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Diffstat (limited to 'src/H5Dchunk.c')
| -rw-r--r-- | src/H5Dchunk.c | 1515 |
1 files changed, 0 insertions, 1515 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c deleted file mode 100644 index baaa5f1..0000000 --- a/src/H5Dchunk.c +++ /dev/null @@ -1,1515 +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 */ -#include "H5Iprivate.h" /* IDs */ -#ifdef H5_HAVE_PARALLEL -#include "H5MMprivate.h" /* Memory management */ -#endif /* H5_HAVE_PARALLEL */ -#include "H5Vprivate.h" /* Vector and array functions */ - - -/****************/ -/* Local Macros */ -/****************/ - -/* Default skip list height for storing list of chunks */ -#define H5D_DEFAULT_SKIPLIST_HEIGHT 8 - -/* Macros for iterating over chunks to operate on */ -#define H5D_CHUNK_GET_FIRST_NODE(map) (map->use_single ? (H5SL_node_t *)(1) : H5SL_first(map->sel_chunks)) -#define H5D_CHUNK_GET_NODE_INFO(map, node) (map->use_single ? map->single_chunk_info : (H5D_chunk_info_t *)H5SL_item(node)) -#define H5D_CHUNK_GET_NEXT_NODE(map, node) (map->use_single ? (H5SL_node_t *)NULL : H5SL_next(node)) - - -/******************/ -/* Local Typedefs */ -/******************/ - - -/********************/ -/* Local Prototypes */ -/********************/ - -/* Chunked layout operation callbacks */ -static herr_t H5D_chunk_io_init(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, H5D_chunk_map_t *fm); -static herr_t H5D_chunk_read(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, - H5D_chunk_map_t *fm); -static herr_t H5D_chunk_write(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, - H5D_chunk_map_t *fm); -static herr_t H5D_chunk_io_term(const H5D_chunk_map_t *fm); - -/* "Null" layout operation callbacks */ -static ssize_t H5D_null_readvv(const H5D_io_info_t *io_info, - size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[], - size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]); - -/* Helper routines */ -static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata); -static herr_t H5D_create_chunk_map_single(H5D_chunk_map_t *fm, - const H5D_io_info_t *io_info); -static herr_t H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, - const H5D_io_info_t *io_info); -static herr_t H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm); -static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, unsigned ndims, - const hsize_t *coords, void *fm); -static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims, - const hsize_t *coords, void *fm); - - - -/*********************/ -/* Package Variables */ -/*********************/ - -/* Compact storage layout I/O ops */ -const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{ - H5D_chunk_io_init, - H5D_chunk_read, - H5D_chunk_write, -#ifdef H5_HAVE_PARALLEL - H5D_chunk_collective_read, - H5D_chunk_collective_write, -#endif /* H5_HAVE_PARALLEL */ - NULL, - NULL, - H5D_chunk_io_term -}}; - - -/*******************/ -/* Local Variables */ -/*******************/ - -/* "null" storage layout I/O ops */ -const H5D_layout_ops_t H5D_LOPS_NULL[1] = {{ - NULL, - NULL, - NULL, -#ifdef H5_HAVE_PARALLEL - NULL, - NULL, -#endif /* H5_HAVE_PARALLEL */ - H5D_null_readvv, - NULL, - NULL -}}; - -/* Declare a free list to manage the H5D_chunk_info_t struct */ -H5FL_DEFINE(H5D_chunk_info_t); - - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_io_init - * - * Purpose: Performs initialization before any sort of I/O on the raw data - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Thursday, March 20, 2008 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_chunk_io_init(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, - H5D_chunk_map_t *fm) -{ - H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ - const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */ - H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */ - hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */ - htri_t file_space_normalized = FALSE; /* File dataspace was normalized */ - hid_t f_tid = (-1); /* Temporary copy of file datatype for iteration */ - hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ - unsigned f_ndims; /* The number of dimensions of the file's dataspace */ - int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */ - H5SL_node_t *curr_node; /* Current node in skip list */ - H5S_sel_type fsel_type; /* Selection type on disk */ - char bogus; /* "bogus" buffer to pass to selection iterator */ - unsigned u; /* Local index variable */ - hbool_t sel_hyper_flag; - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_io_init) - - /* Get layout for dataset */ - fm->layout = &(dataset->shared->layout); - fm->nelmts = nelmts; - - /* Check if the memory space is scalar & make equivalent memory space */ - if((sm_ndims = H5S_GET_EXTENT_NDIMS(mem_space)) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number") - /* Set the number of dimensions for the memory dataspace */ - H5_ASSIGN_OVERFLOW(fm->m_ndims, sm_ndims, int, unsigned); - - /* Get dim number and dimensionality for each dataspace */ - fm->f_ndims = f_ndims = dataset->shared->layout.u.chunk.ndims - 1; - if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality") - - /* Normalize hyperslab selections by adjusting them by the offset */ - /* (It might be worthwhile to normalize both the file and memory dataspaces - * before any (contiguous, chunked, etc) file I/O operation, in order to - * speed up hyperslab calculations by removing the extra checks and/or - * additions involving the offset and the hyperslab selection -QAK) - */ - if((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") - - /* Decide the number of chunks in each dimension*/ - for(u=0; u<f_ndims; u++) { - /* Keep the size of the chunk dimensions as hsize_t for various routines */ - fm->chunk_dim[u]=fm->layout->u.chunk.dim[u]; - - /* Round up to the next integer # of chunks, to accomodate partial chunks */ - fm->chunks[u] = ((fm->f_dims[u]+dataset->shared->layout.u.chunk.dim[u])-1) / dataset->shared->layout.u.chunk.dim[u]; - } /* end for */ - - /* Compute the "down" size of 'chunks' information */ - if(H5V_array_down(f_ndims,fm->chunks,fm->down_chunks) < 0) - HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") - -#ifdef H5_HAVE_PARALLEL - /* Calculate total chunk in file map*/ - fm->select_chunk = NULL; - fm->total_chunks = 1; - for(u = 0; u < fm->f_ndims; u++) - fm->total_chunks = fm->total_chunks * fm->chunks[u]; - if(io_info->using_mpi_vfd) { - H5_CHECK_OVERFLOW(fm->total_chunks, hsize_t, size_t); - if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->total_chunks * sizeof(H5D_chunk_info_t *)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") - } /* end if */ -#endif /* H5_HAVE_PARALLEL */ - - - /* Initialize "last chunk" information */ - fm->last_index = (hsize_t)-1; - fm->last_chunk_info = NULL; - - /* Point at the dataspaces */ - fm->file_space = file_space; - fm->mem_space = mem_space; - - /* Special case for only one element in selection */ - /* (usually appending a record) */ - if(nelmts == 1 -#ifdef H5_HAVE_PARALLEL - && !(io_info->using_mpi_vfd) -#endif /* H5_HAVE_PARALLEL */ - ) { - /* Initialize skip list for chunk selections */ - fm->sel_chunks = NULL; - fm->use_single = TRUE; - - /* Initialize single chunk dataspace */ - if(NULL == dataset->shared->cache.chunk.single_space) { - /* Make a copy of the dataspace for the dataset */ - if((dataset->shared->cache.chunk.single_space = H5S_copy(file_space, TRUE, FALSE)) == NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space") - - /* Resize chunk's dataspace dimensions to size of chunk */ - if(H5S_set_extent_real(dataset->shared->cache.chunk.single_space, fm->chunk_dim) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "can't adjust chunk dimensions") - - /* Set the single chunk dataspace to 'all' selection */ - if(H5S_select_all(dataset->shared->cache.chunk.single_space, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to set all selection") - } /* end if */ - fm->single_space = dataset->shared->cache.chunk.single_space; - HDassert(fm->single_space); - - /* Allocate the single chunk information */ - if(NULL == dataset->shared->cache.chunk.single_chunk_info) { - if(NULL == (dataset->shared->cache.chunk.single_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") - } /* end if */ - fm->single_chunk_info = dataset->shared->cache.chunk.single_chunk_info; - HDassert(fm->single_chunk_info); - - /* Reset chunk template information */ - fm->mchunk_tmpl = NULL; - - /* Set up chunk mapping for single element */ - if(H5D_create_chunk_map_single(fm, io_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element") - } /* end if */ - else { - /* Initialize skip list for chunk selections */ - if(NULL == dataset->shared->cache.chunk.sel_chunks) { - if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_DEFAULT_SKIPLIST_HEIGHT))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections") - } /* end if */ - fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks; - HDassert(fm->sel_chunks); - - /* We are not using single element mode */ - fm->use_single = FALSE; - - /* Get type of selection on disk & in memory */ - if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE) - HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection") - if((fm->msel_type = H5S_GET_SELECT_TYPE(mem_space)) < H5S_SEL_NONE) - HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection") - - /* If the selection is NONE or POINTS, set the flag to FALSE */ - if(fsel_type == H5S_SEL_POINTS || fsel_type == H5S_SEL_NONE) - sel_hyper_flag = FALSE; - else - sel_hyper_flag = TRUE; - - /* Check if file selection is a not a hyperslab selection */ - if(sel_hyper_flag) { - /* Build the file selection for each chunk */ - if(H5D_create_chunk_file_map_hyper(fm, io_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") - - /* Clean file chunks' hyperslab span "scratch" information */ - curr_node = H5SL_first(fm->sel_chunks); - while(curr_node) { - H5D_chunk_info_t *chunk_info; /* Pointer chunk information */ - - /* Get pointer to chunk's information */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); - HDassert(chunk_info); - - /* Clean hyperslab span's "scratch" information */ - if(H5S_hyper_reset_scratch(chunk_info->fspace) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info") - - /* Get the next chunk node in the skip list */ - curr_node = H5SL_next(curr_node); - } /* end while */ - } /* end if */ - else { - /* Create temporary datatypes for selection iteration */ - if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL))) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype") - - /* Spaces might not be the same shape, iterate over the file selection directly */ - if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_file_cb, fm) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") - - /* Reset "last chunk" info */ - fm->last_index = (hsize_t)-1; - fm->last_chunk_info = NULL; - } /* end else */ - - /* Build the memory selection for each chunk */ - if(sel_hyper_flag && H5S_select_shape_same(file_space, mem_space) == TRUE) { - /* Reset chunk template information */ - fm->mchunk_tmpl = NULL; - - /* If the selections are the same shape, use the file chunk information - * to generate the memory chunk information quickly. - */ - if(H5D_create_chunk_mem_map_hyper(fm) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") - } /* end if */ - else { - size_t elmt_size; /* Memory datatype size */ - - /* Make a copy of equivalent memory space */ - if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") - - /* De-select the mem space copy */ - if(H5S_select_none(tmp_mspace) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space") - - /* Save chunk template information */ - fm->mchunk_tmpl = tmp_mspace; - - /* Create temporary datatypes for selection iteration */ - if(f_tid < 0) { - if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL))) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype") - } /* end if */ - - /* Create selection iterator for memory selection */ - if(0 == (elmt_size = H5T_get_size(mem_type))) - HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid") - if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") - iter_init = TRUE; /* Selection iteration info has been initialized */ - - /* Spaces aren't the same shape, iterate over the memory selection directly */ - if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") - - /* Clean up hyperslab stuff, if necessary */ - if(fm->msel_type != H5S_SEL_POINTS) { - /* Clean memory chunks' hyperslab span "scratch" information */ - curr_node = H5SL_first(fm->sel_chunks); - while(curr_node) { - H5D_chunk_info_t *chunk_info; /* Pointer chunk information */ - - /* Get pointer to chunk's information */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); - HDassert(chunk_info); - - /* Clean hyperslab span's "scratch" information */ - if(H5S_hyper_reset_scratch(chunk_info->mspace) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info") - - /* Get the next chunk node in the skip list */ - curr_node = H5SL_next(curr_node); - } /* end while */ - } /* end if */ - } /* end else */ - } /* end else */ - -done: - /* Release the [potentially partially built] chunk mapping information if an error occurs */ - if(ret_value < 0) { - if(tmp_mspace && !fm->mchunk_tmpl) { - if(H5S_close(tmp_mspace) < 0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template") - } /* end if */ - - if(H5D_chunk_io_term(fm) < 0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping") - } /* end if */ - - /* Reset the global dataspace info */ - fm->file_space = NULL; - fm->mem_space = NULL; - - if(iter_init) { - if(H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") - } /* end if */ - if(f_tid!=(-1)) { - if(H5I_dec_ref(f_tid) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") - } /* end if */ - if(file_space_normalized) { - if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_chunk_io_init() */ - - -/*-------------------------------------------------------------------------- - NAME - H5D_free_chunk_info - PURPOSE - Internal routine to destroy a chunk info node - USAGE - void H5D_free_chunk_info(chunk_info) - void *chunk_info; IN: Pointer to chunk info to destroy - RETURNS - No return value - DESCRIPTION - Releases all the memory for a chunk info node. Called by H5SL_free - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5D_free_chunk_info(void *item, void UNUSED *key, void UNUSED *opdata) -{ - H5D_chunk_info_t *chunk_info = (H5D_chunk_info_t *)item; - - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_free_chunk_info) - - HDassert(chunk_info); - - /* Close the chunk's file dataspace, if it's not shared */ - if(!chunk_info->fspace_shared) - (void)H5S_close(chunk_info->fspace); - else - H5S_select_all(chunk_info->fspace, TRUE); - - /* Close the chunk's memory dataspace, if it's not shared */ - if(!chunk_info->mspace_shared) - (void)H5S_close(chunk_info->mspace); - - /* Free the actual chunk info */ - H5FL_FREE(H5D_chunk_info_t, chunk_info); - - FUNC_LEAVE_NOAPI(0) -} /* H5D_free_chunk_info() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_create_chunk_map_single - * - * Purpose: Create chunk selections when appending a single record - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, November 20, 2007 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t -#ifndef H5_HAVE_PARALLEL - UNUSED -#endif /* H5_HAVE_PARALLEL */ - *io_info) -{ - H5D_chunk_info_t *chunk_info; /* Chunk information to insert into skip list */ - hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - unsigned u; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map_single) - - /* Sanity check */ - HDassert(fm->f_ndims > 0); - - /* Get coordinate for selection */ - if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") - - /* Initialize the 'single chunk' file & memory chunk information */ - chunk_info = fm->single_chunk_info; - chunk_info->chunk_points = 1; - - /* Set chunk location & hyperslab size */ - for(u = 0; u < fm->f_ndims; u++) { - HDassert(sel_start[u] == sel_end[u]); - chunk_info->coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u]; - } /* end for */ - chunk_info->coords[fm->f_ndims] = 0; - - /* Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_info->index) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") - - /* Copy selection for file's dataspace into chunk dataspace */ - if(H5S_select_copy(fm->single_space, fm->file_space, FALSE) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file selection") - - /* Move selection back to have correct offset in chunk */ - if(H5S_SELECT_ADJUST_U(fm->single_space, chunk_info->coords) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection") - -#ifdef H5_HAVE_PARALLEL - /* store chunk selection information */ - if(io_info->using_mpi_vfd) - fm->select_chunk[chunk_info->index] = chunk_info; -#endif /* H5_HAVE_PARALLEL */ - - /* Set the file dataspace for the chunk to the shared 'single' dataspace */ - chunk_info->fspace = fm->single_space; - - /* Indicate that the chunk's file dataspace is shared */ - chunk_info->fspace_shared = TRUE; - - /* Just point at the memory dataspace & selection */ - /* (Casting away const OK -QAK) */ - chunk_info->mspace = (H5S_t *)fm->mem_space; - - /* Indicate that the chunk's memory dataspace is shared */ - chunk_info->mspace_shared = TRUE; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_create_chunk_map_single() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_create_chunk_file_map_hyper - * - * Purpose: Create all chunk selections in file. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Thursday, May 29, 2003 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t -#ifndef H5_HAVE_PARALLEL - UNUSED -#endif /* H5_HAVE_PARALLEL */ - *io_info) -{ - hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - hsize_t sel_points; /* Number of elements in file selection */ - hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */ - hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ - hsize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ - hsize_t chunk_index; /* Index of chunk */ - int curr_dim; /* Current dimension to increment */ - unsigned u; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_file_map_hyper) - - /* Sanity check */ - assert(fm->f_ndims>0); - - /* Get number of elements selected in file */ - sel_points = fm->nelmts; - - /* Get bounding box for selection (to reduce the number of chunks to iterate over) */ - if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") - - /* Set initial chunk location & hyperslab size */ - - for(u=0; u<fm->f_ndims; u++) { - start_coords[u]=(sel_start[u]/fm->layout->u.chunk.dim[u])*fm->layout->u.chunk.dim[u]; - coords[u]=start_coords[u]; - end[u]=(coords[u]+fm->chunk_dim[u])-1; - } /* end for */ - - - /* Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") - - /* Iterate through each chunk in the dataset */ - while(sel_points) { - /* Check for intersection of temporary chunk and file selection */ - /* (Casting away const OK - QAK) */ - if(H5S_hyper_intersect_block((H5S_t *)fm->file_space,coords,end)==TRUE) { - H5S_t *tmp_fchunk; /* Temporary file dataspace */ - H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */ - hssize_t schunk_points; /* Number of elements in chunk selection */ - - /* Create "temporary" chunk for selection operations (copy file space) */ - if((tmp_fchunk = H5S_copy(fm->file_space, TRUE, FALSE)) == NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") - - /* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */ - if(H5S_hyper_convert(tmp_fchunk) < 0) { - (void)H5S_close(tmp_fchunk); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees") - } /* end if */ - - /* "AND" temporary chunk and current chunk */ - if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL) < 0) { - (void)H5S_close(tmp_fchunk); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection") - } /* end if */ - - /* Resize chunk's dataspace dimensions to size of chunk */ - if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim) < 0) { - (void)H5S_close(tmp_fchunk); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions") - } /* end if */ - - /* Move selection back to have correct offset in chunk */ - if(H5S_SELECT_ADJUST_U(tmp_fchunk, coords) < 0) { - (void)H5S_close(tmp_fchunk); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection") - } /* end if */ - - /* Add temporary chunk to the list of chunks */ - - /* Allocate the file & memory chunk information */ - if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) { - (void)H5S_close(tmp_fchunk); - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") - } /* end if */ - - /* Initialize the chunk information */ - - /* Set the chunk index */ - new_chunk_info->index=chunk_index; - -#ifdef H5_HAVE_PARALLEL - /* store chunk selection information */ - if(io_info->using_mpi_vfd) - fm->select_chunk[chunk_index] = new_chunk_info; -#endif /* H5_HAVE_PARALLEL */ - - /* Set the file chunk dataspace */ - new_chunk_info->fspace = tmp_fchunk; - new_chunk_info->fspace_shared = FALSE; - - /* Set the memory chunk dataspace */ - new_chunk_info->mspace=NULL; - new_chunk_info->mspace_shared = FALSE; - - /* Copy the chunk's coordinates */ - for(u=0; u<fm->f_ndims; u++) - new_chunk_info->coords[u]=coords[u]; - new_chunk_info->coords[fm->f_ndims]=0; - - /* Insert the new chunk into the skip list */ - if(H5SL_insert(fm->sel_chunks,new_chunk_info,&new_chunk_info->index) < 0) { - H5D_free_chunk_info(new_chunk_info,NULL,NULL); - HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list") - } /* end if */ - - /* Get number of elements selected in chunk */ - if((schunk_points=H5S_GET_SELECT_NPOINTS(tmp_fchunk)) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements") - H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,size_t); - - /* Decrement # of points left in file selection */ - sel_points-=(hsize_t)schunk_points; - - /* Leave if we are done */ - if(sel_points==0) - HGOTO_DONE(SUCCEED) - assert(sel_points>0); - } /* end if */ - - /* Increment chunk index */ - chunk_index++; - - /* Set current increment dimension */ - curr_dim=(int)fm->f_ndims-1; - - /* Increment chunk location in fastest changing dimension */ - H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t); - coords[curr_dim]+=fm->chunk_dim[curr_dim]; - end[curr_dim]+=fm->chunk_dim[curr_dim]; - - /* Bring chunk location back into bounds, if necessary */ - if(coords[curr_dim]>sel_end[curr_dim]) { - do { - /* Reset current dimension's location to 0 */ - coords[curr_dim]=start_coords[curr_dim]; /*lint !e771 The start_coords will always be initialized */ - end[curr_dim]=(coords[curr_dim]+(hssize_t)fm->chunk_dim[curr_dim])-1; - - /* Decrement current dimension */ - curr_dim--; - - /* Increment chunk location in current dimension */ - coords[curr_dim]+=fm->chunk_dim[curr_dim]; - end[curr_dim]=(coords[curr_dim]+fm->chunk_dim[curr_dim])-1; - } while(coords[curr_dim]>sel_end[curr_dim]); - - /* Re-Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") - } /* end if */ - } /* end while */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_create_chunk_file_map_hyper() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_create_chunk_mem_map_hyper - * - * Purpose: Create all chunk selections in memory by copying the file - * chunk selections and adjusting their offsets to be correct - * for the memory. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Thursday, May 29, 2003 - * - * Assumptions: That the file and memory selections are the same shape. - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) -{ - H5SL_node_t *curr_node; /* Current node in skip list */ - hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */ - hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */ - unsigned u; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_mem_map_hyper) - - /* Sanity check */ - assert(fm->f_ndims>0); - - /* Check for all I/O going to a single chunk */ - if(H5SL_count(fm->sel_chunks)==1) { - H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ - - /* Get the node */ - curr_node=H5SL_first(fm->sel_chunks); - - /* Get pointer to chunk's information */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); - assert(chunk_info); - - /* Just point at the memory dataspace & selection */ - /* (Casting away const OK -QAK) */ - chunk_info->mspace=(H5S_t *)fm->mem_space; - - /* Indicate that the chunk's memory space is shared */ - chunk_info->mspace_shared = TRUE; - } /* end if */ - else { - /* Get bounding box for file selection */ - if(H5S_SELECT_BOUNDS(fm->file_space, file_sel_start, file_sel_end) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") - - /* Get bounding box for memory selection */ - if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") - - /* Calculate the adjustment for memory selection from file selection */ - assert(fm->m_ndims==fm->f_ndims); - for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(file_sel_start[u],hsize_t,hssize_t); - H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t); - adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u]; - } /* end for */ - - /* Iterate over each chunk in the chunk list */ - curr_node=H5SL_first(fm->sel_chunks); - while(curr_node) { - H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ - - /* Get pointer to chunk's information */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); - assert(chunk_info); - - /* Copy the information */ - - /* Copy the memory dataspace */ - if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") - - /* Release the current selection */ - if(H5S_SELECT_RELEASE(chunk_info->mspace) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection") - - /* Copy the file chunk's selection */ - if(H5S_select_copy(chunk_info->mspace,chunk_info->fspace,FALSE) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection") - - /* Compensate for the chunk offset */ - for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(chunk_info->coords[u],hsize_t,hssize_t); - chunk_adjust[u]=adjust[u]-(hssize_t)chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */ - } /* end for */ - - /* Adjust the selection */ - if(H5S_hyper_adjust_s(chunk_info->mspace,chunk_adjust) < 0) /*lint !e772 The chunk_adjust array will always be initialized */ - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection") - - /* Get the next chunk node in the skip list */ - curr_node=H5SL_next(curr_node); - } /* end while */ - } /* end else */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_create_chunk_mem_map_hyper() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_file_cb - * - * Purpose: Callback routine for file selection iterator. Used when - * creating selections in file for each point selected. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Wednesday, July 23, 2003 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm) -{ - H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */ - H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ - hsize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ - hsize_t chunk_index; /* Chunk index */ - unsigned u; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb) - - /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") - - /* Find correct chunk in file & memory skip list */ - if(chunk_index==fm->last_index) { - /* If the chunk index is the same as the last chunk index we used, - * get the cached info to operate on. - */ - chunk_info=fm->last_chunk_info; - } /* end if */ - else { - /* If the chunk index is not the same as the last chunk index we used, - * find the chunk in the skip list. - */ - /* Get the chunk node from the skip list */ - if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index))) { - H5S_t *fspace; /* Memory chunk's dataspace */ - - /* Allocate the file & memory chunk information */ - if (NULL==(chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") - - /* Initialize the chunk information */ - - /* Set the chunk index */ - chunk_info->index=chunk_index; - - /* Create a dataspace for the chunk */ - if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) { - H5FL_FREE(H5D_chunk_info_t,chunk_info); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk") - } /* end if */ - - /* De-select the chunk space */ - if(H5S_select_none(fspace) < 0) { - (void)H5S_close(fspace); - H5FL_FREE(H5D_chunk_info_t,chunk_info); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select dataspace") - } /* end if */ - - /* Set the file chunk dataspace */ - chunk_info->fspace = fspace; - chunk_info->fspace_shared = FALSE; - - /* Set the memory chunk dataspace */ - chunk_info->mspace=NULL; - chunk_info->mspace_shared = FALSE; - - /* Set the number of selected elements in chunk to zero */ - chunk_info->chunk_points=0; - - /* Compute the chunk's coordinates */ - for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t); - chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u]; - } /* end for */ - chunk_info->coords[fm->f_ndims]=0; - - /* Insert the new chunk into the skip list */ - if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) { - H5D_free_chunk_info(chunk_info,NULL,NULL); - HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list") - } /* end if */ - } /* end if */ - - /* Update the "last chunk seen" information */ - fm->last_index=chunk_index; - fm->last_chunk_info=chunk_info; - } /* end else */ - - /* Get the coordinates of the element in the chunk */ - for(u=0; u<fm->f_ndims; u++) - coords_in_chunk[u]=coords[u]%fm->layout->u.chunk.dim[u]; - - /* Add point to file selection for chunk */ - if(H5S_select_elements(chunk_info->fspace, H5S_SELECT_APPEND, (size_t)1, coords_in_chunk) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") - - /* Increment the number of elemented selected in chunk */ - chunk_info->chunk_points++; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_chunk_file_cb() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_mem_cb - * - * Purpose: Callback routine for file selection iterator. Used when - * creating selections in memory for each chunk. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Raymond Lu - * Thursday, April 10, 2003 - * - *------------------------------------------------------------------------- - */ -/* ARGSUSED */ -static herr_t -H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm) -{ - H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */ - H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ - hsize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ - hsize_t chunk_index; /* Chunk index */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb) - - /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") - - /* Find correct chunk in file & memory skip list */ - if(chunk_index==fm->last_index) { - /* If the chunk index is the same as the last chunk index we used, - * get the cached spaces to operate on. - */ - chunk_info=fm->last_chunk_info; - } /* end if */ - else { - /* If the chunk index is not the same as the last chunk index we used, - * find the chunk in the skip list. - */ - /* Get the chunk node from the skip list */ - if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index))) - HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list") - - /* Check if the chunk already has a memory space */ - if(chunk_info->mspace==NULL) { - /* Copy the template memory chunk dataspace */ - if((chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE)) == NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space") - } /* end else */ - - /* Update the "last chunk seen" information */ - fm->last_index=chunk_index; - fm->last_chunk_info=chunk_info; - } /* end else */ - - /* Get coordinates of selection iterator for memory */ - if(H5S_SELECT_ITER_COORDS(&fm->mem_iter,coords_in_mem) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates") - - /* Add point to memory selection for chunk */ - if(fm->msel_type==H5S_SEL_POINTS) { - if(H5S_select_elements(chunk_info->mspace, H5S_SELECT_APPEND, (size_t)1, coords_in_mem) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") - } /* end if */ - else { - if(H5S_hyper_add_span_element(chunk_info->mspace, fm->m_ndims, coords_in_mem) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") - } /* end else */ - - /* Move memory selection iterator to next element in selection */ - if(H5S_SELECT_ITER_NEXT(&fm->mem_iter, (size_t)1) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL, "unable to move to next iterator location") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_chunk_mem_cb() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_cacheable - * - * Purpose: A small internal function to if it's possible to load the - * chunk into cache. - * - * Return: TRUE or FALSE - * - * Programmer: Raymond Lu - * 17 July 2007 - * - *------------------------------------------------------------------------- - */ -hbool_t -H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr) -{ - const H5D_t *dataset = io_info->dset; - hbool_t ret_value; - - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cacheable) - - HDassert(io_info); - HDassert(dataset); - - /* Must bring the whole chunk in if there are any filters */ - if(dataset->shared->dcpl_cache.pline.nused > 0) - ret_value = TRUE; - else -#ifdef H5_HAVE_PARALLEL - /* If MPI based VFD is used and the file is opened for write access, must - * bypass the chunk-cache scheme because other MPI processes could - * be writing to other elements in the same chunk. Do a direct - * write-through of only the elements requested. - */ - if(io_info->using_mpi_vfd && (H5F_ACC_RDWR & H5F_INTENT(dataset->oloc.file))) - ret_value = FALSE; - else -#endif /* H5_HAVE_PARALLEL */ - /* If the chunk is too large to keep in the cache and if the address - * for the chunk has been defined, then don't load the chunk into the - * cache, just write the data to it directly. - */ - if(dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes - && H5F_addr_defined(caddr)) - ret_value = FALSE; - else - ret_value = TRUE; - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_chunk_cacheable() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_in_cache - * - * Purpose: Check if a chunk is in the cache. - * - * Return: TRUE or FALSE - * - * Programmer: Quincey Koziol - * 1 April 2008 - * - *------------------------------------------------------------------------- - */ -static hbool_t -H5D_chunk_in_cache(const H5D_io_info_t *io_info) -{ - H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);/*raw data chunk cache*/ - hbool_t found = FALSE; /*already in cache? */ - - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_in_cache) - - HDassert(io_info); - - /* Check if the chunk is in the cache (but hasn't been written to disk yet) */ - if(rdcc->nslots > 0) { - unsigned idx = H5D_CHUNK_HASH(io_info->dset->shared, io_info->store->chunk.index); /* Cache entry index */ - H5D_rdcc_ent_t *ent = rdcc->slot[idx]; /* Cache entry */ - - /* Potential match... */ - if(ent) { - size_t u; /* Local index variable */ - - for(u = 0, found = TRUE; u < io_info->dset->shared->layout.u.chunk.ndims; u++) { - if(io_info->store->chunk.offset[u] != ent->offset[u]) { - found = FALSE; - break; - } /* end if */ - } /* end for */ - } /* end if */ - } /* end if */ - - FUNC_LEAVE_NOAPI(found) -} /* end H5D_chunk_in_cache() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_read - * - * Purpose: Read from a chunked dataset. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Raymond Lu - * Thursday, April 10, 2003 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - hsize_t UNUSED nelmts, const H5S_t UNUSED *file_space, const H5S_t UNUSED *mem_space, - H5D_chunk_map_t *fm) -{ - H5SL_node_t *chunk_node; /* Current node in chunk skip list */ - H5D_io_info_t nul_io_info; /* "null" I/O info object */ - H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - H5D_io_info_t cpt_io_info; /* Compact I/O info object */ - H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */ - hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */ - size_t src_accessed_bytes = 0; /* Total accessed size in a chunk */ - hbool_t skip_missing_chunks = FALSE; /* Whether to skip missing chunks */ - unsigned idx_hint = 0; /* Cache index hint */ - herr_t ret_value = SUCCEED; /*return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read) - - /* Sanity check */ - HDassert(io_info); - HDassert(io_info->u.rbuf); - HDassert(type_info); - HDassert(fm); - - /* Set up "null" I/O info object */ - HDmemcpy(&nul_io_info, io_info, sizeof(nul_io_info)); - nul_io_info.layout_ops = *H5D_LOPS_NULL; - - /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); - ctg_io_info.store = &ctg_store; - ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; - - /* Initialize temporary contiguous storage info */ - ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size; - - /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); - cpt_io_info.store = &cpt_store; - cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; - - /* Initialize temporary compact storage info */ - cpt_store.compact.dirty = &cpt_dirty; - - { - const H5O_fill_t *fill = &(io_info->dset->shared->dcpl_cache.fill); /* Fill value info */ - H5D_fill_value_t fill_status; /* Fill value status */ - - /* Check the fill value status */ - if(H5P_is_fill_value_defined(fill, &fill_status) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") - - /* If we are never to return fill values, or if we would return them - * but they aren't set, set the flag to skip missing chunks. - */ - if(fill->fill_time == H5D_FILL_TIME_NEVER || - (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status != H5D_FILL_VALUE_USER_DEFINED)) - skip_missing_chunks = TRUE; - } - - /* Iterate through nodes in chunk skip list */ - chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm); - while(chunk_node) { - H5D_chunk_info_t *chunk_info; /* Chunk information */ - H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */ - void *chunk; /* Pointer to locked chunk buffer */ - haddr_t chunk_addr; /* Chunk address on disk */ - H5D_istore_ud1_t udata; /* B-tree pass-through */ - - /* Get the actual chunk information from the skip list node */ - chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); - - /* Pass in chunk's coordinates in a union. */ - io_info->store->chunk.offset = chunk_info->coords; - io_info->store->chunk.index = chunk_info->index; - - /* Get the address of the chunk in the file */ - chunk_addr = H5D_istore_get_addr(io_info, &udata); - - /* Check for non-existant chunk & skip it if appropriate */ - if(!H5F_addr_defined(chunk_addr) && !H5D_chunk_in_cache(io_info) - && skip_missing_chunks) { - /* No chunk cached */ - chunk = NULL; - - /* Point I/O info at "null" I/O info for this chunk */ - chk_io_info = &nul_io_info; - } /* end if */ - else { - /* Load the chunk into cache and lock it. */ - if(H5D_chunk_cacheable(io_info, chunk_addr)) { - /* Compute # of bytes accessed in chunk */ - src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size; - - /* Lock the chunk into the cache */ - if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint))) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") - - /* Set up the storage buffer information for this chunk */ - cpt_store.compact.buf = chunk; - - /* Point I/O info at contiguous I/O info for this chunk */ - chk_io_info = &cpt_io_info; - } /* end if */ - else { - /* Sanity check */ - HDassert(H5F_addr_defined(chunk_addr)); - - /* Set up the storage address information for this chunk */ - ctg_store.contig.dset_addr = chunk_addr; - - /* No chunk cached */ - chunk = NULL; - - /* Point I/O info at temporary I/O info for this chunk */ - chk_io_info = &ctg_io_info; - } /* end else */ - } /* end else */ - - /* Perform the actual read operation */ - if((io_info->io_ops.single_read)(chk_io_info, type_info, - (hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed") - - /* Release the cache lock on the chunk. */ - if(chunk && H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, src_accessed_bytes) < 0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") - - /* Advance to next chunk in list */ - chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node); - } /* end while */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5D_chunk_read() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_write - * - * Purpose: Writes to a chunked dataset. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Raymond Lu - * Thursday, April 10, 2003 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - hsize_t UNUSED nelmts, const H5S_t UNUSED *file_space, const H5S_t UNUSED *mem_space, - H5D_chunk_map_t *fm) -{ - H5SL_node_t *chunk_node; /* Current node in chunk skip list */ - H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - H5D_io_info_t cpt_io_info; /* Compact I/O info object */ - H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */ - hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */ - size_t dst_accessed_bytes = 0; /* Total accessed size in a chunk */ - unsigned idx_hint = 0; /* Cache index hint */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write) - - /* Sanity check */ - HDassert(io_info); - HDassert(io_info->u.wbuf); - HDassert(type_info); - HDassert(fm); - - /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); - ctg_io_info.store = &ctg_store; - ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; - - /* Initialize temporary contiguous storage info */ - ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size; - - /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); - cpt_io_info.store = &cpt_store; - cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; - - /* Initialize temporary compact storage info */ - cpt_store.compact.dirty = &cpt_dirty; - - /* Iterate through nodes in chunk skip list */ - chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm); - while(chunk_node) { - H5D_chunk_info_t *chunk_info; /* Chunk information */ - H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */ - void *chunk; /* Pointer to locked chunk buffer */ - haddr_t chunk_addr; /* Chunk address on disk */ - H5D_istore_ud1_t udata; /* B-tree pass-through */ - - /* Get the actual chunk information from the skip list node */ - chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); - - /* Pass in chunk's coordinates in a union. */ - io_info->store->chunk.offset = chunk_info->coords; - io_info->store->chunk.index = chunk_info->index; - - /* Load the chunk into cache. But if the whole chunk is written, - * simply allocate space instead of load the chunk. */ - chunk_addr = H5D_istore_get_addr(io_info, &udata); - if(H5D_chunk_cacheable(io_info, chunk_addr)) { - hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ - - /* Compute # of bytes accessed in chunk */ - dst_accessed_bytes = chunk_info->chunk_points * type_info->dst_type_size; - - /* Determine if we will access all the data in the chunk */ - if(dst_accessed_bytes != ctg_store.contig.dset_size || - (chunk_info->chunk_points * type_info->src_type_size) != ctg_store.contig.dset_size) - entire_chunk = FALSE; - - /* Lock the chunk into the cache */ - if(NULL == (chunk = H5D_istore_lock(io_info, &udata, entire_chunk, &idx_hint))) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") - - /* Set up the storage buffer information for this chunk */ - cpt_store.compact.buf = chunk; - - /* Point I/O info at main I/O info for this chunk */ - chk_io_info = &cpt_io_info; - } /* end if */ - else { - /* Sanity check */ - HDassert(H5F_addr_defined(chunk_addr)); - - /* Set up the storage address information for this chunk */ - ctg_store.contig.dset_addr = chunk_addr; - - /* No chunk cached */ - chunk = NULL; - - /* Point I/O info at temporary I/O info for this chunk */ - chk_io_info = &ctg_io_info; - } /* end else */ - - /* Perform the actual write operation */ - if((io_info->io_ops.single_write)(chk_io_info, type_info, - (hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed") - - /* Release the cache lock on the chunk. */ - if(chunk && H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, dst_accessed_bytes) < 0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") - - /* Advance to next chunk in list */ - chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node); - } /* end while */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5D_chunk_write() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_chunk_io_term - * - * Purpose: Destroy I/O operation information. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Saturday, May 17, 2003 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_chunk_io_term(const H5D_chunk_map_t *fm) -{ - herr_t ret_value = SUCCEED; /*return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_io_term) - - /* Single element I/O vs. multiple element I/O cleanup */ - if(fm->use_single) { - /* Sanity checks */ - HDassert(fm->sel_chunks == NULL); - HDassert(fm->single_chunk_info); - HDassert(fm->single_chunk_info->fspace_shared); - HDassert(fm->single_chunk_info->mspace_shared); - - /* Reset the selection for the single element I/O */ - H5S_select_all(fm->single_space, TRUE); - } /* end if */ - else { - /* Release the nodes on the list of selected chunks */ - if(fm->sel_chunks) - if(H5SL_free(fm->sel_chunks, H5D_free_chunk_info, NULL) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTNEXT, FAIL, "can't iterate over chunks") - } /* end else */ - - /* Free the memory chunk dataspace template */ - if(fm->mchunk_tmpl) - if(H5S_close(fm->mchunk_tmpl) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template") -#ifdef H5_HAVE_PARALLEL - if(fm->select_chunk) - H5MM_xfree(fm->select_chunk); -#endif /* H5_HAVE_PARALLEL */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_chunk_io_term() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_null_readvv - * - * Purpose: Performs "no-op" I/O operation, advancing through two I/O - * vectors, until one runs out. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, April 1, 2008 - * - *------------------------------------------------------------------------- - */ -static ssize_t -H5D_null_readvv(const H5D_io_info_t UNUSED *io_info, - size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[], - size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]) -{ - size_t u, v; /* Local index variables */ - size_t size; /* Size of sequence in bytes */ - ssize_t bytes_processed = 0; /* Eventual return value */ - - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_null_readvv) - - /* Check args */ - HDassert(chunk_len_arr); - HDassert(chunk_offset_arr); - HDassert(mem_len_arr); - HDassert(mem_offset_arr); - - /* Work through all the sequences */ - for(u = *mem_curr_seq, v = *chunk_curr_seq; u < mem_max_nseq && v < chunk_max_nseq; ) { - /* Choose smallest buffer to write */ - if(chunk_len_arr[v] < mem_len_arr[u]) - size = chunk_len_arr[v]; - else - size = mem_len_arr[u]; - - /* Update source information */ - chunk_len_arr[v] -= size; - chunk_offset_arr[v] += size; - if(chunk_len_arr[v] == 0) - v++; - - /* Update destination information */ - mem_len_arr[u] -= size; - mem_offset_arr[u] += size; - if(mem_len_arr[u] == 0) - u++; - - /* Increment number of bytes copied */ - bytes_processed += (ssize_t)size; - } /* end for */ - - /* Update current sequence vectors */ - *mem_curr_seq = u; - *chunk_curr_seq = v; - - FUNC_LEAVE_NOAPI(bytes_processed) -} /* H5D_null_readvv() */ - |