /* Allocate temporary buffer */
+ if(NULL == (type_info->tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
+ type_info->tconv_buf_allocated = TRUE;
+ } /* end if */
+ if(type_info->need_bkg && NULL == (type_info->bkg_buf = (uint8_t *)dxpl_cache->bkgr_buf)) {
+ size_t bkg_size; /* Desired background buffer size */
+
+ /* Compute the background buffer size */
+ /* (don't try to use buffers smaller than the default size) */
+ bkg_size = type_info->request_nelmts * type_info->dst_type_size;
+ if(bkg_size < dxpl_cache->max_temp_buf)
+ bkg_size = dxpl_cache->max_temp_buf;
+
+ /* Allocate background buffer */
+ /* (Need calloc()-like call since memory needs to be initialized) */
+ if(NULL == (type_info->bkg_buf = H5FL_BLK_CALLOC(type_conv, bkg_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
+ type_info->bkg_buf_allocated = TRUE;
} /* end if */
-
- /* Update the "last chunk seen" information */
- fm->last_index=chunk_index;
- fm->last_chunk_info=chunk_info;
- } /* 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->u.chunk.dim[u];
-
- /* Add point to file selection for chunk */
- if(H5S_select_elements(chunk_info->fspace, H5S_SELECT_APPEND, (size_t)1, coords_in_chunk) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
-
- /* Increment the number of elemented selected in chunk */
- chunk_info->chunk_points++;
-
-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
- *
- *-------------------------------------------------------------------------
- */
-/* ARGSUSED */
-static herr_t
-H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm)
-{
- H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */
- H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */
- hsize_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_NOAPI_NOINIT(H5D_chunk_mem_cb)
-
- /* Calculate the index of this chunk */
- if(H5V_chunk_index(ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
-
- /* Find correct chunk in file & memory skip list */
- 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.
- */
- chunk_info=fm->last_chunk_info;
- } /* end if */
- else {
- /* If the chunk index is not the same as the last chunk index we used,
- * find the chunk in the skip list.
- */
- /* Get the chunk node from the skip list */
- if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index)))
- HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list")
-
- /* Check if the chunk already has a memory space */
- if(chunk_info->mspace==NULL) {
- /* Copy the template memory chunk dataspace */
- if((chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE)) == NULL)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
- } /* end else */
-
- /* Update the "last chunk seen" information */
- fm->last_index=chunk_index;
- fm->last_chunk_info=chunk_info;
- } /* 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(chunk_info->mspace, H5S_SELECT_APPEND, (size_t)1, coords_in_mem) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
- } /* end if */
- else {
- if(H5S_hyper_add_span_element(chunk_info->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, (size_t)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() */
+} /* end H5D_typeinfo_init() */
+#ifdef H5_HAVE_PARALLEL
/*-------------------------------------------------------------------------
- * Function: H5D_ioinfo_init
+ * Function: H5D_ioinfo_adjust
*
- * Purpose: Routine for determining correct I/O operations for
- * each I/O action.
+ * Purpose: Adjust operation's I/O info for any parallel I/O
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
- * Thursday, September 30, 2004
+ * Thursday, March 27, 2008
*
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
- const H5S_t
-#if !(defined H5_HAVE_PARALLEL || defined H5S_DEBUG)
- UNUSED
-#endif /* H5_HAVE_PARALLEL */
- *mem_space, const H5S_t
-#if !(defined H5_HAVE_PARALLEL || defined H5S_DEBUG)
- UNUSED
-#endif /* H5_HAVE_PARALLEL */
- *file_space, H5T_path_t
-#ifndef H5_HAVE_PARALLEL
- UNUSED
-#endif /* H5_HAVE_PARALLEL */
- *tpath,
- H5D_io_info_t *io_info)
+H5D_ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset,
+ const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm)
{
herr_t ret_value = SUCCEED; /* Return value */
-#if defined H5_HAVE_PARALLEL || defined H5S_DEBUG
- FUNC_ENTER_NOAPI_NOINIT(H5D_ioinfo_init)
-#else /* defined H5_HAVE_PARALLEL || defined H5S_DEBUG */
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_ioinfo_init)
-#endif /* defined H5_HAVE_PARALLEL || defined H5S_DEBUG */
+ FUNC_ENTER_NOAPI_NOINIT(H5D_ioinfo_adjust)
/* check args */
HDassert(dset);
HDassert(dset->oloc.file);
HDassert(mem_space);
HDassert(file_space);
- HDassert(tpath);
+ HDassert(type_info);
+ HDassert(type_info->tpath);
HDassert(io_info);
- /* Set up "normal" I/O fields */
- io_info->dset=dset;
- io_info->dxpl_cache=dxpl_cache;
- io_info->dxpl_id=dxpl_id;
- io_info->store=NULL; /* Set later in I/O routine? */
-
- /* Set I/O operations to initial values */
- io_info->ops=dset->shared->io_ops;
-
-#ifdef H5_HAVE_PARALLEL
- /* Start in the "not modified" xfer_mode state */
- io_info->xfer_mode_changed = FALSE;
- io_info->using_mpi_vfd = IS_H5FD_MPI(dset->oloc.file);
-
+ /* Make any parallel I/O adjustments */
if(io_info->using_mpi_vfd) {
htri_t opt; /* Flag whether a selection is optimizable */
+ /* Record the original state of parallel I/O transfer options */
+ io_info->orig.xfer_mode = io_info->dxpl_cache->xfer_mode;
+ io_info->orig.coll_opt_mode = io_info->dxpl_cache->coll_opt_mode;
+ io_info->orig.io_ops.single_read = io_info->io_ops.single_read;
+ io_info->orig.io_ops.single_write = io_info->io_ops.single_write;
+
/* Get MPI communicator */
- if((io_info->comm = H5F_mpi_get_comm(dset->oloc.file)) == MPI_COMM_NULL)
+ if(MPI_COMM_NULL == (io_info->comm = H5F_mpi_get_comm(dset->oloc.file)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve MPI communicator")
- /*
- * Check if we can set direct MPI-IO read/write functions
- */
- opt=H5D_mpio_opt_possible(io_info, mem_space, file_space, tpath);
- if(opt==FAIL)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for direct IO dataspace ");
+ /* Check if we can set direct MPI-IO read/write functions */
+ if((opt = H5D_mpio_opt_possible(io_info, file_space, mem_space, type_info, fm)) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for direct IO dataspace ")
/* Check if we can use the optimized parallel I/O routines */
- if(opt==TRUE) {
- /* Set the pointers to the MPI-specific routines */
- io_info->ops.read = H5D_mpio_select_read;
- io_info->ops.write = H5D_mpio_select_write;
+ if(opt == TRUE) {
+ /* Override the I/O op pointers to the MPI-specific routines */
+ io_info->io_ops.multi_read = dset->shared->layout_ops->par_read;
+ io_info->io_ops.multi_write = dset->shared->layout_ops->par_write;
+ io_info->io_ops.single_read = H5D_mpio_select_read;
+ io_info->io_ops.single_write = H5D_mpio_select_write;
} /* end if */
else {
- /* Set the pointers to the non-MPI-specific routines */
- io_info->ops.read = H5D_select_read;
- io_info->ops.write = H5D_select_write;
-
/* If we won't be doing collective I/O, but the user asked for
* collective I/O, change the request to use independent I/O, but
* mark it so that we remember to revert the change.
*/
- if(io_info->dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE) {
+ if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
H5P_genplist_t *dx_plist; /* Data transer property list */
/* Get the dataset transfer property list */
- if (NULL == (dx_plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
+ if(NULL == (dx_plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Change the xfer_mode to independent for handling the I/O */
io_info->dxpl_cache->xfer_mode = H5FD_MPIO_INDEPENDENT;
- if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &io_info->dxpl_cache->xfer_mode) < 0)
+ if(H5P_set(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &io_info->dxpl_cache->xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
-
- /* Indicate that the transfer mode should be restored before returning
- * to user.
- */
- io_info->xfer_mode_changed = TRUE;
} /* end if */
} /* end else */
} /* end if */
- else {
- /* Set the pointers to the non-MPI-specific routines */
- io_info->ops.read = H5D_select_read;
- io_info->ops.write = H5D_select_write;
- } /* end else */
-#else /* H5_HAVE_PARALLEL */
- io_info->ops.read = H5D_select_read;
- io_info->ops.write = H5D_select_write;
-#endif /* H5_HAVE_PARALLEL */
-
-#ifdef H5S_DEBUG
- /* Get the information for the I/O statistics */
- if((io_info->stats=H5S_find(mem_space,file_space))==NULL)
- HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "can't set up selection statistics");
-#endif /* H5S_DEBUG */
-#if defined H5_HAVE_PARALLEL || defined H5S_DEBUG
done:
-#endif /* H5_HAVE_PARALLEL || H5S_DEBUG */
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_ioinfo_init() */
+} /* end H5D_ioinfo_adjust() */
-#ifdef H5_HAVE_PARALLEL
/*-------------------------------------------------------------------------
* Function: H5D_ioinfo_term
@@ -3438,23 +933,69 @@ H5D_ioinfo_term(H5D_io_info_t *io_info)
FUNC_ENTER_NOAPI_NOINIT(H5D_ioinfo_term)
- /* Check if we need to revert the change to the xfer mode */
- if (io_info->xfer_mode_changed) {
- H5P_genplist_t *dx_plist; /* Data transer property list */
+ /* Check if we used the MPI VFD for the I/O */
+ if(io_info->using_mpi_vfd) {
+ /* Check if we need to revert the change to the xfer mode */
+ if(io_info->orig.xfer_mode != io_info->dxpl_cache->xfer_mode) {
+ H5P_genplist_t *dx_plist; /* Data transer property list */
- /* Get the dataset transfer property list */
- if (NULL == (dx_plist = (H5P_genplist_t *)H5I_object(io_info->dxpl_id)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
+ /* Get the dataset transfer property list */
+ if(NULL == (dx_plist = (H5P_genplist_t *)H5I_object(io_info->dxpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
+
+ /* Restore the original parallel I/O mode */
+ if(H5P_set(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &io_info->orig.xfer_mode) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
+ } /* end if */
- /* Restore the original parallel I/O mode */
- io_info->dxpl_cache->xfer_mode = H5FD_MPIO_COLLECTIVE;
- if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &io_info->dxpl_cache->xfer_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
+ /* Check if we need to revert the change to the collective opt mode */
+ if(io_info->orig.coll_opt_mode != io_info->dxpl_cache->coll_opt_mode) {
+ H5P_genplist_t *dx_plist; /* Data transer property list */
+
+ /* Get the dataset transfer property list */
+ if(NULL == (dx_plist = (H5P_genplist_t *)H5I_object(io_info->dxpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
+
+ /* Restore the original parallel I/O mode */
+ if(H5P_set(dx_plist, H5D_XFER_MPIO_COLLECTIVE_OPT_NAME, &io_info->orig.coll_opt_mode) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set collective option mode")
+ } /* end if */
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_ioinfo_term() */
-#endif
+#endif /* H5_HAVE_PARALLEL */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_typeinfo_term
+ *
+ * Purpose: Common logic for terminating a type info object
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, March 6, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_typeinfo_term(const H5D_type_info_t *type_info)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_typeinfo_term)
+
+ /* Check for releasing datatype conversion & background buffers */
+ if(type_info->tconv_buf_allocated) {
+ HDassert(type_info->tconv_buf);
+ (void)H5FL_BLK_FREE(type_conv, type_info->tconv_buf);
+ } /* end if */
+ if(type_info->bkg_buf_allocated) {
+ HDassert(type_info->bkg_buf);
+ (void)H5FL_BLK_FREE(type_conv, type_info->bkg_buf);
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D_typeinfo_term() */