/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 */ #include "H5MMprivate.h" /* Memory management */ #include "H5Vprivate.h" /* Vector and array functions */ /****************/ /* Local Macros */ /****************/ /* Default skip list height for storing list of chunks */ #define H5D_CHUNK_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)) /* * Feature: If this constant is defined then every cache preemption and load * causes a character to be printed on the standard error stream: * * `.': Entry was preempted because it has been completely read or * completely written but not partially read and not partially * written. This is often a good reason for preemption because such * a chunk will be unlikely to be referenced in the near future. * * `:': Entry was preempted because it hasn't been used recently. * * `#': Entry was preempted because another chunk collided with it. This * is usually a relatively bad thing. If there are too many of * these then the number of entries in the cache can be increased. * * c: Entry was preempted because the file is closing. * * w: A chunk read operation was eliminated because the library is * about to write new values to the entire chunk. This is a good * thing, especially on files where the chunk size is the same as * the disk block size, chunks are aligned on disk block boundaries, * and the operating system can also eliminate a read operation. */ /*#define H5D_CHUNK_DEBUG */ /******************/ /* Local Typedefs */ /******************/ /* Callback info for iteration to prune chunks */ typedef struct H5D_chunk_it_ud1_t { H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ const H5D_chk_idx_info_t *idx_info; /* Chunked index info */ const H5D_io_info_t *io_info; /* I/O info for dataset operation */ const hsize_t *dims; /* New dataset dimensions */ const hsize_t *down_chunks; /* "down" size of number of chunks in each dimension */ H5SL_t *outside; /* Skip list to hold chunks outside the new dimensions */ H5S_t *chunk_space; /* Dataspace for a chunk */ uint32_t elmts_per_chunk;/* Elements in chunk */ hsize_t *hyper_start; /* Starting location of hyperslab */ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init; /* Whether the fill value buffer has been initialized */ } H5D_chunk_it_ud1_t; /* Skip list node for storing chunks to remove during a "prune" iteration */ typedef struct H5D_chunk_sl_ck_t { hsize_t index; /* Index of chunk to remove (must be first) */ H5D_chunk_rec_t rec; /* Chunk record */ } H5D_chunk_sl_ck_t; /* Skip list callback info when destroying list & removing chunks during "prune" */ typedef struct H5D_chunk_sl_rm_t { const H5D_chk_idx_info_t *idx_info; /* I/O info for dataset operation */ const H5O_layout_t *mesg; /* Layout message */ } H5D_chunk_sl_rm_t; /* Callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */ typedef struct H5D_chunk_id_ud2_t { /* down */ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ const hsize_t *down_chunks; /* "down chunk" element counts for chunks */ /* up */ haddr_t *chunk_addr; /* Array of chunk addresses to fill in */ } H5D_chunk_it_ud2_t; /* Callback info for iteration to copy data */ typedef struct H5D_chunk_it_ud3_t { H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ H5F_t *file_src; /* Source file for copy */ H5D_chk_idx_info_t *idx_info_dst; /* Dest. chunk index info object */ void *buf; /* Buffer to hold chunk data for read/write */ void *bkg; /* Buffer for background information during type conversion */ size_t buf_size; /* Buffer size */ hbool_t do_convert; /* Whether to perform type conversions */ /* needed for converting variable-length data */ hid_t tid_src; /* Datatype ID for source datatype */ hid_t tid_dst; /* Datatype ID for destination datatype */ hid_t tid_mem; /* Datatype ID for memory datatype */ H5T_t *dt_src; /* Source datatype */ H5T_path_t *tpath_src_mem; /* Datatype conversion path from source file to memory */ H5T_path_t *tpath_mem_dst; /* Datatype conversion path from memory to dest. file */ void *reclaim_buf; /* Buffer for reclaiming data */ size_t reclaim_buf_size; /* Reclaim buffer size */ uint32_t nelmts; /* Number of elements in buffer */ H5S_t *buf_space; /* Dataspace describing buffer */ /* needed for compressed variable-length data */ H5O_pline_t *pline; /* Filter pipeline */ /* needed for copy object pointed by refs */ H5O_copy_t *cpy_info; /* Copy options */ } H5D_chunk_it_ud3_t; /* Callback info for iteration to dump index */ typedef struct H5D_chunk_it_ud4_t { FILE *stream; /* Output stream */ hbool_t header_displayed; /* Node's header is displayed? */ unsigned ndims; /* Number of dimensions for chunk/dataset */ } H5D_chunk_it_ud4_t; /********************/ /* Local Prototypes */ /********************/ /* Chunked layout operation callbacks */ static herr_t H5D_chunk_new(H5F_t *f, hid_t dapl_id, hid_t dxpl_id, H5D_t *dset, const H5P_genplist_t *dc_plist); 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); /* "Nonexistent" layout operation callback */ static ssize_t H5D_nonexistent_readvv(const H5D_io_info_t *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[]); /* Helper routines */ static void *H5D_chunk_alloc(size_t size, const H5O_pline_t *pline); static void *H5D_chunk_xfree(void *chk, const H5O_pline_t *pline); 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 */ /*********************/ /* Chunked storage layout I/O ops */ const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{ H5D_chunk_new, H5D_chunk_is_space_alloc, 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 */ /*******************/ /* "nonexistent" storage layout I/O ops */ const H5D_layout_ops_t H5D_LOPS_NONEXISTENT[1] = {{ NULL, NULL, NULL, NULL, NULL, #ifdef H5_HAVE_PARALLEL NULL, NULL, #endif /* H5_HAVE_PARALLEL */ H5D_nonexistent_readvv, NULL, NULL }}; /* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */ H5FL_SEQ_DEFINE_STATIC(H5D_rdcc_ent_ptr_t); /* Declare a free list to manage H5F_rdcc_ent_t objects */ H5FL_DEFINE_STATIC(H5D_rdcc_ent_t); /* Declare a free list to manage the H5D_chunk_info_t struct */ H5FL_DEFINE(H5D_chunk_info_t); /* Declare a free list to manage the chunk sequence information */ H5FL_BLK_DEFINE_STATIC(chunk); /* Declare a free list to manage H5D_chunk_sl_ck_t objects */ H5FL_DEFINE_STATIC(H5D_chunk_sl_ck_t); /*------------------------------------------------------------------------- * Function: H5D_chunk_new * * Purpose: Constructs new chunked layout information for dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, May 22, 2008 * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_new(H5F_t *f, hid_t dapl_id, hid_t dxpl_id, H5D_t *dset, const H5P_genplist_t *dc_plist) { const H5T_t *type = dset->shared->type; /* Convenience pointer to dataset's datatype */ hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ uint64_t chunk_size; /* Size of chunk in bytes */ int ndims; /* Rank of dataspace */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_new) /* Sanity checks */ HDassert(f); HDassert(dset); HDassert(dc_plist); /* Set up layout information */ if((ndims = H5S_GET_EXTENT_NDIMS(dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get rank") if(dset->shared->layout.u.chunk.ndims != (unsigned)ndims) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dimensionality of chunks doesn't match the dataspace") /* Increment # of chunk dimensions, to account for datatype size as last element */ dset->shared->layout.u.chunk.ndims++; HDassert((unsigned)(dset->shared->layout.u.chunk.ndims) <= NELMTS(dset->shared->layout.u.chunk.dim)); /* Chunked storage is not compatible with external storage (currently) */ if(dset->shared->dcpl_cache.efl.nused > 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "external storage not supported with chunked layout") /* Set the last dimension of the chunk size to the size of the datatype */ dset->shared->layout.u.chunk.dim[dset->shared->layout.u.chunk.ndims - 1] = H5T_GET_SIZE(type); /* Get local copy of dataset dimensions (for sanity checking) */ if(H5S_get_simple_extent_dims(dset->shared->space, NULL, max_dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to query maximum dimensions") /* Sanity check dimensions */ for(u = 0; u < dset->shared->layout.u.chunk.ndims - 1; u++) /* * The chunk size of a dimension with a fixed size cannot exceed * the maximum dimension size */ if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < dset->shared->layout.u.chunk.dim[u]) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be <= maximum dimension size for fixed-sized dimensions") /* Compute the total size of a chunk */ /* (Use 64-bit value to ensure that we can detect >4GB chunks) */ for(u = 1, chunk_size = (uint64_t)dset->shared->layout.u.chunk.dim[0]; u < dset->shared->layout.u.chunk.ndims; u++) chunk_size *= (uint64_t)dset->shared->layout.u.chunk.dim[u]; /* Check for chunk larger than can be represented in 32-bits */ /* (Chunk size is encoded in 32-bit value in v1 B-tree records) */ if(chunk_size > (uint64_t)0xffffffff) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be < 4GB") /* Retain computed chunk size */ H5_ASSIGN_OVERFLOW(dset->shared->layout.u.chunk.size, chunk_size, uint64_t, uint32_t); /* Initialize the chunk cache for the dataset */ if(H5D_chunk_init(f, dapl_id, dxpl_id, dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_new() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_is_space_alloc * * Purpose: Query if space is allocated for layout * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 15, 2009 * *------------------------------------------------------------------------- */ hbool_t H5D_chunk_is_space_alloc(const H5O_layout_t *layout) { hbool_t ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOFUNC(H5D_chunk_is_space_alloc) /* Sanity checks */ HDassert(layout); /* Query index layer */ ret_value = (layout->u.chunk.ops->is_space_alloc)(layout); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_is_space_alloc() */ /*------------------------------------------------------------------------- * 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_CHUNK_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), FALSE)) < 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), FALSE)) < 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, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") } /* end if */ if(file_space_normalized) { /* (Casting away const OK -QAK) */ 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() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_alloc * * Purpose: Allocate space for a chunk in memory. This routine allocates * memory space for non-filtered chunks from a block free list * and uses malloc()/free() for filtered chunks. * * Return: Pointer to memory for chunk on success/NULL on failure * * Programmer: Quincey Koziol * April 22, 2004 * *------------------------------------------------------------------------- */ static void * H5D_chunk_alloc(size_t size, const H5O_pline_t *pline) { void *ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_alloc) HDassert(size); HDassert(pline); if(pline->nused > 0) ret_value = H5MM_malloc(size); else ret_value = H5FL_BLK_MALLOC(chunk, size); FUNC_LEAVE_NOAPI(ret_value) } /* H5D_chunk_alloc() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_xfree * * Purpose: Free space for a chunk in memory. This routine allocates * memory space for non-filtered chunks from a block free list * and uses malloc()/free() for filtered chunks. * * Return: NULL (never fails) * * Programmer: Quincey Koziol * April 22, 2004 * *------------------------------------------------------------------------- */ static void * H5D_chunk_xfree(void *chk, const H5O_pline_t *pline) { FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_xfree) HDassert(pline); if(chk) { if(pline->nused > 0) H5MM_xfree(chk); else (void)H5FL_BLK_FREE(chunk, chk); } /* end if */ FUNC_LEAVE_NOAPI(NULL) } /* H5D_chunk_xfree() */ /*-------------------------------------------------------------------------- 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 */ (void)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(TRUE == H5S_hyper_intersect_block((H5S_t *)fm->file_space, coords, end)) { 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(NULL == (tmp_fchunk = H5S_copy(fm->file_space, TRUE, FALSE))) 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] + 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) { (void)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); (void)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(NULL == chunk_info->mspace) { /* Copy the template memory chunk dataspace */ if(NULL == (chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE))) 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) { 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_max) 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_t *dset, const hsize_t *chunk_offset, hsize_t chunk_idx) { H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/ hbool_t found = FALSE; /*already in cache? */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_in_cache) /* Sanity checks */ HDassert(dset); HDassert(chunk_offset); /* 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(dset->shared, chunk_idx); /* 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 < dset->shared->layout.u.chunk.ndims; u++) { if(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 nonexistent_io_info; /* "nonexistent" 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 "nonexistent" I/O info object */ HDmemcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info)); nonexistent_io_info.layout_ops = *H5D_LOPS_NONEXISTENT; /* 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 */ H5D_chunk_ud_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); /* Get the info for the chunk in the file */ if(H5D_chunk_get_info(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Check for non-existant chunk & skip it if appropriate */ if(H5F_addr_defined(udata.addr) || H5D_chunk_in_cache(io_info->dset, chunk_info->coords, chunk_info->index) || !skip_missing_chunks) { /* Load the chunk into cache and lock it. */ if(H5D_chunk_cacheable(io_info)) { /* Pass in chunk's coordinates in a union. */ io_info->store->chunk.offset = chunk_info->coords; io_info->store->chunk.index = chunk_info->index; /* 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_chunk_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 if(H5F_addr_defined(udata.addr)) { /* Set up the storage address information for this chunk */ ctg_store.contig.dset_addr = udata.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 if */ else { /* No chunk cached */ chunk = NULL; /* Point I/O info at "nonexistent" I/O info for this chunk */ chk_io_info = &nonexistent_io_info; } /* 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_chunk_unlock(io_info, FALSE, idx_hint, chunk, src_accessed_bytes) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") } /* end if */ /* 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 * * Modification:Raymond Lu * 4 Feb 2009 * One case that was considered cacheable was when the chunk * was bigger than the cache size but not allocated on disk. * I moved it to uncacheable branch to bypass the cache to * improve performance. *------------------------------------------------------------------------- */ 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 */ H5D_chunk_ud_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); /* Load the chunk into cache. But if the whole chunk is written, * simply allocate space instead of load the chunk. */ if(H5D_chunk_get_info(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") if(H5D_chunk_cacheable(io_info)) { hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Pass in chunk's coordinates in a union. */ io_info->store->chunk.offset = chunk_info->coords; io_info->store->chunk.index = chunk_info->index; /* 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_chunk_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 { /* If the chunk hasn't been allocated on disk, do so now. */ if(!H5F_addr_defined(udata.addr)) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ /* Compose chunked index info struct */ idx_info.f = io_info->dset->oloc.file; idx_info.dxpl_id = io_info->dxpl_id; idx_info.layout = &(io_info->dset->shared->layout); /* Set up the size of chunk for user data */ udata.nbytes = io_info->dset->shared->layout.u.chunk.size; /* Create the chunk */ if((io_info->dset->shared->layout.u.chunk.ops->insert)(&idx_info, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk") /* Make sure the address of the chunk is returned. */ if(!H5F_addr_defined(udata.addr)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined") } /* Set up the storage address information for this chunk */ ctg_store.contig.dset_addr = udata.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_chunk_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_chunk_init * * Purpose: Initialize the raw data chunk cache for a dataset. This is * called when the dataset is initialized. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Monday, May 18, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_init(H5F_t *f, hid_t dapl_id, hid_t dxpl_id, const H5D_t *dset) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Convenience pointer to dataset's chunk cache */ H5P_genplist_t *dapl; /* Data access property list object pointer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_init, FAIL) /* Sanity check */ HDassert(f); HDassert(dset); if(NULL == (dapl = (H5P_genplist_t *)H5I_object(dapl_id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for fapl ID"); /* Use the properties in dapl_id if they have been set, otherwise use the properties from the file */ if(H5P_get(dapl, H5D_ACS_DATA_CACHE_NUM_SLOTS_NAME, &rdcc->nslots) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET,FAIL, "can't get data cache number of slots"); if(rdcc->nslots == H5D_CHUNK_CACHE_NSLOTS_DEFAULT) rdcc->nslots = H5F_RDCC_NSLOTS(f); if(H5P_get(dapl, H5D_ACS_DATA_CACHE_BYTE_SIZE_NAME, &rdcc->nbytes_max) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET,FAIL, "can't get data cache byte size"); if(rdcc->nbytes_max == H5D_CHUNK_CACHE_NBYTES_DEFAULT) rdcc->nbytes_max = H5F_RDCC_NBYTES(f); if(H5P_get(dapl, H5D_ACS_PREEMPT_READ_CHUNKS_NAME, &rdcc->w0) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET,FAIL, "can't get preempt read chunks"); if(rdcc->w0 < 0) rdcc->w0 = H5F_RDCC_W0(f); /* If nbytes_max or nslots is 0, set them both to 0 and avoid allocating space */ if(!rdcc->nbytes_max || !rdcc->nslots) rdcc->nbytes_max = rdcc->nslots = 0; else { rdcc->slot = H5FL_SEQ_CALLOC(H5D_rdcc_ent_ptr_t, rdcc->nslots); if(NULL == rdcc->slot) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") /* Reset any cached chunk info for this dataset */ H5D_chunk_cinfo_cache_reset(&(rdcc->last)); } /* end else */ /* Compose chunked index info struct */ idx_info.f = f; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Allocate any indexing structures */ if((dset->shared->layout.u.chunk.ops->init)(&idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_init() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_idx_reset * * Purpose: Reset index information * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 15, 2009 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_idx_reset(H5O_layout_t *layout) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_idx_reset, FAIL) /* Sanity checks */ HDassert(layout); HDassert(layout->u.chunk.ops); /* Reset index structures */ if((layout->u.chunk.ops->reset)(layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset chunk index info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_idx_reset() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_cinfo_cache_reset * * Purpose: Reset the cached chunk info * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * November 27, 2007 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_cinfo_cache_reset(H5D_chunk_cached_t *last) { FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_reset) /* Sanity check */ HDassert(last); /* Indicate that the cached info is not valid */ last->valid = FALSE; FUNC_LEAVE_NOAPI(SUCCEED) } /* H5D_chunk_cinfo_cache_reset() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_cinfo_cache_update * * Purpose: Update the cached chunk info * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * November 27, 2007 * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *udata) { unsigned u; /* Local index variable */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_update) /* Sanity check */ HDassert(last); HDassert(udata); HDassert(udata->common.mesg); HDassert(udata->common.offset); /* Stored the information to cache */ for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++) last->offset[u] = udata->common.offset[u]; last->nbytes = udata->nbytes; last->filter_mask = udata->filter_mask; last->addr = udata->addr; /* Indicate that the cached info is valid */ last->valid = TRUE; FUNC_LEAVE_NOAPI(SUCCEED) } /* H5D_chunk_cinfo_cache_update() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_cinfo_cache_found * * Purpose: Look for chunk info in cache * * Return: TRUE/FALSE/FAIL * * Programmer: Quincey Koziol * November 27, 2007 * *------------------------------------------------------------------------- */ static hbool_t H5D_chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *udata) { hbool_t ret_value = FALSE; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_found) /* Sanity check */ HDassert(last); HDassert(udata); HDassert(udata->common.mesg); HDassert(udata->common.offset); /* Check if the cached information is what is desired */ if(last->valid) { unsigned u; /* Local index variable */ /* Check that the offset is the same */ for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++) if(last->offset[u] != udata->common.offset[u]) HGOTO_DONE(FALSE) /* Retrieve the information from the cache */ udata->nbytes = last->nbytes; udata->filter_mask = last->filter_mask; udata->addr = last->addr; /* Indicate that the data was found */ HGOTO_DONE(TRUE) } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_chunk_cinfo_cache_found() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_create * * Purpose: Creates a new chunked storage index and initializes the * layout information with information about the storage. The * layout info should be immediately written to the object header. * * Return: Non-negative on success (with the layout information initialized * and ready to write to an object header). Negative on failure. * * Programmer: Quincey Koziol * Thursday, May 22, 2008 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_create, FAIL) /* Check args */ HDassert(dset); HDassert(H5D_CHUNKED == dset->shared->layout.type); HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS); #ifndef NDEBUG { unsigned u; /* Local index variable */ for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++) HDassert(dset->shared->layout.u.chunk.dim[u] > 0); } #endif /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Create the index for the chunks */ if((dset->shared->layout.u.chunk.ops->create)(&idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_create() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_get_info * * Purpose: Get the info about a chunk if file space has been * assigned. Save the retrieved information in the udata * supplied. * * Return: Non-negative on success/Negative on failure * * Programmer: Albert Cheng * June 27, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_get_info(const H5D_t *dset, hid_t dxpl_id, const hsize_t *chunk_offset, H5D_chunk_ud_t *udata) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_get_info) HDassert(dset); HDassert(dset->shared->layout.u.chunk.ndims > 0); HDassert(chunk_offset); HDassert(udata); /* Initialize the query information about the chunk we are looking for */ udata->common.mesg = &(dset->shared->layout); udata->common.offset = chunk_offset; /* Reset information about the chunk we are looking for */ udata->nbytes = 0; udata->filter_mask = 0; udata->addr = HADDR_UNDEF; /* Check for cached information */ if(!H5D_chunk_cinfo_cache_found(&dset->shared->cache.chunk.last, udata)) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Go get the chunk information */ if((dset->shared->layout.u.chunk.ops->get_addr)(&idx_info, udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address") /* Cache the information retrieved */ H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata); } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_chunk_get_info() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_flush_entry * * Purpose: Writes a chunk to disk. If RESET is non-zero then the * entry is cleared -- it's slightly faster to flush a chunk if * the RESET flag is turned on because it results in one fewer * memory copy. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache, H5D_rdcc_ent_t *ent, hbool_t reset) { void *buf = NULL; /* Temporary buffer */ hbool_t point_of_no_return = FALSE; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_flush_entry) HDassert(dset); HDassert(dxpl_cache); HDassert(ent); HDassert(!ent->locked); buf = ent->chunk; if(ent->dirty) { H5D_chunk_ud_t udata; /* pass through B-tree */ hbool_t must_insert = FALSE; /* Whether the chunk must go through the "insert" method */ /* Set up user data for index callbacks */ udata.common.mesg = &dset->shared->layout; udata.common.offset = ent->offset; udata.filter_mask = 0; udata.nbytes = ent->chunk_size; udata.addr = ent->chunk_addr; /* Should the chunk be filtered before writing it to disk? */ if(dset->shared->dcpl_cache.pline.nused) { size_t alloc = ent->alloc_size; /* Bytes allocated for BUF */ size_t nbytes; /* Chunk size (in bytes) */ if(!reset) { /* * Copy the chunk to a new buffer before running it through * the pipeline because we'll want to save the original buffer * for later. */ H5_ASSIGN_OVERFLOW(alloc, ent->chunk_size, uint32_t, size_t); if(NULL == (buf = H5MM_malloc(alloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline") HDmemcpy(buf, ent->chunk, ent->chunk_size); } /* end if */ else { /* * If we are reseting and something goes wrong after this * point then it's too late to recover because we may have * destroyed the original data by calling H5Z_pipeline(). * The only safe option is to continue with the reset * even if we can't write the data to disk. */ point_of_no_return = TRUE; ent->chunk = NULL; } /* end else */ H5_ASSIGN_OVERFLOW(nbytes, udata.nbytes, uint32_t, size_t); if(H5Z_pipeline(&(dset->shared->dcpl_cache.pline), 0, &(udata.filter_mask), dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &alloc, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed") H5_ASSIGN_OVERFLOW(udata.nbytes, nbytes, size_t, uint32_t); /* Indicate that the chunk must go through 'insert' method */ must_insert = TRUE; } /* end if */ else if(!H5F_addr_defined(udata.addr)) /* Indicate that the chunk must go through 'insert' method */ must_insert = TRUE; /* Check if the chunk needs to be 'inserted' (could exist already and * the 'insert' operation could resize it) */ if(must_insert) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Create the chunk it if it doesn't exist, or reallocate the chunk * if its size changed. */ if((dset->shared->layout.u.chunk.ops->insert)(&idx_info, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk") /* Update the chunk entry's address, in case it was allocated or relocated */ ent->chunk_addr = udata.addr; } /* end if */ /* Write the data to the file */ HDassert(H5F_addr_defined(udata.addr)); if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.nbytes, dxpl_id, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") /* Cache the chunk's info, in case it's accessed again shortly */ H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata); /* Mark cache entry as clean */ ent->dirty = FALSE; /* Increment # of flushed entries */ dset->shared->cache.chunk.stats.nflushes++; } /* end if */ /* Reset, but do not free or removed from list */ if(reset) { point_of_no_return = FALSE; if(buf == ent->chunk) buf = NULL; if(ent->chunk != NULL) ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline)); } /* end if */ done: /* Free the temp buffer only if it's different than the entry chunk */ if(buf != ent->chunk) H5MM_xfree(buf); /* * If we reached the point of no return then we have no choice but to * reset the entry. This can only happen if RESET is true but the * output pipeline failed. Do not free the entry or remove it from the * list. */ if(ret_value < 0 && point_of_no_return) { if(ent->chunk) ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline)); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_flush_entry() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_cache_evict * * Purpose: Preempts the specified entry from the cache, flushing it to * disk if necessary. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache, H5D_rdcc_ent_t *ent, hbool_t flush) { H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_evict) HDassert(dset); HDassert(dxpl_cache); HDassert(ent); HDassert(!ent->locked); HDassert(ent->idx < rdcc->nslots); if(flush) { /* Flush */ if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") } /* end if */ else { /* Don't flush, just free chunk */ if(ent->chunk != NULL) ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline)); } /* end else */ /* Unlink from list */ if(ent->prev) ent->prev->next = ent->next; else rdcc->head = ent->next; if(ent->next) ent->next->prev = ent->prev; else rdcc->tail = ent->prev; ent->prev = ent->next = NULL; /* Remove from cache */ rdcc->slot[ent->idx] = NULL; ent->idx = UINT_MAX; rdcc->nbytes_used -= ent->chunk_size; --rdcc->nused; /* Free */ (void)H5FL_FREE(H5D_rdcc_ent_t, ent); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_cache_evict() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_cache_prune * * Purpose: Prune the cache by preempting some things until the cache has * room for something which is SIZE bytes. Only unlocked * entries are considered for preemption. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_cache_prune(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache, size_t size) { const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); size_t total = rdcc->nbytes_max; const int nmeth = 2; /*number of methods */ int w[1]; /*weighting as an interval */ H5D_rdcc_ent_t *p[2], *cur; /*list pointers */ H5D_rdcc_ent_t *n[2]; /*list next pointers */ int nerrors = 0; /* Accumulated error count during preemptions */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_prune) /* * Preemption is accomplished by having multiple pointers (currently two) * slide down the list beginning at the head. Pointer p(N+1) will start * traversing the list when pointer pN reaches wN percent of the original * list. In other words, preemption method N gets to consider entries in * approximate least recently used order w0 percent before method N+1 * where 100% means tha method N will run to completion before method N+1 * begins. The pointers participating in the list traversal are each * given a chance at preemption before any of the pointers are advanced. */ w[0] = (int)(rdcc->nused * rdcc->w0); p[0] = rdcc->head; p[1] = NULL; while((p[0] || p[1]) && (rdcc->nbytes_used + size) > total) { int i; /* Local index variable */ /* Introduce new pointers */ for(i = 0; i < nmeth - 1; i++) if(0 == w[i]) p[i + 1] = rdcc->head; /* Compute next value for each pointer */ for(i = 0; i < nmeth; i++) n[i] = p[i] ? p[i]->next : NULL; /* Give each method a chance */ for(i = 0; i < nmeth && (rdcc->nbytes_used + size) > total; i++) { if(0 == i && p[0] && !p[0]->locked && ((0 == p[0]->rd_count && 0 == p[0]->wr_count) || (0 == p[0]->rd_count && p[0]->chunk_size == p[0]->wr_count) || (p[0]->chunk_size == p[0]->rd_count && 0 == p[0]->wr_count))) { /* * Method 0: Preempt entries that have been completely written * and/or completely read but not entries that are partially * written or partially read. */ cur = p[0]; } else if(1 == i && p[1] && !p[1]->locked) { /* * Method 1: Preempt the entry without regard to * considerations other than being locked. This is the last * resort preemption. */ cur = p[1]; } else { /* Nothing to preempt at this point */ cur = NULL; } if(cur) { int j; /* Local index variable */ for(j = 0; j < nmeth; j++) { if(p[j] == cur) p[j] = NULL; if(n[j] == cur) n[j] = cur->next; } /* end for */ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, cur, TRUE) < 0) nerrors++; } /* end if */ } /* end for */ /* Advance pointers */ for(i = 0; i < nmeth; i++) p[i] = n[i]; for(i = 0; i < nmeth - 1; i++) w[i] -= 1; } /* end while */ if(nerrors) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to preempt one or more raw data cache entry") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_cache_prune() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_lock * * Purpose: Return a pointer to a dataset chunk. The pointer points * directly into the chunk cache and should not be freed * by the caller but will be valid until it is unlocked. The * input value IDX_HINT is used to speed up cache lookups and * it's output value should be given to H5F_chunk_unlock(). * IDX_HINT is ignored if it is out of range, and if it points * to the wrong entry then we fall back to the normal search * method. * * If RELAX is non-zero and the chunk isn't in the cache then * don't try to read it from the file, but just allocate an * uninitialized buffer to hold the result. This is intended * for output functions that are about to overwrite the entire * chunk. * * Return: Success: Ptr to a file chunk. * * Failure: NULL * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ void * H5D_chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax, unsigned *idx_hint/*in,out*/) { H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache*/ H5D_rdcc_ent_t *ent = NULL; /*cache entry */ unsigned idx = 0; /*hash index number */ hbool_t found = FALSE; /*already in cache? */ haddr_t chunk_addr = HADDR_UNDEF; /* Address of chunk on disk */ size_t chunk_size; /*size of a chunk */ void *chunk = NULL; /*the file chunk */ unsigned u; /*counters */ void *ret_value; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_lock) HDassert(io_info); HDassert(io_info->dxpl_cache); HDassert(io_info->store); HDassert(udata); HDassert(dset); HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER)); /* Get the chunk's size */ HDassert(layout->u.chunk.size > 0); H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t); /* Search for the chunk in the cache */ if(rdcc->nslots > 0) { idx = H5D_CHUNK_HASH(dset->shared, io_info->store->chunk.index); ent = rdcc->slot[idx]; if(ent) for(u = 0, found = TRUE; u < layout->u.chunk.ndims; u++) if(io_info->store->chunk.offset[u] != ent->offset[u]) { found = FALSE; break; } /* end if */ } /* end if */ if(found) { /* * Already in the cache. Count a hit. */ rdcc->stats.nhits++; } /* end if */ else if(relax) { /* * Not in the cache, but we're about to overwrite the whole thing * anyway, so just allocate a buffer for it but don't initialize that * buffer with the file contents. Count this as a hit instead of a * miss because we saved ourselves lots of work. */ rdcc->stats.nhits++; if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") /* In the case that some dataset functions look through this data, * clear it to all 0s. */ HDmemset(chunk, 0, chunk_size); } /* end if */ else { /* * Not in the cache. Count this as a miss if it's in the file * or an init if it isn't. */ /* Save the chunk address */ chunk_addr = udata->addr; /* Check if the chunk exists on disk */ if(H5F_addr_defined(chunk_addr)) { size_t chunk_alloc = 0; /*allocated chunk size */ /* Chunk size on disk isn't [likely] the same size as the final chunk * size in memory, so allocate memory big enough. */ H5_ASSIGN_OVERFLOW(chunk_alloc, udata->nbytes, uint32_t, size_t); if(NULL == (chunk = H5D_chunk_alloc(chunk_alloc, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, chunk_addr, chunk_alloc, io_info->dxpl_id, chunk) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk") if(pline->nused) { if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &(udata->filter_mask), io_info->dxpl_cache->err_detect, io_info->dxpl_cache->filter_cb, &chunk_alloc, &chunk_alloc, &chunk) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, NULL, "data pipeline read failed") H5_ASSIGN_OVERFLOW(udata->nbytes, chunk_alloc, size_t, uint32_t); } /* end if */ /* Increment # of cache misses */ rdcc->stats.nmisses++; } /* end if */ else { H5D_fill_value_t fill_status; /* Chunk size on disk isn't [likely] the same size as the final chunk * size in memory, so allocate memory big enough. */ if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") if(H5P_is_fill_value_defined(fill, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined") if(fill->fill_time == H5D_FILL_TIME_ALLOC || (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { /* * The chunk doesn't exist in the file. Replicate the fill * value throughout the chunk, if the fill value is defined. */ /* Initialize the fill value buffer */ /* (use the compact dataset storage buffer as the fill value buffer) */ if(H5D_fill_init(&fb_info, chunk, FALSE, NULL, NULL, NULL, NULL, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, (size_t)0, chunk_size, io_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize fill buffer info") fb_info_init = TRUE; /* Check for VL datatype & non-default fill value */ if(fb_info.has_vlen_fill_type) /* Fill the buffer with VL datatype fill values */ if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, io_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, NULL, "can't refill fill value buffer") } /* end if */ else HDmemset(chunk, 0, chunk_size); /* Increment # of creations */ rdcc->stats.ninits++; } /* end else */ } /* end else */ HDassert(found || chunk_size > 0); if(!found && rdcc->nslots > 0 && chunk_size <= rdcc->nbytes_max && (!ent || !ent->locked)) { /* * Add the chunk to the cache only if the slot is not already locked. * Preempt enough things from the cache to make room. */ if(ent) { if(H5D_chunk_cache_evict(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, ent, TRUE) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk from cache") } /* end if */ if(H5D_chunk_cache_prune(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, chunk_size) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk(s) from cache") /* Create a new entry */ ent = H5FL_MALLOC(H5D_rdcc_ent_t); ent->locked = 0; ent->dirty = FALSE; ent->chunk_addr = chunk_addr; H5_ASSIGN_OVERFLOW(ent->chunk_size, chunk_size, size_t, uint32_t); ent->alloc_size = chunk_size; for(u = 0; u < layout->u.chunk.ndims; u++) ent->offset[u] = io_info->store->chunk.offset[u]; H5_ASSIGN_OVERFLOW(ent->rd_count, chunk_size, size_t, uint32_t); H5_ASSIGN_OVERFLOW(ent->wr_count, chunk_size, size_t, uint32_t); ent->chunk = (uint8_t *)chunk; /* Add it to the cache */ HDassert(NULL == rdcc->slot[idx]); rdcc->slot[idx] = ent; ent->idx = idx; rdcc->nbytes_used += chunk_size; rdcc->nused++; /* Add it to the linked list */ ent->next = NULL; if(rdcc->tail) { rdcc->tail->next = ent; ent->prev = rdcc->tail; rdcc->tail = ent; } /* end if */ else { rdcc->head = rdcc->tail = ent; ent->prev = NULL; } /* end else */ found = TRUE; } else if(!found) { /* * The chunk is larger than the entire cache so we don't cache it. * This is the reason all those arguments have to be repeated for the * unlock function. */ ent = NULL; idx = UINT_MAX; } else { /* * The chunk is not at the beginning of the cache; move it backward * by one slot. This is how we implement the LRU preemption * algorithm. */ HDassert(ent); if(ent->next) { if(ent->next->next) ent->next->next->prev = ent; else rdcc->tail = ent; ent->next->prev = ent->prev; if(ent->prev) ent->prev->next = ent->next; else rdcc->head = ent->next; ent->prev = ent->next; ent->next = ent->next->next; ent->prev->next = ent; } /* end if */ } /* end else */ /* Lock the chunk into the cache */ if(ent) { HDassert(!ent->locked); ent->locked = TRUE; chunk = ent->chunk; } /* end if */ if(idx_hint) *idx_hint = idx; /* Set return value */ ret_value = chunk; done: /* Release the fill buffer info, if it's been initialized */ if(fb_info_init && H5D_fill_term(&fb_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "Can't release fill buffer info") /* Release the chunk allocated, on error */ if(!ret_value) if(chunk) chunk = H5D_chunk_xfree(chunk, pline); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_lock() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_unlock * * Purpose: Unlocks a previously locked chunk. The LAYOUT, COMP, and * OFFSET arguments should be the same as for H5D_chunk_lock(). * The DIRTY argument should be set to non-zero if the chunk has * been modified since it was locked. The IDX_HINT argument is * the returned index hint from the lock operation and BUF is * the return value from the lock. * * The NACCESSED argument should be the number of bytes accessed * for reading or writing (depending on the value of DIRTY). * It's only purpose is to provide additional information to the * preemption policy. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_unlock(const H5D_io_info_t *io_info, hbool_t dirty, unsigned idx_hint, void *chunk, uint32_t naccessed) { const H5O_layout_t *layout = &(io_info->dset->shared->layout); /* Dataset layout */ const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk); H5D_rdcc_ent_t *ent = NULL; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_unlock) HDassert(io_info); if(UINT_MAX == idx_hint) { /* * It's not in the cache, probably because it's too big. If it's * dirty then flush it to disk. In any case, free the chunk. * Note: we have to copy the layout and filter messages so we * don't discard the `const' qualifier. */ if(dirty) { H5D_rdcc_ent_t x; HDmemset(&x, 0, sizeof(x)); x.dirty = TRUE; HDmemcpy(x.offset, io_info->store->chunk.offset, layout->u.chunk.ndims * sizeof(x.offset[0])); HDassert(layout->u.chunk.size > 0); x.chunk_addr = HADDR_UNDEF; x.chunk_size = layout->u.chunk.size; H5_ASSIGN_OVERFLOW(x.alloc_size, x.chunk_size, uint32_t, size_t); x.chunk = (uint8_t *)chunk; if(H5D_chunk_flush_entry(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, &x, TRUE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") } /* end if */ else { if(chunk) chunk = H5D_chunk_xfree(chunk, &(io_info->dset->shared->dcpl_cache.pline)); } /* end else */ } /* end if */ else { /* Sanity check */ HDassert(idx_hint < rdcc->nslots); HDassert(rdcc->slot[idx_hint]); HDassert(rdcc->slot[idx_hint]->chunk == chunk); /* * It's in the cache so unlock it. */ ent = rdcc->slot[idx_hint]; HDassert(ent->locked); if(dirty) { ent->dirty = TRUE; ent->wr_count -= MIN(ent->wr_count, naccessed); } /* end if */ else ent->rd_count -= MIN(ent->rd_count, naccessed); ent->locked = FALSE; } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_unlock() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_flush * * Purpose: Writes all dirty chunks to disk and optionally preempts them * from the cache. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags) { H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); unsigned nerrors = 0; H5D_rdcc_ent_t *ent, *next; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_flush, FAIL) /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Loop over all entries in the chunk cache */ for(ent = rdcc->head; ent; ent = next) { next = ent->next; if((flags & H5F_FLUSH_INVALIDATE)) { if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0) nerrors++; } else { if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0) nerrors++; } } /* end for */ if(nerrors) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_flush() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_allocated_cb * * Purpose: Simply counts the number of chunks for a dataset. * * Return: Success: Non-negative * Failure: Negative * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { hsize_t *nbytes = (hsize_t *)_udata; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_allocated_cb) *(hsize_t *)nbytes += chunk_rec->nbytes; FUNC_LEAVE_NOAPI(H5_ITER_CONT) } /* H5D_chunk_allocated_cb() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_allocated * * Purpose: Return the number of bytes allocated in the file for storage * of raw data in the chunked dataset * * Return: Success: Number of bytes stored in all chunks. * Failure: 0 * * Programmer: Quincey Koziol * Tuesday, May 20, 2008 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */ H5D_rdcc_ent_t *ent; /* Cache entry */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ hsize_t chunk_bytes = 0; /* Number of bytes allocated for chunks */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_allocated, FAIL) HDassert(dset); /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Search for cached chunks that haven't been written out */ for(ent = rdcc->head; ent; ent = ent->next) { /* Flush the chunk out to disk, to make certain the size is correct later */ if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") } /* end for */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Call the index-specific "get all the allocated chunks sizes" routine */ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_allocated_cb, &chunk_bytes) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index") /* Set number of bytes for caller */ *nbytes = chunk_bytes; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_allocated() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_allocate * * Purpose: Allocate file space for all chunks that are not allocated yet. * Return SUCCEED if all needed allocation succeed, otherwise * FAIL. * * Return: Non-negative on success/Negative on failure * * Programmer: Albert Cheng * June 26, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ const H5D_chunk_ops_t *ops = dset->shared->layout.u.chunk.ops; /* Chunk operations */ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */ size_t orig_chunk_size; /* Original size of chunk in bytes */ unsigned filter_mask = 0; /* Filter mask for chunks that have them */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */ const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */ H5D_fill_value_t fill_status; /* The fill value status */ hbool_t should_fill = FALSE; /* Whether fill values should be written */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ #ifdef H5_HAVE_PARALLEL MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */ int mpi_rank = (-1); /* This process's rank */ int mpi_code; /* MPI return code */ hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */ hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ #endif /* H5_HAVE_PARALLEL */ hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ int space_ndims; /* Dataset's space rank */ hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ hid_t data_dxpl_id; /* DXPL ID to use for raw data I/O operations */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_allocate, FAIL) /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER)); /* Retrieve the dataset dimensions */ if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info") space_dim[space_ndims] = layout->u.chunk.dim[space_ndims]; #ifdef H5_HAVE_PARALLEL /* Retrieve MPI parameters */ if(IS_H5FD_MPI(dset->oloc.file)) { /* Get the MPI communicator */ if(MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file))) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator") /* Get the MPI rank */ if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file)) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank") /* Set the MPI-capable file driver flag */ using_mpi = TRUE; /* Use the internal "independent" DXPL */ data_dxpl_id = H5AC_ind_dxpl_id; } /* end if */ else { #endif /* H5_HAVE_PARALLEL */ /* Use the DXPL we were given */ data_dxpl_id = dxpl_id; #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(data_dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Get original chunk size */ H5_ASSIGN_OVERFLOW(orig_chunk_size, layout->u.chunk.size, uint32_t, size_t); /* Check the dataset's 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 filling the dataset on allocation or "if set" and * the fill value _is_ set, _and_ we are not overwriting the new blocks, * or if there are any pipeline filters defined, * set the "should fill" flag */ if((!full_overwrite && (fill->fill_time == H5D_FILL_TIME_ALLOC || (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED))) || pline->nused > 0) should_fill = TRUE; /* Check if fill values should be written to chunks */ if(should_fill) { /* Initialize the fill value buffer */ /* (delay allocating fill buffer for VL datatypes until refilling) */ /* (casting away const OK - QAK) */ if(H5D_fill_init(&fb_info, NULL, (hbool_t)(pline->nused > 0), (H5MM_allocate_t)H5D_chunk_alloc, (void *)pline, (H5MM_free_t)H5D_chunk_xfree, (void *)pline, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, (size_t)0, orig_chunk_size, data_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info") fb_info_init = TRUE; /* Check if there are filters which need to be applied to the chunk */ /* (only do this in advance when the chunk info can be re-used (i.e. * it doesn't contain any non-default VL datatype fill values) */ if(!fb_info.has_vlen_fill_type && pline->nused > 0) { size_t buf_size = orig_chunk_size; /* Push the chunk through the filters */ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed") } /* end if */ } /* end if */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Reset the chunk offset indices */ HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0]))); /* Loop over all chunks */ carry = FALSE; while(!carry) { H5D_chunk_ud_t udata; /* User data for querying chunk info */ int i; /* Local index variable */ /* Get the chunk's info */ if(H5D_chunk_get_info(dset, dxpl_id, chunk_offset, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Check if the chunk exists yet on disk */ if(!H5F_addr_defined(udata.addr)) { const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */ H5D_rdcc_ent_t *ent; /* Cache entry */ hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */ unsigned u; /* Local index variable */ /* Didn't find the chunk on disk */ chunk_exists = FALSE; /* Look for chunk in cache */ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) { /* Assume a match */ chunk_exists = TRUE; for(u = 0; u < layout->u.chunk.ndims; u++) if(ent->offset[u] != chunk_offset[u]) { chunk_exists = FALSE; /* Reset if no match */ break; } /* end if */ } /* end for */ /* Chunk wasn't in cache either, create it now */ if(!chunk_exists) { size_t chunk_size; /* Size of chunk in bytes, possibly filtered */ /* Check for VL datatype & non-default fill value */ if(fb_info_init && fb_info.has_vlen_fill_type) { /* Sanity check */ HDassert(should_fill); /* Fill the buffer with VL datatype fill values */ if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") /* Check if there are filters which need to be applied to the chunk */ if(pline->nused > 0) { size_t buf_size = orig_chunk_size; size_t nbytes = fb_info.fill_buf_size; /* Push the chunk through the filters */ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &fb_info.fill_buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed") /* Keep the number of bytes the chunk turned in to */ chunk_size = nbytes; } /* end if */ else H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t); } /* end if */ else chunk_size = orig_chunk_size; /* Initialize the chunk information */ udata.common.mesg = layout; udata.common.offset = chunk_offset; H5_ASSIGN_OVERFLOW(udata.nbytes, chunk_size, size_t, uint32_t); udata.filter_mask = filter_mask; udata.addr = HADDR_UNDEF; /* Allocate the chunk with all processes */ if((ops->insert)(&idx_info, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert record into chunk index") HDassert(H5F_addr_defined(udata.addr)); /* Check if fill values should be written to chunks */ if(should_fill) { /* Sanity check */ HDassert(fb_info_init); HDassert(udata.nbytes == chunk_size); #ifdef H5_HAVE_PARALLEL /* Check if this file is accessed with an MPI-capable file driver */ if(using_mpi) { /* Write the chunks out from only one process */ /* !! Use the internal "independent" DXPL!! -QAK */ if(H5_PAR_META_WRITE == mpi_rank) if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") /* Indicate that blocks are being written */ blocks_written = TRUE; } /* end if */ else { #endif /* H5_HAVE_PARALLEL */ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ } /* end if */ /* Release the fill buffer if we need to re-allocate it each time */ if(fb_info_init && fb_info.has_vlen_fill_type && pline->nused > 0) H5D_fill_release(&fb_info); } /* end if */ } /* end if */ /* Increment indices */ carry = TRUE; for(i = (int)(space_ndims - 1); i >= 0; --i) { chunk_offset[i] += layout->u.chunk.dim[i]; if(chunk_offset[i] >= space_dim[i]) chunk_offset[i] = 0; else { carry = FALSE; break; } /* end else */ } /* end for */ } /* end while */ #ifdef H5_HAVE_PARALLEL /* Only need to block at the barrier if we actually initialized a chunk */ /* using an MPI-capable file driver */ if(using_mpi && blocks_written) { /* Wait at barrier to avoid race conditions where some processes are * still writing out chunks and other processes race ahead to read * them in, getting bogus data. */ if(MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) } /* end if */ #endif /* H5_HAVE_PARALLEL */ /* Reset any cached chunk info for this dataset */ H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); done: /* Release the fill buffer info, if it's been initialized */ if(fb_info_init && H5D_fill_term(&fb_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_allocate() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_prune_cb * * Purpose: Search for chunks that are no longer inside the pruned * dataset's extent * * Return: Non-negative on success/Negative on failure * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * March 26, 2002 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_chunk_prune_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_chunk_it_ud1_t *udata = (H5D_chunk_it_ud1_t *)_udata; /* User data */ H5D_chunk_sl_ck_t *sl_node = NULL; /* Skip list node for chunk to remove */ unsigned rank; /* Current # of dimensions */ hbool_t should_delete = FALSE; /* Whether the chunk should be deleted */ hbool_t needs_fill = FALSE; /* Whether the chunk overlaps the new extent and needs fill valiues */ unsigned u; /* Local index variable */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_cb) /* Figure out what chunks are no longer in use for the specified extent and release them */ rank = udata->common.mesg->u.chunk.ndims - 1; for(u = 0; u < rank; u++) /* The chunk record points to a chunk of storage that contains the * beginning of the logical address space represented by UDATA. */ if(chunk_rec->offset[u] >= udata->dims[u]) { /* Indicate that the chunk will be deleted */ should_delete = TRUE; /* Break out of loop, we know the chunk is outside the current dimensions */ break; } /* end if */ /* Check for chunk that overlaps new extent and will need fill values */ else if((chunk_rec->offset[u] + udata->common.mesg->u.chunk.dim[u]) > udata->dims[u]) /* Indicate that the chunk needs filling */ /* (but continue in loop, since it could be outside the extent in * another dimension -QAK) */ needs_fill = TRUE; /* Check for chunk to delete */ if(should_delete) { /* Allocate space for the shared structure */ if(NULL == (sl_node = H5FL_MALLOC(H5D_chunk_sl_ck_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for shared B-tree info") /* Calculate the index of this chunk */ if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &sl_node->index) < 0) HGOTO_ERROR(H5E_IO, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index") /* Store the key for the chunk */ sl_node->rec = *chunk_rec; /* Insert the chunk description in the skip list */ if(H5SL_insert(udata->outside, sl_node, &sl_node->index) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINSERT, H5_ITER_ERROR, "can't insert chunk into skip list") } /* end if */ /* Check for chunk that overlaps the new dataset dimensions and needs filling */ else if(needs_fill) { const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */ H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */ hssize_t sel_nelmts; /* Number of elements in selection */ hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */ void *chunk; /* The file chunk */ unsigned idx_hint; /* Which chunk we're dealing with */ H5D_chunk_ud_t chk_udata; /* User data for locking chunk */ uint32_t bytes_accessed; /* Bytes accessed in chunk */ /* Initialize the fill value buffer, if necessary */ if(!udata->fb_info_init) { H5_CHECK_OVERFLOW(udata->elmts_per_chunk, uint32_t, size_t); if(H5D_fill_init(&udata->fb_info, NULL, FALSE, NULL, NULL, NULL, NULL, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk, io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't initialize fill buffer info") udata->fb_info_init = TRUE; } /* end if */ /* Compute the # of elements to leave with existing value, in each dimension */ for(u = 0; u < rank; u++) { count[u] = MIN(layout->u.chunk.dim[u], (udata->dims[u] - chunk_rec->offset[u])); HDassert(count[u] > 0); } /* end for */ /* Select all elements in chunk, to begin with */ if(H5S_select_all(udata->chunk_space, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select space") /* "Subtract out" the elements to keep */ if(H5S_select_hyperslab(udata->chunk_space, H5S_SELECT_NOTB, udata->hyper_start, NULL, count, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select hyperslab") /* Calculate the index of this chunk */ if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, udata->down_chunks, &io_info->store->chunk.index) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't get chunk index") /* Lock the chunk into the cache, to get a pointer to the chunk buffer */ /* (Casting away const OK -QAK) */ io_info->store->chunk.offset = (hsize_t *)chunk_rec->offset; chk_udata.common.mesg = layout; chk_udata.common.offset = chunk_rec->offset; chk_udata.nbytes = chunk_rec->nbytes; chk_udata.filter_mask = chunk_rec->filter_mask; chk_udata.addr = chunk_rec->chunk_addr; if(NULL == (chunk = (void *)H5D_chunk_lock(udata->io_info, &chk_udata, FALSE, &idx_hint))) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "unable to lock raw data chunk") /* Fill the selection in the memory buffer */ /* Use the size of the elements in the chunk directly instead of */ /* relying on the fill.size, which might be set to 0 if there is */ /* no fill-value defined for the dataset -QAK */ /* Get the number of elements in the selection */ sel_nelmts = H5S_GET_SELECT_NPOINTS(udata->chunk_space); HDassert(sel_nelmts >= 0); H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, size_t); /* Check for VL datatype & non-default fill value */ if(udata->fb_info.has_vlen_fill_type) /* Re-fill the buffer to use for this I/O operation */ if(H5D_fill_refill_vl(&udata->fb_info, (size_t)sel_nelmts, io_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, H5_ITER_ERROR, "can't refill fill value buffer") /* Create a selection iterator for scattering the elements to memory buffer */ if(H5S_select_iter_init(&chunk_iter, udata->chunk_space, layout->u.chunk.dim[rank]) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "unable to initialize chunk selection information") /* Scatter the data into memory */ if(H5D_scatter_mem(udata->fb_info.fill_buf, udata->chunk_space, &chunk_iter, (size_t)sel_nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) { H5S_SELECT_ITER_RELEASE(&chunk_iter); HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "scatter failed") } /* end if */ /* Release the selection iterator */ if(H5S_SELECT_ITER_RELEASE(&chunk_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "Can't release selection iterator") /* The number of bytes accessed in the chunk */ /* (i.e. the bytes replaced with fill values) */ H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, uint32_t); bytes_accessed = (uint32_t)sel_nelmts * layout->u.chunk.dim[rank]; /* Release lock on chunk */ if(H5D_chunk_unlock(io_info, TRUE, idx_hint, chunk, bytes_accessed) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5_ITER_ERROR, "unable to unlock raw data chunk") } /* end else-if */ done: if(ret_value != H5_ITER_CONT && sl_node) (void)H5FL_FREE(H5D_chunk_sl_ck_t, sl_node); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_prune_cb() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_prune_sl_rm_cb * * Purpose: Destroy a skip list node for "pruning" chunks, also removes * the chunk from the index. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol, koziol@hdfgroup.org * May 3, 2007 * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_prune_sl_rm_cb(void *item, void UNUSED *key, void *op_data) { H5D_chunk_sl_ck_t *sl_node = (H5D_chunk_sl_ck_t *)item; /* Temporary pointer to chunk to remove */ H5D_chunk_sl_rm_t *rm_info = (H5D_chunk_sl_rm_t *)op_data; /* Information needed for removing chunk from B-tree */ H5D_chunk_common_ud_t idx_udata; /* User data for index removal routine */ herr_t ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_sl_rm_cb) /* Sanity checks */ HDassert(sl_node); HDassert(rm_info); /* Initialize the user data for the index callback */ idx_udata.mesg = rm_info->mesg; idx_udata.offset = sl_node->rec.offset; /* Remove */ if((rm_info->idx_info->layout->u.chunk.ops->remove)(rm_info->idx_info, &idx_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, H5_ITER_ERROR, "unable to remove chunk entry from index") done: (void)H5FL_FREE(H5D_chunk_sl_ck_t, sl_node); FUNC_LEAVE_NOAPI(ret_value) } /* H5D_chunk_prune_sl_rm_cb() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_prune_by_extent * * Purpose: This function searches for chunks that are no longer necessary * both in the raw data cache and in the chunk index. * * Return: Non-negative on success/Negative on failure * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Algorithm: Robb Matzke * March 27, 2002 * * The algorithm is: * * For chunks that are no longer necessary: * * 1. Search in the raw data cache for each chunk * 2. If found then preempt it from the cache * 3. Search in the B-tree for each chunk * 4. If found then remove it from the B-tree and deallocate file storage for the chunk * * This example shows a 2d dataset of 90x90 with a chunk size of 20x20. * * * 0 20 40 60 80 90 100 * 0 +---------+---------+---------+---------+-----+...+ * |:::::X:::::::::::::: : : | : * |:::::::X:::::::::::: : : | : Key * |::::::::::X::::::::: : : | : -------- * |::::::::::::X::::::: : : | : +-+ Dataset * 20+::::::::::::::::::::.........:.........:.....+...: | | Extent * | :::::X::::: : : | : +-+ * | ::::::::::: : : | : * | ::::::::::: : : | : ... Chunk * | :::::::X::: : : | : : : Boundary * 40+.........:::::::::::.........:.........:.....+...: :.: * | : : : : | : * | : : : : | : ... Allocated * | : : : : | : ::: & Filled * | : : : : | : ::: Chunk * 60+.........:.........:.........:.........:.....+...: * | : :::::::X::: : | : X Element * | : ::::::::::: : | : Written * | : ::::::::::: : | : * | : ::::::::::: : | : * 80+.........:.........:::::::::::.........:.....+...: O Fill Val * | : : ::::::::::: | : Explicitly * | : : ::::::X:::: | : Written * 90+---------+---------+---------+---------+-----+ : * : : : ::::::::::: : * 100:.........:.........:.........:::::::::::.........: * * * We have 25 total chunks for this dataset, 5 of which have space * allocated in the file because they were written to one or more * elements. These five chunks (and only these five) also have entries in * the storage B-tree for this dataset. * * Now lets say we want to shrink the dataset down to 70x70: * * * 0 20 40 60 70 80 90 100 * 0 +---------+---------+---------+----+----+-----+...+ * |:::::X:::::::::::::: : | : | : * |:::::::X:::::::::::: : | : | : Key * |::::::::::X::::::::: : | : | : -------- * |::::::::::::X::::::: : | : | : +-+ Dataset * 20+::::::::::::::::::::.........:....+....:.....|...: | | Extent * | :::::X::::: : | : | : +-+ * | ::::::::::: : | : | : * | ::::::::::: : | : | : ... Chunk * | :::::::X::: : | : | : : : Boundary * 40+.........:::::::::::.........:....+....:.....|...: :.: * | : : : | : | : * | : : : | : | : ... Allocated * | : : : | : | : ::: & Filled * | : : : | : | : ::: Chunk * 60+.........:.........:.........:....+....:.....|...: * | : :::::::X::: | : | : X Element * | : ::::::::::: | : | : Written * +---------+---------+---------+----+ : | : * | : ::::::::::: : | : * 80+.........:.........:::::::::X:.........:.....|...: O Fill Val * | : : ::::::::::: | : Explicitly * | : : ::::::X:::: | : Written * 90+---------+---------+---------+---------+-----+ : * : : : ::::::::::: : * 100:.........:.........:.........:::::::::::.........: * * * That means that the nine chunks along the bottom and right side should * no longer exist. Of those nine chunks, (0,80), (20,80), (40,80), * (60,80), (80,80), (80,60), (80,40), (80,20), and (80,0), one is actually allocated * that needs to be released. * To release the chunks, we traverse the B-tree to obtain a list of unused * allocated chunks, and then call H5B_remove() for each chunk. * *------------------------------------------------------------------------- */ herr_t H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_io_info_t chk_io_info; /* Chunked I/O info object */ H5D_storage_t chk_store; /* Chunk storage information */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Cache entries */ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dataspace dimensions */ H5D_chunk_it_ud1_t udata; /* Chunk index iterator user data */ hbool_t udata_init = FALSE; /* Whether the chunk index iterator user data has been initialized */ H5D_chunk_sl_rm_t rm_info; /* User data for skip list destroy callback */ H5S_t *chunk_space = NULL; /* Dataspace for a chunk */ hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Current number of chunks in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */ hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */ uint32_t elmts_per_chunk; /* Elements in chunk */ unsigned rank; /* Current # of dimensions */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_prune_by_extent, FAIL) /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); HDassert(dxpl_cache); /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Go get the rank & dimensions (including the element size) */ rank = layout->u.chunk.ndims - 1; if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") curr_dims[rank] = layout->u.chunk.dim[rank]; /*------------------------------------------------------------------------- * Figure out what chunks are no longer in use for the specified extent * and release them from the linked list raw data cache *------------------------------------------------------------------------- */ for(ent = rdcc->head; ent; ent = next) { /* Get pointer to next extry in cache, in case this one is evicted */ next = ent->next; /* Check for chunk offset outside of new dimensions */ for(u = 0; u < rank; u++) if((hsize_t)ent->offset[u] >= curr_dims[u]) { /* Evict the entry from the cache, but do not flush it to disk */ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") /* Break out of loop, chunk is evicted */ break; } /* end if */ } /* end for */ /* Round up to the next integer # of chunks, to accomodate partial chunks */ /* (also compute the number of elements per chunk) */ /* (also copy the chunk dimensions into 'hsize_t' array for creating dataspace) */ elmts_per_chunk = 1; for(u = 0; u < rank; u++) { chunks[u] = ((old_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u]; elmts_per_chunk *= layout->u.chunk.dim[u]; chunk_dims[u] = layout->u.chunk.dim[u]; } /* end for */ /* Get the "down" sizes for each dimension */ if(H5V_array_down(rank, chunks, down_chunks) < 0) HGOTO_ERROR(H5E_IO, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") /* Create a dataspace for a chunk & set the extent */ if(NULL == (chunk_space = H5S_create_simple(rank, chunk_dims, NULL))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* Reset hyperslab start array */ /* (hyperslabs will always start from origin) */ HDmemset(hyper_start, 0, sizeof(hyper_start)); /* Set up chunked I/O info object, for operations on chunks (in callback) */ /* (Casting away const OK -QAK) */ H5D_BUILD_IO_INFO_RD(&chk_io_info, dset, dxpl_cache, dxpl_id, &chk_store, NULL); /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Initialize the user data for the iteration */ HDmemset(&udata, 0, sizeof udata); udata.common.mesg = layout; udata.io_info = &chk_io_info; udata.idx_info = &idx_info; udata.dims = curr_dims; udata.down_chunks = down_chunks; udata.elmts_per_chunk = elmts_per_chunk; udata.chunk_space = chunk_space; udata.hyper_start = hyper_start; udata_init = TRUE; /* Initialize the skip list that will hold the chunks outside the dimensions */ if(NULL == (udata.outside = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT))) HGOTO_ERROR(H5E_IO, H5E_CANTCREATE, FAIL, "can't create skip list for chunks outside new dimensions") /* Iterate over the chunks */ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_prune_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve prune chunks from index") /* Set up user data for skip list callback */ rm_info.idx_info = &idx_info; rm_info.mesg = layout; /* Destroy the skip list, deleting the chunks in the callback */ H5SL_destroy(udata.outside, H5D_chunk_prune_sl_rm_cb, &rm_info); /* Reset any cached chunk info for this dataset */ H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); done: /* Release resources */ if(chunk_space && H5S_close(chunk_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") if(udata_init) { if(udata.fb_info_init && H5D_fill_term(&udata.fb_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_prune_by_extent() */ #ifdef H5_HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5D_chunk_addrmap_cb * * Purpose: Callback when obtaining the chunk addresses for all existing chunks * * Return: Success: Non-negative * Failure: Negative * * Programmer: Kent Yang * Tuesday, November 15, 2005 * *------------------------------------------------------------------------- */ static int H5D_chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_chunk_it_ud2_t *udata = (H5D_chunk_it_ud2_t *)_udata; /* User data for callback */ unsigned rank = udata->common.mesg->u.chunk.ndims - 1; /* # of dimensions of dataset */ hsize_t chunk_index; int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_addrmap_cb) /* Compute the index for this chunk */ if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index") /* Set it in the userdata to return */ udata->chunk_addr[chunk_index] = chunk_rec->chunk_addr; done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_chunk_addrmap_cb() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_addrmap * * Purpose: Obtain the chunk addresses for all existing chunks * * Return: Success: Non-negative on succeed. * Failure: negative value * * Programmer: Kent Yang * November 15, 2005 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[], const hsize_t down_chunks[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ H5D_chunk_it_ud2_t udata; /* User data for iteration callback */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_addrmap, FAIL) HDassert(dset); HDassert(chunk_addr); HDassert(down_chunks); /* Set up user data for B-tree callback */ HDmemset(&udata, 0, sizeof(udata)); udata.common.mesg = &dset->shared->layout; udata.down_chunks = down_chunks; udata.chunk_addr = chunk_addr; /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = io_info->dxpl_id; idx_info.layout = &dset->shared->layout; /* Iterate over chunks to build mapping of chunk addresses */ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_addrmap_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to iterate over chunk index to build address map") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_addrmap() */ #endif /* H5_HAVE_PARALLEL */ /*------------------------------------------------------------------------- * Function: H5D_chunk_delete * * Purpose: Delete raw data storage for entire dataset (i.e. all chunks) * * Return: Success: Non-negative * Failure: negative * * Programmer: Quincey Koziol * Thursday, March 20, 2003 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_delete, FAIL) /* Compose chunked index info struct */ idx_info.f = f; idx_info.dxpl_id = dxpl_id; idx_info.layout = layout; /* Delete the chunked storage information in the file */ if((layout->u.chunk.ops->delete)(&idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk index") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_delete() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_update_cache * * Purpose: Update any cached chunks index values after the dataspace * size has changed * * Return: Success: Non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, May 29, 2004 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id) { H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent, *next; /*cache entry */ H5D_rdcc_ent_t *old_ent; /* Old cache entry */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ unsigned rank; /*current # of dimensions */ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */ unsigned u; /*counters */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_update_cache, FAIL) /* Check args */ HDassert(dset && H5D_CHUNKED == dset->shared->layout.type); HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS); /* Get the rank */ rank = dset->shared->layout.u.chunk.ndims-1; HDassert(rank > 0); /* 1-D dataset's chunks can't have their index change */ if(rank == 1) HGOTO_DONE(SUCCEED) /* Go get the dimensions */ if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") /* Round up to the next integer # of chunks, to accomodate partial chunks */ for(u = 0; u < rank; u++) chunks[u] = ((curr_dims[u] + dset->shared->layout.u.chunk.dim[u]) - 1) / dset->shared->layout.u.chunk.dim[u]; /* Get the "down" sizes for each dimension */ if(H5V_array_down(rank, chunks, down_chunks) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Recompute the index for each cached chunk that is in a dataset */ for(ent = rdcc->head; ent; ent = next) { hsize_t idx; /* Chunk index */ unsigned old_idx; /* Previous index number */ /* Get the pointer to the next cache entry */ next = ent->next; /* Calculate the index of this chunk */ if(H5V_chunk_index(rank, ent->offset, dset->shared->layout.u.chunk.dim, down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Compute the index for the chunk entry */ old_idx = ent->idx; /* Save for later */ ent->idx = H5D_CHUNK_HASH(dset->shared, idx); if(old_idx != ent->idx) { /* Check if there is already a chunk at this chunk's new location */ old_ent = rdcc->slot[ent->idx]; if(old_ent != NULL) { HDassert(old_ent->locked == 0); /* Check if we are removing the entry we would walk to next */ if(old_ent == next) next = old_ent->next; /* Remove the old entry from the cache */ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, old_ent, TRUE) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") } /* end if */ /* Insert this chunk into correct location in hash table */ rdcc->slot[ent->idx] = ent; /* Null out previous location */ rdcc->slot[old_idx] = NULL; } /* end if */ } /* end for */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_update_cache() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_copy_cb * * Purpose: Copy chunked raw data from source file and insert to the * index in the destination file * * Return: Non-negative on success/Negative on failure * * Programmer: Peter Cao * August 20, 2005 * *------------------------------------------------------------------------- */ static int H5D_chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_chunk_it_ud3_t *udata = (H5D_chunk_it_ud3_t *)_udata; /* User data for callback */ H5D_chunk_ud_t udata_dst; /* User data about new destination chunk */ hbool_t is_vlen = FALSE; /* Whether datatype is variable-length */ hbool_t fix_ref = FALSE; /* Whether to fix up references in the dest. file */ /* General information about chunk copy */ void *bkg = udata->bkg; /* Background buffer for datatype conversion */ void *buf = udata->buf; /* Chunk buffer for I/O & datatype conversions */ size_t buf_size = udata->buf_size; /* Size of chunk buffer */ H5O_pline_t *pline = udata->pline; /* I/O pipeline for applying filters */ /* needed for commpressed variable length data */ hbool_t has_filters = FALSE; /* Whether chunk has filters */ size_t nbytes; /* Size of chunk in file (in bytes) */ H5Z_cb_t cb_struct; /* Filter failure callback struct */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_copy_cb) /* Get 'size_t' local value for number of bytes in chunk */ H5_ASSIGN_OVERFLOW(nbytes, chunk_rec->nbytes, uint32_t, size_t); /* Check parameter for type conversion */ if(udata->do_convert) { if(H5T_detect_class(udata->dt_src, H5T_VLEN) > 0) is_vlen = TRUE; else if((H5T_get_class(udata->dt_src, FALSE) == H5T_REFERENCE) && (udata->file_src != udata->idx_info_dst->f)) fix_ref = TRUE; else HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements") } /* end if */ /* Check for filtered chunks */ if(pline && pline->nused) { has_filters = TRUE; cb_struct.func = NULL; /* no callback function when failed */ } /* end if */ /* Resize the buf if it is too small to hold the data */ if(nbytes > buf_size) { void *new_buf; /* New buffer for data */ /* Re-allocate memory for copying the chunk */ if(NULL == (new_buf = H5MM_realloc(udata->buf, nbytes))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk") udata->buf = new_buf; if(udata->bkg) { if(NULL == (new_buf = H5MM_realloc(udata->bkg, nbytes))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk") udata->bkg = new_buf; if(!udata->cpy_info->expand_ref) HDmemset((uint8_t *)udata->bkg + buf_size, 0, (size_t)(nbytes - buf_size)); bkg = udata->bkg; } /* end if */ buf = udata->buf; udata->buf_size = buf_size = nbytes; } /* end if */ /* read chunk data from the source file */ if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk") /* Need to uncompress variable-length & reference data elements */ if(has_filters && (is_vlen || fix_ref)) { unsigned filter_mask = chunk_rec->filter_mask; if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "data pipeline read failed") } /* end if */ /* Perform datatype conversion, if necessary */ if(is_vlen) { H5T_path_t *tpath_src_mem = udata->tpath_src_mem; H5T_path_t *tpath_mem_dst = udata->tpath_mem_dst; H5S_t *buf_space = udata->buf_space; hid_t tid_src = udata->tid_src; hid_t tid_dst = udata->tid_dst; hid_t tid_mem = udata->tid_mem; void *reclaim_buf = udata->reclaim_buf; size_t reclaim_buf_size = udata->reclaim_buf_size; /* Convert from source file to memory */ H5_CHECK_OVERFLOW(udata->nelmts, uint32_t, size_t); if(H5T_convert(tpath_src_mem, tid_src, tid_mem, (size_t)udata->nelmts, (size_t)0, (size_t)0, buf, NULL, udata->idx_info_dst->dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ HDmemcpy(reclaim_buf, buf, reclaim_buf_size); /* Set background buffer to all zeros */ HDmemset(bkg, 0, buf_size); /* Convert from memory to destination file */ if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, udata->nelmts, (size_t)0, (size_t)0, buf, bkg, udata->idx_info_dst->dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed") /* Reclaim space from variable length data */ if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, H5_ITER_ERROR, "unable to reclaim variable-length data") } /* end if */ else if(fix_ref) { /* Check for expanding references */ /* (background buffer has already been zeroed out, if not expanding) */ if(udata->cpy_info->expand_ref) { size_t ref_count; /* Determine # of reference elements to copy */ ref_count = nbytes / H5T_get_size(udata->dt_src); /* Copy the reference elements */ if(H5O_copy_expand_ref(udata->file_src, buf, udata->idx_info_dst->dxpl_id, udata->idx_info_dst->f, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute") } /* end if */ /* After fix ref, copy the new reference elements to the buffer to write out */ HDmemcpy(buf, bkg, buf_size); } /* end if */ /* Set up destination chunk callback information for insertion */ udata_dst.common.mesg = udata->idx_info_dst->layout; udata_dst.common.offset = chunk_rec->offset; udata_dst.nbytes = chunk_rec->nbytes; udata_dst.filter_mask = chunk_rec->filter_mask; udata_dst.addr = HADDR_UNDEF; /* Need to compress variable-length & reference data elements before writing to file */ if(has_filters && (is_vlen || fix_ref) ) { if(H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed") H5_ASSIGN_OVERFLOW(udata_dst.nbytes, nbytes, size_t, uint32_t); udata->buf = buf; udata->buf_size = buf_size; } /* end if */ /* Insert chunk into the destination index */ if((udata->idx_info_dst->layout->u.chunk.ops->insert)(udata->idx_info_dst, &udata_dst) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk into index") /* Write chunk data to destination file */ HDassert(H5F_addr_defined(udata_dst.addr)); if(H5F_block_write(udata->idx_info_dst->f, H5FD_MEM_DRAW, udata_dst.addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_copy_cb() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_copy * * Purpose: Copy chunked storage from SRC file to DST file. * * Return: Success: Non-negative * Failure: negative * * Programmer: Peter Cao * August 20, 2005 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, H5O_pline_t *pline, hid_t dxpl_id) { H5D_chunk_it_ud3_t udata; /* User data for iteration callback */ H5D_chk_idx_info_t idx_info_dst; /* Dest. chunked index info */ H5D_chk_idx_info_t idx_info_src; /* Source chunked index info */ H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ hid_t tid_src = -1; /* Datatype ID for source datatype */ hid_t tid_dst = -1; /* Datatype ID for destination datatype */ hid_t tid_mem = -1; /* Datatype ID for memory datatype */ size_t buf_size; /* Size of copy buffer */ size_t reclaim_buf_size; /* Size of reclaim buffer */ void *buf = NULL; /* Buffer for copying data */ void *bkg = NULL; /* Buffer for background during type conversion */ void *reclaim_buf = NULL; /* Buffer for reclaiming data */ H5S_t *buf_space = NULL; /* Dataspace describing buffer */ hid_t sid_buf = -1; /* ID for buffer dataspace */ uint32_t nelmts = 0; /* Number of elements in buffer */ hbool_t do_convert = FALSE; /* Indicate that type conversions should be performed */ hbool_t copy_setup_done = FALSE; /* Indicate that 'copy setup' is done */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_copy, FAIL) /* Check args */ HDassert(f_src); HDassert(f_dst); HDassert(layout_src && H5D_CHUNKED == layout_src->type); HDassert(layout_dst && H5D_CHUNKED == layout_dst->type); HDassert(dt_src); /* Compose source & dest chunked index info structs */ idx_info_src.f = f_src; idx_info_src.dxpl_id = dxpl_id; idx_info_src.layout = layout_src; idx_info_dst.f = f_dst; idx_info_dst.dxpl_id = dxpl_id; idx_info_dst.layout = layout_dst; /* Call the index-specific "copy setup" routine */ if((layout_src->u.chunk.ops->copy_setup)(&idx_info_src, &idx_info_dst) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up index-specific chunk copying information") copy_setup_done = TRUE; /* Create datatype ID for src datatype */ if((tid_src = H5I_register(H5I_DATATYPE, dt_src, FALSE)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype") /* If there's a VLEN source datatype, set up type conversion information */ if(H5T_detect_class(dt_src, H5T_VLEN) > 0) { H5T_t *dt_dst; /* Destination datatype */ H5T_t *dt_mem; /* Memory datatype */ size_t mem_dt_size; /* Memory datatype size */ size_t tmp_dt_size; /* Temp. datatype size */ size_t max_dt_size; /* Max atatype size */ hsize_t buf_dim; /* Dimension for buffer */ unsigned u; /* create a memory copy of the variable-length datatype */ if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy") if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype") /* create variable-length datatype at the destinaton file */ if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy") if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk") if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst, FALSE)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype") /* Set up the conversion functions */ if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes") if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes") /* Determine largest datatype size */ if(0 == (max_dt_size = H5T_get_size(dt_src))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") if(0 == (mem_dt_size = H5T_get_size(dt_mem))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") max_dt_size = MAX(max_dt_size, mem_dt_size); if(0 == (tmp_dt_size = H5T_get_size(dt_dst))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") max_dt_size = MAX(max_dt_size, tmp_dt_size); /* Compute the number of elements per chunk */ nelmts = 1; for(u = 0; u < (layout_src->u.chunk.ndims - 1); u++) nelmts *= layout_src->u.chunk.dim[u]; /* Create the space and set the initial extent */ buf_dim = nelmts; if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* Atomize */ if((sid_buf = H5I_register(H5I_DATASPACE, buf_space, FALSE)) < 0) { H5S_close(buf_space); HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID") } /* end if */ /* Set initial buffer sizes */ buf_size = nelmts * max_dt_size; reclaim_buf_size = nelmts * mem_dt_size; /* Allocate memory for reclaim buf */ if(NULL == (reclaim_buf = H5MM_malloc(reclaim_buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") /* Indicate that type conversion should be performed */ do_convert = TRUE; } /* end if */ else { if(H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) { /* Indicate that type conversion should be performed */ do_convert = TRUE; } /* end if */ H5_ASSIGN_OVERFLOW(buf_size, layout_src->u.chunk.size, uint32_t, size_t); reclaim_buf_size = 0; } /* end else */ /* Set up conversion buffer, if appropriate */ if(do_convert) { /* Allocate background memory for converting the chunk */ if(NULL == (bkg = H5MM_malloc(buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") /* Check for reference datatype and no expanding references & clear background buffer */ if(!cpy_info->expand_ref && ((H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) && (f_src != f_dst))) /* Reset value to zero */ HDmemset(bkg, 0, buf_size); } /* end if */ /* Allocate memory for copying the chunk */ if(NULL == (buf = H5MM_malloc(buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") /* Initialize the callback structure for the source */ HDmemset(&udata, 0, sizeof udata); udata.common.mesg = layout_src; udata.file_src = f_src; udata.idx_info_dst = &idx_info_dst; udata.buf = buf; udata.bkg = bkg; udata.buf_size = buf_size; udata.tid_src = tid_src; udata.tid_mem = tid_mem; udata.tid_dst = tid_dst; udata.dt_src = dt_src; udata.do_convert = do_convert; udata.tpath_src_mem = tpath_src_mem; udata.tpath_mem_dst = tpath_mem_dst; udata.reclaim_buf = reclaim_buf; udata.reclaim_buf_size = reclaim_buf_size; udata.buf_space = buf_space; udata.nelmts = nelmts; udata.pline = pline; udata.cpy_info = cpy_info; /* Iterate over chunks to copy data */ if((layout_src->u.chunk.ops->iterate)(&idx_info_src, H5D_chunk_copy_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to copy data") /* I/O buffers may have been re-allocated */ buf = udata.buf; bkg = udata.bkg; done: if(sid_buf > 0 && H5I_dec_ref(sid_buf, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't decrement temporary dataspace ID") if(tid_src > 0) if(H5I_dec_ref(tid_src, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(tid_dst > 0) if(H5I_dec_ref(tid_dst, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(tid_mem > 0) if(H5I_dec_ref(tid_mem, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(buf) H5MM_xfree(buf); if(bkg) H5MM_xfree(bkg); if(reclaim_buf) H5MM_xfree(reclaim_buf); /* Clean up any index information */ if(copy_setup_done) if((layout_src->u.chunk.ops->copy_shutdown)(layout_src, layout_dst) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to shut down index copying info") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_copy() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_bh_size * * Purpose: Retrieve the amount of index storage for chunked dataset * * Return: Success: Non-negative * Failure: negative * * Programmer: Vailin Choi * June 8, 2007 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout, hsize_t *index_size) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_bh_info, FAIL) /* Check args */ HDassert(f); HDassert(layout); HDassert(index_size); /* Compose chunked index info struct */ idx_info.f = f; idx_info.dxpl_id = dxpl_id; idx_info.layout = layout; /* Get size of index structure */ if((layout->u.chunk.ops->size)(&idx_info, index_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve chunk index info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_bh_info() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_iter_dump * * Purpose: If the UDATA.STREAM member is non-null then debugging * information is written to that stream. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_chunk_it_ud4_t *udata = (H5D_chunk_it_ud4_t *)_udata; /* User data from caller */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_dump_index_cb) if(udata->stream) { unsigned u; /* Local index variable */ /* Print header if not already displayed */ if(!udata->header_displayed) { HDfprintf(udata->stream, " Flags Bytes Address Logical Offset\n"); HDfprintf(udata->stream, " ========== ======== ========== ==============================\n"); /* Set flag that the headers has been printed */ udata->header_displayed = TRUE; } /* end if */ /* Print information about this chunk */ HDfprintf(udata->stream, " 0x%08x %8Zu %10a [", chunk_rec->filter_mask, chunk_rec->nbytes, chunk_rec->chunk_addr); for(u = 0; u < udata->ndims; u++) HDfprintf(udata->stream, "%s%Hd", (u ? ", " : ""), chunk_rec->offset[u]); HDfputs("]\n", udata->stream); } /* end if */ FUNC_LEAVE_NOAPI(H5_ITER_CONT) } /* H5D_chunk_dump_index_cb() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_dump_index * * Purpose: Prints information about the storage index to the specified * stream. * * Return: Success: Non-negative * Failure: negative * * Programmer: Robb Matzke * Wednesday, April 28, 1999 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_dump_index, FAIL) /* Sanity check */ HDassert(dset); /* Only display info if stream is defined */ if(stream) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_chunk_it_ud4_t udata; /* User data for callback */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Display info for index */ if((dset->shared->layout.u.chunk.ops->dump)(&idx_info, stream) < 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to dump chunk index info") /* Set up user data for callback */ udata.stream = stream; udata.header_displayed = FALSE; udata.ndims = dset->shared->layout.u.chunk.ndims; /* Iterate over index and dump chunk info */ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_dump_index_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to dump chunk info") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_dump_index() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_dest * * Purpose: Destroy the entire chunk cache by flushing dirty entries, * preempting all entries, and freeing the cache itself. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Dataset's chunk cache */ H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Pointer to current & next cache entries */ int nerrors = 0; /* Accumulated count of errors */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_dest, FAIL) HDassert(f); HDassert(dset); /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Flush all the cached chunks */ for(ent = rdcc->head; ent; ent = next) { next = ent->next; if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0) nerrors++; } /* end for */ if(nerrors) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") /* Release cache structures */ if(rdcc->slot) rdcc->slot = H5FL_SEQ_FREE(H5D_rdcc_ent_ptr_t, rdcc->slot); HDmemset(rdcc, 0, sizeof(H5D_rdcc_t)); /* Compose chunked index info struct */ idx_info.f = f; idx_info.dxpl_id = dxpl_id; idx_info.layout = &dset->shared->layout; /* Free any index structures */ if((dset->shared->layout.u.chunk.ops->dest)(&idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_dest() */ #ifdef H5D_CHUNK_DEBUG /*------------------------------------------------------------------------- * Function: H5D_chunk_stats * * Purpose: Print raw data cache statistics to the debug stream. If * HEADERS is non-zero then print table column headers, * otherwise assume that the H5AC layer has already printed them. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_chunk_stats(const H5D_t *dset, hbool_t headers) { H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); double miss_rate; char ascii[32]; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_stats, FAIL) if (!H5DEBUG(AC)) HGOTO_DONE(SUCCEED) if (headers) { fprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n"); fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n", "Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes"); fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n", "-----", "----", "------", "--------", "-----", "-------"); } #ifdef H5AC_DEBUG if (H5DEBUG(AC)) headers = TRUE; #endif if (headers) { if (rdcc->nhits>0 || rdcc->nmisses>0) { miss_rate = 100.0 * rdcc->nmisses / (rdcc->nhits + rdcc->nmisses); } else { miss_rate = 0.0; } if (miss_rate > 100) { sprintf(ascii, "%7d%%", (int) (miss_rate + 0.5)); } else { sprintf(ascii, "%7.2f%%", miss_rate); } fprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", "raw data chunks", rdcc->nhits, rdcc->nmisses, ascii, rdcc->ninits, (long)(rdcc->nflushes)-(long)(rdcc->ninits)); } done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_stats() */ #endif /* H5D_CHUNK_DEBUG */ /*------------------------------------------------------------------------- * Function: H5D_nonexistent_readvv * * Purpose: When the chunk doesn't exist on disk and the chunk is bigger * than the cache size, performs fill value I/O operation on * memory buffer, advancing through two I/O vectors, until one * runs out. * * Note: This algorithm is pretty inefficient about initializing and * terminating the fill buffer info structure and it would be * faster to refactor this into a "real" initialization routine, * and a "vectorized fill" routine. -QAK * * Return: Non-negative on success/Negative on failure * * Programmer: Raymond Lu * 6 Feb 2009 * *------------------------------------------------------------------------- */ static ssize_t H5D_nonexistent_readvv(const H5D_io_info_t *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[]) { H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ ssize_t bytes_processed = 0; /* Eventual return value */ size_t u, v; /* Local index variables */ ssize_t ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_nonexistent_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; ) { unsigned char *buf; /* Temporary pointer into read buffer */ size_t size; /* Size of sequence in bytes */ /* 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]; /* Compute offset in memory */ buf = (unsigned char *)io_info->u.rbuf + mem_offset_arr[v]; /* Initialize the fill value buffer */ if(H5D_fill_init(&fb_info, buf, FALSE, NULL, NULL, NULL, NULL, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, (size_t)0, size, io_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info") fb_info_init = TRUE; /* Check for VL datatype & fill the buffer with VL datatype fill values */ if(fb_info.has_vlen_fill_type && H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, io_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") /* Release the fill buffer info */ if(H5D_fill_term(&fb_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") fb_info_init = FALSE; /* 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; /* Set return value */ ret_value = bytes_processed; done: /* Release the fill buffer info, if it's been initialized */ if(fb_info_init && H5D_fill_term(&fb_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") FUNC_LEAVE_NOAPI(ret_value) } /* H5D_nonexistent_readvv() */