90aea941c5
Description: When writing data to a dataset, the data transform was performed after type conversion. This caused an error if the file type was non-native. This has been changed so data transforms are always performed on the memory type. Tested: jam, linew. smirom (h5committest)
902 lines
37 KiB
C
902 lines
37 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/****************/
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/* Module Setup */
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/****************/
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#define H5D_PACKAGE /*suppress error about including H5Dpkg */
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/***********/
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/* Headers */
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/***********/
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#include "H5private.h" /* Generic Functions */
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#include "H5Dpkg.h" /* Dataset functions */
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#include "H5Eprivate.h" /* Error handling */
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#include "H5FLprivate.h" /* Free Lists */
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/****************/
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/* Local Macros */
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/****************/
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/******************/
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/* Local Typedefs */
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/******************/
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/********************/
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/* Local Prototypes */
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/********************/
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static size_t H5D_gather_file(const H5D_io_info_t *io_info,
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const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts,
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void *buf);
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static herr_t H5D_scatter_file(const H5D_io_info_t *io_info,
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const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts,
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const void *buf);
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static size_t H5D_gather_mem(const void *_buf,
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const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
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const H5D_dxpl_cache_t *dxpl_cache, void *_tgath_buf/*out*/);
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static herr_t H5D_compound_opt_read(size_t nelmts, const H5S_t *mem_space,
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H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache,
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const H5D_type_info_t *type_info, void *user_buf/*out*/);
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static herr_t H5D_compound_opt_write(size_t nelmts, const H5D_type_info_t *type_info);
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/*********************/
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/* Package Variables */
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/*********************/
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/*******************/
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/* Local Variables */
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/*******************/
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/* Declare a free list to manage sequences of size_t */
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H5FL_SEQ_EXTERN(size_t);
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/* Declare a free list to manage sequences of hsize_t */
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H5FL_SEQ_EXTERN(hsize_t);
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/*-------------------------------------------------------------------------
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* Function: H5D_scatter_file
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*
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* Purpose: Scatters dataset elements from the type conversion buffer BUF
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* to the file F where the data points are arranged according to
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* the file dataspace FILE_SPACE and stored according to
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* LAYOUT and EFL. Each element is ELMT_SIZE bytes.
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* The caller is requesting that NELMTS elements are copied.
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Quincey Koziol
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* Thursday, June 20, 2002
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5D_scatter_file(const H5D_io_info_t *_io_info,
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const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
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const void *_buf)
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{
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H5D_io_info_t tmp_io_info; /* Temporary I/O info object */
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hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
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hsize_t *off = NULL; /* Pointer to sequence offsets */
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hsize_t mem_off; /* Offset in memory */
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size_t mem_curr_seq; /* "Current sequence" in memory */
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size_t dset_curr_seq; /* "Current sequence" in dataset */
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size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
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size_t *len = NULL; /* Array to store sequence lengths */
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size_t orig_mem_len, mem_len; /* Length of sequence in memory */
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size_t nseq; /* Number of sequences generated */
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size_t nelem; /* Number of elements used in sequences */
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_NOAPI_NOINIT(H5D_scatter_file)
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/* Check args */
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HDassert(_io_info);
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HDassert(space);
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HDassert(iter);
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HDassert(nelmts > 0);
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HDassert(_buf);
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/* Set up temporary I/O info object */
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HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
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tmp_io_info.op_type = H5D_IO_OP_WRITE;
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tmp_io_info.u.wbuf = _buf;
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/* Allocate the vector I/O arrays */
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if(tmp_io_info.dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
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if(NULL == (len = H5FL_SEQ_MALLOC(size_t, tmp_io_info.dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array")
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if(NULL == (off = H5FL_SEQ_MALLOC(hsize_t, tmp_io_info.dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array")
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} /* end if */
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else {
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len = _len;
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off = _off;
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} /* end else */
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/* Loop until all elements are written */
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while(nelmts > 0) {
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/* Get list of sequences for selection to write */
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if(H5S_SELECT_GET_SEQ_LIST(space, H5S_GET_SEQ_LIST_SORTED, iter, tmp_io_info.dxpl_cache->vec_size, nelmts, &nseq, &nelem, off, len) < 0)
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HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
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/* Reset the current sequence information */
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mem_curr_seq = dset_curr_seq = 0;
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orig_mem_len = mem_len = nelem * iter->elmt_size;
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mem_off = 0;
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/* Write sequence list out */
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if((*tmp_io_info.layout_ops.writevv)(&tmp_io_info, nseq, &dset_curr_seq,
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len, off, (size_t)1, &mem_curr_seq, &mem_len, &mem_off) < 0)
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HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
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/* Update buffer */
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tmp_io_info.u.wbuf = (const uint8_t *)tmp_io_info.u.wbuf + orig_mem_len;
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/* Decrement number of elements left to process */
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nelmts -= nelem;
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} /* end while */
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done:
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/* Release resources, if allocated */
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if(len && len != _len)
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len = H5FL_SEQ_FREE(size_t, len);
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if(off && off != _off)
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off = H5FL_SEQ_FREE(hsize_t, off);
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FUNC_LEAVE_NOAPI(ret_value)
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} /* H5D_scatter_file() */
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/*-------------------------------------------------------------------------
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* Function: H5D_gather_file
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*
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* Purpose: Gathers data points from file F and accumulates them in the
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* type conversion buffer BUF. The LAYOUT argument describes
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* how the data is stored on disk and EFL describes how the data
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* is organized in external files. ELMT_SIZE is the size in
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* bytes of a datum which this function treats as opaque.
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* FILE_SPACE describes the dataspace of the dataset on disk
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* and the elements that have been selected for reading (via
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* hyperslab, etc). This function will copy at most NELMTS
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* elements.
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*
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* Return: Success: Number of elements copied.
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* Failure: 0
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*
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* Programmer: Quincey Koziol
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* Monday, June 24, 2002
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*
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*-------------------------------------------------------------------------
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*/
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static size_t
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H5D_gather_file(const H5D_io_info_t *_io_info,
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const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
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void *_buf/*out*/)
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{
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H5D_io_info_t tmp_io_info; /* Temporary I/O info object */
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hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
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hsize_t *off = NULL; /* Pointer to sequence offsets */
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hsize_t mem_off; /* Offset in memory */
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size_t mem_curr_seq; /* "Current sequence" in memory */
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size_t dset_curr_seq; /* "Current sequence" in dataset */
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size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
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size_t *len = NULL; /* Pointer to sequence lengths */
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size_t orig_mem_len, mem_len; /* Length of sequence in memory */
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size_t nseq; /* Number of sequences generated */
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size_t nelem; /* Number of elements used in sequences */
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size_t ret_value = nelmts; /* Return value */
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FUNC_ENTER_NOAPI_NOINIT(H5D_gather_file)
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/* Check args */
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HDassert(_io_info);
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HDassert(_io_info->dset);
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HDassert(_io_info->store);
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HDassert(space);
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HDassert(iter);
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HDassert(nelmts > 0);
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HDassert(_buf);
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/* Set up temporary I/O info object */
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HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
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tmp_io_info.op_type = H5D_IO_OP_READ;
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tmp_io_info.u.rbuf = _buf;
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/* Allocate the vector I/O arrays */
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if(tmp_io_info.dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
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if(NULL == (len = H5FL_SEQ_MALLOC(size_t, tmp_io_info.dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O length vector array")
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if(NULL == (off = H5FL_SEQ_MALLOC(hsize_t, tmp_io_info.dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O offset vector array")
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} /* end if */
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else {
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len = _len;
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off = _off;
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} /* end else */
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/* Loop until all elements are read */
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while(nelmts > 0) {
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/* Get list of sequences for selection to read */
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if(H5S_SELECT_GET_SEQ_LIST(space, H5S_GET_SEQ_LIST_SORTED, iter, tmp_io_info.dxpl_cache->vec_size, nelmts, &nseq, &nelem, off, len) < 0)
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HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed")
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/* Reset the current sequence information */
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mem_curr_seq = dset_curr_seq = 0;
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orig_mem_len = mem_len = nelem * iter->elmt_size;
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mem_off = 0;
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/* Read sequence list in */
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if((*tmp_io_info.layout_ops.readvv)(&tmp_io_info, nseq, &dset_curr_seq,
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len, off, (size_t)1, &mem_curr_seq, &mem_len, &mem_off) < 0)
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HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error")
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/* Update buffer */
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tmp_io_info.u.rbuf = (uint8_t *)tmp_io_info.u.rbuf + orig_mem_len;
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/* Decrement number of elements left to process */
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nelmts -= nelem;
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} /* end while */
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done:
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/* Release resources, if allocated */
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if(len && len != _len)
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len = H5FL_SEQ_FREE(size_t, len);
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if(off && off != _off)
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off = H5FL_SEQ_FREE(hsize_t, off);
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FUNC_LEAVE_NOAPI(ret_value)
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} /* H5D_gather_file() */
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/*-------------------------------------------------------------------------
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* Function: H5D_scatter_mem
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*
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* Purpose: Scatters NELMTS data points from the scatter buffer
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* TSCAT_BUF to the application buffer BUF. Each element is
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* ELMT_SIZE bytes and they are organized in application memory
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* according to SPACE.
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Quincey Koziol
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* Monday, July 8, 2002
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*
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*-------------------------------------------------------------------------
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*/
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herr_t
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H5D_scatter_mem (const void *_tscat_buf, const H5S_t *space,
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H5S_sel_iter_t *iter, size_t nelmts, const H5D_dxpl_cache_t *dxpl_cache,
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void *_buf/*out*/)
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{
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uint8_t *buf = (uint8_t *)_buf; /* Get local copies for address arithmetic */
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const uint8_t *tscat_buf = (const uint8_t *)_tscat_buf;
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hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
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hsize_t *off = NULL; /* Pointer to sequence offsets */
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size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
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size_t *len = NULL; /* Pointer to sequence lengths */
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size_t curr_len; /* Length of bytes left to process in sequence */
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size_t nseq; /* Number of sequences generated */
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size_t curr_seq; /* Current sequence being processed */
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size_t nelem; /* Number of elements used in sequences */
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herr_t ret_value = SUCCEED; /* Number of elements scattered */
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FUNC_ENTER_NOAPI(H5D_scatter_mem, FAIL)
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/* Check args */
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HDassert(tscat_buf);
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HDassert(space);
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HDassert(iter);
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HDassert(nelmts > 0);
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HDassert(buf);
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/* Allocate the vector I/O arrays */
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if(dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
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if(NULL == (len = H5FL_SEQ_MALLOC(size_t, dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array")
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if(NULL == (off = H5FL_SEQ_MALLOC(hsize_t, dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array")
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} /* end if */
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else {
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len = _len;
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off = _off;
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} /* end else */
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/* Loop until all elements are written */
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while(nelmts > 0) {
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/* Get list of sequences for selection to write */
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if(H5S_SELECT_GET_SEQ_LIST(space, 0, iter, dxpl_cache->vec_size, nelmts, &nseq, &nelem, off, len) < 0)
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HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed")
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/* Loop, while sequences left to process */
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for(curr_seq = 0; curr_seq < nseq; curr_seq++) {
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/* Get the number of bytes in sequence */
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curr_len = len[curr_seq];
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HDmemcpy(buf + off[curr_seq], tscat_buf, curr_len);
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/* Advance offset in destination buffer */
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tscat_buf += curr_len;
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} /* end for */
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/* Decrement number of elements left to process */
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nelmts -= nelem;
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} /* end while */
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done:
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/* Release resources, if allocated */
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if(len && len != _len)
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len = H5FL_SEQ_FREE(size_t, len);
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if(off && off != _off)
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off = H5FL_SEQ_FREE(hsize_t, off);
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FUNC_LEAVE_NOAPI(ret_value)
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} /* H5D_scatter_mem() */
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/*-------------------------------------------------------------------------
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* Function: H5D_gather_mem
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*
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* Purpose: Gathers dataset elements from application memory BUF and
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* copies them into the gather buffer TGATH_BUF.
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* Each element is ELMT_SIZE bytes and arranged in application
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* memory according to SPACE.
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* The caller is requesting that at most NELMTS be gathered.
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*
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* Return: Success: Number of elements copied.
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* Failure: 0
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*
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* Programmer: Quincey Koziol
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* Monday, June 24, 2002
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*
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*-------------------------------------------------------------------------
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*/
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static size_t
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H5D_gather_mem(const void *_buf, const H5S_t *space,
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H5S_sel_iter_t *iter, size_t nelmts, const H5D_dxpl_cache_t *dxpl_cache,
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void *_tgath_buf/*out*/)
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{
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const uint8_t *buf = (const uint8_t *)_buf; /* Get local copies for address arithmetic */
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uint8_t *tgath_buf = (uint8_t *)_tgath_buf;
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hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
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hsize_t *off = NULL; /* Pointer to sequence offsets */
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size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
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size_t *len = NULL; /* Pointer to sequence lengths */
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size_t curr_len; /* Length of bytes left to process in sequence */
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size_t nseq; /* Number of sequences generated */
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size_t curr_seq; /* Current sequence being processed */
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size_t nelem; /* Number of elements used in sequences */
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size_t ret_value = nelmts; /* Number of elements gathered */
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FUNC_ENTER_NOAPI_NOINIT(H5D_gather_mem)
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/* Check args */
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HDassert(buf);
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HDassert(space);
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HDassert(iter);
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HDassert(nelmts > 0);
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HDassert(tgath_buf);
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/* Allocate the vector I/O arrays */
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if(dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
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if(NULL == (len = H5FL_SEQ_MALLOC(size_t, dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O length vector array")
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if(NULL == (off = H5FL_SEQ_MALLOC(hsize_t, dxpl_cache->vec_size)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O offset vector array")
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} /* end if */
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else {
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len = _len;
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off = _off;
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} /* end else */
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/* Loop until all elements are written */
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while(nelmts > 0) {
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/* Get list of sequences for selection to write */
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if(H5S_SELECT_GET_SEQ_LIST(space, 0, iter, dxpl_cache->vec_size, nelmts, &nseq, &nelem, off, len) < 0)
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HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed")
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/* Loop, while sequences left to process */
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for(curr_seq = 0; curr_seq < nseq; curr_seq++) {
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/* Get the number of bytes in sequence */
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curr_len = len[curr_seq];
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|
||
HDmemcpy(tgath_buf, buf + off[curr_seq], curr_len);
|
||
|
||
/* Advance offset in gather buffer */
|
||
tgath_buf += curr_len;
|
||
} /* end for */
|
||
|
||
/* Decrement number of elements left to process */
|
||
nelmts -= nelem;
|
||
} /* end while */
|
||
|
||
done:
|
||
/* Release resources, if allocated */
|
||
if(len && len != _len)
|
||
len = H5FL_SEQ_FREE(size_t, len);
|
||
if(off && off != _off)
|
||
off = H5FL_SEQ_FREE(hsize_t, off);
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* H5D_gather_mem() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5D_scatgath_read
|
||
*
|
||
* Purpose: Perform scatter/gather ead from a contiguous [piece of a] dataset.
|
||
*
|
||
* Return: Non-negative on success/Negative on failure
|
||
*
|
||
* Programmer: Quincey Koziol
|
||
* Thursday, March 6, 2008
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
herr_t
|
||
H5D_scatgath_read(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
|
||
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space)
|
||
{
|
||
const H5D_dxpl_cache_t *dxpl_cache = io_info->dxpl_cache; /* Local pointer to dataset transfer info */
|
||
void *buf = io_info->u.rbuf; /* Local pointer to application buffer */
|
||
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 */
|
||
hsize_t smine_start; /*strip mine start loc */
|
||
size_t smine_nelmts; /*elements per strip */
|
||
herr_t ret_value = SUCCEED; /*return value */
|
||
|
||
FUNC_ENTER_NOAPI_NOINIT(H5D_scatgath_read)
|
||
|
||
/* Sanity check */
|
||
HDassert(io_info);
|
||
HDassert(type_info);
|
||
HDassert(mem_space);
|
||
HDassert(file_space);
|
||
HDassert(buf);
|
||
|
||
/* Check for NOOP read */
|
||
if(nelmts == 0)
|
||
HGOTO_DONE(SUCCEED)
|
||
|
||
/* Figure out the strip mine size. */
|
||
if(H5S_select_iter_init(&file_iter, file_space, type_info->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, mem_space, type_info->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, mem_space, type_info->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 */
|
||
|
||
/* Start strip mining... */
|
||
for(smine_start = 0; smine_start < nelmts; smine_start += smine_nelmts) {
|
||
size_t n; /* Elements operated on */
|
||
|
||
/* Go figure out how many elements to read from the file */
|
||
HDassert(H5S_SELECT_ITER_NELMTS(&file_iter) == (nelmts - smine_start));
|
||
smine_nelmts = (size_t)MIN(type_info->request_nelmts, (nelmts - smine_start));
|
||
|
||
/*
|
||
* Gather the data from disk into the datatype conversion
|
||
* buffer. Also gather data from application to background buffer
|
||
* if necessary.
|
||
*/
|
||
|
||
/*
|
||
* Gather data
|
||
*/
|
||
n = H5D_gather_file(io_info, file_space, &file_iter, smine_nelmts,
|
||
type_info->tconv_buf/*out*/);
|
||
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.
|
||
*/
|
||
if(type_info->cmpd_subset && H5T_SUBSET_FALSE != type_info->cmpd_subset->subset) {
|
||
if(H5D_compound_opt_read(smine_nelmts, mem_space, &mem_iter, dxpl_cache,
|
||
type_info, buf /*out*/) < 0)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
|
||
} /* end if */
|
||
else {
|
||
if(H5T_BKG_YES == type_info->need_bkg) {
|
||
n = H5D_gather_mem(buf, mem_space, &bkg_iter, smine_nelmts,
|
||
dxpl_cache, type_info->bkg_buf/*out*/);
|
||
if(n != smine_nelmts)
|
||
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
|
||
} /* end if */
|
||
|
||
/*
|
||
* Perform datatype conversion.
|
||
*/
|
||
if(H5T_convert(type_info->tpath, type_info->src_type_id, type_info->dst_type_id,
|
||
smine_nelmts, (size_t)0, (size_t)0, type_info->tconv_buf,
|
||
type_info->bkg_buf, io_info->dxpl_id) < 0)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed")
|
||
|
||
/* Do the data transform after the conversion (since we're using type mem_type) */
|
||
if(!type_info->is_xform_noop)
|
||
if(H5Z_xform_eval(dxpl_cache->data_xform_prop, type_info->tconv_buf, smine_nelmts, type_info->mem_type) < 0)
|
||
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
|
||
|
||
/*
|
||
* Scatter the data into memory.
|
||
*/
|
||
if(H5D_scatter_mem(type_info->tconv_buf, mem_space, &mem_iter,
|
||
smine_nelmts, dxpl_cache, buf/*out*/) < 0)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
|
||
} /* end else */
|
||
} /* 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 */
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5D_scatgath_read() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5D_scatgath_write
|
||
*
|
||
* Purpose: Perform scatter/gather write to a contiguous [piece of a] dataset.
|
||
*
|
||
* Return: Non-negative on success/Negative on failure
|
||
*
|
||
* Programmer: Quincey Koziol
|
||
* Thursday, March 6, 2008
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
herr_t
|
||
H5D_scatgath_write(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
|
||
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space)
|
||
{
|
||
const H5D_dxpl_cache_t *dxpl_cache = io_info->dxpl_cache; /* Local pointer to dataset transfer info */
|
||
const void *buf = io_info->u.wbuf; /* Local pointer to application buffer */
|
||
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 */
|
||
hsize_t smine_start; /*strip mine start loc */
|
||
size_t smine_nelmts; /*elements per strip */
|
||
herr_t ret_value = SUCCEED; /*return value */
|
||
|
||
FUNC_ENTER_NOAPI_NOINIT(H5D_scatgath_write)
|
||
|
||
/* Sanity check */
|
||
HDassert(io_info);
|
||
HDassert(type_info);
|
||
HDassert(mem_space);
|
||
HDassert(file_space);
|
||
HDassert(buf);
|
||
|
||
/* Check for NOOP write */
|
||
if(nelmts == 0)
|
||
HGOTO_DONE(SUCCEED)
|
||
|
||
/* Figure out the strip mine size. */
|
||
if(H5S_select_iter_init(&file_iter, file_space, type_info->dst_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, mem_space, type_info->src_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, file_space, type_info->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 */
|
||
|
||
/* Start strip mining... */
|
||
for(smine_start = 0; smine_start < nelmts; smine_start += smine_nelmts) {
|
||
size_t n; /* Elements operated on */
|
||
|
||
/* Go figure out how many elements to read from the file */
|
||
HDassert(H5S_SELECT_ITER_NELMTS(&file_iter) == (nelmts - smine_start));
|
||
smine_nelmts = (size_t)MIN(type_info->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.
|
||
*/
|
||
n = H5D_gather_mem(buf, mem_space, &mem_iter, smine_nelmts,
|
||
dxpl_cache, type_info->tconv_buf/*out*/);
|
||
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.
|
||
*/
|
||
if(type_info->cmpd_subset && H5T_SUBSET_DST == type_info->cmpd_subset->subset
|
||
&& type_info->dst_type_size == type_info->cmpd_subset->copy_size) {
|
||
if(H5D_compound_opt_write(smine_nelmts, type_info) < 0)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed")
|
||
} /* end if */
|
||
else {
|
||
if(H5T_BKG_YES == type_info->need_bkg) {
|
||
n = H5D_gather_file(io_info, file_space, &bkg_iter, smine_nelmts,
|
||
type_info->bkg_buf/*out*/);
|
||
if(n != smine_nelmts)
|
||
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
|
||
} /* end if */
|
||
|
||
/* Do the data transform before the type conversion (since
|
||
* transforms must be done in the memory type). */
|
||
if(!type_info->is_xform_noop)
|
||
if(H5Z_xform_eval(dxpl_cache->data_xform_prop, type_info->tconv_buf, smine_nelmts, type_info->mem_type) < 0)
|
||
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
|
||
|
||
/*
|
||
* Perform datatype conversion.
|
||
*/
|
||
if(H5T_convert(type_info->tpath, type_info->src_type_id, type_info->dst_type_id,
|
||
smine_nelmts, (size_t)0, (size_t)0, type_info->tconv_buf,
|
||
type_info->bkg_buf, io_info->dxpl_id) < 0)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed")
|
||
} /* end else */
|
||
|
||
/*
|
||
* Scatter the data out to the file.
|
||
*/
|
||
if(H5D_scatter_file(io_info, file_space, &file_iter, smine_nelmts,
|
||
type_info->tconv_buf) < 0)
|
||
HGOTO_ERROR(H5E_DATASET, 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 */
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5D_scatgath_write() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5D_compound_opt_read
|
||
*
|
||
* Purpose: 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_read(size_t nelmts, const H5S_t *space,
|
||
H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache,
|
||
const H5D_type_info_t *type_info, void *user_buf/*out*/)
|
||
{
|
||
uint8_t *ubuf = (uint8_t *)user_buf; /* Cast for pointer arithmetic */
|
||
uint8_t *xdbuf; /* Pointer into dataset buffer */
|
||
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 src_stride, dst_stride, copy_size;
|
||
herr_t ret_value = SUCCEED; /*return value */
|
||
|
||
FUNC_ENTER_NOAPI_NOINIT(H5D_compound_opt_read)
|
||
|
||
/* Check args */
|
||
HDassert(nelmts > 0);
|
||
HDassert(space);
|
||
HDassert(iter);
|
||
HDassert(dxpl_cache);
|
||
HDassert(type_info);
|
||
HDassert(type_info->cmpd_subset);
|
||
HDassert(H5T_SUBSET_SRC == type_info->cmpd_subset->subset ||
|
||
H5T_SUBSET_DST == type_info->cmpd_subset->subset);
|
||
HDassert(user_buf);
|
||
|
||
/* Allocate the vector I/O arrays */
|
||
if(dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
|
||
if(NULL == (len = H5FL_SEQ_MALLOC(size_t, dxpl_cache->vec_size)))
|
||
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array")
|
||
if(NULL == (off = H5FL_SEQ_MALLOC(hsize_t, dxpl_cache->vec_size)))
|
||
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array")
|
||
} /* end if */
|
||
else {
|
||
len = _len;
|
||
off = _off;
|
||
} /* end else */
|
||
|
||
/* Get source & destination strides */
|
||
src_stride = type_info->src_type_size;
|
||
dst_stride = type_info->dst_type_size;
|
||
|
||
/* Get the size, in bytes, to copy for each element */
|
||
copy_size = type_info->cmpd_subset->copy_size;
|
||
|
||
/* Loop until all elements are written */
|
||
xdbuf = type_info->tconv_buf;
|
||
while(nelmts > 0) {
|
||
size_t nseq; /* Number of sequences generated */
|
||
size_t curr_seq; /* Current sequence being processed */
|
||
size_t elmtno; /* Element counter */
|
||
|
||
/* 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++) {
|
||
size_t curr_off; /* Offset of bytes left to process in sequence */
|
||
size_t curr_len; /* Length of bytes left to process in sequence */
|
||
size_t curr_nelmts; /* Number of elements to process in sequence */
|
||
uint8_t *xubuf;
|
||
size_t i; /* Local index variable */
|
||
|
||
/* Get the number of bytes and offset in sequence */
|
||
curr_len = len[curr_seq];
|
||
H5_CHECK_OVERFLOW(off[curr_seq], hsize_t, size_t);
|
||
curr_off = (size_t)off[curr_seq];
|
||
|
||
/* Decide the number of elements and position in the buffer. */
|
||
curr_nelmts = curr_len / dst_stride;
|
||
xubuf = ubuf + curr_off;
|
||
|
||
/* Copy the data into the right place. */
|
||
for(i = 0; i < curr_nelmts; i++) {
|
||
HDmemmove(xubuf, xdbuf, copy_size);
|
||
|
||
/* Update pointers */
|
||
xdbuf += src_stride;
|
||
xubuf += dst_stride;
|
||
} /* end for */
|
||
} /* end for */
|
||
|
||
/* Decrement number of elements left to process */
|
||
nelmts -= elmtno;
|
||
} /* end while */
|
||
|
||
done:
|
||
/* Release resources, if allocated */
|
||
if(len && len != _len)
|
||
len = H5FL_SEQ_FREE(size_t, len);
|
||
if(off && off != _off)
|
||
off = H5FL_SEQ_FREE(hsize_t, off);
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5D_compound_opt_read() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5D_compound_opt_write
|
||
*
|
||
* Purpose: 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, const H5D_type_info_t *type_info)
|
||
{
|
||
uint8_t *xsbuf, *xdbuf; /* Source & destination pointers into dataset buffer */
|
||
size_t src_stride, dst_stride; /* Strides through source & destination datatypes */
|
||
size_t i; /* Local index variable */
|
||
|
||
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_compound_opt_write)
|
||
|
||
/* Check args */
|
||
HDassert(nelmts > 0);
|
||
HDassert(type_info);
|
||
|
||
/* Initialize values for loop */
|
||
src_stride = type_info->src_type_size;
|
||
dst_stride = type_info->dst_type_size;
|
||
|
||
/* Loop until all elements are written */
|
||
xsbuf = (uint8_t *)type_info->tconv_buf;
|
||
xdbuf = (uint8_t *)type_info->tconv_buf;
|
||
for(i = 0; i < nelmts; i++) {
|
||
HDmemmove(xdbuf, xsbuf, dst_stride);
|
||
|
||
/* Update pointers */
|
||
xsbuf += src_stride;
|
||
xdbuf += dst_stride;
|
||
} /* end for */
|
||
|
||
FUNC_LEAVE_NOAPI(SUCCEED)
|
||
} /* end H5D_compound_opt_write() */
|
||
|