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Diffstat (limited to 'src/H5Dscatgath.c')
| -rw-r--r-- | src/H5Dscatgath.c | 899 |
1 files changed, 0 insertions, 899 deletions
diff --git a/src/H5Dscatgath.c b/src/H5Dscatgath.c deleted file mode 100644 index 3ea4c69..0000000 --- a/src/H5Dscatgath.c +++ /dev/null @@ -1,899 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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() */ - |