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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Quincey Koziol
* Thursday, September 30, 2004
*
* Purpose: Dataspace I/O functions.
*/
/****************/
/* Module Setup */
/****************/
#include "H5Dmodule.h" /* This source code file is part of the H5D module */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Local Prototypes */
/********************/
static herr_t H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5S_t *file_space,
H5S_t *mem_space);
/*********************/
/* Package Variables */
/*********************/
/*******************/
/* Local Variables */
/*******************/
/* Declare a free list to manage sequences of size_t */
H5FL_SEQ_DEFINE(size_t);
/* Declare a free list to manage sequences of hsize_t */
H5FL_SEQ_DEFINE(hsize_t);
/* Declare extern free list to manage the H5S_sel_iter_t struct */
H5FL_EXTERN(H5S_sel_iter_t);
/*-------------------------------------------------------------------------
* Function: H5D__select_io
*
* Purpose: Perform I/O directly from application memory and a file
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 27, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5S_t *file_space,
H5S_t *mem_space)
{
H5S_sel_iter_t *mem_iter = NULL; /* Memory selection iteration info */
hbool_t mem_iter_init = FALSE; /* Memory selection iteration info has been initialized */
H5S_sel_iter_t *file_iter = NULL; /* File selection iteration info */
hbool_t file_iter_init = FALSE; /* File selection iteration info has been initialized */
hsize_t * mem_off = NULL; /* Pointer to sequence offsets in memory */
hsize_t * file_off = NULL; /* Pointer to sequence offsets in the file */
size_t * mem_len = NULL; /* Pointer to sequence lengths in memory */
size_t * file_len = NULL; /* Pointer to sequence lengths in the file */
size_t curr_mem_seq; /* Current memory sequence to operate on */
size_t curr_file_seq; /* Current file sequence to operate on */
size_t mem_nseq; /* Number of sequences generated in the file */
size_t file_nseq; /* Number of sequences generated in memory */
size_t dxpl_vec_size; /* Vector length from API context's DXPL */
size_t vec_size; /* Vector length */
ssize_t tmp_file_len; /* Temporary number of bytes in file sequence */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(io_info);
HDassert(io_info->dset);
HDassert(io_info->store);
HDassert(io_info->u.rbuf);
if (elmt_size == 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "invalid elmt_size of 0")
/* Check for only one element in selection */
if (nelmts == 1) {
hsize_t single_mem_off; /* Offset in memory */
hsize_t single_file_off; /* Offset in the file */
size_t single_mem_len; /* Length in memory */
size_t single_file_len; /* Length in the file */
/* Get offset of first element in selections */
if (H5S_SELECT_OFFSET(file_space, &single_file_off) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve file selection offset")
if (H5S_SELECT_OFFSET(mem_space, &single_mem_off) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve memory selection offset")
/* Set up necessary information for I/O operation */
file_nseq = mem_nseq = 1;
curr_mem_seq = curr_file_seq = 0;
single_file_off *= elmt_size;
single_mem_off *= elmt_size;
single_file_len = single_mem_len = elmt_size;
/* Perform I/O on memory and file sequences */
if (io_info->op_type == H5D_IO_OP_READ) {
if ((tmp_file_len = (*io_info->layout_ops.readvv)(
io_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, mem_nseq,
&curr_mem_seq, &single_mem_len, &single_mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error")
} /* end if */
else {
HDassert(io_info->op_type == H5D_IO_OP_WRITE);
if ((tmp_file_len = (*io_info->layout_ops.writevv)(
io_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, mem_nseq,
&curr_mem_seq, &single_mem_len, &single_mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
} /* end else */
/* Decrement number of elements left to process */
HDassert(((size_t)tmp_file_len % elmt_size) == 0);
} /* end if */
else {
size_t mem_nelem; /* Number of elements used in memory sequences */
size_t file_nelem; /* Number of elements used in file sequences */
/* Get info from API context */
if (H5CX_get_vec_size(&dxpl_vec_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve I/O vector size")
/* Allocate the vector I/O arrays */
if (dxpl_vec_size > H5D_IO_VECTOR_SIZE)
vec_size = dxpl_vec_size;
else
vec_size = H5D_IO_VECTOR_SIZE;
if (NULL == (mem_len = H5FL_SEQ_MALLOC(size_t, vec_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array")
if (NULL == (mem_off = H5FL_SEQ_MALLOC(hsize_t, vec_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array")
if (NULL == (file_len = H5FL_SEQ_MALLOC(size_t, vec_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array")
if (NULL == (file_off = H5FL_SEQ_MALLOC(hsize_t, vec_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array")
/* Allocate the iterators */
if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate memory iterator")
if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate file iterator")
/* Initialize file iterator */
if (H5S_select_iter_init(file_iter, file_space, elmt_size, H5S_SEL_ITER_GET_SEQ_LIST_SORTED) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
file_iter_init = 1; /* File selection iteration info has been initialized */
/* Initialize memory iterator */
if (H5S_select_iter_init(mem_iter, mem_space, elmt_size, 0) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
mem_iter_init = 1; /* Memory selection iteration info has been initialized */
/* Initialize sequence counts */
curr_mem_seq = curr_file_seq = 0;
mem_nseq = file_nseq = 0;
/* Loop, until all bytes are processed */
while (nelmts > 0) {
/* Check if more file sequences are needed */
if (curr_file_seq >= file_nseq) {
/* Get sequences for file selection */
if (H5S_SELECT_ITER_GET_SEQ_LIST(file_iter, vec_size, nelmts, &file_nseq, &file_nelem,
file_off, file_len) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
/* Start at the beginning of the sequences again */
curr_file_seq = 0;
} /* end if */
/* Check if more memory sequences are needed */
if (curr_mem_seq >= mem_nseq) {
/* Get sequences for memory selection */
if (H5S_SELECT_ITER_GET_SEQ_LIST(mem_iter, vec_size, nelmts, &mem_nseq, &mem_nelem, mem_off,
mem_len) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
/* Start at the beginning of the sequences again */
curr_mem_seq = 0;
} /* end if */
/* Perform I/O on memory and file sequences */
if (io_info->op_type == H5D_IO_OP_READ) {
if ((tmp_file_len =
(*io_info->layout_ops.readvv)(io_info, file_nseq, &curr_file_seq, file_len, file_off,
mem_nseq, &curr_mem_seq, mem_len, mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error")
} /* end if */
else {
HDassert(io_info->op_type == H5D_IO_OP_WRITE);
if ((tmp_file_len = (*io_info->layout_ops.writevv)(io_info, file_nseq, &curr_file_seq,
file_len, file_off, mem_nseq,
&curr_mem_seq, mem_len, mem_off)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
} /* end else */
/* Decrement number of elements left to process */
HDassert(((size_t)tmp_file_len % elmt_size) == 0);
nelmts -= ((size_t)tmp_file_len / elmt_size);
} /* end while */
} /* end else */
done:
/* Release selection iterators */
if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
if (file_iter)
file_iter = H5FL_FREE(H5S_sel_iter_t, file_iter);
if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
if (mem_iter)
mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter);
/* Release vector arrays, if allocated */
if (file_len)
file_len = H5FL_SEQ_FREE(size_t, file_len);
if (file_off)
file_off = H5FL_SEQ_FREE(hsize_t, file_off);
if (mem_len)
mem_len = H5FL_SEQ_FREE(size_t, mem_len);
if (mem_off)
mem_off = H5FL_SEQ_FREE(hsize_t, mem_off);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__select_io() */
/*-------------------------------------------------------------------------
* Function: H5D_select_io_mem
*
* Purpose: Perform memory copies directly between two memory buffers
* according to the selections in the `dst_space` and
* `src_space` dataspaces.
*
* Note: This routine is [basically] the same as H5D__select_io,
* with the only difference being that the readvv/writevv
* calls are exchanged for H5VM_memcpyvv calls. Changes should
* be made to both routines.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_select_io_mem(void *dst_buf, H5S_t *dst_space, const void *src_buf, H5S_t *src_space, size_t elmt_size,
size_t nelmts)
{
H5S_sel_iter_t *dst_sel_iter = NULL; /* Destination dataspace iteration info */
H5S_sel_iter_t *src_sel_iter = NULL; /* Source dataspace iteration info */
hbool_t dst_sel_iter_init = FALSE; /* Destination dataspace selection iterator initialized? */
hbool_t src_sel_iter_init = FALSE; /* Source dataspace selection iterator initialized? */
hsize_t * dst_off = NULL; /* Pointer to sequence offsets in destination buffer */
hsize_t * src_off = NULL; /* Pointer to sequence offsets in source buffer */
size_t * dst_len = NULL; /* Pointer to sequence lengths in destination buffer */
size_t * src_len = NULL; /* Pointer to sequence lengths in source buffer */
size_t curr_dst_seq; /* Current destination buffer sequence to operate on */
size_t curr_src_seq; /* Current source buffer sequence to operate on */
size_t dst_nseq; /* Number of sequences generated for destination buffer */
size_t src_nseq; /* Number of sequences generated for source buffer */
size_t dxpl_vec_size; /* Vector length from API context's DXPL */
size_t vec_size; /* Vector length */
ssize_t bytes_copied;
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
HDassert(dst_buf);
HDassert(dst_space);
HDassert(src_buf);
HDassert(src_space);
if (elmt_size == 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "invalid elmt_size of 0")
/* Check for only one element in selection */
if (nelmts == 1) {
hsize_t single_dst_off; /* Offset in dst_space */
hsize_t single_src_off; /* Offset in src_space */
size_t single_dst_len; /* Length in dst_space */
size_t single_src_len; /* Length in src_space */
/* Get offset of first element in selections */
if (H5S_SELECT_OFFSET(dst_space, &single_dst_off) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve destination selection offset")
if (H5S_SELECT_OFFSET(src_space, &single_src_off) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve source selection offset")
/* Set up necessary information for I/O operation */
dst_nseq = src_nseq = 1;
curr_dst_seq = curr_src_seq = 0;
single_dst_off *= elmt_size;
single_src_off *= elmt_size;
single_dst_len = single_src_len = elmt_size;
/* Perform vectorized memcpy from src_buf to dst_buf */
if ((bytes_copied =
H5VM_memcpyvv(dst_buf, dst_nseq, &curr_dst_seq, &single_dst_len, &single_dst_off, src_buf,
src_nseq, &curr_src_seq, &single_src_len, &single_src_off)) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
HDassert(((size_t)bytes_copied % elmt_size) == 0);
}
else {
unsigned sel_iter_flags = H5S_SEL_ITER_GET_SEQ_LIST_SORTED | H5S_SEL_ITER_SHARE_WITH_DATASPACE;
size_t dst_nelem; /* Number of elements used in destination buffer sequences */
size_t src_nelem; /* Number of elements used in source buffer sequences */
/* Get info from API context */
if (H5CX_get_vec_size(&dxpl_vec_size) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "can't retrieve I/O vector size")
/* Allocate the vector I/O arrays */
if (dxpl_vec_size > H5D_IO_VECTOR_SIZE)
vec_size = dxpl_vec_size;
else
vec_size = H5D_IO_VECTOR_SIZE;
if (NULL == (dst_len = H5FL_SEQ_MALLOC(size_t, vec_size)))
HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array")
if (NULL == (dst_off = H5FL_SEQ_MALLOC(hsize_t, vec_size)))
HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array")
if (NULL == (src_len = H5FL_SEQ_MALLOC(size_t, vec_size)))
HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array")
if (NULL == (src_off = H5FL_SEQ_MALLOC(hsize_t, vec_size)))
HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array")
/* Allocate the dataspace selection iterators */
if (NULL == (dst_sel_iter = H5FL_MALLOC(H5S_sel_iter_t)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate destination selection iterator")
if (NULL == (src_sel_iter = H5FL_MALLOC(H5S_sel_iter_t)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate source selection iterator")
/* Initialize destination selection iterator */
if (H5S_select_iter_init(dst_sel_iter, dst_space, elmt_size, sel_iter_flags) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
dst_sel_iter_init = TRUE; /* Destination selection iteration info has been initialized */
/* Initialize source selection iterator */
if (H5S_select_iter_init(src_sel_iter, src_space, elmt_size, H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
src_sel_iter_init = TRUE; /* Source selection iteration info has been initialized */
/* Initialize sequence counts */
curr_dst_seq = curr_src_seq = 0;
dst_nseq = src_nseq = 0;
/* Loop, until all bytes are processed */
while (nelmts > 0) {
/* Check if more destination buffer sequences are needed */
if (curr_dst_seq >= dst_nseq) {
/* Get sequences for destination selection */
if (H5S_SELECT_ITER_GET_SEQ_LIST(dst_sel_iter, vec_size, nelmts, &dst_nseq, &dst_nelem,
dst_off, dst_len) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "sequence length generation failed")
/* Start at the beginning of the sequences again */
curr_dst_seq = 0;
}
/* Check if more source buffer sequences are needed */
if (curr_src_seq >= src_nseq) {
/* Get sequences for source selection */
if (H5S_SELECT_ITER_GET_SEQ_LIST(src_sel_iter, vec_size, nelmts, &src_nseq, &src_nelem,
src_off, src_len) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "sequence length generation failed")
/* Start at the beginning of the sequences again */
curr_src_seq = 0;
} /* end if */
/* Perform vectorized memcpy from src_buf to dst_buf */
if ((bytes_copied = H5VM_memcpyvv(dst_buf, dst_nseq, &curr_dst_seq, dst_len, dst_off, src_buf,
src_nseq, &curr_src_seq, src_len, src_off)) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
/* Decrement number of elements left to process */
HDassert(((size_t)bytes_copied % elmt_size) == 0);
nelmts -= ((size_t)bytes_copied / elmt_size);
}
}
done:
/* Release selection iterators */
if (src_sel_iter) {
if (src_sel_iter_init && H5S_SELECT_ITER_RELEASE(src_sel_iter) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
src_sel_iter = H5FL_FREE(H5S_sel_iter_t, src_sel_iter);
}
if (dst_sel_iter) {
if (dst_sel_iter_init && H5S_SELECT_ITER_RELEASE(dst_sel_iter) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
dst_sel_iter = H5FL_FREE(H5S_sel_iter_t, dst_sel_iter);
}
/* Release vector arrays, if allocated */
if (src_off)
src_off = H5FL_SEQ_FREE(hsize_t, src_off);
if (src_len)
src_len = H5FL_SEQ_FREE(size_t, src_len);
if (dst_off)
dst_off = H5FL_SEQ_FREE(hsize_t, dst_off);
if (dst_len)
dst_len = H5FL_SEQ_FREE(size_t, dst_len);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_select_io_mem() */
/*-------------------------------------------------------------------------
* Function: H5D__select_read
*
* Purpose: Reads directly from file into application memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, July 23, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__select_read(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts,
H5S_t *file_space, H5S_t *mem_space)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Call generic selection operation */
H5_CHECK_OVERFLOW(nelmts, hsize_t, size_t);
if (H5D__select_io(io_info, type_info->src_type_size, (size_t)nelmts, file_space, mem_space) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__select_read() */
/*-------------------------------------------------------------------------
* Function: H5D__select_write
*
* Purpose: Writes directly from application memory into a file
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, July 23, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__select_write(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts,
H5S_t *file_space, H5S_t *mem_space)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Call generic selection operation */
H5_CHECK_OVERFLOW(nelmts, hsize_t, size_t);
if (H5D__select_io(io_info, type_info->dst_type_size, (size_t)nelmts, file_space, mem_space) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__select_write() */
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