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diff --git a/src/H5Dscatgath.c b/src/H5Dscatgath.c
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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 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
- * access to either file, you may request a copy from help@hdfgroup.org. *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-/****************/
-/* 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 "H5FLprivate.h" /* Free Lists */
-
-
-/****************/
-/* Local Macros */
-/****************/
-
-
-/******************/
-/* Local Typedefs */
-/******************/
-
-
-/********************/
-/* Local Prototypes */
-/********************/
-static size_t H5D_gather_file(const H5D_io_info_t *io_info,
- const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts,
- void *buf);
-static herr_t H5D_scatter_file(const H5D_io_info_t *io_info,
- const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts,
- const void *buf);
-static size_t H5D_gather_mem(const void *_buf,
- const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
- const H5D_dxpl_cache_t *dxpl_cache, void *_tgath_buf/*out*/);
-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,
- const H5D_type_info_t *type_info, void *user_buf/*out*/);
-static herr_t H5D_compound_opt_write(size_t nelmts, const H5D_type_info_t *type_info);
-
-
-/*********************/
-/* Package Variables */
-/*********************/
-
-
-/*******************/
-/* Local Variables */
-/*******************/
-
-/* Declare a free list to manage sequences of size_t */
-H5FL_SEQ_EXTERN(size_t);
-
-/* Declare a free list to manage sequences of hsize_t */
-H5FL_SEQ_EXTERN(hsize_t);
-
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_scatter_file
- *
- * Purpose: Scatters dataset elements from the type conversion buffer BUF
- * to the file F where the data points are arranged according to
- * the file dataspace FILE_SPACE and stored according to
- * LAYOUT and EFL. Each element is ELMT_SIZE bytes.
- * The caller is requesting that NELMTS elements are copied.
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Quincey Koziol
- * Thursday, June 20, 2002
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_scatter_file(const H5D_io_info_t *_io_info,
- const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
- const void *_buf)
-{
- H5D_io_info_t tmp_io_info; /* Temporary I/O info object */
- hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
- hsize_t *off = NULL; /* Pointer to sequence offsets */
- hsize_t mem_off; /* Offset in memory */
- size_t mem_curr_seq; /* "Current sequence" in memory */
- size_t dset_curr_seq; /* "Current sequence" in dataset */
- size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
- size_t *len = NULL; /* Array to store sequence lengths */
- size_t orig_mem_len, mem_len; /* Length of sequence in memory */
- size_t nseq; /* Number of sequences generated */
- size_t nelem; /* Number of elements used in sequences */
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_scatter_file)
-
- /* Check args */
- HDassert(_io_info);
- HDassert(space);
- HDassert(iter);
- HDassert(nelmts > 0);
- HDassert(_buf);
-
- /* Set up temporary I/O info object */
- HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
- tmp_io_info.op_type = H5D_IO_OP_WRITE;
- tmp_io_info.u.wbuf = _buf;
-
- /* Allocate the vector I/O arrays */
- if(tmp_io_info.dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
- if(NULL == (len = H5FL_SEQ_MALLOC(size_t, tmp_io_info.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, tmp_io_info.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 */
-
- /* Loop until all elements are written */
- while(nelmts > 0) {
- /* Get list of sequences for selection to write */
- 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)
- HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
-
- /* Reset the current sequence information */
- mem_curr_seq = dset_curr_seq = 0;
- orig_mem_len = mem_len = nelem * iter->elmt_size;
- mem_off = 0;
-
- /* Write sequence list out */
- if((*tmp_io_info.layout_ops.writevv)(&tmp_io_info, nseq, &dset_curr_seq,
- len, off, (size_t)1, &mem_curr_seq, &mem_len, &mem_off) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error")
-
- /* Update buffer */
- tmp_io_info.u.wbuf = (const uint8_t *)tmp_io_info.u.wbuf + orig_mem_len;
-
- /* Decrement number of elements left to process */
- nelmts -= nelem;
- } /* end while */
-
-done:
- /* Release resources, if allocated */
- if(len && len != _len)
- H5FL_SEQ_FREE(size_t, len);
- if(off && off != _off)
- H5FL_SEQ_FREE(hsize_t, off);
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_scatter_file() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_gather_file
- *
- * Purpose: Gathers data points from file F and accumulates them in the
- * type conversion buffer BUF. The LAYOUT argument describes
- * how the data is stored on disk and EFL describes how the data
- * is organized in external files. ELMT_SIZE is the size in
- * bytes of a datum which this function treats as opaque.
- * FILE_SPACE describes the dataspace of the dataset on disk
- * and the elements that have been selected for reading (via
- * hyperslab, etc). This function will copy at most NELMTS
- * elements.
- *
- * Return: Success: Number of elements copied.
- * Failure: 0
- *
- * Programmer: Quincey Koziol
- * Monday, June 24, 2002
- *
- *-------------------------------------------------------------------------
- */
-static size_t
-H5D_gather_file(const H5D_io_info_t *_io_info,
- const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
- void *_buf/*out*/)
-{
- H5D_io_info_t tmp_io_info; /* Temporary I/O info object */
- hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
- hsize_t *off = NULL; /* Pointer to sequence offsets */
- hsize_t mem_off; /* Offset in memory */
- size_t mem_curr_seq; /* "Current sequence" in memory */
- size_t dset_curr_seq; /* "Current sequence" in dataset */
- size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
- size_t *len = NULL; /* Pointer to sequence lengths */
- size_t orig_mem_len, mem_len; /* Length of sequence in memory */
- size_t nseq; /* Number of sequences generated */
- size_t nelem; /* Number of elements used in sequences */
- size_t ret_value = nelmts; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_gather_file)
-
- /* Check args */
- HDassert(_io_info);
- HDassert(_io_info->dset);
- HDassert(_io_info->store);
- HDassert(space);
- HDassert(iter);
- HDassert(nelmts > 0);
- HDassert(_buf);
-
- /* Set up temporary I/O info object */
- HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
- tmp_io_info.op_type = H5D_IO_OP_READ;
- tmp_io_info.u.rbuf = _buf;
-
- /* Allocate the vector I/O arrays */
- if(tmp_io_info.dxpl_cache->vec_size > H5D_IO_VECTOR_SIZE) {
- if(NULL == (len = H5FL_SEQ_MALLOC(size_t, tmp_io_info.dxpl_cache->vec_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O length vector array")
- if(NULL == (off = H5FL_SEQ_MALLOC(hsize_t, tmp_io_info.dxpl_cache->vec_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O offset vector array")
- } /* end if */
- else {
- len = _len;
- off = _off;
- } /* end else */
-
- /* Loop until all elements are read */
- while(nelmts > 0) {
- /* Get list of sequences for selection to read */
- 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)
- HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed")
-
- /* Reset the current sequence information */
- mem_curr_seq = dset_curr_seq = 0;
- orig_mem_len = mem_len = nelem * iter->elmt_size;
- mem_off = 0;
-
- /* Read sequence list in */
- if((*tmp_io_info.layout_ops.readvv)(&tmp_io_info, nseq, &dset_curr_seq,
- len, off, (size_t)1, &mem_curr_seq, &mem_len, &mem_off) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error")
-
- /* Update buffer */
- tmp_io_info.u.rbuf = (uint8_t *)tmp_io_info.u.rbuf + orig_mem_len;
-
- /* Decrement number of elements left to process */
- nelmts -= nelem;
- } /* end while */
-
-done:
- /* Release resources, if allocated */
- if(len && len != _len)
- H5FL_SEQ_FREE(size_t, len);
- if(off && off != _off)
- H5FL_SEQ_FREE(hsize_t, off);
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_gather_file() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_scatter_mem
- *
- * Purpose: Scatters NELMTS data points from the scatter buffer
- * TSCAT_BUF to the application buffer BUF. Each element is
- * ELMT_SIZE bytes and they are organized in application memory
- * according to SPACE.
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Quincey Koziol
- * Monday, July 8, 2002
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5D_scatter_mem (const void *_tscat_buf, const H5S_t *space,
- H5S_sel_iter_t *iter, size_t nelmts, const H5D_dxpl_cache_t *dxpl_cache,
- void *_buf/*out*/)
-{
- uint8_t *buf = (uint8_t *)_buf; /* Get local copies for address arithmetic */
- const uint8_t *tscat_buf = (const uint8_t *)_tscat_buf;
- 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 curr_len; /* Length of bytes left to process in sequence */
- size_t nseq; /* Number of sequences generated */
- size_t curr_seq; /* Current sequence being processed */
- size_t nelem; /* Number of elements used in sequences */
- herr_t ret_value = SUCCEED; /* Number of elements scattered */
-
- FUNC_ENTER_NOAPI(H5D_scatter_mem, FAIL)
-
- /* Check args */
- HDassert(tscat_buf);
- HDassert(space);
- HDassert(iter);
- HDassert(nelmts > 0);
- HDassert(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 */
-
- /* 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, &nelem, 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 in sequence */
- curr_len = len[curr_seq];
-
- HDmemcpy(buf + off[curr_seq], tscat_buf, curr_len);
-
- /* Advance offset in destination buffer */
- tscat_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)
- H5FL_SEQ_FREE(size_t, len);
- if(off && off != _off)
- H5FL_SEQ_FREE(hsize_t, off);
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_scatter_mem() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_gather_mem
- *
- * Purpose: Gathers dataset elements from application memory BUF and
- * copies them into the gather buffer TGATH_BUF.
- * Each element is ELMT_SIZE bytes and arranged in application
- * memory according to SPACE.
- * The caller is requesting that at most NELMTS be gathered.
- *
- * Return: Success: Number of elements copied.
- * Failure: 0
- *
- * Programmer: Quincey Koziol
- * Monday, June 24, 2002
- *
- *-------------------------------------------------------------------------
- */
-static size_t
-H5D_gather_mem(const void *_buf, const H5S_t *space,
- H5S_sel_iter_t *iter, size_t nelmts, const H5D_dxpl_cache_t *dxpl_cache,
- void *_tgath_buf/*out*/)
-{
- const uint8_t *buf = (const uint8_t *)_buf; /* Get local copies for address arithmetic */
- uint8_t *tgath_buf = (uint8_t *)_tgath_buf;
- 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 curr_len; /* Length of bytes left to process in sequence */
- size_t nseq; /* Number of sequences generated */
- size_t curr_seq; /* Current sequence being processed */
- size_t nelem; /* Number of elements used in sequences */
- size_t ret_value = nelmts; /* Number of elements gathered */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_gather_mem)
-
- /* Check args */
- HDassert(buf);
- HDassert(space);
- HDassert(iter);
- HDassert(nelmts > 0);
- HDassert(tgath_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, 0, "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, 0, "can't allocate I/O offset vector array")
- } /* end if */
- else {
- len = _len;
- off = _off;
- } /* end else */
-
- /* 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, &nelem, 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 in sequence */
- curr_len = len[curr_seq];
-
- 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)
- H5FL_SEQ_FREE(size_t, len);
- if(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(H5T_SUBSET_FALSE != type_info->cmpd_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(H5T_SUBSET_DST == type_info->cmpd_subset) {
- 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 */
-
- /*
- * 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 type conversion (since we're using dataset->shared->type). */
- if(!type_info->is_xform_noop)
- if(H5Z_xform_eval(dxpl_cache->data_xform_prop, type_info->tconv_buf, smine_nelmts, type_info->dset_type) < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
- } /* 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, type_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(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;
-
- if(H5T_SUBSET_SRC == type_info->cmpd_subset)
- type_size = src_stride;
- else {
- HDassert(H5T_SUBSET_DST == type_info->cmpd_subset);
- type_size = dst_stride;
- } /* end else */
-
- /* 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];
- 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;
-
- /* Copy the data into the right place. */
- for(i = 0; i < curr_nelmts; i++) {
- HDmemmove(xubuf, xdbuf, type_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)
- H5FL_SEQ_FREE(size_t, len);
- if(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() */
-