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Diffstat (limited to 'src/H5Dchunk.c')
| -rw-r--r-- | src/H5Dchunk.c | 1515 |
1 files changed, 1515 insertions, 0 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c new file mode 100644 index 0000000..baaa5f1 --- /dev/null +++ b/src/H5Dchunk.c @@ -0,0 +1,1515 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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() */ + |