/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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; uf_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, uint32_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) } /* 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; uf_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; uf_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. */ H5_CHECK_OVERFLOW(dataset->shared->layout.u.chunk.size, uint32_t, size_t); if((size_t)dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes && H5F_addr_defined(caddr)) ret_value = FALSE; else ret_value = TRUE; #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ } /* end else */ 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 */ uint32_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 */ H5_ASSIGN_OVERFLOW(ctg_store.contig.dset_size, io_info->dset->shared->layout.u.chunk.size, uint32_t, hsize_t); /* 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)) { size_t tmp_src_accessed_bytes; /* Total accessed size in a chunk */ /* Compute # of bytes accessed in chunk */ tmp_src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size; H5_ASSIGN_OVERFLOW(src_accessed_bytes, tmp_src_accessed_bytes, size_t, uint32_t); /* 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 */ uint32_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 */ H5_ASSIGN_OVERFLOW(ctg_store.contig.dset_size, io_info->dset->shared->layout.u.chunk.size, uint32_t, hsize_t); /* 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 */ size_t tmp_dst_accessed_bytes; /* Total accessed size in a chunk */ /* Compute # of bytes accessed in chunk */ tmp_dst_accessed_bytes = chunk_info->chunk_points * type_info->dst_type_size; H5_ASSIGN_OVERFLOW(dst_accessed_bytes, tmp_dst_accessed_bytes, size_t, uint32_t); /* 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() */