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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Raymond Lu <slu@ncsa.uiuc.edu>
* August 5, 2002
*
* Purpose: Compact dataset I/O functions. These routines are similar
* H5D_contig_* and H5D_istore_*.
*/
/****************/
/* Module Setup */
/****************/
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* Files */
#include "H5FDprivate.h" /* File drivers */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5Oprivate.h" /* Object headers */
#include "H5Vprivate.h" /* Vector and array functions */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Local Prototypes */
/********************/
/*********************/
/* Package Variables */
/*********************/
/*******************/
/* Local Variables */
/*******************/
/* Declare extern the free list to manage blocks of type conversion data */
H5FL_BLK_EXTERN(type_conv);
/*-------------------------------------------------------------------------
* Function: H5D_compact_readvv
*
* Purpose: Reads some data vectors from a dataset into a buffer.
* The data is in compact dataset. The address is relative
* to the beginning address of the dataset. The offsets and
* sequence lengths are in bytes.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* May 7, 2003
*
* Notes:
* Offsets in the sequences must be monotonically increasing
*
*-------------------------------------------------------------------------
*/
ssize_t
H5D_compact_readvv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
void *buf)
{
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_compact_readvv, FAIL)
assert(io_info->dset);
/* Use the vectorized memory copy routine to do actual work */
if((ret_value=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr,io_info->dset->shared->layout.u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr))<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_compact_readvv() */
/*-------------------------------------------------------------------------
* Function: H5D_compact_writevv
*
* Purpose: Writes some data vectors from a dataset into a buffer.
* The data is in compact dataset. The address is relative
* to the beginning address for the file. The offsets and
* sequence lengths are in bytes. This function only copies
* data into the buffer in the LAYOUT struct and mark it
* as DIRTY. Later in H5D_close, the data is copied into
* header message in memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* May 2, 2003
*
* Notes:
* Offsets in the sequences must be monotonically increasing
*
*-------------------------------------------------------------------------
*/
ssize_t
H5D_compact_writevv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
const void *buf)
{
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_compact_writevv, FAIL)
assert(io_info->dset);
/* Use the vectorized memory copy routine to do actual work */
if((ret_value=H5V_memcpyvv(io_info->dset->shared->layout.u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr))<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
/* Mark the compact dataset's buffer as dirty */
io_info->dset->shared->layout.u.compact.dirty = TRUE;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_compact_writevv() */
/*-------------------------------------------------------------------------
* Function: H5D_compact_copy
*
* Purpose: Copy compact storage raw data from SRC file to DST file.
*
* Return: Non-negative on success, negative on failure.
*
* Programmer: Peter Cao
* December 11, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst,
H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, hid_t dxpl_id)
{
hid_t tid_src = -1; /* Datatype ID for source datatype */
hid_t tid_dst = -1; /* Datatype ID for destination datatype */
hid_t tid_mem = -1; /* Datatype ID for memory datatype */
void *buf = NULL; /* Buffer for copying data */
void *bkg = NULL; /* Temporary buffer for copying data */
void *reclaim_buf = NULL; /* Buffer for reclaiming data */
hid_t buf_sid = -1; /* ID for buffer dataspace */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_compact_copy, FAIL)
/* Check args */
HDassert(layout_src && H5D_COMPACT == layout_src->type);
HDassert(f_src);
HDassert(f_dst);
HDassert(layout_dst && H5D_COMPACT == layout_dst->type);
/* If there's a source datatype, set up type conversion information */
if(!dt_src)
/* Type conversion not necessary */
HDmemcpy(layout_dst->u.compact.buf, layout_src->u.compact.buf, layout_src->u.compact.size);
else if(H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) {
/* Create datatype ID for src datatype, so it gets freed */
if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
if(f_src != f_dst) {
/* Check for expanding references */
if(cpy_info->expand_ref) {
size_t ref_count;
/* Determine # of reference elements to copy */
ref_count = layout_src->u.compact.size / H5T_get_size(dt_src);
/* Copy objects referenced in source buffer to destination file and set destination elements */
if(H5O_copy_expand_ref(f_src, layout_src->u.compact.buf, dxpl_id, f_dst,
layout_dst->u.compact.buf, ref_count, H5T_get_ref_type(dt_src), cpy_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute")
} /* end if */
else
/* Reset value to zero */
HDmemset(layout_dst->u.compact.buf, 0, layout_src->u.compact.size);
} /* end if */
else
/* Type conversion not necessary */
HDmemcpy(layout_dst->u.compact.buf, layout_src->u.compact.buf, layout_src->u.compact.size);
} /* end if */
else if(H5T_detect_class(dt_src, H5T_VLEN) > 0) {
H5T_path_t *tpath_src_mem, *tpath_mem_dst; /* Datatype conversion paths */
H5T_t *dt_dst; /* Destination datatype */
H5T_t *dt_mem; /* Memory datatype */
H5S_t *buf_space; /* Dataspace describing buffer */
size_t buf_size; /* Size of copy buffer */
size_t nelmts; /* Number of elements in buffer */
size_t src_dt_size; /* Source datatype size */
size_t tmp_dt_size; /* Temporary datatype size */
size_t max_dt_size; /* Max atatype size */
hsize_t buf_dim; /* Dimension for buffer */
/* Create datatype ID for src datatype */
if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
/* create a memory copy of the variable-length datatype */
if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
/* create variable-length datatype at the destinaton file */
if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
/* Set up the conversion functions */
if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
/* Determine largest datatype size */
if(0 == (src_dt_size = H5T_get_size(dt_src)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
if(0 == (tmp_dt_size = H5T_get_size(dt_mem)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
max_dt_size = MAX(src_dt_size, tmp_dt_size);
if(0 == (tmp_dt_size = H5T_get_size(dt_dst)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
max_dt_size = MAX(max_dt_size, tmp_dt_size);
/* Set number of whole elements that fit in buffer */
if(0 == (nelmts = layout_src->u.compact.size / src_dt_size))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "element size too large")
/* Set up number of bytes to copy, and initial buffer size */
buf_size = nelmts * max_dt_size;
/* Create dataspace for number of elements in buffer */
buf_dim = nelmts;
/* Create the space and set the initial extent */
if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
/* Atomize */
if((buf_sid = H5I_register(H5I_DATASPACE, buf_space)) < 0) {
H5S_close(buf_space);
HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
} /* end if */
/* Allocate memory for recclaim buf */
if(NULL == (reclaim_buf = H5FL_BLK_MALLOC(type_conv, buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Allocate memory for copying the chunk */
if(NULL == (buf = H5FL_BLK_MALLOC(type_conv, buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
HDmemcpy(buf, layout_src->u.compact.buf, layout_src->u.compact.size);
/* Convert from source file to memory */
if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
HDmemcpy(reclaim_buf, buf, buf_size);
/* allocate temporary bkg buff for data conversion */
if(NULL == (bkg = H5FL_BLK_CALLOC(type_conv, buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Convert from memory to destination file */
if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
HDmemcpy(layout_dst->u.compact.buf, buf, layout_dst->u.compact.size);
if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data")
} /* end if */
else
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements")
done:
if(buf_sid > 0)
if(H5I_dec_ref(buf_sid) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID")
if(tid_src > 0)
if(H5I_dec_ref(tid_src) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(tid_dst > 0)
if(H5I_dec_ref(tid_dst) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(tid_mem > 0)
if(H5I_dec_ref(tid_mem) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(buf)
H5FL_BLK_FREE(type_conv, buf);
if(reclaim_buf)
H5FL_BLK_FREE(type_conv, reclaim_buf);
if(bkg)
H5FL_BLK_FREE(type_conv, bkg);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_compact_copy() */
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