/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 COPYING file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* Programmer: Quincey Koziol * Thursday, April 24, 2008 * * Purpose: Abstract indexed (chunked) I/O functions. The logical * multi-dimensional dataspace is regularly partitioned into * same-sized "chunks", the first of which is aligned with the * logical origin. The chunks are indexed by different methods, * that map a chunk index to disk address. Each chunk can be * compressed independently and the chunks may move around in the * file as their storage requirements change. * * Cache: Disk I/O is performed in units of chunks and H5MF_alloc() * contains code to optionally align chunks on disk block * boundaries for performance. * * The chunk cache is an extendible hash indexed by a function * of storage B-tree address and chunk N-dimensional offset * within the dataset. Collisions are not resolved -- one of * the two chunks competing for the hash slot must be preempted * from the cache. All entries in the hash also participate in * a doubly-linked list and entries are penalized by moving them * toward the front of the list. When a new chunk is about to * be added to the cache the heap is pruned by preempting * entries near the front of the list to make room for the new * entry which is added to the end of the list. */ /****************/ /* Module Setup */ /****************/ #include "H5Dmodule.h" /* This source code file is part of the H5D module */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #ifdef H5_HAVE_PARALLEL #include "H5ACprivate.h" /* Metadata cache */ #endif /* H5_HAVE_PARALLEL */ #include "H5CXprivate.h" /* API Contexts */ #include "H5Dpkg.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5Fprivate.h" /* File functions */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5MFprivate.h" /* File memory management */ #include "H5VMprivate.h" /* Vector and array functions */ /****************/ /* Local Macros */ /****************/ /* 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)) /* Sanity check on chunk index types: commonly used by a lot of routines in this file */ #define H5D_CHUNK_STORAGE_INDEX_CHK(storage) \ HDassert((H5D_CHUNK_IDX_EARRAY == (storage)->idx_type && H5D_COPS_EARRAY == (storage)->ops) || \ (H5D_CHUNK_IDX_FARRAY == (storage)->idx_type && H5D_COPS_FARRAY == (storage)->ops) || \ (H5D_CHUNK_IDX_BT2 == (storage)->idx_type && H5D_COPS_BT2 == (storage)->ops) || \ (H5D_CHUNK_IDX_BTREE == (storage)->idx_type && H5D_COPS_BTREE == (storage)->ops) || \ (H5D_CHUNK_IDX_SINGLE == (storage)->idx_type && H5D_COPS_SINGLE == (storage)->ops) || \ (H5D_CHUNK_IDX_NONE == (storage)->idx_type && H5D_COPS_NONE == (storage)->ops)); /* * 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 */ /* Flags for the "edge_chunk_state" field below */ #define H5D_RDCC_DISABLE_FILTERS 0x01u /* Disable filters on this chunk */ #define H5D_RDCC_NEWLY_DISABLED_FILTERS \ 0x02u /* Filters have been disabled since \ * the last flush */ /******************/ /* Local Typedefs */ /******************/ /* Raw data chunks are cached. Each entry in the cache is: */ typedef struct H5D_rdcc_ent_t { hbool_t locked; /*entry is locked in cache */ hbool_t dirty; /*needs to be written to disk? */ hbool_t deleted; /*chunk about to be deleted */ unsigned edge_chunk_state; /*states related to edge chunks (see above) */ hsize_t scaled[H5O_LAYOUT_NDIMS]; /*scaled chunk 'name' (coordinates) */ uint32_t rd_count; /*bytes remaining to be read */ uint32_t wr_count; /*bytes remaining to be written */ H5F_block_t chunk_block; /*offset/length of chunk in file */ hsize_t chunk_idx; /*index of chunk in dataset */ uint8_t * chunk; /*the unfiltered chunk data */ unsigned idx; /*index in hash table */ struct H5D_rdcc_ent_t *next; /*next item in doubly-linked list */ struct H5D_rdcc_ent_t *prev; /*previous item in doubly-linked list */ struct H5D_rdcc_ent_t *tmp_next; /*next item in temporary doubly-linked list */ struct H5D_rdcc_ent_t *tmp_prev; /*previous item in temporary doubly-linked list */ } H5D_rdcc_ent_t; typedef H5D_rdcc_ent_t *H5D_rdcc_ent_ptr_t; /* For free lists */ /* 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 * space_dim; /* New dataset dimensions */ const hbool_t * shrunk_dim; /* Dimensions which have been shrunk */ 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; /* 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_it_ud2_t { /* down */ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ /* 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 */ const 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 */ const H5O_pline_t *pline; /* Filter pipeline */ unsigned dset_ndims; /* Number of dimensions in dataset */ const hsize_t * dset_dims; /* Dataset dimensions */ /* needed for copy object pointed by refs */ H5O_copy_t *cpy_info; /* Copy options */ /* needed for getting raw data from chunk cache */ hbool_t chunk_in_cache; uint8_t *chunk; /* the unfiltered chunk data */ } 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 */ uint32_t *chunk_dim; /* Chunk dimensions */ } H5D_chunk_it_ud4_t; /* Callback info for iteration to format convert chunks */ typedef struct H5D_chunk_it_ud5_t { H5D_chk_idx_info_t *new_idx_info; /* Dest. chunk index info object */ unsigned dset_ndims; /* Number of dimensions in dataset */ hsize_t * dset_dims; /* Dataset dimensions */ } H5D_chunk_it_ud5_t; /* Callback info for nonexistent readvv operation */ typedef struct H5D_chunk_readvv_ud_t { unsigned char *rbuf; /* Read buffer to initialize */ const H5D_t * dset; /* Dataset to operate on */ } H5D_chunk_readvv_ud_t; /* Typedef for chunk info iterator callback */ typedef struct H5D_chunk_info_iter_ud_t { hsize_t scaled[H5O_LAYOUT_NDIMS]; /* Logical offset of the chunk */ hsize_t ndims; /* Number of dimensions in the dataset */ uint32_t nbytes; /* Size of stored data in the chunk */ unsigned filter_mask; /* Excluded filters */ haddr_t chunk_addr; /* Address of the chunk in file */ hsize_t chunk_idx; /* Chunk index, where the iteration needs to stop */ hsize_t curr_idx; /* Current index, where the iteration is */ unsigned idx_hint; /* Index of chunk in cache, if present */ hbool_t found; /* Whether the chunk was found */ } H5D_chunk_info_iter_ud_t; /* Callback info for file selection iteration */ typedef struct H5D_chunk_file_iter_ud_t { H5D_chunk_map_t *fm; /* File->memory chunk mapping info */ #ifdef H5_HAVE_PARALLEL const H5D_io_info_t *io_info; /* I/O info for operation */ #endif /* H5_HAVE_PARALLEL */ } H5D_chunk_file_iter_ud_t; #ifdef H5_HAVE_PARALLEL /* information to construct a collective I/O operation for filling chunks */ typedef struct H5D_chunk_coll_fill_info_t { size_t num_chunks; /* Number of chunks in the write operation */ struct chunk_coll_fill_info { haddr_t addr; /* File address of the chunk */ size_t chunk_size; /* Size of the chunk in the file */ hbool_t unfiltered_partial_chunk; } * chunk_info; } H5D_chunk_coll_fill_info_t; #endif /* H5_HAVE_PARALLEL */ /********************/ /* Local Prototypes */ /********************/ /* Chunked layout operation callbacks */ static herr_t H5D__chunk_construct(H5F_t *f, H5D_t *dset); static herr_t H5D__chunk_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id); 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_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, 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_flush(H5D_t *dset); static herr_t H5D__chunk_io_term(const H5D_chunk_map_t *fm); static herr_t H5D__chunk_dest(H5D_t *dset); /* Chunk query operation callbacks */ static int H5D__get_num_chunks_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata); static int H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata); static int H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata); /* "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[]); /* Format convert cb */ static int H5D__chunk_format_convert_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata); /* Helper routines */ static herr_t H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims, const hsize_t *curr_dims, const hsize_t *max_dims); static herr_t H5D__chunk_cinfo_cache_reset(H5D_chunk_cached_t *last); static herr_t H5D__chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *udata); static hbool_t H5D__chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *udata); 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_all(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_1d(const H5D_chunk_map_t *fm); static herr_t H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm); static herr_t H5D__chunk_file_cb(void *elem, const H5T_t *type, unsigned ndims, const hsize_t *coords, void *fm); static herr_t H5D__chunk_mem_cb(void *elem, const H5T_t *type, unsigned ndims, const hsize_t *coords, void *fm); static unsigned H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *scaled); static herr_t H5D__chunk_flush_entry(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset); static herr_t H5D__chunk_cache_evict(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t flush); static void * H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax, hbool_t prev_unfilt_chunk); static herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty, void *chunk, uint32_t naccessed); static herr_t H5D__chunk_cache_prune(const H5D_t *dset, size_t size); static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfilt_chunk); #ifdef H5_HAVE_PARALLEL static herr_t H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_fill_info, const void *fill_buf, const void *partial_chunk_fill_buf); static int H5D__chunk_cmp_coll_fill_info(const void *_entry1, const void *_entry2); #endif /* H5_HAVE_PARALLEL */ /* Debugging helper routine callback */ static int H5D__chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata); /*********************/ /* Package Variables */ /*********************/ /* Chunked storage layout I/O ops */ const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = { {H5D__chunk_construct, H5D__chunk_init, H5D__chunk_is_space_alloc, H5D__chunk_is_data_cached, 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_flush, H5D__chunk_io_term, H5D__chunk_dest}}; /*******************/ /* Local Variables */ /*******************/ /* "nonexistent" storage layout I/O ops */ const H5D_layout_ops_t H5D_LOPS_NONEXISTENT[1] = {{NULL, NULL, NULL, NULL, NULL, NULL, NULL, #ifdef H5_HAVE_PARALLEL NULL, NULL, #endif /* H5_HAVE_PARALLEL */ H5D__nonexistent_readvv, NULL, NULL, 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 H5D_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 extern free list to manage the H5S_sel_iter_t struct */ H5FL_EXTERN(H5S_sel_iter_t); /*------------------------------------------------------------------------- * Function: H5D__chunk_direct_write * * Purpose: Internal routine to write a chunk directly into the file. * * Return: Non-negative on success/Negative on failure * * Programmer: Raymond Lu * 30 July 2012 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters, hsize_t *offset, uint32_t data_size, const void *buf) { const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ H5D_chunk_ud_t udata; /* User data for querying chunk info */ H5F_block_t old_chunk; /* Offset/length of old chunk */ H5D_chk_idx_info_t idx_info; /* Chunked index info */ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */ hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) /* Sanity checks */ HDassert(layout->type == H5D_CHUNKED); /* Allocate dataspace and initialize it if it hasn't been. */ if (!H5D__chunk_is_space_alloc(&layout->storage)) { H5D_io_info_t io_info; /* to hold the dset info */ io_info.dset = dset; io_info.f_sh = H5F_SHARED(dset->oloc.file); /* Allocate storage */ if (H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, FALSE, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") } /* Calculate the index of this chunk */ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled); scaled[dset->shared->ndims] = 0; /* Find out the file address of the chunk (if any) */ if (H5D__chunk_lookup(dset, scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Sanity check */ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) || (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0)); /* Set the file block information for the old chunk */ /* (Which is only defined when overwriting an existing chunk) */ old_chunk.offset = udata.chunk_block.offset; old_chunk.length = udata.chunk_block.length; /* Check if the chunk needs to be inserted (it also could exist already * and the chunk allocate operation could resize it) */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &(dset->shared->dcpl_cache.pline); idx_info.layout = &(dset->shared->layout.u.chunk); idx_info.storage = &(dset->shared->layout.storage.u.chunk); /* Set up the size of chunk for user data */ udata.chunk_block.length = data_size; if (0 == idx_info.pline->nused && H5F_addr_defined(old_chunk.offset)) /* If there are no filters and we are overwriting the chunk we can just set values */ need_insert = FALSE; else { /* Otherwise, create the chunk it if it doesn't exist, or reallocate the chunk * if its size has changed. */ if (H5D__chunk_file_alloc(&idx_info, &old_chunk, &udata.chunk_block, &need_insert, scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") /* Cache the new chunk information */ H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata); } /* end else */ /* Make sure the address of the chunk is returned. */ if (!H5F_addr_defined(udata.chunk_block.offset)) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk address isn't defined") /* Evict the (old) entry from the cache if present, but do not flush * it to disk */ if (UINT_MAX != udata.idx_hint) { const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ if (H5D__chunk_cache_evict(dset, rdcc->slot[udata.idx_hint], FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") } /* end if */ /* Write the data to the file */ if (H5F_shared_block_write(H5F_SHARED(dset->oloc.file), H5FD_MEM_DRAW, udata.chunk_block.offset, data_size, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data to file") /* Insert the chunk record into the index */ if (need_insert && layout->storage.u.chunk.ops->insert) { /* Set the chunk's filter mask to the new settings */ udata.filter_mask = filters; if ((layout->storage.u.chunk.ops->insert)(&idx_info, &udata, dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") } /* end if */ done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__chunk_direct_write() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_direct_read * * Purpose: Internal routine to read a chunk directly from the file. * * Return: Non-negative on success/Negative on failure * * Programmer: Matthew Strong (GE Healthcare) * 14 February 2016 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_direct_read(const H5D_t *dset, hsize_t *offset, uint32_t *filters, void *buf) { const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ const H5D_rdcc_t * rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */ H5D_chunk_ud_t udata; /* User data for querying chunk info */ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(offset); HDassert(filters); HDassert(buf); *filters = 0; /* Allocate dataspace and initialize it if it hasn't been. */ if (!H5D__chunk_is_space_alloc(&layout->storage) && !H5D__chunk_is_data_cached(dset->shared)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "storage is not initialized") /* Calculate the index of this chunk */ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled); scaled[dset->shared->ndims] = 0; /* Reset fields about the chunk we are looking for */ udata.filter_mask = 0; udata.chunk_block.offset = HADDR_UNDEF; udata.chunk_block.length = 0; udata.idx_hint = UINT_MAX; /* Find out the file address of the chunk */ if (H5D__chunk_lookup(dset, scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Sanity check */ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) || (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0)); /* Check if the requested chunk exists in the chunk cache */ if (UINT_MAX != udata.idx_hint) { H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint]; hbool_t flush; /* Sanity checks */ HDassert(udata.idx_hint < rdcc->nslots); HDassert(rdcc->slot[udata.idx_hint]); flush = (ent->dirty == TRUE) ? TRUE : FALSE; /* Flush the chunk to disk and clear the cache entry */ if (H5D__chunk_cache_evict(dset, rdcc->slot[udata.idx_hint], flush) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") /* Reset fields about the chunk we are looking for */ udata.filter_mask = 0; udata.chunk_block.offset = HADDR_UNDEF; udata.chunk_block.length = 0; udata.idx_hint = UINT_MAX; /* Get the new file address / chunk size after flushing */ if (H5D__chunk_lookup(dset, scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") } /* Make sure the address of the chunk is returned. */ if (!H5F_addr_defined(udata.chunk_block.offset)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined") /* Read the chunk data into the supplied buffer */ if (H5F_shared_block_read(H5F_SHARED(dset->oloc.file), H5FD_MEM_DRAW, udata.chunk_block.offset, udata.chunk_block.length, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") /* Return the filter mask */ *filters = udata.filter_mask; done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__chunk_direct_read() */ /*------------------------------------------------------------------------- * Function: H5D__get_chunk_storage_size * * Purpose: Internal routine to read the storage size of a chunk on disk. * * Return: Non-negative on success/Negative on failure * * Programmer: Matthew Strong (GE Healthcare) * 20 October 2016 * *------------------------------------------------------------------------- */ herr_t H5D__get_chunk_storage_size(H5D_t *dset, const hsize_t *offset, hsize_t *storage_size) { const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ const H5D_rdcc_t * rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */ H5D_chunk_ud_t udata; /* User data for querying chunk info */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(offset); HDassert(storage_size); *storage_size = 0; /* Allocate dataspace and initialize it if it hasn't been. */ if (!(*layout->ops->is_space_alloc)(&layout->storage)) HGOTO_DONE(SUCCEED) /* Calculate the index of this chunk */ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled); scaled[dset->shared->ndims] = 0; /* Reset fields about the chunk we are looking for */ udata.chunk_block.offset = HADDR_UNDEF; udata.chunk_block.length = 0; udata.idx_hint = UINT_MAX; /* Find out the file address of the chunk */ if (H5D__chunk_lookup(dset, scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Sanity check */ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) || (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0)); /* The requested chunk is not in cache or on disk */ if (!H5F_addr_defined(udata.chunk_block.offset) && UINT_MAX == udata.idx_hint) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk storage is not allocated") /* Check if there are filters registered to the dataset */ if (dset->shared->dcpl_cache.pline.nused > 0) { /* Check if the requested chunk exists in the chunk cache */ if (UINT_MAX != udata.idx_hint) { H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint]; /* Sanity checks */ HDassert(udata.idx_hint < rdcc->nslots); HDassert(rdcc->slot[udata.idx_hint]); /* If the cached chunk is dirty, it must be flushed to get accurate size */ if (ent->dirty == TRUE) { /* Flush the chunk to disk and clear the cache entry */ if (H5D__chunk_cache_evict(dset, rdcc->slot[udata.idx_hint], TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") /* Reset fields about the chunk we are looking for */ udata.chunk_block.offset = HADDR_UNDEF; udata.chunk_block.length = 0; udata.idx_hint = UINT_MAX; /* Get the new file address / chunk size after flushing */ if (H5D__chunk_lookup(dset, scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") } } /* Make sure the address of the chunk is returned. */ if (!H5F_addr_defined(udata.chunk_block.offset)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined") /* Return the chunk size on disk */ *storage_size = udata.chunk_block.length; } /* There are no filters registered, return the chunk size from the storage layout */ else *storage_size = dset->shared->layout.u.chunk.size; done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* H5D__get_chunk_storage_size */ /*------------------------------------------------------------------------- * Function: H5D__chunk_set_info_real * * Purpose: Internal routine to set the information about chunks for a dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Tuesday, June 30, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims, const hsize_t *curr_dims, const hsize_t *max_dims) { unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity checks */ HDassert(layout); HDassert(ndims > 0); HDassert(curr_dims); /* Compute the # of chunks in dataset dimensions */ for (u = 0, layout->nchunks = 1, layout->max_nchunks = 1; u < ndims; u++) { /* Round up to the next integer # of chunks, to accommodate partial chunks */ layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u]; if (H5S_UNLIMITED == max_dims[u]) layout->max_chunks[u] = H5S_UNLIMITED; else { /* Sanity check */ if (layout->dim[u] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dimension size must be > 0, dim = %u ", u) layout->max_chunks[u] = ((max_dims[u] + layout->dim[u]) - 1) / layout->dim[u]; } /* Accumulate the # of chunks */ layout->nchunks *= layout->chunks[u]; layout->max_nchunks *= layout->max_chunks[u]; } /* end for */ /* Get the "down" sizes for each dimension */ H5VM_array_down(ndims, layout->chunks, layout->down_chunks); H5VM_array_down(ndims, layout->max_chunks, layout->max_down_chunks); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_set_info_real() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_set_info * * Purpose: Sets the information about chunks for a dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Tuesday, June 30, 2009 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_set_info(const H5D_t *dset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity checks */ HDassert(dset); /* Set the base layout information */ if (H5D__chunk_set_info_real(&dset->shared->layout.u.chunk, dset->shared->ndims, dset->shared->curr_dims, dset->shared->max_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout's chunk info") /* Call the index's "resize" callback */ if (dset->shared->layout.storage.u.chunk.ops->resize && (dset->shared->layout.storage.u.chunk.ops->resize)(&dset->shared->layout.u.chunk) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to resize chunk index information") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_set_info() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_set_sizes * * Purpose: Sets chunk and type sizes. * * Return: SUCCEED/FAIL * * Programmer: Dana Robinson * December 2015 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_set_sizes(H5D_t *dset) { uint64_t chunk_size; /* Size of chunk in bytes */ unsigned max_enc_bytes_per_dim; /* Max. number of bytes required to encode this dimension */ unsigned u; /* Iterator */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* Sanity checks */ HDassert(dset); /* Increment # of chunk dimensions, to account for datatype size as last element */ dset->shared->layout.u.chunk.ndims++; /* 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] = (uint32_t)H5T_GET_SIZE(dset->shared->type); /* Compute number of bytes to use for encoding chunk dimensions */ max_enc_bytes_per_dim = 0; for (u = 0; u < (unsigned)dset->shared->layout.u.chunk.ndims; u++) { unsigned enc_bytes_per_dim; /* Number of bytes required to encode this dimension */ /* Get encoded size of dim, in bytes */ enc_bytes_per_dim = (H5VM_log2_gen(dset->shared->layout.u.chunk.dim[u]) + 8) / 8; /* Check if this is the largest value so far */ if (enc_bytes_per_dim > max_enc_bytes_per_dim) max_enc_bytes_per_dim = enc_bytes_per_dim; } /* end for */ HDassert(max_enc_bytes_per_dim > 0 && max_enc_bytes_per_dim <= 8); dset->shared->layout.u.chunk.enc_bytes_per_dim = max_enc_bytes_per_dim; /* Compute and store 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") H5_CHECKED_ASSIGN(dset->shared->layout.u.chunk.size, uint32_t, chunk_size, uint64_t); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_set_sizes */ /*------------------------------------------------------------------------- * Function: H5D__chunk_construct * * 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_construct(H5F_t H5_ATTR_UNUSED *f, H5D_t *dset) { unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity checks */ HDassert(f); HDassert(dset); /* Check for invalid chunk dimension rank */ if (0 == dset->shared->layout.u.chunk.ndims) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "no chunk information set?") if (dset->shared->layout.u.chunk.ndims != dset->shared->ndims) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dimensionality of chunks doesn't match the dataspace") /* Set chunk sizes */ if (H5D__chunk_set_sizes(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "unable to set chunk sizes") 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") /* Sanity check dimensions */ for (u = 0; u < dset->shared->layout.u.chunk.ndims - 1; u++) { /* Don't allow zero-sized chunk dimensions */ if (0 == dset->shared->layout.u.chunk.dim[u]) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be > 0, dim = %u ", u) /* * The chunk size of a dimension with a fixed size cannot exceed * the maximum dimension size. If any dimension size is zero, there * will be no such restriction. */ if (dset->shared->curr_dims[u] && dset->shared->max_dims[u] != H5S_UNLIMITED && dset->shared->max_dims[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") } /* end for */ /* Reset address and pointer of the array struct for the chunked storage index */ if (H5D_chunk_idx_reset(&dset->shared->layout.storage.u.chunk, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to reset chunked storage index") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_construct() */ /*------------------------------------------------------------------------- * 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 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_init(H5F_t *f, const H5D_t *const dset, hid_t dapl_id) { 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 */ H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(f); HDassert(dset); H5D_CHUNK_STORAGE_INDEX_CHK(sc); 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 */ /* Compute scaled dimension info, if dataset dims > 1 */ if (dset->shared->ndims > 1) { unsigned u; /* Local index value */ for (u = 0; u < dset->shared->ndims; u++) { hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */ /* Initial scaled dimension sizes */ if (dset->shared->layout.u.chunk.dim[u] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u) /* Round up to the next integer # of chunks, to accommodate partial chunks */ rdcc->scaled_dims[u] = (dset->shared->curr_dims[u] + dset->shared->layout.u.chunk.dim[u] - 1) / dset->shared->layout.u.chunk.dim[u]; if (!(scaled_power2up = H5VM_power2up(rdcc->scaled_dims[u]))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get the next power of 2") /* Initial 'power2up' values for scaled dimensions */ rdcc->scaled_power2up[u] = scaled_power2up; /* Number of bits required to encode scaled dimension size */ rdcc->scaled_encode_bits[u] = H5VM_log2_gen(rdcc->scaled_power2up[u]); } /* end for */ } /* end if */ /* Compose chunked index info struct */ idx_info.f = f; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Allocate any indexing structures */ if (sc->ops->init && (sc->ops->init)(&idx_info, dset->shared->space, dset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information") /* Set the number of chunks in dataset, etc. */ if (H5D__chunk_set_info(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set # of chunks for dataset") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_init() */ /*------------------------------------------------------------------------- * 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_storage_t *storage) { const H5O_storage_chunk_t *sc = &(storage->u.chunk); hbool_t ret_value = FALSE; /* Return value */ FUNC_ENTER_PACKAGE_NOERR /* Sanity checks */ HDassert(storage); H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Query index layer */ ret_value = (sc->ops->is_space_alloc)(sc); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_is_space_alloc() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_is_data_cached * * Purpose: Query if raw data is cached for dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * Wednessday, March 6, 2016 * *------------------------------------------------------------------------- */ hbool_t H5D__chunk_is_data_cached(const H5D_shared_t *shared_dset) { FUNC_ENTER_PACKAGE_NOERR /* Sanity checks */ HDassert(shared_dset); FUNC_LEAVE_NOAPI(shared_dset->cache.chunk.nused > 0) } /* end H5D__chunk_is_data_cached() */ /*------------------------------------------------------------------------- * 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) { const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */ htri_t file_space_normalized = FALSE; /* File dataspace was normalized */ 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) */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* 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_CHECKED_ASSIGN(fm->m_ndims, unsigned, sm_ndims, int); /* Get rank for file dataspace */ fm->f_ndims = f_ndims = dataset->shared->layout.u.chunk.ndims - 1; /* 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_CANTSET, FAIL, "unable to normalize selection") /* 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]; #ifdef H5_HAVE_PARALLEL /* Calculate total chunk in file map*/ fm->select_chunk = NULL; if (io_info->using_mpi_vfd) { H5_CHECK_OVERFLOW(fm->layout->u.chunk.nchunks, hsize_t, size_t); if (fm->layout->u.chunk.nchunks) if (NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc( (size_t)fm->layout->u.chunk.nchunks * 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; if (H5D__chunk_io_init_selections(io_info, type_info, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file and memory chunk selections") done: /* Reset the global dataspace info */ fm->file_space = NULL; fm->mem_space = NULL; if (file_space_normalized == TRUE) if (H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0) /* (Casting away const OK -QAK) */ HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't denormalize selection") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_io_init() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_io_init_selections * * Purpose: Initialize the chunk mappings * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, March 20, 2008 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm) { const 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 */ H5T_t * file_type = NULL; /* Temporary copy of file datatype for iteration */ hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ char bogus; /* "bogus" buffer to pass to selection iterator */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Special case for only one element in selection */ /* (usually appending a record) */ if (fm->nelmts == 1 #ifdef H5_HAVE_PARALLEL && !(io_info->using_mpi_vfd) #endif /* H5_HAVE_PARALLEL */ && H5S_SEL_ALL != H5S_GET_SELECT_TYPE(fm->file_space)) { /* 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(fm->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") 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 { hbool_t sel_hyper_flag; /* Whether file selection is a hyperslab */ /* 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, NULL))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections") 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 ((fm->fsel_type = H5S_GET_SELECT_TYPE(fm->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(fm->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 (fm->fsel_type == H5S_SEL_POINTS || fm->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 (H5S_SEL_ALL == fm->fsel_type) { if (H5D__create_chunk_file_map_all(fm, io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") } /* end if */ else { /* Sanity check */ HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS); if (H5D__create_chunk_file_map_hyper(fm, io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") } /* end else */ } /* end if */ else { H5S_sel_iter_op_t iter_op; /* Operator for iteration */ H5D_chunk_file_iter_ud_t udata; /* User data for iteration */ /* Create temporary datatypes for selection iteration */ if (NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype") /* Initialize the user data */ udata.fm = fm; #ifdef H5_HAVE_PARALLEL udata.io_info = io_info; #endif /* H5_HAVE_PARALLEL */ iter_op.op_type = H5S_SEL_ITER_OP_LIB; iter_op.u.lib_op = H5D__chunk_file_cb; /* Spaces might not be the same shape, iterate over the file selection directly */ if (H5S_select_iterate(&bogus, file_type, fm->file_space, &iter_op, &udata) < 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(fm->file_space, fm->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 if (sel_hyper_flag && fm->f_ndims == 1 && fm->m_ndims == 1 && H5S_SELECT_IS_REGULAR(fm->mem_space) && H5S_SELECT_IS_SINGLE(fm->mem_space)) { if (H5D__create_chunk_mem_map_1d(fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") } /* end else-if */ else { H5S_sel_iter_op_t iter_op; /* Operator for iteration */ size_t elmt_size; /* Memory datatype size */ /* Make a copy of equivalent memory space */ if ((tmp_mspace = H5S_copy(fm->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 (!file_type) if (NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype") /* 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), fm->mem_space, elmt_size, 0) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") iter_init = TRUE; /* Selection iteration info has been initialized */ iter_op.op_type = H5S_SEL_ITER_OP_LIB; iter_op.u.lib_op = H5D__chunk_mem_cb; /* Spaces aren't the same shape, iterate over the memory selection directly */ if (H5S_select_iterate(&bogus, file_type, fm->file_space, &iter_op, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") } /* 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") if (H5D__chunk_io_term(fm) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping") } /* end if */ if (iter_init && H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") if (file_type && (H5T_close_real(file_type) < 0)) HDONE_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "Can't free temporary datatype") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_io_init_selections() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_mem_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 * *------------------------------------------------------------------------- */ void * H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline) { void *ret_value = NULL; /* Return value */ FUNC_ENTER_STATIC_NOERR HDassert(size); if (pline && pline->nused) ret_value = H5MM_malloc(size); else ret_value = H5FL_BLK_MALLOC(chunk, size); FUNC_LEAVE_NOAPI(ret_value) } /* H5D__chunk_mem_alloc() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_mem_xfree * * Purpose: Free space for a chunk in memory. This routine releases * 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 * *------------------------------------------------------------------------- */ void * H5D__chunk_mem_xfree(void *chk, const void *_pline) { const H5O_pline_t *pline = (const H5O_pline_t *)_pline; FUNC_ENTER_STATIC_NOERR if (chk) { if (pline && pline->nused) H5MM_xfree(chk); else chk = H5FL_BLK_FREE(chunk, chk); } /* end if */ FUNC_LEAVE_NOAPI(NULL) } /* H5D__chunk_mem_xfree() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_mem_free * * Purpose: Wrapper with H5MM_free_t-compatible signature that just * calls H5D__chunk_mem_xfree and discards the return value. *------------------------------------------------------------------------- */ void H5D__chunk_mem_free(void *chk, const void *_pline) { (void)H5D__chunk_mem_xfree(chk, _pline); } /*------------------------------------------------------------------------- * Function: H5D__chunk_mem_realloc * * Purpose: Reallocate 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: Neil Fortner * May 3, 2010 * *------------------------------------------------------------------------- */ void * H5D__chunk_mem_realloc(void *chk, size_t size, const H5O_pline_t *pline) { void *ret_value = NULL; /* Return value */ FUNC_ENTER_STATIC_NOERR HDassert(size); HDassert(pline); if (pline->nused > 0) ret_value = H5MM_realloc(chk, size); else ret_value = H5FL_BLK_REALLOC(chunk, chk, size); FUNC_LEAVE_NOAPI(ret_value) } /* H5D__chunk_mem_realloc() */ /*-------------------------------------------------------------------------- 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 H5_ATTR_UNUSED *key, void H5_ATTR_UNUSED *opdata) { H5D_chunk_info_t *chunk_info = (H5D_chunk_info_t *)item; FUNC_ENTER_STATIC_NOERR 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 && chunk_info->mspace) (void)H5S_close(chunk_info->mspace); /* Free the actual chunk info */ chunk_info = H5FL_FREE(H5D_chunk_info_t, chunk_info); FUNC_LEAVE_NOAPI(0) } /* H5D__free_chunk_info() */ /*------------------------------------------------------------------------- * Function: H5D__create_chunk_map_single * * Purpose: Create chunk selections when appending a single record * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Tuesday, November 20, 2007 * *------------------------------------------------------------------------- */ static herr_t H5D__create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t #ifndef H5_HAVE_PARALLEL H5_ATTR_UNUSED #endif /* H5_HAVE_PARALLEL */ *io_info) { H5D_chunk_info_t *chunk_info; /* Chunk information to insert into skip list */ hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk */ 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_STATIC /* 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++) { /* Validate this chunk dimension */ if (fm->layout->u.chunk.dim[u] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u) HDassert(sel_start[u] == sel_end[u]); chunk_info->scaled[u] = sel_start[u] / fm->layout->u.chunk.dim[u]; coords[u] = chunk_info->scaled[u] * fm->layout->u.chunk.dim[u]; } /* end for */ chunk_info->scaled[fm->f_ndims] = 0; /* Calculate the index of this chunk */ chunk_info->index = H5VM_array_offset_pre(fm->f_ndims, fm->layout->u.chunk.down_chunks, chunk_info->scaled); /* 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, 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_all * * Purpose: Create all chunk selections in file, for an "all" selection. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Monday, January 21, 2019 * *------------------------------------------------------------------------- */ static herr_t H5D__create_chunk_file_map_all(H5D_chunk_map_t *fm, const H5D_io_info_t #ifndef H5_HAVE_PARALLEL H5_ATTR_UNUSED #endif /* H5_HAVE_PARALLEL */ *io_info) { H5S_t * tmp_fchunk = NULL; /* Temporary file dataspace */ hsize_t file_dims[H5S_MAX_RANK]; /* File dataspace dims */ hsize_t sel_points; /* Number of elements in file selection */ hsize_t zeros[H5S_MAX_RANK]; /* All zero vector (for start parameter to setting hyperslab on partial chunks) */ hsize_t coords[H5S_MAX_RANK]; /* Current coordinates of chunk */ hsize_t end[H5S_MAX_RANK]; /* Final coordinates of chunk */ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */ hsize_t chunk_index; /* "Index" of chunk */ hsize_t curr_partial_clip[H5S_MAX_RANK]; /* Current partial dimension sizes to clip against */ hsize_t partial_dim_size[H5S_MAX_RANK]; /* Size of a partial dimension */ hbool_t is_partial_dim[H5S_MAX_RANK]; /* Whether a dimension is currently a partial chunk */ unsigned num_partial_dims; /* Current number of partial dimensions */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(fm->f_ndims > 0); /* Get number of elements selected in file */ sel_points = fm->nelmts; /* Get dataspace dimensions */ if (H5S_get_simple_extent_dims(fm->file_space, file_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") /* Set initial chunk location, partial dimensions, etc */ num_partial_dims = 0; HDmemset(zeros, 0, sizeof(zeros)); for (u = 0; u < fm->f_ndims; u++) { /* Validate this chunk dimension */ if (fm->layout->u.chunk.dim[u] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u) /* Set up start / end coordinates for first chunk */ scaled[u] = 0; coords[u] = 0; end[u] = fm->chunk_dim[u] - 1; /* Iniitialize partial chunk dimension information */ partial_dim_size[u] = file_dims[u] % fm->chunk_dim[u]; if (file_dims[u] < fm->chunk_dim[u]) { curr_partial_clip[u] = partial_dim_size[u]; is_partial_dim[u] = TRUE; num_partial_dims++; } /* end if */ else { curr_partial_clip[u] = fm->chunk_dim[u]; is_partial_dim[u] = FALSE; } /* end else */ } /* end for */ /* Set the index of this chunk */ chunk_index = 0; /* Create "temporary" chunk for selection operations (copy file space) */ if (NULL == (tmp_fchunk = H5S_create_simple(fm->f_ndims, fm->chunk_dim, NULL))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk") /* Iterate through each chunk in the dataset */ while (sel_points) { H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */ hsize_t chunk_points; /* Number of elements in chunk selection */ /* 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))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk info") /* Initialize the chunk information */ /* Set the chunk index */ new_chunk_info->index = chunk_index; #ifdef H5_HAVE_PARALLEL /* Store chunk selection information, for multi-chunk I/O */ if (io_info->using_mpi_vfd) fm->select_chunk[chunk_index] = new_chunk_info; #endif /* H5_HAVE_PARALLEL */ /* Set the file chunk dataspace */ if (NULL == (new_chunk_info->fspace = H5S_copy(tmp_fchunk, TRUE, FALSE))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy chunk dataspace") new_chunk_info->fspace_shared = FALSE; /* If there are partial dimensions for this chunk, set the hyperslab for them */ if (num_partial_dims > 0) if (H5S_select_hyperslab(new_chunk_info->fspace, H5S_SELECT_SET, zeros, NULL, curr_partial_clip, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk selection") /* Set the memory chunk dataspace */ new_chunk_info->mspace = NULL; new_chunk_info->mspace_shared = FALSE; /* Copy the chunk's scaled coordinates */ H5MM_memcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); new_chunk_info->scaled[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 */ chunk_points = H5S_GET_SELECT_NPOINTS(new_chunk_info->fspace); H5_CHECKED_ASSIGN(new_chunk_info->chunk_points, uint32_t, chunk_points, hsize_t); /* Decrement # of points left in file selection */ sel_points -= chunk_points; /* Advance to next chunk if we are not done */ if (sel_points > 0) { int curr_dim; /* Current dimension to increment */ /* Increment chunk index */ chunk_index++; /* Set current increment dimension */ curr_dim = (int)fm->f_ndims - 1; /* Increment chunk location in fastest changing dimension */ coords[curr_dim] += fm->chunk_dim[curr_dim]; scaled[curr_dim]++; end[curr_dim] += fm->chunk_dim[curr_dim]; /* Bring chunk location back into bounds, if necessary */ if (coords[curr_dim] >= file_dims[curr_dim]) { do { /* Reset current dimension's location to 0 */ coords[curr_dim] = 0; scaled[curr_dim] = 0; end[curr_dim] = fm->chunk_dim[curr_dim] - 1; /* Check for previous partial chunk in this dimension */ if (is_partial_dim[curr_dim] && end[curr_dim] < file_dims[curr_dim]) { /* Sanity check */ HDassert(num_partial_dims > 0); /* Reset partial chunk information for this dimension */ curr_partial_clip[curr_dim] = fm->chunk_dim[curr_dim]; is_partial_dim[curr_dim] = FALSE; num_partial_dims--; } /* end if */ /* Decrement current dimension */ curr_dim--; /* Check for valid current dim */ if (curr_dim >= 0) { /* Increment chunk location in current dimension */ coords[curr_dim] += fm->chunk_dim[curr_dim]; scaled[curr_dim]++; end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1; } /* end if */ } while (curr_dim >= 0 && (coords[curr_dim] >= file_dims[curr_dim])); } /* end if */ /* Check for valid current dim */ if (curr_dim >= 0) { /* Check for partial chunk in this dimension */ if (!is_partial_dim[curr_dim] && file_dims[curr_dim] <= end[curr_dim]) { /* Set partial chunk information for this dimension */ curr_partial_clip[curr_dim] = partial_dim_size[curr_dim]; is_partial_dim[curr_dim] = TRUE; num_partial_dims++; /* Sanity check */ HDassert(num_partial_dims <= fm->f_ndims); } /* end if */ } /* end if */ } /* end if */ } /* end while */ done: /* Clean up */ if (tmp_fchunk && H5S_close(tmp_fchunk) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release temporary dataspace") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__create_chunk_file_map_all() */ /*------------------------------------------------------------------------- * Function: H5D__create_chunk_file_map_hyper * * Purpose: Create all chunk selections in file, for a hyperslab selection. * * 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 H5_ATTR_UNUSED #endif /* H5_HAVE_PARALLEL */ *io_info) { H5S_t * tmp_fchunk = NULL; /* Temporary file dataspace */ 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]; /* Final coordinates of chunk */ hsize_t chunk_index; /* Index of chunk */ hsize_t start_scaled[H5S_MAX_RANK]; /* Starting scaled coordinates of selection */ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */ int curr_dim; /* Current dimension to increment */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(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++) { /* Validate this chunk dimension */ if (fm->layout->u.chunk.dim[u] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u) scaled[u] = start_scaled[u] = sel_start[u] / fm->layout->u.chunk.dim[u]; coords[u] = start_coords[u] = scaled[u] * fm->layout->u.chunk.dim[u]; end[u] = (coords[u] + fm->chunk_dim[u]) - 1; } /* end for */ /* Calculate the index of this chunk */ chunk_index = H5VM_array_offset_pre(fm->f_ndims, fm->layout->u.chunk.down_chunks, scaled); /* Iterate through each chunk in the dataset */ while (sel_points) { /* Check for intersection of current chunk and file selection */ /* (Casting away const OK - QAK) */ if (TRUE == H5S_SELECT_INTERSECT_BLOCK(fm->file_space, coords, end)) { H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */ hsize_t chunk_points; /* Number of elements in chunk selection */ /* Create dataspace for chunk, 'AND'ing the overall selection with * the current chunk. */ if (H5S_combine_hyperslab(fm->file_space, H5S_SELECT_AND, coords, NULL, fm->chunk_dim, NULL, &tmp_fchunk) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to combine file space selection with chunk block") /* Resize chunk's dataspace dimensions to size of chunk */ if (H5S_set_extent_real(tmp_fchunk, fm->chunk_dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions") /* Move selection back to have correct offset in chunk */ if (H5S_SELECT_ADJUST_U(tmp_fchunk, coords) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't adjust chunk selection") /* 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))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk info") /* Initialize the chunk information */ /* Set the chunk index */ new_chunk_info->index = chunk_index; #ifdef H5_HAVE_PARALLEL /* Store chunk selection information, for multi-chunk I/O */ 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; tmp_fchunk = NULL; /* Set the memory chunk dataspace */ new_chunk_info->mspace = NULL; new_chunk_info->mspace_shared = FALSE; /* Copy the chunk's scaled coordinates */ H5MM_memcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); new_chunk_info->scaled[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 */ chunk_points = H5S_GET_SELECT_NPOINTS(new_chunk_info->fspace); H5_CHECKED_ASSIGN(new_chunk_info->chunk_points, uint32_t, chunk_points, hsize_t); /* Decrement # of points left in file selection */ sel_points -= chunk_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 */ coords[curr_dim] += fm->chunk_dim[curr_dim]; end[curr_dim] += fm->chunk_dim[curr_dim]; scaled[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 */ scaled[curr_dim] = start_scaled[curr_dim]; 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--; /* Check for valid current dim */ if (curr_dim >= 0) { /* Increment chunk location in current dimension */ scaled[curr_dim]++; coords[curr_dim] += fm->chunk_dim[curr_dim]; end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1; } /* end if */ } while (curr_dim >= 0 && (coords[curr_dim] > sel_end[curr_dim])); /* Re-calculate the index of this chunk */ chunk_index = H5VM_array_offset_pre(fm->f_ndims, fm->layout->u.chunk.down_chunks, scaled); } /* end if */ } /* end while */ done: /* Clean up on failure */ if (ret_value < 0) if (tmp_fchunk && H5S_close(tmp_fchunk) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release temporary dataspace") 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) { H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ H5SL_node_t * curr_node; /* Current node in skip list */ hsize_t file_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ hsize_t file_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ hssize_t adjust[H5S_MAX_RANK]; /* Adjustment to make to all file chunks */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(fm->f_ndims > 0); /* Check for all I/O going to a single chunk */ if (H5SL_count(fm->sel_chunks) == 1) { /* 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); HDassert(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 */ HDassert(fm->m_ndims == fm->f_ndims); for (u = 0; u < fm->f_ndims; u++) { H5_CHECK_OVERFLOW(file_sel_start[u], hsize_t, hssize_t); H5_CHECK_OVERFLOW(mem_sel_start[u], hsize_t, hssize_t); adjust[u] = (hssize_t)file_sel_start[u] - (hssize_t)mem_sel_start[u]; } /* end for */ /* Iterate over each chunk in the chunk list */ curr_node = H5SL_first(fm->sel_chunks); while (curr_node) { hsize_t coords[H5S_MAX_RANK]; /* Current coordinates of chunk */ hssize_t chunk_adjust[H5S_MAX_RANK]; /* Adjustment to make to a particular chunk */ H5S_sel_type chunk_sel_type; /* Chunk's selection type */ /* Get pointer to chunk's information */ chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); HDassert(chunk_info); /* Compute the chunk coordinates from the scaled coordinates */ for (u = 0; u < fm->f_ndims; u++) coords[u] = chunk_info->scaled[u] * fm->layout->u.chunk.dim[u]; /* 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") /* Get the chunk's selection type */ if ((chunk_sel_type = H5S_GET_SELECT_TYPE(chunk_info->fspace)) < H5S_SEL_NONE) HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection") /* Set memory selection for "all" chunk selections */ if (H5S_SEL_ALL == chunk_sel_type) { /* Adjust the chunk coordinates */ for (u = 0; u < fm->f_ndims; u++) coords[u] = (hsize_t)((hssize_t)coords[u] - adjust[u]); /* Set to same shape as chunk */ if (H5S_select_hyperslab(chunk_info->mspace, H5S_SELECT_SET, coords, NULL, fm->chunk_dim, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk memory selection") } /* end if */ else { /* Sanity check */ HDassert(H5S_SEL_HYPERSLABS == chunk_sel_type); /* 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") /* Compute the adjustment for this chunk */ for (u = 0; u < fm->f_ndims; u++) { /* Compensate for the chunk offset */ H5_CHECK_OVERFLOW(coords[u], hsize_t, hssize_t); chunk_adjust[u] = adjust[u] - (hssize_t)coords[u]; } /* end for */ /* Adjust the selection */ if (H5S_SELECT_ADJUST_S(chunk_info->mspace, chunk_adjust) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to adjust selection") } /* end else */ /* 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__create_mem_map_1d * * Purpose: Create all chunk selections for 1-dimensional regular memory space * that has only one single block in the selection * * Return: Non-negative on success/Negative on failure * * Programmer: Vailin Choi * Sept 18, 2019 * *------------------------------------------------------------------------- */ static herr_t H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm) { H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ H5SL_node_t * curr_node; /* Current node in skip list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(fm->f_ndims > 0); /* Check for all I/O going to a single chunk */ if (H5SL_count(fm->sel_chunks) == 1) { /* 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); HDassert(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 { hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ HDassert(fm->m_ndims == 1); 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") /* Iterate over each chunk in the chunk list */ curr_node = H5SL_first(fm->sel_chunks); while (curr_node) { hsize_t chunk_points; /* Number of elements in chunk selection */ hsize_t tmp_count = 1; /* Get pointer to chunk's information */ chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); HDassert(chunk_info); /* 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") chunk_points = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); if (H5S_select_hyperslab(chunk_info->mspace, H5S_SELECT_SET, mem_sel_start, NULL, &tmp_count, &chunk_points) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk memory selection") mem_sel_start[0] += chunk_points; /* 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_1d() */ /*------------------------------------------------------------------------- * 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 H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, unsigned ndims, const hsize_t *coords, void *_udata) { H5D_chunk_file_iter_ud_t *udata = (H5D_chunk_file_iter_ud_t *)_udata; /* User data for operation */ H5D_chunk_map_t * fm = udata->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 */ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Calculate the index of this chunk */ chunk_index = H5VM_chunk_index_scaled(ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, scaled); /* 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) { chunk_info = 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); chunk_info = 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; /* Set the chunk's scaled coordinates */ H5MM_memcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); chunk_info->scaled[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 */ #ifdef H5_HAVE_PARALLEL /* Store chunk selection information, for collective multi-chunk I/O */ if (udata->io_info->using_mpi_vfd) fm->select_chunk[chunk_index] = chunk_info; #endif /* H5_HAVE_PARALLEL */ /* Update the "last chunk seen" information */ fm->last_index = chunk_index; fm->last_chunk_info = chunk_info; } /* end else */ /* Get the offset of the element within the chunk */ for (u = 0; u < fm->f_ndims; u++) coords_in_chunk[u] = coords[u] - (scaled[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 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, 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[H5S_MAX_RANK]; /* Coordinates of element in memory */ hsize_t chunk_index; /* Chunk index */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Calculate the index of this chunk */ chunk_index = H5VM_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks); /* 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, H5_ITER_ERROR, "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, H5_ITER_ERROR, "unable to copy file space") /* 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, H5_ITER_ERROR, "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, H5_ITER_ERROR, "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, H5_ITER_ERROR, "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, H5_ITER_ERROR, "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 * *------------------------------------------------------------------------- */ htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_op) { const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ hbool_t has_filters = FALSE; /* Whether there are filters on the chunk or not */ htri_t ret_value = FAIL; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(io_info); HDassert(dataset); /* Must bring the whole chunk in if there are any filters on the chunk. * Make sure to check if filters are on the dataset but disabled for the * chunk because it is a partial edge chunk. */ if (dataset->shared->dcpl_cache.pline.nused > 0) { if (dataset->shared->layout.u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) { has_filters = !H5D__chunk_is_partial_edge_chunk( io_info->dset->shared->ndims, io_info->dset->shared->layout.u.chunk.dim, io_info->store->chunk.scaled, io_info->dset->shared->curr_dims); } /* end if */ else has_filters = TRUE; } /* end if */ if (has_filters) 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 we don't * need to write the fill value, 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) { if (write_op && !H5F_addr_defined(caddr)) { const H5O_fill_t *fill = &(dataset->shared->dcpl_cache.fill); /* Fill value info */ H5D_fill_value_t fill_status; /* Fill value status */ /* Revtrieve 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 the fill value needs to be written then we will need * to use the cache to write the fill value */ if (fill->fill_time == H5D_FILL_TIME_ALLOC || (fill->fill_time == H5D_FILL_TIME_IFSET && (fill_status == H5D_FILL_VALUE_USER_DEFINED || fill_status == H5D_FILL_VALUE_DEFAULT))) ret_value = TRUE; else ret_value = FALSE; } else ret_value = FALSE; } else ret_value = TRUE; #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_cacheable() */ /*------------------------------------------------------------------------- * 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 H5_ATTR_UNUSED nelmts, const H5S_t H5_ATTR_UNUSED *file_space, const H5S_t H5_ATTR_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 */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(io_info); HDassert(io_info->u.rbuf); HDassert(type_info); HDassert(fm); /* Set up "nonexistent" I/O info object */ H5MM_memcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info)); nonexistent_io_info.layout_ops = *H5D_LOPS_NONEXISTENT; /* Set up contiguous I/O info object */ H5MM_memcpy(&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_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t); /* Set up compact I/O info object */ H5MM_memcpy(&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 && fill_status != H5D_FILL_VALUE_DEFAULT)) 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_chunk_ud_t udata; /* Chunk index 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_lookup(io_info->dset, chunk_info->scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Sanity check */ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) || (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0)); /* Check for non-existent chunk & skip it if appropriate */ if (H5F_addr_defined(udata.chunk_block.offset) || UINT_MAX != udata.idx_hint || !skip_missing_chunks) { H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */ void * chunk = NULL; /* Pointer to locked chunk buffer */ htri_t cacheable; /* Whether the chunk is cacheable */ /* Set chunk's [scaled] coordinates */ io_info->store->chunk.scaled = chunk_info->scaled; /* Determine if we should use the chunk cache */ if ((cacheable = H5D__chunk_cacheable(io_info, udata.chunk_block.offset, FALSE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") if (cacheable) { /* Load the chunk into cache and lock it. */ /* Compute # of bytes accessed in chunk */ H5_CHECK_OVERFLOW(type_info->src_type_size, /*From:*/ size_t, /*To:*/ uint32_t); src_accessed_bytes = chunk_info->chunk_points * (uint32_t)type_info->src_type_size; /* Lock the chunk into the cache */ if (NULL == (chunk = H5D__chunk_lock(io_info, &udata, FALSE, FALSE))) 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.chunk_block.offset)) { /* Set up the storage address information for this chunk */ ctg_store.contig.dset_addr = udata.chunk_block.offset; /* Point I/O info at temporary I/O info for this chunk */ chk_io_info = &ctg_io_info; } /* end else if */ else { /* 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, &udata, FALSE, 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 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t H5_ATTR_UNUSED nelmts, const H5S_t H5_ATTR_UNUSED *file_space, const H5S_t H5_ATTR_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 */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(io_info); HDassert(io_info->u.wbuf); HDassert(type_info); HDassert(fm); /* Set up contiguous I/O info object */ H5MM_memcpy(&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_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t); /* Set up compact I/O info object */ H5MM_memcpy(&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_chk_idx_info_t idx_info; /* Chunked index info */ 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; /* Index pass-through */ htri_t cacheable; /* Whether the chunk is cacheable */ hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */ /* Get the actual chunk information from the skip list node */ chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); /* Look up the chunk */ if (H5D__chunk_lookup(io_info->dset, chunk_info->scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Sanity check */ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) || (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0)); /* Set chunk's [scaled] coordinates */ io_info->store->chunk.scaled = chunk_info->scaled; /* Determine if we should use the chunk cache */ if ((cacheable = H5D__chunk_cacheable(io_info, udata.chunk_block.offset, TRUE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") if (cacheable) { /* Load the chunk into cache. But if the whole chunk is written, * simply allocate space instead of load the chunk. */ hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Compute # of bytes accessed in chunk */ H5_CHECK_OVERFLOW(type_info->dst_type_size, /*From:*/ size_t, /*To:*/ uint32_t); dst_accessed_bytes = chunk_info->chunk_points * (uint32_t)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 || fm->fsel_type == H5S_SEL_POINTS) entire_chunk = FALSE; /* Lock the chunk into the cache */ if (NULL == (chunk = H5D__chunk_lock(io_info, &udata, entire_chunk, FALSE))) 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.chunk_block.offset)) { /* Compose chunked index info struct */ idx_info.f = io_info->dset->oloc.file; idx_info.pline = &(io_info->dset->shared->dcpl_cache.pline); idx_info.layout = &(io_info->dset->shared->layout.u.chunk); idx_info.storage = &(io_info->dset->shared->layout.storage.u.chunk); /* Set up the size of chunk for user data */ udata.chunk_block.length = io_info->dset->shared->layout.u.chunk.size; /* Allocate the chunk */ if (H5D__chunk_file_alloc(&idx_info, NULL, &udata.chunk_block, &need_insert, chunk_info->scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") /* Make sure the address of the chunk is returned. */ if (!H5F_addr_defined(udata.chunk_block.offset)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined") /* Cache the new chunk information */ H5D__chunk_cinfo_cache_update(&io_info->dset->shared->cache.chunk.last, &udata); } /* end if */ /* Set up the storage address information for this chunk */ ctg_store.contig.dset_addr = udata.chunk_block.offset; /* 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, or insert chunk into index. */ if (chunk) { if (H5D__chunk_unlock(io_info, &udata, TRUE, chunk, dst_accessed_bytes) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") } /* end if */ else { if (need_insert && io_info->dset->shared->layout.storage.u.chunk.ops->insert) if ((io_info->dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") } /* end else */ /* 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_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 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_flush(H5D_t *dset) { H5D_rdcc_t * rdcc = &(dset->shared->cache.chunk); H5D_rdcc_ent_t *ent, *next; unsigned nerrors = 0; /* Count of any errors encountered when flushing chunks */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(dset); /* Loop over all entries in the chunk cache */ for (ent = rdcc->head; ent; ent = next) { next = ent->next; if (H5D__chunk_flush_entry(dset, ent, FALSE) < 0) nerrors++; } /* end for */ if (nerrors) HGOTO_ERROR(H5E_DATASET, 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_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_STATIC /* 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_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 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_dest(H5D_t *dset) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ 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 */ H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC_TAG(dset->oloc.addr) /* Sanity checks */ HDassert(dset); H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Flush all the cached chunks */ for (ent = rdcc->head; ent; ent = next) { next = ent->next; if (H5D__chunk_cache_evict(dset, ent, TRUE) < 0) nerrors++; } /* end for */ /* Continue even if there are failures. */ if (nerrors) HDONE_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 = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Free any index structures */ if (sc->ops->dest && (sc->ops->dest)(&idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__chunk_dest() */ /*------------------------------------------------------------------------- * 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_storage_chunk_t *storage, hbool_t reset_addr) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* Sanity checks */ HDassert(storage); HDassert(storage->ops); H5D_CHUNK_STORAGE_INDEX_CHK(storage); /* Reset index structures */ if ((storage->ops->reset)(storage, reset_addr) < 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 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_cinfo_cache_reset(H5D_chunk_cached_t *last) { FUNC_ENTER_STATIC_NOERR /* 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) { FUNC_ENTER_STATIC_NOERR /* Sanity check */ HDassert(last); HDassert(udata); HDassert(udata->common.layout); HDassert(udata->common.scaled); /* Stored the information to cache */ H5MM_memcpy(last->scaled, udata->common.scaled, sizeof(hsize_t) * udata->common.layout->ndims); last->addr = udata->chunk_block.offset; H5_CHECKED_ASSIGN(last->nbytes, uint32_t, udata->chunk_block.length, hsize_t); last->chunk_idx = udata->chunk_idx; last->filter_mask = udata->filter_mask; /* 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_STATIC_NOERR /* Sanity check */ HDassert(last); HDassert(udata); HDassert(udata->common.layout); HDassert(udata->common.scaled); /* Check if the cached information is what is desired */ if (last->valid) { unsigned u; /* Local index variable */ /* Check that the scaled offset is the same */ for (u = 0; u < udata->common.layout->ndims; u++) if (last->scaled[u] != udata->common.scaled[u]) HGOTO_DONE(FALSE) /* Retrieve the information from the cache */ udata->chunk_block.offset = last->addr; udata->chunk_block.length = last->nbytes; udata->chunk_idx = last->chunk_idx; udata->filter_mask = last->filter_mask; /* 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(const H5D_t *dset /*in,out*/) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* 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); H5D_CHUNK_STORAGE_INDEX_CHK(sc); #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.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Create the index for the chunks */ if ((sc->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_hash_val * * Purpose: To calculate an index based on the dataset's scaled * coordinates and sizes of the faster dimensions. * * Return: Hash value index * * Programmer: Vailin Choi; Nov 2014 * *------------------------------------------------------------------------- */ static unsigned H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *scaled) { hsize_t val; /* Intermediate value */ unsigned ndims = shared->ndims; /* Rank of dataset */ unsigned ret = 0; /* Value to return */ unsigned u; /* Local index variable */ FUNC_ENTER_STATIC_NOERR /* Sanity check */ HDassert(shared); HDassert(scaled); /* If the fastest changing dimension doesn't have enough entropy, use * other dimensions too */ val = scaled[0]; for (u = 1; u < ndims; u++) { val <<= shared->cache.chunk.scaled_encode_bits[u]; val ^= scaled[u]; } /* end for */ /* Modulo value against the number of array slots */ ret = (unsigned)(val % shared->cache.chunk.nslots); FUNC_LEAVE_NOAPI(ret) } /* H5D__chunk_hash_val() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_lookup * * Purpose: Loops up a chunk in cache and on disk, and retrieves * information about that chunk. * * Return: Non-negative on success/Negative on failure * * Programmer: Albert Cheng * June 27, 1998 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udata) { H5D_rdcc_ent_t * ent = NULL; /* Cache entry */ H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); unsigned idx = 0; /* Index of chunk in cache, if present */ hbool_t found = FALSE; /* In cache? */ #ifdef H5_HAVE_PARALLEL H5P_coll_md_read_flag_t md_reads_file_flag; hbool_t md_reads_context_flag; hbool_t restore_md_reads_state = FALSE; #endif herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity checks */ HDassert(dset); HDassert(dset->shared->layout.u.chunk.ndims > 0); H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(scaled); HDassert(udata); /* Initialize the query information about the chunk we are looking for */ udata->common.layout = &(dset->shared->layout.u.chunk); udata->common.storage = sc; udata->common.scaled = scaled; /* Reset information about the chunk we are looking for */ udata->chunk_block.offset = HADDR_UNDEF; udata->chunk_block.length = 0; udata->filter_mask = 0; udata->new_unfilt_chunk = FALSE; /* Check for chunk in cache */ if (dset->shared->cache.chunk.nslots > 0) { /* Determine the chunk's location in the hash table */ idx = H5D__chunk_hash_val(dset->shared, scaled); /* Get the chunk cache entry for that location */ ent = dset->shared->cache.chunk.slot[idx]; if (ent) { unsigned u; /* Counter */ /* Speculatively set the 'found' flag */ found = TRUE; /* Verify that the cache entry is the correct chunk */ for (u = 0; u < dset->shared->ndims; u++) if (scaled[u] != ent->scaled[u]) { found = FALSE; break; } /* end if */ } /* end if */ } /* end if */ /* Retrieve chunk addr */ if (found) { udata->idx_hint = idx; udata->chunk_block.offset = ent->chunk_block.offset; udata->chunk_block.length = ent->chunk_block.length; ; udata->chunk_idx = ent->chunk_idx; } /* end if */ else { /* Invalidate idx_hint, to signal that the chunk is not in cache */ udata->idx_hint = UINT_MAX; /* 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.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; #ifdef H5_HAVE_PARALLEL /* Disable collective metadata read for chunk indexes as it is * highly unlikely that users would read the same chunks from all * processes. */ if (H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) { md_reads_file_flag = H5P_FORCE_FALSE; md_reads_context_flag = FALSE; H5F_set_coll_metadata_reads(idx_info.f, &md_reads_file_flag, &md_reads_context_flag); restore_md_reads_state = TRUE; } #endif /* H5_HAVE_PARALLEL */ /* Go get the chunk information */ if ((sc->ops->get_addr)(&idx_info, udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address") /* * Cache the information retrieved. * * Note that if we are writing to the dataset in parallel and filters * are involved, we skip caching this information as it is highly likely * that the chunk information will be invalidated as a result of the * filter operation (e.g. the chunk gets re-allocated to a different * address in the file and/or gets re-allocated with a different size). * If we were to cache this information, subsequent reads/writes would * retrieve the invalid information and cause a variety of issues. * * It has been verified that in the serial library, when writing to chunks * with the real chunk cache disabled and with filters involved, the * functions within this file are correctly called in such a manner that * this single chunk cache is always updated correctly. Therefore, this * check is not needed for the serial library. * * This is an ugly and potentially frail check, but the * H5D__chunk_cinfo_cache_reset() function is not currently available * to functions outside of this file, so outside functions can not * invalidate this single chunk cache. Even if the function were available, * this check prevents us from doing the work of going through and caching * each chunk in the write operation, when we're only going to invalidate * the cache at the end of a parallel write anyway. * * - JTH (7/13/2018) */ #ifdef H5_HAVE_PARALLEL if (!((H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) && (H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR) && dset->shared->dcpl_cache.pline.nused)) #endif H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata); } /* end if */ } /* end else */ done: #ifdef H5_HAVE_PARALLEL /* Re-enable collective metadata reads if we disabled them */ if (restore_md_reads_state) H5F_set_coll_metadata_reads(dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag); #endif /* H5_HAVE_PARALLEL */ FUNC_LEAVE_NOAPI(ret_value) } /* H5D__chunk_lookup() */ /*------------------------------------------------------------------------- * 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, H5D_rdcc_ent_t *ent, hbool_t reset) { void * buf = NULL; /* Temporary buffer */ hbool_t point_of_no_return = FALSE; H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC HDassert(dset); HDassert(dset->shared); H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(ent); HDassert(!ent->locked); buf = ent->chunk; if (ent->dirty) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_chunk_ud_t udata; /* pass through B-tree */ hbool_t must_alloc = FALSE; /* Whether the chunk must be allocated */ hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */ /* Set up user data for index callbacks */ udata.common.layout = &dset->shared->layout.u.chunk; udata.common.storage = sc; udata.common.scaled = ent->scaled; udata.chunk_block.offset = ent->chunk_block.offset; udata.chunk_block.length = dset->shared->layout.u.chunk.size; udata.filter_mask = 0; udata.chunk_idx = ent->chunk_idx; /* Should the chunk be filtered before writing it to disk? */ if (dset->shared->dcpl_cache.pline.nused && !(ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS)) { H5Z_EDC_t err_detect; /* Error detection info */ H5Z_cb_t filter_cb; /* I/O filter callback function */ size_t alloc = udata.chunk_block.length; /* Bytes allocated for BUF */ size_t nbytes; /* Chunk size (in bytes) */ /* Retrieve filter settings from API context */ if (H5CX_get_err_detect(&err_detect) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info") if (H5CX_get_filter_cb(&filter_cb) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function") 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. */ if (NULL == (buf = H5MM_malloc(alloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline") H5MM_memcpy(buf, ent->chunk, alloc); } /* end if */ else { /* * If we are resetting 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_CHECKED_ASSIGN(nbytes, size_t, udata.chunk_block.length, hsize_t); if (H5Z_pipeline(&(dset->shared->dcpl_cache.pline), 0, &(udata.filter_mask), err_detect, filter_cb, &nbytes, &alloc, &buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 /* Check for the chunk expanding too much to encode in a 32-bit value */ if (nbytes > ((size_t)0xffffffff)) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") #endif /* H5_SIZEOF_SIZE_T > 4 */ H5_CHECKED_ASSIGN(udata.chunk_block.length, hsize_t, nbytes, size_t); /* Indicate that the chunk must be allocated */ must_alloc = TRUE; } /* end if */ else if (!H5F_addr_defined(udata.chunk_block.offset)) { /* Indicate that the chunk must be allocated */ must_alloc = TRUE; /* This flag could be set for this chunk, just remove and ignore it */ ent->edge_chunk_state &= ~H5D_RDCC_NEWLY_DISABLED_FILTERS; } /* end else */ else if (ent->edge_chunk_state & H5D_RDCC_NEWLY_DISABLED_FILTERS) { /* Chunk on disk is still filtered, must insert to allocate correct * size */ must_alloc = TRUE; /* Set the disable filters field back to the standard disable * filters setting, as it no longer needs to be inserted with every * flush */ ent->edge_chunk_state &= ~H5D_RDCC_NEWLY_DISABLED_FILTERS; } /* end else */ HDassert(!(ent->edge_chunk_state & H5D_RDCC_NEWLY_DISABLED_FILTERS)); /* Check if the chunk needs to be allocated (it also could exist already * and the chunk alloc operation could resize it) */ if (must_alloc) { /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Create the chunk it if it doesn't exist, or reallocate the chunk * if its size changed. */ if (H5D__chunk_file_alloc(&idx_info, &(ent->chunk_block), &udata.chunk_block, &need_insert, ent->scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") /* Update the chunk entry's info, in case it was allocated or relocated */ ent->chunk_block.offset = udata.chunk_block.offset; ent->chunk_block.length = udata.chunk_block.length; } /* end if */ /* Write the data to the file */ HDassert(H5F_addr_defined(udata.chunk_block.offset)); H5_CHECK_OVERFLOW(udata.chunk_block.length, hsize_t, size_t); if (H5F_shared_block_write(H5F_SHARED(dset->oloc.file), H5FD_MEM_DRAW, udata.chunk_block.offset, (size_t)udata.chunk_block.length, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data to file") /* Insert the chunk record into the index */ if (need_insert && sc->ops->insert) if ((sc->ops->insert)(&idx_info, &udata, dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") /* 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_mem_xfree(ent->chunk, ((ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS) ? NULL : &(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_mem_xfree(ent->chunk, ((ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS) ? NULL : &(dset->shared->dcpl_cache.pline))); 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, 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_STATIC /* Sanity checks */ HDassert(dset); HDassert(ent); HDassert(!ent->locked); HDassert(ent->idx < rdcc->nslots); if (flush) { /* Flush */ if (H5D__chunk_flush_entry(dset, ent, TRUE) < 0) HDONE_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_mem_xfree(ent->chunk, ((ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS) ? NULL : &(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; /* Unlink from temporary list */ if (ent->tmp_prev) { HDassert(rdcc->tmp_head->tmp_next); ent->tmp_prev->tmp_next = ent->tmp_next; if (ent->tmp_next) { ent->tmp_next->tmp_prev = ent->tmp_prev; ent->tmp_next = NULL; } /* end if */ ent->tmp_prev = NULL; } /* end if */ else /* Only clear hash table slot if the chunk was not on the temporary list */ rdcc->slot[ent->idx] = NULL; /* Remove from cache */ HDassert(rdcc->slot[ent->idx] != ent); ent->idx = UINT_MAX; rdcc->nbytes_used -= dset->shared->layout.u.chunk.size; --rdcc->nused; /* Free */ ent = H5FL_FREE(H5D_rdcc_ent_t, ent); 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, 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_STATIC /* * 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 that 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 && dset->shared->layout.u.chunk.size == p[0]->wr_count) || (dset->shared->layout.u.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, 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 H5D__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 * *------------------------------------------------------------------------- */ static void * H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax, hbool_t prev_unfilt_chunk) { const 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 - always equal to the pline passed to H5D__chunk_mem_alloc */ const H5O_pline_t * old_pline = pline; /* Old pipeline, i.e. pipeline used to read the chunk */ 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; /*cache entry */ size_t chunk_size; /*size of a chunk */ hbool_t disable_filters = FALSE; /* Whether to disable filters (when adding to cache) */ void * chunk = NULL; /*the file chunk */ void * ret_value = NULL; /* Return value */ FUNC_ENTER_STATIC /* Sanity checks */ HDassert(io_info); HDassert(io_info->store); HDassert(udata); HDassert(dset); HDassert(!(udata->new_unfilt_chunk && prev_unfilt_chunk)); HDassert(!rdcc->tmp_head); /* Get the chunk's size */ HDassert(layout->u.chunk.size > 0); H5_CHECKED_ASSIGN(chunk_size, size_t, layout->u.chunk.size, uint32_t); /* Check if the chunk is in the cache */ if (UINT_MAX != udata->idx_hint) { /* Sanity check */ HDassert(udata->idx_hint < rdcc->nslots); HDassert(rdcc->slot[udata->idx_hint]); /* Get the entry */ ent = rdcc->slot[udata->idx_hint]; #ifndef NDEBUG { unsigned u; /*counters */ /* Make sure this is the right chunk */ for (u = 0; u < layout->u.chunk.ndims - 1; u++) HDassert(io_info->store->chunk.scaled[u] == ent->scaled[u]); } #endif /* NDEBUG */ /* * Already in the cache. Count a hit. */ rdcc->stats.nhits++; /* Make adjustments if the edge chunk status changed recently */ if (pline->nused) { /* If the chunk recently became an unfiltered partial edge chunk * while in cache, we must make some changes to the entry */ if (udata->new_unfilt_chunk) { /* If this flag is set then partial chunk filters must be * disabled, and the chunk must not have previously been a * partial chunk (with disabled filters) */ HDassert(layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); HDassert(!(ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS)); HDassert(old_pline->nused); /* Disable filters. Set pline to NULL instead of just the * default pipeline to make a quick failure more likely if the * code is changed in an inappropriate/incomplete way. */ pline = NULL; /* Reallocate the chunk so H5D__chunk_mem_xfree doesn't get confused */ if (NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") H5MM_memcpy(chunk, ent->chunk, chunk_size); ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline); ent->chunk = (uint8_t *)chunk; chunk = NULL; /* Mark the chunk as having filters disabled as well as "newly * disabled" so it is inserted on flush */ ent->edge_chunk_state |= H5D_RDCC_DISABLE_FILTERS; ent->edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS; } /* end if */ else if (prev_unfilt_chunk) { /* If this flag is set then partial chunk filters must be * disabled, and the chunk must have previously been a partial * chunk (with disabled filters) */ HDassert(layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); HDassert((ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS)); HDassert(pline->nused); /* Mark the old pipeline as having been disabled */ old_pline = NULL; /* Reallocate the chunk so H5D__chunk_mem_xfree doesn't get confused */ if (NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") H5MM_memcpy(chunk, ent->chunk, chunk_size); ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline); ent->chunk = (uint8_t *)chunk; chunk = NULL; /* Mark the chunk as having filters enabled */ ent->edge_chunk_state &= ~(H5D_RDCC_DISABLE_FILTERS | H5D_RDCC_NEWLY_DISABLED_FILTERS); } /* end else */ } /* end if */ /* * If 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. */ 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 if */ else { haddr_t chunk_addr; /* Address of chunk on disk */ hsize_t chunk_alloc; /* Length of chunk on disk */ /* Save the chunk info so the cache stays consistent */ chunk_addr = udata->chunk_block.offset; chunk_alloc = udata->chunk_block.length; /* Check if we should disable filters on this chunk */ if (pline->nused) { if (udata->new_unfilt_chunk) { HDassert(layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); /* Disable the filters for writing */ disable_filters = TRUE; pline = NULL; } /* end if */ else if (prev_unfilt_chunk) { HDassert(layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); /* Mark the filters as having been previously disabled (for the * chunk as currently on disk) - disable the filters for reading */ old_pline = NULL; } /* end if */ else if (layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) { /* Check if this is an edge chunk */ if (H5D__chunk_is_partial_edge_chunk(io_info->dset->shared->ndims, layout->u.chunk.dim, io_info->store->chunk.scaled, io_info->dset->shared->curr_dims)) { /* Disable the filters for both writing and reading */ disable_filters = TRUE; old_pline = NULL; pline = NULL; } /* end if */ } /* end if */ } /* end if */ 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_mem_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. */ /* Check if the chunk exists on disk */ if (H5F_addr_defined(chunk_addr)) { size_t my_chunk_alloc = chunk_alloc; /* Allocated buffer size */ size_t buf_alloc = chunk_alloc; /* [Re-]allocated buffer size */ /* 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_mem_alloc(my_chunk_alloc, (udata->new_unfilt_chunk ? old_pline : pline)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") if (H5F_shared_block_read(H5F_SHARED(dset->oloc.file), H5FD_MEM_DRAW, chunk_addr, my_chunk_alloc, chunk) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk") if (old_pline && old_pline->nused) { H5Z_EDC_t err_detect; /* Error detection info */ H5Z_cb_t filter_cb; /* I/O filter callback function */ /* Retrieve filter settings from API context */ if (H5CX_get_err_detect(&err_detect) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get error detection info") if (H5CX_get_filter_cb(&filter_cb) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get I/O filter callback function") if (H5Z_pipeline(old_pline, H5Z_FLAG_REVERSE, &(udata->filter_mask), err_detect, filter_cb, &my_chunk_alloc, &buf_alloc, &chunk) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, NULL, "data pipeline read failed") /* Reallocate chunk if necessary */ if (udata->new_unfilt_chunk) { void *tmp_chunk = chunk; if (NULL == (chunk = H5D__chunk_mem_alloc(my_chunk_alloc, pline))) { (void)H5D__chunk_mem_xfree(tmp_chunk, old_pline); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") } /* end if */ H5MM_memcpy(chunk, tmp_chunk, chunk_size); (void)H5D__chunk_mem_xfree(tmp_chunk, old_pline); } /* end if */ } /* end if */ /* Increment # of cache misses */ rdcc->stats.nmisses++; } /* end if */ else { H5D_fill_value_t fill_status; /* Sanity check */ HDassert(fill->alloc_time != H5D_ALLOC_TIME_EARLY); /* 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_mem_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 || fill_status == H5D_FILL_VALUE_DEFAULT))) { /* * 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, NULL, NULL, NULL, NULL, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, (size_t)0, chunk_size) < 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) < 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 */ /* See if the chunk can be cached */ if (rdcc->nslots > 0 && chunk_size <= rdcc->nbytes_max) { /* Calculate the index */ udata->idx_hint = H5D__chunk_hash_val(io_info->dset->shared, udata->common.scaled); /* Add the chunk to the cache only if the slot is not already locked */ ent = rdcc->slot[udata->idx_hint]; if (!ent || !ent->locked) { /* Preempt enough things from the cache to make room */ if (ent) { if (H5D__chunk_cache_evict(io_info->dset, 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, chunk_size) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk(s) from cache") /* Create a new entry */ if (NULL == (ent = H5FL_CALLOC(H5D_rdcc_ent_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate raw data chunk entry") ent->edge_chunk_state = disable_filters ? H5D_RDCC_DISABLE_FILTERS : 0; if (udata->new_unfilt_chunk) ent->edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS; /* Initialize the new entry */ ent->chunk_block.offset = chunk_addr; ent->chunk_block.length = chunk_alloc; ent->chunk_idx = udata->chunk_idx; H5MM_memcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); H5_CHECKED_ASSIGN(ent->rd_count, uint32_t, chunk_size, size_t); H5_CHECKED_ASSIGN(ent->wr_count, uint32_t, chunk_size, size_t); ent->chunk = (uint8_t *)chunk; /* Add it to the cache */ HDassert(NULL == rdcc->slot[udata->idx_hint]); rdcc->slot[udata->idx_hint] = ent; ent->idx = udata->idx_hint; rdcc->nbytes_used += chunk_size; rdcc->nused++; /* Add it to the linked list */ if (rdcc->tail) { rdcc->tail->next = ent; ent->prev = rdcc->tail; rdcc->tail = ent; } /* end if */ else rdcc->head = rdcc->tail = ent; ent->tmp_next = NULL; ent->tmp_prev = NULL; } /* end if */ else /* We did not add the chunk to cache */ ent = NULL; } /* end else */ else /* No cache set up, or chunk is too large: chunk is uncacheable */ ent = NULL; } /* end else */ /* Lock the chunk into the cache */ if (ent) { HDassert(!ent->locked); ent->locked = TRUE; chunk = ent->chunk; } /* end if */ else /* * The chunk cannot be placed in cache so we don't cache it. This is the * reason all those arguments have to be repeated for the unlock * function. */ udata->idx_hint = UINT_MAX; /* 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_mem_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 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty, 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); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(io_info); HDassert(udata); if (UINT_MAX == udata->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. */ hbool_t is_unfiltered_edge_chunk = FALSE; /* Whether the chunk is an unfiltered edge chunk */ /* Check if we should disable filters on this chunk */ if (udata->new_unfilt_chunk) { HDassert(layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); is_unfiltered_edge_chunk = TRUE; } /* end if */ else if (layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) { /* Check if the chunk is an edge chunk, and disable filters if so */ is_unfiltered_edge_chunk = H5D__chunk_is_partial_edge_chunk( io_info->dset->shared->ndims, layout->u.chunk.dim, io_info->store->chunk.scaled, io_info->dset->shared->curr_dims); } /* end if */ if (dirty) { H5D_rdcc_ent_t fake_ent; /* "fake" chunk cache entry */ HDmemset(&fake_ent, 0, sizeof(fake_ent)); fake_ent.dirty = TRUE; if (is_unfiltered_edge_chunk) fake_ent.edge_chunk_state = H5D_RDCC_DISABLE_FILTERS; if (udata->new_unfilt_chunk) fake_ent.edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS; H5MM_memcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); HDassert(layout->u.chunk.size > 0); fake_ent.chunk_idx = udata->chunk_idx; fake_ent.chunk_block.offset = udata->chunk_block.offset; fake_ent.chunk_block.length = udata->chunk_block.length; fake_ent.chunk = (uint8_t *)chunk; if (H5D__chunk_flush_entry(io_info->dset, &fake_ent, TRUE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") } /* end if */ else { if (chunk) chunk = H5D__chunk_mem_xfree( chunk, (is_unfiltered_edge_chunk ? NULL : &(io_info->dset->shared->dcpl_cache.pline))); } /* end else */ } /* end if */ else { H5D_rdcc_ent_t *ent; /* Chunk's entry in the cache */ /* Sanity check */ HDassert(udata->idx_hint < rdcc->nslots); HDassert(rdcc->slot[udata->idx_hint]); HDassert(rdcc->slot[udata->idx_hint]->chunk == chunk); /* * It's in the cache so unlock it. */ ent = rdcc->slot[udata->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_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 * *------------------------------------------------------------------------- */ static int H5D__chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { hsize_t *nbytes = (hsize_t *)_udata; FUNC_ENTER_STATIC_NOERR *(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(const H5D_t *dset, 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 */ hsize_t chunk_bytes = 0; /* Number of bytes allocated for chunks */ H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE HDassert(dset); HDassert(dset->shared); H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* 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, ent, FALSE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Iterate over the chunks */ if ((sc->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(const H5D_io_info_t *io_info, hbool_t full_overwrite, const hsize_t old_dim[]) { const H5D_t * dset = io_info->dset; /* the dataset pointer */ H5D_chk_idx_info_t idx_info; /* Chunked index info */ const H5D_chunk_ops_t *ops = dset->shared->layout.storage.u.chunk.ops; /* Chunk operations */ hsize_t min_unalloc[H5O_LAYOUT_NDIMS]; /* First chunk in each dimension that is unallocated (in scaled coordinates) */ hsize_t max_unalloc[H5O_LAYOUT_NDIMS]; /* Last chunk in each dimension that is unallocated (in scaled coordinates) */ hsize_t scaled[H5O_LAYOUT_NDIMS]; /* Offset of current chunk (in scaled coordinates) */ size_t orig_chunk_size; /* Original size of chunk in bytes */ size_t chunk_size; /* Actual size of chunk in bytes, possibly filtered */ 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_pline_t def_pline = H5O_CRT_PIPELINE_DEF; /* Default pipeline */ 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 */ void * unfilt_fill_buf = NULL; /* Unfiltered fill value buffer */ void ** fill_buf = NULL; /* Pointer to the fill buffer to use for a chunk */ #ifdef H5_HAVE_PARALLEL 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 */ H5D_chunk_coll_fill_info_t chunk_fill_info; /* chunk address information for doing I/O */ #endif /* H5_HAVE_PARALLEL */ hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ unsigned space_ndims; /* Dataset's space rank */ const hsize_t * space_dim; /* Dataset's dataspace dimensions */ const uint32_t * chunk_dim = layout->u.chunk.dim; /* Convenience pointer to chunk dimensions */ unsigned op_dim; /* Current operating dimension */ 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 */ hbool_t has_unfilt_edge_chunks = FALSE; /* Whether there are partial edge chunks with disabled filters */ hbool_t unfilt_edge_chunk_dim[H5O_LAYOUT_NDIMS]; /* Whether there are unfiltered edge chunks at the edge of each dimension */ hsize_t edge_chunk_scaled[H5O_LAYOUT_NDIMS]; /* Offset of the unfiltered edge chunks at the edge of each dimension */ unsigned nunfilt_edge_chunk_dims = 0; /* Number of dimensions on an edge */ H5O_storage_chunk_t *sc = &(layout->storage.u.chunk); /* Convenience variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Retrieve the dataset dimensions */ space_dim = dset->shared->curr_dims; space_ndims = dset->shared->ndims; /* The last dimension in scaled chunk coordinates is always 0 */ scaled[space_ndims] = (hsize_t)0; /* Check if any space dimensions are 0, if so we do not have to do anything */ for (op_dim = 0; op_dim < (unsigned)space_ndims; op_dim++) if (space_dim[op_dim] == 0) { /* Reset any cached chunk info for this dataset */ H5D__chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); HGOTO_DONE(SUCCEED) } /* end if */ #ifdef H5_HAVE_PARALLEL /* Retrieve MPI parameters */ if (H5F_HAS_FEATURE(dset->oloc.file, H5FD_FEAT_HAS_MPI)) { /* Set the MPI-capable file driver flag */ using_mpi = TRUE; /* init chunk info stuff for collective I/O */ chunk_fill_info.num_chunks = 0; chunk_fill_info.chunk_info = NULL; } /* end if */ #endif /* H5_HAVE_PARALLEL */ /* Calculate the minimum and maximum chunk offsets in each dimension, and * determine if there are any unfiltered partial edge chunks. Note that we * assume here that all elements of space_dim are > 0. This is checked at * the top of this function. */ for (op_dim = 0; op_dim < space_ndims; op_dim++) { /* Validate this chunk dimension */ if (chunk_dim[op_dim] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", op_dim) min_unalloc[op_dim] = (old_dim[op_dim] + chunk_dim[op_dim] - 1) / chunk_dim[op_dim]; max_unalloc[op_dim] = (space_dim[op_dim] - 1) / chunk_dim[op_dim]; /* Calculate if there are unfiltered edge chunks at the edge of this * dimension. Note the edge_chunk_scaled is uninitialized for * dimensions where unfilt_edge_chunk_dim is FALSE. Also */ if ((layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) && pline->nused > 0 && space_dim[op_dim] % chunk_dim[op_dim] != 0) { has_unfilt_edge_chunks = TRUE; unfilt_edge_chunk_dim[op_dim] = TRUE; edge_chunk_scaled[op_dim] = max_unalloc[op_dim]; } /* end if */ else unfilt_edge_chunk_dim[op_dim] = FALSE; } /* end for */ /* Get original chunk size */ H5_CHECKED_ASSIGN(orig_chunk_size, size_t, layout->u.chunk.size, uint32_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 || fill_status == H5D_FILL_VALUE_DEFAULT)))) || 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, (H5MM_allocate_t)H5D__chunk_mem_alloc, (void *)pline, (H5MM_free_t)H5D__chunk_mem_free, (void *)pline, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, (size_t)0, orig_chunk_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info") fb_info_init = TRUE; /* Initialize the fill_buf pointer to the buffer in fb_info. If edge * chunk filters are disabled, we will switch the buffer as appropriate * for each chunk. */ fill_buf = &fb_info.fill_buf; /* 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) { H5Z_EDC_t err_detect; /* Error detection info */ H5Z_cb_t filter_cb; /* I/O filter callback function */ size_t buf_size = orig_chunk_size; /* If the dataset has disabled partial chunk filters, create a copy * of the unfiltered fill_buf to use for partial chunks */ if (has_unfilt_edge_chunks) { if (NULL == (unfilt_fill_buf = H5D__chunk_mem_alloc(orig_chunk_size, &def_pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") H5MM_memcpy(unfilt_fill_buf, fb_info.fill_buf, orig_chunk_size); } /* end if */ /* Retrieve filter settings from API context */ if (H5CX_get_err_detect(&err_detect) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info") if (H5CX_get_filter_cb(&filter_cb) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function") /* Push the chunk through the filters */ if (H5Z_pipeline(pline, 0, &filter_mask, err_detect, filter_cb, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 /* Check for the chunk expanding too much to encode in a 32-bit value */ if (orig_chunk_size > ((size_t)0xffffffff)) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") #endif /* H5_SIZEOF_SIZE_T > 4 */ } /* end if */ } /* end if */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Loop over all chunks */ /* The algorithm is: * For each dimension: * -Allocate all chunks in the new dataspace that are beyond the original * dataspace in the operating dimension, except those that have already * been allocated. * * This is accomplished mainly using the min_unalloc and max_unalloc arrays. * min_unalloc represents the lowest offset in each dimension of chunks that * have not been allocated (whether or not they need to be). max_unalloc * represents the highest offset in each dimension of chunks in the new * dataset that have not been allocated by this routine (they may have been * allocated previously). * * Every time the algorithm finishes allocating chunks allocated beyond a * certain dimension, max_unalloc is updated in order to avoid allocating * those chunks again. * * Note that min_unalloc & max_unalloc are in scaled coordinates. * */ chunk_size = orig_chunk_size; for (op_dim = 0; op_dim < space_ndims; op_dim++) { H5D_chunk_ud_t udata; /* User data for querying chunk info */ unsigned u; /* Local index variable */ int i; /* Local index variable */ /* Check if allocation along this dimension is really necessary */ if (min_unalloc[op_dim] > max_unalloc[op_dim]) continue; else { /* Reset the chunk offset indices */ HDmemset(scaled, 0, (space_ndims * sizeof(scaled[0]))); scaled[op_dim] = min_unalloc[op_dim]; if (has_unfilt_edge_chunks) { /* Initialize nunfilt_edge_chunk_dims */ nunfilt_edge_chunk_dims = 0; for (u = 0; u < space_ndims; u++) if (unfilt_edge_chunk_dim[u] && scaled[u] == edge_chunk_scaled[u]) nunfilt_edge_chunk_dims++; /* Initialize chunk_size and fill_buf */ if (should_fill && !fb_info.has_vlen_fill_type) { HDassert(fb_info_init); HDassert(unfilt_fill_buf); if (nunfilt_edge_chunk_dims) { fill_buf = &unfilt_fill_buf; chunk_size = layout->u.chunk.size; } /* end if */ else { fill_buf = &fb_info.fill_buf; chunk_size = orig_chunk_size; } /* end else */ } /* end if */ } /* end if */ carry = FALSE; } /* end else */ while (!carry) { hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */ /* Look up this chunk */ if (H5D__chunk_lookup(dset, scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") #ifndef NDEBUG /* None of the chunks should be allocated */ if (H5D_CHUNK_IDX_NONE != sc->idx_type) HDassert(!H5F_addr_defined(udata.chunk_block.offset)); /* Make sure the chunk is really in the dataset and outside the * original dimensions */ { unsigned v; /* Local index variable */ hbool_t outside_orig = FALSE; for (v = 0; v < space_ndims; v++) { HDassert((scaled[v] * chunk_dim[v]) < space_dim[v]); if ((scaled[v] * chunk_dim[v]) >= old_dim[v]) outside_orig = TRUE; } /* end for */ HDassert(outside_orig); } /* end block */ #endif /* NDEBUG */ /* Check for VL datatype & non-default fill value */ if (fb_info_init && fb_info.has_vlen_fill_type) { /* Sanity check */ HDassert(should_fill); HDassert(!unfilt_fill_buf); #ifdef H5_HAVE_PARALLEL HDassert(!using_mpi); /* Can't write VL datatypes in parallel currently */ #endif /* Check to make sure the buffer is large enough. It is * possible (though ill-advised) for the filter to shrink the * buffer. */ if (fb_info.fill_buf_size < orig_chunk_size) { if (NULL == (fb_info.fill_buf = H5D__chunk_mem_realloc(fb_info.fill_buf, orig_chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory reallocation failed for raw data chunk") fb_info.fill_buf_size = orig_chunk_size; } /* end if */ /* Fill the buffer with VL datatype fill values */ if (H5D__fill_refill_vl(&fb_info, fb_info.elmts_per_buf) < 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) && !nunfilt_edge_chunk_dims) { H5Z_EDC_t err_detect; /* Error detection info */ H5Z_cb_t filter_cb; /* I/O filter callback function */ size_t nbytes = orig_chunk_size; /* Retrieve filter settings from API context */ if (H5CX_get_err_detect(&err_detect) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info") if (H5CX_get_filter_cb(&filter_cb) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function") /* Push the chunk through the filters */ if (H5Z_pipeline(pline, 0, &filter_mask, err_detect, filter_cb, &nbytes, &fb_info.fill_buf_size, &fb_info.fill_buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 /* Check for the chunk expanding too much to encode in a 32-bit value */ if (nbytes > ((size_t)0xffffffff)) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") #endif /* H5_SIZEOF_SIZE_T > 4 */ /* Keep the number of bytes the chunk turned in to */ chunk_size = nbytes; } /* end if */ else chunk_size = layout->u.chunk.size; HDassert(*fill_buf == fb_info.fill_buf); } /* end if */ /* Initialize the chunk information */ udata.common.layout = &layout->u.chunk; udata.common.storage = sc; udata.common.scaled = scaled; udata.chunk_block.offset = HADDR_UNDEF; H5_CHECKED_ASSIGN(udata.chunk_block.length, uint32_t, chunk_size, size_t); udata.filter_mask = filter_mask; /* Allocate the chunk (with all processes) */ if (H5D__chunk_file_alloc(&idx_info, NULL, &udata.chunk_block, &need_insert, scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") HDassert(H5F_addr_defined(udata.chunk_block.offset)); /* Check if fill values should be written to chunks */ if (should_fill) { /* Sanity check */ HDassert(fb_info_init); HDassert(udata.chunk_block.length == chunk_size); #ifdef H5_HAVE_PARALLEL /* Check if this file is accessed with an MPI-capable file driver */ if (using_mpi) { /* collect all chunk addresses to be written to write collectively at the end */ /* allocate/resize chunk info array if no more space left */ if (0 == chunk_fill_info.num_chunks % 1024) { void *tmp_realloc; if (NULL == (tmp_realloc = H5MM_realloc(chunk_fill_info.chunk_info, (chunk_fill_info.num_chunks + 1024) * sizeof(struct chunk_coll_fill_info)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed for chunk fill info") chunk_fill_info.chunk_info = tmp_realloc; } /* Store info about the chunk for later */ chunk_fill_info.chunk_info[chunk_fill_info.num_chunks].addr = udata.chunk_block.offset; chunk_fill_info.chunk_info[chunk_fill_info.num_chunks].chunk_size = chunk_size; chunk_fill_info.chunk_info[chunk_fill_info.num_chunks].unfiltered_partial_chunk = (*fill_buf == unfilt_fill_buf); chunk_fill_info.num_chunks++; /* Indicate that blocks will be written */ blocks_written = TRUE; } /* end if */ else { #endif /* H5_HAVE_PARALLEL */ if (H5F_shared_block_write(H5F_SHARED(dset->oloc.file), H5FD_MEM_DRAW, udata.chunk_block.offset, chunk_size, *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 */ /* Insert the chunk record into the index */ if (need_insert && ops->insert) if ((ops->insert)(&idx_info, &udata, dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") /* Increment indices and adjust the edge chunk state */ carry = TRUE; for (i = ((int)space_ndims - 1); i >= 0; --i) { scaled[i]++; if (scaled[i] > max_unalloc[i]) { if ((unsigned)i == op_dim) scaled[i] = min_unalloc[i]; else scaled[i] = 0; /* Check if we just left the edge in this dimension */ if (unfilt_edge_chunk_dim[i] && edge_chunk_scaled[i] == max_unalloc[i] && scaled[i] < edge_chunk_scaled[i]) { nunfilt_edge_chunk_dims--; if (should_fill && nunfilt_edge_chunk_dims == 0 && !fb_info.has_vlen_fill_type) { HDassert( !H5D__chunk_is_partial_edge_chunk(space_ndims, chunk_dim, scaled, space_dim)); fill_buf = &fb_info.fill_buf; chunk_size = orig_chunk_size; } /* end if */ } /* end if */ } /* end if */ else { /* Check if we just entered the edge in this dimension */ if (unfilt_edge_chunk_dim[i] && scaled[i] == edge_chunk_scaled[i]) { HDassert(edge_chunk_scaled[i] == max_unalloc[i]); nunfilt_edge_chunk_dims++; if (should_fill && nunfilt_edge_chunk_dims == 1 && !fb_info.has_vlen_fill_type) { HDassert( H5D__chunk_is_partial_edge_chunk(space_ndims, chunk_dim, scaled, space_dim)); fill_buf = &unfilt_fill_buf; chunk_size = layout->u.chunk.size; } /* end if */ } /* end if */ carry = FALSE; break; } /* end else */ } /* end for */ } /* end while(!carry) */ /* Adjust max_unalloc so we don't allocate the same chunk twice. Also * check if this dimension started from 0 (and hence allocated all of * the chunks. */ if (min_unalloc[op_dim] == 0) break; else max_unalloc[op_dim] = min_unalloc[op_dim] - 1; } /* end for(op_dim=0...) */ #ifdef H5_HAVE_PARALLEL /* do final collective I/O */ if (using_mpi && blocks_written) if (H5D__chunk_collective_fill(dset, &chunk_fill_info, fb_info.fill_buf, unfilt_fill_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") #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") /* Free the unfiltered fill value buffer */ unfilt_fill_buf = H5D__chunk_mem_xfree(unfilt_fill_buf, &def_pline); #ifdef H5_HAVE_PARALLEL if (using_mpi && chunk_fill_info.chunk_info) H5MM_free(chunk_fill_info.chunk_info); #endif FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_allocate() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_update_old_edge_chunks * * Purpose: Update all chunks which were previously partial edge * chunks and are now complete. Determines exactly which * chunks need to be updated and locks each into cache using * the 'prev_unfilt_chunk' flag, then unlocks it, causing * filters to be applied as necessary. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * April 14, 2010 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_update_old_edge_chunks(H5D_t *dset, hsize_t old_dim[]) { hsize_t old_edge_chunk_sc[H5O_LAYOUT_NDIMS]; /* Offset of first previously incomplete chunk in each dimension */ hsize_t max_edge_chunk_sc[H5O_LAYOUT_NDIMS]; /* largest offset of chunks that might need to be modified in each dimension */ hbool_t new_full_dim[H5O_LAYOUT_NDIMS]; /* Whether the plane of chunks in this dimension needs to be modified */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ hsize_t chunk_sc[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */ const uint32_t * chunk_dim = layout->u.chunk.dim; /* Convenience pointer to chunk dimensions */ unsigned space_ndims; /* Dataset's space rank */ const hsize_t * space_dim; /* Dataset's dataspace dimensions */ unsigned op_dim; /* Current operationg dimension */ H5D_io_info_t chk_io_info; /* Chunked I/O info object */ H5D_chunk_ud_t chk_udata; /* User data for locking chunk */ H5D_storage_t chk_store; /* Chunk storage information */ void * chunk; /* The file chunk */ hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); H5D_CHUNK_STORAGE_INDEX_CHK(&layout->storage.u.chunk); HDassert(dset->shared->dcpl_cache.pline.nused > 0); HDassert(layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); /* Retrieve the dataset dimensions */ space_dim = dset->shared->curr_dims; space_ndims = dset->shared->ndims; /* The last dimension in chunk_offset is always 0 */ chunk_sc[space_ndims] = (hsize_t)0; /* Check if any current dimensions are smaller than the chunk size, or if * any old dimensions are 0. If so we do not have to do anything. */ for (op_dim = 0; op_dim < space_ndims; op_dim++) if ((space_dim[op_dim] < chunk_dim[op_dim]) || old_dim[op_dim] == 0) { /* Reset any cached chunk info for this dataset */ H5D__chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); HGOTO_DONE(SUCCEED) } /* end if */ /* Set up chunked I/O info object, for operations on chunks (in callback). * Note that we only need to set chunk_offset once, as the array's address * will never change. */ chk_store.chunk.scaled = chunk_sc; H5D_BUILD_IO_INFO_RD(&chk_io_info, dset, &chk_store, NULL); /* * Determine the edges of the dataset which need to be modified */ for (op_dim = 0; op_dim < space_ndims; op_dim++) { /* Start off with this dimension marked as not needing to be modified */ new_full_dim[op_dim] = FALSE; /* Validate this chunk dimension */ if (chunk_dim[op_dim] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", op_dim) /* Calculate offset of first previously incomplete chunk in this * dimension */ old_edge_chunk_sc[op_dim] = (old_dim[op_dim] / chunk_dim[op_dim]); /* Calculate the largest offset of chunks that might need to be * modified in this dimension */ max_edge_chunk_sc[op_dim] = MIN((old_dim[op_dim] - 1) / chunk_dim[op_dim], MAX((space_dim[op_dim] / chunk_dim[op_dim]), 1) - 1); /* Check for old_dim aligned with chunk boundary in this dimension, if * so we do not need to modify chunks along the edge in this dimension */ if (old_dim[op_dim] % chunk_dim[op_dim] == 0) continue; /* Check if the dataspace expanded enough to cause the old edge chunks * in this dimension to become full */ if ((space_dim[op_dim] / chunk_dim[op_dim]) >= (old_edge_chunk_sc[op_dim] + 1)) new_full_dim[op_dim] = TRUE; } /* end for */ /* Main loop: fix old edge chunks */ for (op_dim = 0; op_dim < space_ndims; op_dim++) { /* Check if allocation along this dimension is really necessary */ if (!new_full_dim[op_dim]) continue; else { HDassert(max_edge_chunk_sc[op_dim] == old_edge_chunk_sc[op_dim]); /* Reset the chunk offset indices */ HDmemset(chunk_sc, 0, (space_ndims * sizeof(chunk_sc[0]))); chunk_sc[op_dim] = old_edge_chunk_sc[op_dim]; carry = FALSE; } /* end if */ while (!carry) { int i; /* Local index variable */ /* Make sure the chunk is really a former edge chunk */ HDassert(H5D__chunk_is_partial_edge_chunk(space_ndims, chunk_dim, chunk_sc, old_dim) && !H5D__chunk_is_partial_edge_chunk(space_ndims, chunk_dim, chunk_sc, space_dim)); /* Lookup the chunk */ if (H5D__chunk_lookup(dset, chunk_sc, &chk_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* If this chunk does not exist in cache or on disk, no need to do * anything */ if (H5F_addr_defined(chk_udata.chunk_block.offset) || (UINT_MAX != chk_udata.idx_hint)) { /* Lock the chunk into cache. H5D__chunk_lock will take care of * updating the chunk to no longer be an edge chunk. */ if (NULL == (chunk = (void *)H5D__chunk_lock(&chk_io_info, &chk_udata, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to lock raw data chunk") /* Unlock the chunk */ if (H5D__chunk_unlock(&chk_io_info, &chk_udata, TRUE, chunk, (uint32_t)0) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk") } /* end if */ /* Increment indices */ carry = TRUE; for (i = ((int)space_ndims - 1); i >= 0; --i) { if ((unsigned)i != op_dim) { ++chunk_sc[i]; if (chunk_sc[i] > (hsize_t)max_edge_chunk_sc[i]) chunk_sc[i] = 0; else { carry = FALSE; break; } /* end else */ } /* end if */ } /* end for */ } /* end while(!carry) */ /* Adjust max_edge_chunk_sc so we don't modify the same chunk twice. * Also check if this dimension started from 0 (and hence modified all * of the old edge chunks. */ if (old_edge_chunk_sc[op_dim] == 0) break; else --max_edge_chunk_sc[op_dim]; } /* end for(op_dim=0...) */ /* Reset any cached chunk info for this dataset */ H5D__chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_update_old_edge_chunks() */ #ifdef H5_HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5D__chunk_collective_fill * * Purpose: Use MPIO collective write to fill the chunks (if number of * chunks to fill is greater than the number of MPI procs; * otherwise use independent I/O). * * Return: Non-negative on success/Negative on failure * * Programmer: Mohamad Chaarawi * July 30, 2014 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_fill_info, const void *fill_buf, const void *partial_chunk_fill_buf) { MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */ int mpi_rank = (-1); /* This process's rank */ int mpi_size = (-1); /* MPI Comm size */ int mpi_code; /* MPI return code */ size_t num_blocks; /* Number of blocks between processes. */ size_t leftover_blocks; /* Number of leftover blocks to handle */ int blocks, leftover; /* converted to int for MPI */ MPI_Aint * chunk_disp_array = NULL; MPI_Aint * block_disps = NULL; int * block_lens = NULL; MPI_Datatype mem_type = MPI_BYTE, file_type = MPI_BYTE; H5FD_mpio_xfer_t prev_xfer_mode; /* Previous data xfer mode */ hbool_t have_xfer_mode = FALSE; /* Whether the previous xffer mode has been retrieved */ hbool_t need_sort = FALSE; size_t i; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* * If a separate fill buffer is provided for partial chunks, ensure * that the "don't filter partial edge chunks" flag is set. */ if (partial_chunk_fill_buf) HDassert(dset->shared->layout.u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); /* 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") /* Get the MPI size */ if ((mpi_size = H5F_mpi_get_size(dset->oloc.file)) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size") /* Distribute evenly the number of blocks between processes. */ if (mpi_size == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Resulted in division by zero") num_blocks = (size_t)(chunk_fill_info->num_chunks / (size_t)mpi_size); /* value should be the same on all procs */ /* After evenly distributing the blocks between processes, are there any * leftover blocks for each individual process (round-robin)? */ leftover_blocks = (size_t)(chunk_fill_info->num_chunks % (size_t)mpi_size); /* Cast values to types needed by MPI */ H5_CHECKED_ASSIGN(blocks, int, num_blocks, size_t); H5_CHECKED_ASSIGN(leftover, int, leftover_blocks, size_t); /* Check if we have any chunks to write on this rank */ if (num_blocks > 0 || (leftover && leftover > mpi_rank)) { MPI_Aint partial_fill_buf_disp = 0; hbool_t all_same_block_len = TRUE; /* Allocate buffers */ if (NULL == (chunk_disp_array = (MPI_Aint *)H5MM_malloc((size_t)(blocks + 1) * sizeof(MPI_Aint)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file displacement buffer") if (partial_chunk_fill_buf) { MPI_Aint fill_buf_addr; MPI_Aint partial_fill_buf_addr; /* Calculate the displacement between the fill buffer and partial chunk fill buffer */ if (MPI_SUCCESS != (mpi_code = MPI_Get_address(fill_buf, &fill_buf_addr))) HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code) if (MPI_SUCCESS != (mpi_code = MPI_Get_address(partial_chunk_fill_buf, &partial_fill_buf_addr))) HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code) #if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1 partial_fill_buf_disp = MPI_Aint_diff(partial_fill_buf_addr, fill_buf_addr); #else partial_fill_buf_disp = partial_fill_buf_addr - fill_buf_addr; #endif /* * Allocate all-zero block displacements array. If a block's displacement * is left as zero, that block will be written to from the regular fill * buffer. If a block represents an unfiltered partial edge chunk, its * displacement will be set so that the block is written to from the * unfiltered fill buffer. */ if (NULL == (block_disps = (MPI_Aint *)H5MM_calloc((size_t)(blocks + 1) * sizeof(MPI_Aint)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate block displacements buffer") } /* * Perform initial scan of chunk info list to: * - make sure that chunk addresses are monotonically non-decreasing * - check if all blocks have the same length */ for (i = 1; i < chunk_fill_info->num_chunks; i++) { if (chunk_fill_info->chunk_info[i].addr < chunk_fill_info->chunk_info[i - 1].addr) need_sort = TRUE; if (chunk_fill_info->chunk_info[i].chunk_size != chunk_fill_info->chunk_info[i - 1].chunk_size) all_same_block_len = FALSE; } if (need_sort) HDqsort(chunk_fill_info->chunk_info, chunk_fill_info->num_chunks, sizeof(struct chunk_coll_fill_info), H5D__chunk_cmp_coll_fill_info); /* Allocate buffer for block lengths if necessary */ if (!all_same_block_len) if (NULL == (block_lens = (int *)H5MM_malloc((size_t)(blocks + 1) * sizeof(int)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk lengths buffer") for (i = 0; i < (size_t)blocks; i++) { size_t idx = i + (size_t)(mpi_rank * blocks); /* store the chunk address as an MPI_Aint */ chunk_disp_array[i] = (MPI_Aint)(chunk_fill_info->chunk_info[idx].addr); if (!all_same_block_len) H5_CHECKED_ASSIGN(block_lens[i], int, chunk_fill_info->chunk_info[idx].chunk_size, size_t); if (chunk_fill_info->chunk_info[idx].unfiltered_partial_chunk) { HDassert(partial_chunk_fill_buf); block_disps[i] = partial_fill_buf_disp; } } /* end for */ /* Calculate if there are any leftover blocks after evenly * distributing. If there are, then round-robin the distribution * to processes 0 -> leftover. */ if (leftover && leftover > mpi_rank) { chunk_disp_array[blocks] = (MPI_Aint)chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].addr; if (!all_same_block_len) H5_CHECKED_ASSIGN(block_lens[blocks], int, chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].chunk_size, size_t); if (chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].unfiltered_partial_chunk) { HDassert(partial_chunk_fill_buf); block_disps[blocks] = partial_fill_buf_disp; } blocks++; } /* Create file and memory types for the write operation */ if (all_same_block_len) { int block_len; H5_CHECKED_ASSIGN(block_len, int, chunk_fill_info->chunk_info[0].chunk_size, size_t); mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, &file_type); if (mpi_code != MPI_SUCCESS) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code) if (partial_chunk_fill_buf) { /* * If filters are disabled for partial edge chunks, those chunks could * potentially have the same block length as the other chunks, but still * need to be written to using the unfiltered fill buffer. Use an hindexed * block type rather than an hvector. */ mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, block_disps, MPI_BYTE, &mem_type); if (mpi_code != MPI_SUCCESS) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code) } else { mpi_code = MPI_Type_create_hvector(blocks, block_len, 0, MPI_BYTE, &mem_type); if (mpi_code != MPI_SUCCESS) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) } } else { /* * Currently, different block lengths implies that there are partial * edge chunks and the "don't filter partial edge chunks" flag is set. */ HDassert(partial_chunk_fill_buf); HDassert(block_lens); HDassert(block_disps); mpi_code = MPI_Type_create_hindexed(blocks, block_lens, chunk_disp_array, MPI_BYTE, &file_type); if (mpi_code != MPI_SUCCESS) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) mpi_code = MPI_Type_create_hindexed(blocks, block_lens, block_disps, MPI_BYTE, &mem_type); if (mpi_code != MPI_SUCCESS) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) } if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&file_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&mem_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) } /* end if */ /* Set MPI-IO VFD properties */ /* Set MPI datatypes for operation */ if (H5CX_set_mpi_coll_datatypes(mem_type, file_type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O properties") /* Get current transfer mode */ if (H5CX_get_io_xfer_mode(&prev_xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set transfer mode") have_xfer_mode = TRUE; /* Set transfer mode */ if (H5CX_set_io_xfer_mode(H5FD_MPIO_COLLECTIVE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set transfer mode") /* Low-level write (collective) */ if (H5F_shared_block_write(H5F_SHARED(dset->oloc.file), H5FD_MEM_DRAW, (haddr_t)0, (blocks) ? (size_t)1 : (size_t)0, fill_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") /* Barrier so processes don't race ahead */ if (MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) done: if (have_xfer_mode) /* Set transfer mode */ if (H5CX_set_io_xfer_mode(prev_xfer_mode) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set transfer mode") /* free things */ if (MPI_BYTE != file_type) if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) if (MPI_BYTE != mem_type) if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) H5MM_xfree(chunk_disp_array); H5MM_xfree(block_disps); H5MM_xfree(block_lens); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_collective_fill() */ static int H5D__chunk_cmp_coll_fill_info(const void *_entry1, const void *_entry2) { const struct chunk_coll_fill_info *entry1; const struct chunk_coll_fill_info *entry2; FUNC_ENTER_STATIC_NOERR entry1 = (const struct chunk_coll_fill_info *)_entry1; entry2 = (const struct chunk_coll_fill_info *)_entry2; FUNC_LEAVE_NOAPI(H5F_addr_cmp(entry1->addr, entry2->addr)) } /* end H5D__chunk_cmp_coll_fill_info() */ #endif /* H5_HAVE_PARALLEL */ /*------------------------------------------------------------------------- * Function: H5D__chunk_prune_fill * * Purpose: Write the fill value to the parts of the chunk that are no * longer part of the dataspace * * Return: Non-negative on success/Negative on failure * * Programmer: Pedro Vicente * March 26, 2002 * *------------------------------------------------------------------------- */ static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfilt_chunk) { const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */ const H5D_t * dset = io_info->dset; /* Local pointer to the dataset info */ const H5O_layout_t * layout = &(dset->shared->layout); /* Dataset's layout */ unsigned rank = udata->common.layout->ndims - 1; /* Dataset rank */ const hsize_t * scaled = udata->common.scaled; /* Scaled chunk offset */ H5S_sel_iter_t * chunk_iter = NULL; /* Memory selection iteration info */ hbool_t chunk_iter_init = FALSE; /* Whether the chunk iterator has been initialized */ hsize_t sel_nelmts; /* Number of elements in selection */ hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */ size_t chunk_size; /*size of a chunk */ void * chunk; /* The file chunk */ H5D_chunk_ud_t chk_udata; /* User data for locking chunk */ uint32_t bytes_accessed; /* Bytes accessed in chunk */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Get the chunk's size */ HDassert(layout->u.chunk.size > 0); H5_CHECKED_ASSIGN(chunk_size, size_t, layout->u.chunk.size, uint32_t); /* Get the info for the chunk in the file */ if (H5D__chunk_lookup(dset, scaled, &chk_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") chk_udata.new_unfilt_chunk = new_unfilt_chunk; /* If this chunk does not exist in cache or on disk, no need to do anything */ if (!H5F_addr_defined(chk_udata.chunk_block.offset) && UINT_MAX == chk_udata.idx_hint) HGOTO_DONE(SUCCEED) /* 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, NULL, NULL, NULL, NULL, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk, chunk_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "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->space_dim[u] - (scaled[u] * layout->u.chunk.dim[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, FAIL, "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, FAIL, "unable to select hyperslab") /* Lock the chunk into the cache, to get a pointer to the chunk buffer */ if (NULL == (chunk = (void *)H5D__chunk_lock(io_info, &chk_udata, FALSE, FALSE))) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "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); H5_CHECK_OVERFLOW(sel_nelmts, hsize_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) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") /* Allocate the chunk selection iterator */ if (NULL == (chunk_iter = H5FL_MALLOC(H5S_sel_iter_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk selection iterator") /* 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) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunk selection information") chunk_iter_init = TRUE; /* Scatter the data into memory */ if (H5D__scatter_mem(udata->fb_info.fill_buf, chunk_iter, (size_t)sel_nelmts, chunk /*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed") /* The number of bytes accessed in the chunk */ /* (i.e. the bytes replaced with fill values) */ H5_CHECK_OVERFLOW(sel_nelmts, hsize_t, uint32_t); bytes_accessed = (uint32_t)sel_nelmts * layout->u.chunk.dim[rank]; /* Release lock on chunk */ if (H5D__chunk_unlock(io_info, &chk_udata, TRUE, chunk, bytes_accessed) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk") done: /* Release the selection iterator */ if (chunk_iter_init && H5S_SELECT_ITER_RELEASE(chunk_iter) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") if (chunk_iter) chunk_iter = H5FL_FREE(H5S_sel_iter_t, chunk_iter); FUNC_LEAVE_NOAPI(ret_value) } /* H5D__chunk_prune_fill */ /*------------------------------------------------------------------------- * 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 * 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, const hsize_t *old_dim) { hsize_t min_mod_chunk_sc[H5O_LAYOUT_NDIMS]; /* Scaled offset of first chunk to modify in each dimension */ hsize_t max_mod_chunk_sc[H5O_LAYOUT_NDIMS]; /* Scaled offset of last chunk to modify in each dimension */ hssize_t max_fill_chunk_sc[H5O_LAYOUT_NDIMS]; /* Scaled offset of last chunk that might be filled in each dimension */ hbool_t fill_dim[H5O_LAYOUT_NDIMS]; /* Whether the plane of edge chunks in this dimension needs to be filled */ hsize_t min_partial_chunk_sc[H5O_LAYOUT_NDIMS]; /* Offset of first partial (or empty) chunk in each dimension */ hbool_t new_unfilt_dim[H5O_LAYOUT_NDIMS]; /* Whether the plane of edge chunks in this dimension are newly unfiltered */ 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 */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ const H5D_rdcc_t * rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ unsigned space_ndims; /* Dataset's space rank */ const hsize_t * space_dim; /* Current dataspace dimensions */ unsigned op_dim; /* Current operating dimension */ hbool_t shrunk_dim[H5O_LAYOUT_NDIMS]; /* Dimensions which have shrunk */ 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_common_ud_t idx_udata; /* User data for index removal routine */ H5S_t * chunk_space = NULL; /* Dataspace for a chunk */ hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */ hsize_t scaled[H5O_LAYOUT_NDIMS]; /* Scaled offset of current chunk */ hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */ uint32_t elmts_per_chunk; /* Elements in chunk */ hbool_t disable_edge_filters = FALSE; /* Whether to disable filters on partial edge chunks */ hbool_t new_unfilt_chunk = FALSE; /* Whether the chunk is newly unfiltered */ unsigned u; /* Local index variable */ const H5O_storage_chunk_t *sc = &(layout->storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Go get the rank & dimensions (including the element size) */ space_dim = dset->shared->curr_dims; space_ndims = dset->shared->ndims; /* The last dimension in scaled is always 0 */ scaled[space_ndims] = (hsize_t)0; /* Check if any old dimensions are 0, if so we do not have to do anything */ for (op_dim = 0; op_dim < (unsigned)space_ndims; op_dim++) if (old_dim[op_dim] == 0) { /* Reset any cached chunk info for this dataset */ H5D__chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last); HGOTO_DONE(SUCCEED) } /* end if */ /* Round up to the next integer # of chunks, to accommodate partial chunks */ /* Use current dims because the indices have already been updated! -NAF */ /* (also compute the number of elements per chunk) */ /* (also copy the chunk dimensions into 'hsize_t' array for creating dataspace) */ /* (also compute the dimensions which have been shrunk) */ elmts_per_chunk = 1; for (u = 0; u < space_ndims; u++) { elmts_per_chunk *= layout->u.chunk.dim[u]; chunk_dim[u] = layout->u.chunk.dim[u]; shrunk_dim[u] = (space_dim[u] < old_dim[u]); } /* end for */ /* Create a dataspace for a chunk & set the extent */ if (NULL == (chunk_space = H5S_create_simple(space_ndims, chunk_dim, 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) * Note that we only need to set scaled once, as the array's address * will never change. */ chk_store.chunk.scaled = scaled; H5D_BUILD_IO_INFO_RD(&chk_io_info, dset, &chk_store, NULL); /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = &dset->shared->layout.storage.u.chunk; /* Initialize the user data for the iteration */ HDmemset(&udata, 0, sizeof udata); udata.common.layout = &layout->u.chunk; udata.common.storage = sc; udata.common.scaled = scaled; udata.io_info = &chk_io_info; udata.idx_info = &idx_info; udata.space_dim = space_dim; udata.shrunk_dim = shrunk_dim; udata.elmts_per_chunk = elmts_per_chunk; udata.chunk_space = chunk_space; udata.hyper_start = hyper_start; udata_init = TRUE; /* Initialize user data for removal */ idx_udata.layout = &layout->u.chunk; idx_udata.storage = sc; /* Determine if partial edge chunk filters are disabled */ disable_edge_filters = (layout->u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) && (idx_info.pline->nused > 0); /* * Determine the chunks which need to be filled or removed */ HDmemset(min_mod_chunk_sc, 0, sizeof(min_mod_chunk_sc)); HDmemset(max_mod_chunk_sc, 0, sizeof(max_mod_chunk_sc)); for (op_dim = 0; op_dim < (unsigned)space_ndims; op_dim++) { /* Validate this chunk dimension */ if (chunk_dim[op_dim] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", op_dim) /* Calculate the largest offset of chunks that might need to be * modified in this dimension */ max_mod_chunk_sc[op_dim] = (old_dim[op_dim] - 1) / chunk_dim[op_dim]; /* Calculate the largest offset of chunks that might need to be * filled in this dimension */ if (0 == space_dim[op_dim]) max_fill_chunk_sc[op_dim] = -1; else max_fill_chunk_sc[op_dim] = (hssize_t)(((MIN(space_dim[op_dim], old_dim[op_dim]) - 1) / chunk_dim[op_dim])); if (shrunk_dim[op_dim]) { /* Calculate the smallest offset of chunks that might need to be * modified in this dimension. Note that this array contains * garbage for all dimensions which are not shrunk. These locations * must not be read from! */ min_mod_chunk_sc[op_dim] = space_dim[op_dim] / chunk_dim[op_dim]; /* Determine if we need to fill chunks in this dimension */ if ((hssize_t)min_mod_chunk_sc[op_dim] == max_fill_chunk_sc[op_dim]) { fill_dim[op_dim] = TRUE; /* If necessary, check if chunks in this dimension that need to * be filled are new partial edge chunks */ if (disable_edge_filters && old_dim[op_dim] >= (min_mod_chunk_sc[op_dim] + 1)) new_unfilt_dim[op_dim] = TRUE; else new_unfilt_dim[op_dim] = FALSE; } /* end if */ else { fill_dim[op_dim] = FALSE; new_unfilt_dim[op_dim] = FALSE; } /* end else */ } /* end if */ else { fill_dim[op_dim] = FALSE; new_unfilt_dim[op_dim] = FALSE; } /* end else */ /* If necessary, calculate the smallest offset of non-previously full * chunks in this dimension, so we know these chunks were previously * unfiltered */ if (disable_edge_filters) min_partial_chunk_sc[op_dim] = old_dim[op_dim] / chunk_dim[op_dim]; } /* end for */ /* Main loop: fill or remove chunks */ for (op_dim = 0; op_dim < (unsigned)space_ndims; op_dim++) { hbool_t dims_outside_fill[H5O_LAYOUT_NDIMS]; /* Dimensions in chunk offset outside fill dimensions */ int ndims_outside_fill; /* Number of dimensions in chunk offset outside fill dimensions */ hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ /* Check if modification along this dimension is really necessary */ if (!shrunk_dim[op_dim]) continue; else { HDassert(max_mod_chunk_sc[op_dim] >= min_mod_chunk_sc[op_dim]); /* Reset the chunk offset indices */ HDmemset(scaled, 0, (space_ndims * sizeof(scaled[0]))); scaled[op_dim] = min_mod_chunk_sc[op_dim]; /* Initialize "dims_outside_fill" array */ ndims_outside_fill = 0; for (u = 0; u < space_ndims; u++) if ((hssize_t)scaled[u] > max_fill_chunk_sc[u]) { dims_outside_fill[u] = TRUE; ndims_outside_fill++; } /* end if */ else dims_outside_fill[u] = FALSE; } /* end else */ carry = FALSE; while (!carry) { int i; /* Local index variable */ udata.common.scaled = scaled; if (0 == ndims_outside_fill) { HDassert(fill_dim[op_dim]); HDassert(scaled[op_dim] == min_mod_chunk_sc[op_dim]); /* Make sure this is an edge chunk */ HDassert( H5D__chunk_is_partial_edge_chunk(space_ndims, layout->u.chunk.dim, scaled, space_dim)); /* Determine if the chunk just became an unfiltered chunk */ if (new_unfilt_dim[op_dim]) { new_unfilt_chunk = TRUE; for (u = 0; u < space_ndims; u++) if (scaled[u] == min_partial_chunk_sc[u]) { new_unfilt_chunk = FALSE; break; } /* end if */ } /* end if */ /* Make sure that, if we think this is a new unfiltered chunk, * it was previously not an edge chunk */ HDassert(!new_unfilt_dim[op_dim] || (!new_unfilt_chunk != !H5D__chunk_is_partial_edge_chunk( space_ndims, layout->u.chunk.dim, scaled, old_dim))); HDassert(!new_unfilt_chunk || new_unfilt_dim[op_dim]); /* Fill the unused parts of the chunk */ if (H5D__chunk_prune_fill(&udata, new_unfilt_chunk) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write fill value") } /* end if */ else { H5D_chunk_ud_t chk_udata; /* User data for getting chunk info */ #ifndef NDEBUG /* Make sure this chunk is really outside the new dimensions */ { hbool_t outside_dim = FALSE; for (u = 0; u < space_ndims; u++) if ((scaled[u] * chunk_dim[u]) >= space_dim[u]) { outside_dim = TRUE; break; } /* end if */ HDassert(outside_dim); } /* end block */ #endif /* NDEBUG */ /* Check if the chunk exists in cache or on disk */ if (H5D__chunk_lookup(dset, scaled, &chk_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk") /* Evict the entry from the cache if present, but do not flush * it to disk */ if (UINT_MAX != chk_udata.idx_hint) if (H5D__chunk_cache_evict(dset, rdcc->slot[chk_udata.idx_hint], FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") /* Remove the chunk from disk, if present */ if (H5F_addr_defined(chk_udata.chunk_block.offset)) { /* Update the offset in idx_udata */ idx_udata.scaled = udata.common.scaled; /* Remove the chunk from disk */ if ((sc->ops->remove)(&idx_info, &idx_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to remove chunk entry from index") } /* end if */ } /* end else */ /* Increment indices */ carry = TRUE; for (i = (int)(space_ndims - 1); i >= 0; --i) { scaled[i]++; if (scaled[i] > max_mod_chunk_sc[i]) { /* Left maximum dimensions, "wrap around" and check if this * dimension is no longer outside the fill dimension */ if ((unsigned)i == op_dim) { scaled[i] = min_mod_chunk_sc[i]; if (dims_outside_fill[i] && fill_dim[i]) { dims_outside_fill[i] = FALSE; ndims_outside_fill--; } /* end if */ } /* end if */ else { scaled[i] = 0; if (dims_outside_fill[i] && max_fill_chunk_sc[i] >= 0) { dims_outside_fill[i] = FALSE; ndims_outside_fill--; } /* end if */ } /* end else */ } /* end if */ else { /* Check if we just went outside the fill dimension */ if (!dims_outside_fill[i] && (hssize_t)scaled[i] > max_fill_chunk_sc[i]) { dims_outside_fill[i] = TRUE; ndims_outside_fill++; } /* end if */ /* We found the next chunk, so leave the loop */ carry = FALSE; break; } /* end else */ } /* end for */ } /* end while(!carry) */ /* Adjust max_mod_chunk_sc so we don't modify the same chunk twice. * Also check if this dimension started from 0 (and hence removed all * of the chunks). */ if (min_mod_chunk_sc[op_dim] == 0) break; else max_mod_chunk_sc[op_dim] = min_mod_chunk_sc[op_dim] - 1; } /* end for(op_dim=0...) */ /* 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") 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.layout->ndims - 1; /* # of dimensions of dataset */ hsize_t chunk_index; FUNC_ENTER_STATIC_NOERR /* Compute the index for this chunk */ chunk_index = H5VM_array_offset_pre(rank, udata->common.layout->down_chunks, chunk_rec->scaled); /* Set it in the userdata to return */ udata->chunk_addr[chunk_index] = chunk_rec->chunk_addr; FUNC_LEAVE_NOAPI(H5_ITER_CONT) } /* 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[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ const H5D_t * dset = io_info->dset; /* Local pointer to dataset info */ H5D_chunk_it_ud2_t udata; /* User data for iteration callback */ H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE HDassert(dset); HDassert(dset->shared); H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(chunk_addr); /* Set up user data for B-tree callback */ HDmemset(&udata, 0, sizeof(udata)); udata.common.layout = &dset->shared->layout.u.chunk; udata.common.storage = sc; udata.chunk_addr = chunk_addr; /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Iterate over chunks to build mapping of chunk addresses */ if ((sc->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, H5O_t *oh, H5O_storage_t *storage) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5O_layout_t layout; /* Dataset layout message */ hbool_t layout_read = FALSE; /* Whether the layout message was read from the file */ H5O_pline_t pline; /* I/O pipeline message */ hbool_t pline_read = FALSE; /* Whether the I/O pipeline message was read from the file */ htri_t exists; /* Flag if header message of interest exists */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(f); HDassert(oh); HDassert(storage); H5D_CHUNK_STORAGE_INDEX_CHK(&storage->u.chunk); /* Check for I/O pipeline message */ if ((exists = H5O_msg_exists_oh(oh, H5O_PLINE_ID)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to check for object header message") else if (exists) { if (NULL == H5O_msg_read_oh(f, oh, H5O_PLINE_ID, &pline)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O pipeline message") pline_read = TRUE; } /* end else if */ else HDmemset(&pline, 0, sizeof(pline)); /* Retrieve dataset layout message */ if ((exists = H5O_msg_exists_oh(oh, H5O_LAYOUT_ID)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to check for object header message") else if (exists) { if (NULL == H5O_msg_read_oh(f, oh, H5O_LAYOUT_ID, &layout)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout message") layout_read = TRUE; } /* end else if */ else HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "can't find layout message") /* Compose chunked index info struct */ idx_info.f = f; idx_info.pline = &pline; idx_info.layout = &layout.u.chunk; idx_info.storage = &storage->u.chunk; /* Delete the chunked storage information in the file */ if ((storage->u.chunk.ops->idx_delete)(&idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk index") done: /* Clean up any messages read in */ if (pline_read) if (H5O_msg_reset(H5O_PLINE_ID, &pline) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset I/O pipeline message") if (layout_read) if (H5O_msg_reset(H5O_LAYOUT_ID, &layout) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset layout message") 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) { H5D_rdcc_t * rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent, *next; /*cache entry */ H5D_rdcc_ent_t tmp_head; /* Sentinel entry for temporary entry list */ H5D_rdcc_ent_t *tmp_tail; /* Tail pointer for temporary entry list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* 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); /* Check the rank */ HDassert((dset->shared->layout.u.chunk.ndims - 1) > 1); /* Add temporary entry list to rdcc */ (void)HDmemset(&tmp_head, 0, sizeof(tmp_head)); rdcc->tmp_head = &tmp_head; tmp_tail = &tmp_head; /* Recompute the index for each cached chunk that is in a dataset */ for (ent = rdcc->head; ent; ent = next) { unsigned old_idx; /* Previous index number */ /* Get the pointer to the next cache entry */ next = ent->next; /* Compute the index for the chunk entry */ old_idx = ent->idx; /* Save for later */ ent->idx = H5D__chunk_hash_val(dset->shared, ent->scaled); if (old_idx != ent->idx) { H5D_rdcc_ent_t *old_ent; /* Old cache entry */ /* 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 == FALSE); HDassert(old_ent->deleted == FALSE); /* Insert the old entry into the temporary list, but do not * evict (yet). Make sure we do not make any calls to the index * until all chunks have updated indices! */ HDassert(!old_ent->tmp_next); HDassert(!old_ent->tmp_prev); tmp_tail->tmp_next = old_ent; old_ent->tmp_prev = tmp_tail; tmp_tail = old_ent; } /* end if */ /* Insert this chunk into correct location in hash table */ rdcc->slot[ent->idx] = ent; /* If this chunk was previously on the temporary list and therefore * not in the hash table, remove it from the temporary list. * Otherwise clear the old hash table slot. */ if (ent->tmp_prev) { HDassert(tmp_head.tmp_next); HDassert(tmp_tail != &tmp_head); ent->tmp_prev->tmp_next = ent->tmp_next; if (ent->tmp_next) { ent->tmp_next->tmp_prev = ent->tmp_prev; ent->tmp_next = NULL; } /* end if */ else { HDassert(tmp_tail == ent); tmp_tail = ent->tmp_prev; } /* end else */ ent->tmp_prev = NULL; } /* end if */ else rdcc->slot[old_idx] = NULL; } /* end if */ } /* end for */ /* tmp_tail is no longer needed, and will be invalidated by * H5D_chunk_cache_evict anyways. */ tmp_tail = NULL; /* Evict chunks that are still on the temporary list */ while (tmp_head.tmp_next) { ent = tmp_head.tmp_next; /* Remove the old entry from the cache */ if (H5D__chunk_cache_evict(dset, ent, TRUE) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") } /* end while */ done: /* Remove temporary list from rdcc */ rdcc->tmp_head = NULL; 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 */ hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */ /* 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 */ const H5O_pline_t *pline = udata->pline; /* I/O pipeline for applying filters */ /* needed for compressed variable length data */ hbool_t must_filter = FALSE; /* Whether chunk must be filtered during copy */ size_t nbytes; /* Size of chunk in file (in bytes) */ H5Z_cb_t filter_cb; /* Filter failure callback struct */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_STATIC /* Get 'size_t' local value for number of bytes in chunk */ H5_CHECKED_ASSIGN(nbytes, size_t, chunk_rec->nbytes, uint32_t); /* Initialize the filter callback struct */ filter_cb.op_data = NULL; filter_cb.func = NULL; /* no callback function when failed */ /* Check for filtered chunks */ /* Check for an edge chunk that is not filtered */ if (pline && pline->nused) { must_filter = TRUE; if ((udata->common.layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) && H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, udata->common.layout->dim, chunk_rec->scaled, udata->dset_dims)) must_filter = FALSE; } /* Check parameter for type conversion */ if (udata->do_convert) { if (H5T_detect_class(udata->dt_src, H5T_VLEN, FALSE) > 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, H5_ITER_ERROR, "unable to copy dataset elements") } /* 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 */ if (udata->chunk_in_cache && udata->chunk) { HDassert(!H5F_addr_defined(chunk_rec->chunk_addr)); H5MM_memcpy(buf, udata->chunk, nbytes); udata->chunk = NULL; } else { H5D_rdcc_ent_t *ent = NULL; /* Cache entry */ unsigned idx; /* Index of chunk in cache, if present */ unsigned u; /* Counter */ H5D_shared_t * shared_fo = (H5D_shared_t *)udata->cpy_info->shared_fo; /* See if the written chunk is in the chunk cache */ if (shared_fo && shared_fo->cache.chunk.nslots > 0) { /* Determine the chunk's location in the hash table */ idx = H5D__chunk_hash_val(shared_fo, chunk_rec->scaled); /* Get the chunk cache entry for that location */ ent = shared_fo->cache.chunk.slot[idx]; if (ent) { /* Speculatively set the 'found' flag */ udata->chunk_in_cache = TRUE; /* Verify that the cache entry is the correct chunk */ for (u = 0; u < shared_fo->ndims; u++) if (chunk_rec->scaled[u] != ent->scaled[u]) { udata->chunk_in_cache = FALSE; break; } /* end if */ } /* end if */ } /* end if */ if (udata->chunk_in_cache) { HDassert(H5F_addr_defined(chunk_rec->chunk_addr)); HDassert(H5F_addr_defined(ent->chunk_block.offset)); H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t); H5MM_memcpy(buf, ent->chunk, nbytes); } else { /* read chunk data from the source file */ if (H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk") } } /* Need to uncompress filtered variable-length & reference data elements that are not found in chunk cache */ if (must_filter && (is_vlen || fix_ref) && !udata->chunk_in_cache) { unsigned filter_mask = chunk_rec->filter_mask; if (H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, H5Z_NO_EDC, filter_cb, &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, bkg) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ H5MM_memcpy(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) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed") /* Reclaim space from variable length data */ if (H5T_reclaim(tid_mem, buf_space, 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) { /* Copy the reference elements */ if (H5O_copy_expand_ref(udata->file_src, udata->tid_src, udata->dt_src, buf, nbytes, udata->idx_info_dst->f, bkg, udata->cpy_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, H5_ITER_ERROR, "unable to copy reference attribute") } /* end if */ /* After fix ref, copy the new reference elements to the buffer to write out */ H5MM_memcpy(buf, bkg, buf_size); } /* end if */ /* Set up destination chunk callback information for insertion */ udata_dst.common.layout = udata->idx_info_dst->layout; udata_dst.common.storage = udata->idx_info_dst->storage; udata_dst.common.scaled = chunk_rec->scaled; udata_dst.chunk_block.offset = HADDR_UNDEF; udata_dst.chunk_block.length = chunk_rec->nbytes; udata_dst.filter_mask = chunk_rec->filter_mask; /* Need to compress variable-length or reference data elements or a chunk found in cache before writing to * file */ if (must_filter && (is_vlen || fix_ref || udata->chunk_in_cache)) { if (H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), H5Z_NO_EDC, filter_cb, &nbytes, &buf_size, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 /* Check for the chunk expanding too much to encode in a 32-bit value */ if (nbytes > ((size_t)0xffffffff)) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, H5_ITER_ERROR, "chunk too large for 32-bit length") #endif /* H5_SIZEOF_SIZE_T > 4 */ H5_CHECKED_ASSIGN(udata_dst.chunk_block.length, uint32_t, nbytes, size_t); udata->buf = buf; udata->buf_size = buf_size; } /* end if */ udata->chunk_in_cache = FALSE; udata_dst.chunk_idx = H5VM_array_offset_pre(udata_dst.common.layout->ndims - 1, udata_dst.common.layout->max_down_chunks, udata_dst.common.scaled); /* Allocate chunk in the file */ if (H5D__chunk_file_alloc(udata->idx_info_dst, NULL, &udata_dst.chunk_block, &need_insert, udata_dst.common.scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") /* Write chunk data to destination file */ HDassert(H5F_addr_defined(udata_dst.chunk_block.offset)); if (H5F_block_write(udata->idx_info_dst->f, H5FD_MEM_DRAW, udata_dst.chunk_block.offset, nbytes, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file") /* Set metadata tag in API context */ H5_BEGIN_TAG(H5AC__COPIED_TAG); /* Insert chunk record into index */ if (need_insert && udata->idx_info_dst->storage->ops->insert) if ((udata->idx_info_dst->storage->ops->insert)(udata->idx_info_dst, &udata_dst, NULL) < 0) HGOTO_ERROR_TAG(H5E_DATASET, H5E_CANTINSERT, H5_ITER_ERROR, "unable to insert chunk addr into index") /* Reset metadata tag in API context */ H5_END_TAG 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_storage_chunk_t *storage_src, H5O_layout_chunk_t *layout_src, H5F_t *f_dst, H5O_storage_chunk_t *storage_dst, const H5S_extent_t *ds_extent_src, const H5T_t *dt_src, const H5O_pline_t *pline_src, H5O_copy_t *cpy_info) { 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 */ int sndims; /* Rank of dataspace */ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Curr. size of dataset dimensions */ hsize_t max_dims[H5O_LAYOUT_NDIMS]; /* Curr. size of dataset dimensions */ H5O_pline_t _pline; /* Temporary pipeline info */ const H5O_pline_t *pline; /* Pointer to pipeline info to use */ 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_PACKAGE /* Check args */ HDassert(f_src); HDassert(storage_src); H5D_CHUNK_STORAGE_INDEX_CHK(storage_src); HDassert(layout_src); HDassert(f_dst); HDassert(storage_dst); H5D_CHUNK_STORAGE_INDEX_CHK(storage_dst); HDassert(ds_extent_src); HDassert(dt_src); /* Initialize the temporary pipeline info */ if (NULL == pline_src) { HDmemset(&_pline, 0, sizeof(_pline)); pline = &_pline; } /* end if */ else pline = pline_src; /* Layout is not created in the destination file, reset index address */ if (H5D_chunk_idx_reset(storage_dst, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to reset chunked storage index in dest") /* Initialize layout information */ { unsigned ndims; /* Rank of dataspace */ /* Get the dim info for dataset */ if ((sndims = H5S_extent_get_dims(ds_extent_src, curr_dims, max_dims)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace dimensions") H5_CHECKED_ASSIGN(ndims, unsigned, sndims, int); /* Set the source layout chunk information */ if (H5D__chunk_set_info_real(layout_src, ndims, curr_dims, max_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout's chunk info") } /* end block */ /* Compose source & dest chunked index info structs */ idx_info_src.f = f_src; idx_info_src.pline = pline; idx_info_src.layout = layout_src; idx_info_src.storage = storage_src; idx_info_dst.f = f_dst; idx_info_dst.pline = pline; /* Use same I/O filter pipeline for dest. */ idx_info_dst.layout = layout_src /* Use same layout for dest. */; idx_info_dst.storage = storage_dst; /* Call the index-specific "copy setup" routine */ if ((storage_src->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, FALSE) > 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) { (void)H5T_close_real(dt_mem); HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype") } /* end if */ /* 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, H5F_VOL_OBJ(f_dst), H5T_LOC_DISK) < 0) { (void)H5T_close_real(dt_dst); HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk") } /* end if */ if ((tid_dst = H5I_register(H5I_DATATYPE, dt_dst, FALSE)) < 0) { (void)H5T_close_real(dt_dst); HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype") } /* end if */ /* Set up the conversion functions */ if (NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem))) 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))) 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->ndims - 1); u++) nelmts *= layout_src->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) { (void)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_CHECKED_ASSIGN(buf_size, size_t, layout_src->size, uint32_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.layout = layout_src; udata.common.storage = storage_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.dset_ndims = (unsigned)sndims; udata.dset_dims = curr_dims; udata.cpy_info = cpy_info; udata.chunk_in_cache = FALSE; udata.chunk = NULL; /* Iterate over chunks to copy data */ if ((storage_src->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") /* Iterate over the chunk cache to copy data for chunks with undefined address */ if (udata.cpy_info->shared_fo) { H5D_rdcc_ent_t *ent, *next; H5D_chunk_rec_t chunk_rec; H5D_shared_t * shared_fo = (H5D_shared_t *)udata.cpy_info->shared_fo; chunk_rec.nbytes = layout_src->size; chunk_rec.filter_mask = 0; chunk_rec.chunk_addr = HADDR_UNDEF; for (ent = shared_fo->cache.chunk.head; ent; ent = next) { if (!H5F_addr_defined(ent->chunk_block.offset)) { H5MM_memcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled)); udata.chunk = ent->chunk; udata.chunk_in_cache = TRUE; if (H5D__chunk_copy_cb(&chunk_rec, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy chunk data in cache") } next = ent->next; } /* end for */ } /* I/O buffers may have been re-allocated */ buf = udata.buf; bkg = udata.bkg; done: if (sid_buf > 0 && H5I_dec_ref(sid_buf) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't decrement temporary dataspace ID") if (tid_src > 0 && H5I_dec_ref(tid_src) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if (tid_dst > 0 && H5I_dec_ref(tid_dst) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if (tid_mem > 0 && H5I_dec_ref(tid_mem) < 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 (storage_src->ops->copy_shutdown && (storage_src->ops->copy_shutdown)(storage_src, storage_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_info * * 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(const H5O_loc_t *loc, H5O_t *oh, H5O_layout_t *layout, hsize_t *index_size) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5S_t * space = NULL; /* Dataset's dataspace */ H5O_pline_t pline; /* I/O pipeline message */ H5O_storage_chunk_t *sc = &(layout->storage.u.chunk); htri_t exists; /* Flag if header message of interest exists */ hbool_t idx_info_init = FALSE; /* Whether the chunk index info has been initialized */ hbool_t pline_read = FALSE; /* Whether the I/O pipeline message was read */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(loc); HDassert(loc->file); HDassert(H5F_addr_defined(loc->addr)); HDassert(layout); H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(index_size); /* Check for I/O pipeline message */ if ((exists = H5O_msg_exists_oh(oh, H5O_PLINE_ID)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header") else if (exists) { if (NULL == H5O_msg_read_oh(loc->file, oh, H5O_PLINE_ID, &pline)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't find I/O pipeline message") pline_read = TRUE; } /* end else if */ else HDmemset(&pline, 0, sizeof(pline)); /* Compose chunked index info struct */ idx_info.f = loc->file; idx_info.pline = &pline; idx_info.layout = &layout->u.chunk; idx_info.storage = sc; /* Get the dataspace for the dataset */ if (NULL == (space = H5S_read(loc))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") /* Allocate any indexing structures */ if (sc->ops->init && (sc->ops->init)(&idx_info, space, loc->addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information") idx_info_init = TRUE; /* Get size of index structure */ if (sc->ops->size && (sc->ops->size)(&idx_info, index_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve chunk index info") done: /* Free resources, if they've been initialized */ if (idx_info_init && sc->ops->dest && (sc->ops->dest)(&idx_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") if (pline_read && H5O_msg_reset(H5O_PLINE_ID, &pline) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset I/O pipeline message") if (space && H5S_close(space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_bh_info() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_dump_index_cb * * 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 * *------------------------------------------------------------------------- */ 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_STATIC_NOERR 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 %8" PRIu32 " %10" PRIuHADDR " [", chunk_rec->filter_mask, chunk_rec->nbytes, chunk_rec->chunk_addr); for (u = 0; u < udata->ndims; u++) HDfprintf(udata->stream, "%s%" PRIuHSIZE, (u ? ", " : ""), (chunk_rec->scaled[u] * udata->chunk_dim[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, FILE *stream) { H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(dset); H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* 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 */ /* Display info for index */ if ((sc->ops->dump)(sc, stream) < 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to dump chunk index info") /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = sc; /* Set up user data for callback */ udata.stream = stream; udata.header_displayed = FALSE; udata.ndims = dset->shared->layout.u.chunk.ndims; udata.chunk_dim = dset->shared->layout.u.chunk.dim; /* Iterate over index and dump chunk info */ if ((sc->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() */ #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_PACKAGE_NOERR if (!H5DEBUG(AC)) HGOTO_DONE(SUCCEED) if (headers) { HDfprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n"); HDfprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n", "Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes"); HDfprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n", "-----", "----", "------", "--------", "-----", "-------"); } #ifdef H5AC_DEBUG if (H5DEBUG(AC)) headers = TRUE; #endif if (headers) { if (rdcc->stats.nhits > 0 || rdcc->stats.nmisses > 0) { miss_rate = 100.0 * rdcc->stats.nmisses / (rdcc->stats.nhits + rdcc->stats.nmisses); } else { miss_rate = 0.0; } if (miss_rate > 100) { HDsnprintf(ascii, sizeof(ascii), "%7d%%", (int)(miss_rate + 0.5)); } else { HDsnprintf(ascii, sizeof(ascii), "%7.2f%%", miss_rate); } HDfprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", "raw data chunks", rdcc->stats.nhits, rdcc->stats.nmisses, ascii, rdcc->stats.ninits, (long)(rdcc->stats.nflushes) - (long)(rdcc->stats.ninits)); } done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_stats() */ #endif /* H5D_CHUNK_DEBUG */ /*------------------------------------------------------------------------- * Function: H5D__nonexistent_readvv_cb * * Purpose: Callback operation for performing fill value I/O operation * on memory buffer. * * 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: Quincey Koziol * 30 Sep 2010 * *------------------------------------------------------------------------- */ static herr_t H5D__nonexistent_readvv_cb(hsize_t H5_ATTR_UNUSED dst_off, hsize_t src_off, size_t len, void *_udata) { H5D_chunk_readvv_ud_t *udata = (H5D_chunk_readvv_ud_t *)_udata; /* User data for H5VM_opvv() operator */ 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 */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Initialize the fill value buffer */ if (H5D__fill_init(&fb_info, (udata->rbuf + src_off), NULL, NULL, NULL, NULL, &udata->dset->shared->dcpl_cache.fill, udata->dset->shared->type, udata->dset->shared->type_id, (size_t)0, len) < 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) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") 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_cb() */ /*------------------------------------------------------------------------- * 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_off_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_off_arr[]) { H5D_chunk_readvv_ud_t udata; /* User data for H5VM_opvv() operator */ ssize_t ret_value = -1; /* Return value */ FUNC_ENTER_STATIC /* Check args */ HDassert(io_info); HDassert(chunk_curr_seq); HDassert(chunk_len_arr); HDassert(chunk_off_arr); HDassert(mem_curr_seq); HDassert(mem_len_arr); HDassert(mem_off_arr); /* Set up user data for H5VM_opvv() */ udata.rbuf = (unsigned char *)io_info->u.rbuf; udata.dset = io_info->dset; /* Call generic sequence operation routine */ if ((ret_value = H5VM_opvv(chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_off_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_off_arr, H5D__nonexistent_readvv_cb, &udata)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPERATE, FAIL, "can't perform vectorized fill value init") done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__nonexistent_readvv() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_is_partial_edge_chunk * * Purpose: Checks to see if the chunk is a partial edge chunk. * Either dset or (dset_dims and dset_ndims) must be * provided. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * 19 Nov 2009 * *------------------------------------------------------------------------- */ hbool_t H5D__chunk_is_partial_edge_chunk(unsigned dset_ndims, const uint32_t *chunk_dims, const hsize_t scaled[], const hsize_t *dset_dims) { unsigned u; /* Local index variable */ hbool_t ret_value = FALSE; /* Return value */ FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(scaled); HDassert(dset_ndims > 0); HDassert(dset_dims); HDassert(chunk_dims); /* check if this is a partial edge chunk */ for (u = 0; u < dset_ndims; u++) if (((scaled[u] + 1) * chunk_dims[u]) > dset_dims[u]) HGOTO_DONE(TRUE); done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__chunk_is_partial_edge_chunk() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_file_alloc() * * Purpose: Chunk allocation: * Create the chunk if it doesn't exist, or reallocate the * chunk if its size changed. * The coding is moved and modified from each index structure. * * Return: Non-negative on success/Negative on failure * * Programmer: Vailin Choi; June 2014 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_file_alloc(const H5D_chk_idx_info_t *idx_info, const H5F_block_t *old_chunk, H5F_block_t *new_chunk, hbool_t *need_insert, const hsize_t *scaled) { hbool_t alloc_chunk = FALSE; /* Whether to allocate chunk */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(new_chunk); HDassert(need_insert); *need_insert = FALSE; /* Check for filters on chunks */ if (idx_info->pline->nused > 0) { /* Sanity/error checking block */ HDassert(idx_info->storage->idx_type != H5D_CHUNK_IDX_NONE); { unsigned allow_chunk_size_len; /* Allowed size of encoded chunk size */ unsigned new_chunk_size_len; /* Size of encoded chunk size */ /* Compute the size required for encoding the size of a chunk, allowing * for an extra byte, in case the filter makes the chunk larger. */ allow_chunk_size_len = 1 + ((H5VM_log2_gen((uint64_t)(idx_info->layout->size)) + 8) / 8); if (allow_chunk_size_len > 8) allow_chunk_size_len = 8; /* Compute encoded size of chunk */ new_chunk_size_len = (H5VM_log2_gen((uint64_t)(new_chunk->length)) + 8) / 8; if (new_chunk_size_len > 8) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "encoded chunk size is more than 8 bytes?!?") /* Check if the chunk became too large to be encoded */ if (new_chunk_size_len > allow_chunk_size_len) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk size can't be encoded") } /* end block */ if (old_chunk && H5F_addr_defined(old_chunk->offset)) { /* Sanity check */ HDassert(!H5F_addr_defined(new_chunk->offset) || H5F_addr_eq(new_chunk->offset, old_chunk->offset)); /* Check for chunk being same size */ if (new_chunk->length != old_chunk->length) { /* Release previous chunk */ /* Only free the old location if not doing SWMR writes - otherwise * we must keep the old chunk around in case a reader has an * outdated version of the B-tree node */ if (!(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE)) if (H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, old_chunk->offset, old_chunk->length) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk") alloc_chunk = TRUE; } /* end if */ else { /* Don't need to reallocate chunk, but send its address back up */ if (!H5F_addr_defined(new_chunk->offset)) new_chunk->offset = old_chunk->offset; } /* end else */ } /* end if */ else { HDassert(!H5F_addr_defined(new_chunk->offset)); alloc_chunk = TRUE; } /* end else */ } /* end if */ else { HDassert(!H5F_addr_defined(new_chunk->offset)); HDassert(new_chunk->length == idx_info->layout->size); alloc_chunk = TRUE; } /* end else */ /* Actually allocate space for the chunk in the file */ if (alloc_chunk) { switch (idx_info->storage->idx_type) { case H5D_CHUNK_IDX_NONE: { H5D_chunk_ud_t udata; udata.common.scaled = scaled; if ((idx_info->storage->ops->get_addr)(idx_info, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address") new_chunk->offset = udata.chunk_block.offset; HDassert(new_chunk->length == udata.chunk_block.length); break; } case H5D_CHUNK_IDX_EARRAY: case H5D_CHUNK_IDX_FARRAY: case H5D_CHUNK_IDX_BT2: case H5D_CHUNK_IDX_BTREE: case H5D_CHUNK_IDX_SINGLE: HDassert(new_chunk->length > 0); H5_CHECK_OVERFLOW(new_chunk->length, /*From: */ uint32_t, /*To: */ hsize_t); new_chunk->offset = H5MF_alloc(idx_info->f, H5FD_MEM_DRAW, (hsize_t)new_chunk->length); if (!H5F_addr_defined(new_chunk->offset)) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "file allocation failed") *need_insert = TRUE; break; case H5D_CHUNK_IDX_NTYPES: default: HDassert(0 && "This should never be executed!"); break; } /* end switch */ } /* end if */ HDassert(H5F_addr_defined(new_chunk->offset)); done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__chunk_file_alloc() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_format_convert_cb * * Purpose: Callback routine to insert chunk address into v1 B-tree * chunk index. * * Return: Success: Non-negative * Failure: Negative * * Programmer: Vailin Choi * Feb 2015 * *------------------------------------------------------------------------- */ static int H5D__chunk_format_convert_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_chunk_it_ud5_t *udata = (H5D_chunk_it_ud5_t *)_udata; /* User data */ H5D_chk_idx_info_t *new_idx_info; /* The new chunk index information */ H5D_chunk_ud_t insert_udata; /* Chunk information to be inserted */ haddr_t chunk_addr; /* Chunk address */ size_t nbytes; /* Chunk size */ void * buf = NULL; /* Pointer to buffer of chunk data */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_STATIC /* Set up */ new_idx_info = udata->new_idx_info; H5_CHECKED_ASSIGN(nbytes, size_t, chunk_rec->nbytes, uint32_t); chunk_addr = chunk_rec->chunk_addr; if (new_idx_info->pline->nused && (new_idx_info->layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) && (H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, new_idx_info->layout->dim, chunk_rec->scaled, udata->dset_dims))) { /* This is a partial non-filtered edge chunk */ /* Convert the chunk to a filtered edge chunk for v1 B-tree chunk index */ unsigned filter_mask = chunk_rec->filter_mask; H5Z_cb_t filter_cb; /* Filter failure callback struct */ size_t read_size = nbytes; /* Bytes to read */ HDassert(read_size == new_idx_info->layout->size); /* Initialize the filter callback struct */ filter_cb.op_data = NULL; filter_cb.func = NULL; /* no callback function when failed */ /* Allocate buffer for chunk data */ if (NULL == (buf = H5MM_malloc(read_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk") /* Read the non-filtered edge chunk */ if (H5F_block_read(new_idx_info->f, H5FD_MEM_DRAW, chunk_addr, read_size, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk") /* Pass the chunk through the pipeline */ if (H5Z_pipeline(new_idx_info->pline, 0, &filter_mask, H5Z_NO_EDC, filter_cb, &nbytes, &read_size, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 /* Check for the chunk expanding too much to encode in a 32-bit value */ if (nbytes > ((size_t)0xffffffff)) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, H5_ITER_ERROR, "chunk too large for 32-bit length") #endif /* H5_SIZEOF_SIZE_T > 4 */ /* Allocate space for the filtered chunk */ if ((chunk_addr = H5MF_alloc(new_idx_info->f, H5FD_MEM_DRAW, (hsize_t)nbytes)) == HADDR_UNDEF) HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, H5_ITER_ERROR, "file allocation failed for filtered chunk") HDassert(H5F_addr_defined(chunk_addr)); /* Write the filtered chunk to disk */ if (H5F_block_write(new_idx_info->f, H5FD_MEM_DRAW, chunk_addr, nbytes, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file") } /* end if */ /* Set up chunk information for insertion to chunk index */ insert_udata.chunk_block.offset = chunk_addr; insert_udata.chunk_block.length = nbytes; insert_udata.filter_mask = chunk_rec->filter_mask; insert_udata.common.scaled = chunk_rec->scaled; insert_udata.common.layout = new_idx_info->layout; insert_udata.common.storage = new_idx_info->storage; /* Insert chunk into the v1 B-tree chunk index */ if ((new_idx_info->storage->ops->insert)(new_idx_info, &insert_udata, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, H5_ITER_ERROR, "unable to insert chunk addr into index") done: if (buf) H5MM_xfree(buf); FUNC_LEAVE_NOAPI(ret_value) } /* H5D__chunk_format_convert_cb() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_format_convert * * Purpose: Iterate over the chunks for the current chunk index and insert the * the chunk addresses into v1 B-tree chunk index via callback. * * Return: Non-negative on success/Negative on failure * * Programmer: Vailin Choi * Feb 2015 * *------------------------------------------------------------------------- */ herr_t H5D__chunk_format_convert(H5D_t *dset, H5D_chk_idx_info_t *idx_info, H5D_chk_idx_info_t *new_idx_info) { H5D_chunk_it_ud5_t udata; /* User data */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dset); /* Set up user data */ udata.new_idx_info = new_idx_info; udata.dset_ndims = dset->shared->ndims; udata.dset_dims = dset->shared->curr_dims; /* Iterate over the chunks in the current index and insert the chunk addresses into version 1 B-tree index */ if ((idx_info->storage->ops->iterate)(idx_info, H5D__chunk_format_convert_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to chunk info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_format_convert() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_index_empty_cb * * Purpose: Callback function that simply stops iteration and sets the * `empty` parameter to FALSE if called. If this callback is * entered, it means that the chunk index contains at least * one chunk, so is not empty. * * Return: H5_ITER_STOP * *------------------------------------------------------------------------- */ static int H5D__chunk_index_empty_cb(const H5D_chunk_rec_t H5_ATTR_UNUSED *chunk_rec, void *_udata) { hbool_t *empty = (hbool_t *)_udata; int ret_value = H5_ITER_STOP; FUNC_ENTER_STATIC_NOERR *empty = FALSE; FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_index_empty_cb() */ /*------------------------------------------------------------------------- * Function: H5D__chunk_index_empty * * Purpose: Determines whether a chunk index is empty (has no chunks * inserted into it yet). * * Note: This routine is meant to be a little more performant than * just counting the number of chunks in the index. In the * future, this is probably a callback that the chunk index * ops structure should provide. * * Return: Non-negative on Success/Negative on failure * *------------------------------------------------------------------------- */ herr_t H5D__chunk_index_empty(const H5D_t *dset, hbool_t *empty) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_rdcc_ent_t * ent; /* Cache entry */ const H5D_rdcc_t * rdcc = NULL; /* Raw data chunk cache */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) HDassert(dset); HDassert(dset->shared); HDassert(empty); rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */ HDassert(rdcc); /* 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, ent, FALSE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = &dset->shared->layout.storage.u.chunk; *empty = TRUE; if (H5F_addr_defined(idx_info.storage->idx_addr)) { /* Iterate over the allocated chunks */ if ((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__chunk_index_empty_cb, empty) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index") } done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__chunk_index_empty() */ /*------------------------------------------------------------------------- * Function: H5D__get_num_chunks_cb * * Purpose: Callback function that increments the number of written * chunks in the dataset. * * Note: Currently, this function only gets the number of all written * chunks, regardless the dataspace. * * Return: H5_ITER_CONT * * Programmer: Binh-Minh Ribler * June 2019 (HDFFV-10677) * *------------------------------------------------------------------------- */ static int H5D__get_num_chunks_cb(const H5D_chunk_rec_t H5_ATTR_UNUSED *chunk_rec, void *_udata) { hsize_t *num_chunks = (hsize_t *)_udata; int ret_value = H5_ITER_CONT; /* Callback return value */ FUNC_ENTER_STATIC_NOERR HDassert(num_chunks); (*num_chunks)++; FUNC_LEAVE_NOAPI(ret_value) } /* H5D__get_num_chunks_cb() */ /*------------------------------------------------------------------------- * Function: H5D__get_num_chunks * * Purpose: Gets the number of written chunks in a dataset. * * Note: Currently, this function only gets the number of all written * chunks, regardless the dataspace. * * Return: Success: Non-negative * Failure: Negative * * Programmer: Binh-Minh Ribler * June 2019 (HDFFV-10677) * *------------------------------------------------------------------------- */ herr_t H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_t *nchunks) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ hsize_t num_chunks = 0; /* Number of written chunks */ H5D_rdcc_ent_t * ent; /* Cache entry */ const H5D_rdcc_t * rdcc = NULL; /* Raw data chunk cache */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) HDassert(dset); HDassert(dset->shared); HDassert(space); HDassert(nchunks); rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */ HDassert(rdcc); /* 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, ent, FALSE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = &dset->shared->layout.storage.u.chunk; /* If the dataset is not written, number of chunks will be 0 */ if (!H5F_addr_defined(idx_info.storage->idx_addr)) *nchunks = 0; else { /* Iterate over the allocated chunks */ if ((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_num_chunks_cb, &num_chunks) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index") *nchunks = num_chunks; } done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__get_num_chunks() */ /*------------------------------------------------------------------------- * Function: H5D__get_chunk_info_cb * * Purpose: Get the chunk info of the queried chunk, given by its index. * * Return: Success: H5_ITER_CONT or H5_ITER_STOP * H5_ITER_STOP indicates the queried chunk is found * Failure: Negative (H5_ITER_ERROR) * * Programmer: Binh-Minh Ribler * June 2019 (HDFFV-10677) * *------------------------------------------------------------------------- */ static int H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_chunk_info_iter_ud_t *chunk_info = (H5D_chunk_info_iter_ud_t *)_udata; int ret_value = H5_ITER_CONT; /* Callback return value */ FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(chunk_rec); HDassert(chunk_info); /* If this is the queried chunk, retrieve its info and stop iterating */ if (chunk_info->curr_idx == chunk_info->chunk_idx) { hsize_t ii = 0; /* Dimension index */ /* Copy info */ chunk_info->filter_mask = chunk_rec->filter_mask; chunk_info->chunk_addr = chunk_rec->chunk_addr; chunk_info->nbytes = chunk_rec->nbytes; for (ii = 0; ii < chunk_info->ndims; ii++) chunk_info->scaled[ii] = chunk_rec->scaled[ii]; chunk_info->found = TRUE; /* Stop iterating */ ret_value = H5_ITER_STOP; } /* Go to the next chunk */ else chunk_info->curr_idx++; FUNC_LEAVE_NOAPI(ret_value) } /* H5D__get_chunk_info_cb() */ /*------------------------------------------------------------------------- * Function: H5D__get_chunk_info * * Purpose: Iterate over the chunks in the dataset to get the info * of the desired chunk. * * Note: Currently, the domain of the index in this function is of all * the written chunks, regardless the dataspace. * * Return: Success: SUCCEED * Failure: FAIL * * Programmer: Binh-Minh Ribler * June 2019 (HDFFV-10677) * *------------------------------------------------------------------------- */ herr_t H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_t chk_index, hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_chunk_info_iter_ud_t udata; /* User data for callback */ const H5D_rdcc_t * rdcc = NULL; /* Raw data chunk cache */ H5D_rdcc_ent_t * ent; /* Cache entry index */ hsize_t ii = 0; /* Dimension index */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) HDassert(dset); HDassert(dset->shared); HDassert(space); /* Get the raw data chunk cache */ rdcc = &(dset->shared->cache.chunk); HDassert(rdcc); /* 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, ent, FALSE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = &dset->shared->layout.storage.u.chunk; /* Set addr & size for when dset is not written or queried chunk is not found */ if (addr) *addr = HADDR_UNDEF; if (size) *size = 0; /* If the chunk is written, get its info, otherwise, return without error */ if (H5F_addr_defined(idx_info.storage->idx_addr)) { /* Initialize before iteration */ udata.chunk_idx = chk_index; udata.curr_idx = 0; udata.ndims = dset->shared->ndims; udata.nbytes = 0; udata.filter_mask = 0; udata.chunk_addr = HADDR_UNDEF; udata.found = FALSE; /* Iterate over the allocated chunks */ if ((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_chunk_info_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index") /* Obtain requested info if the chunk is found */ if (udata.found) { if (filter_mask) *filter_mask = udata.filter_mask; if (addr) *addr = udata.chunk_addr; if (size) *size = udata.nbytes; if (offset) for (ii = 0; ii < udata.ndims; ii++) offset[ii] = udata.scaled[ii] * dset->shared->layout.u.chunk.dim[ii]; } /* end if */ } /* end if H5F_addr_defined */ done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__get_chunk_info() */ /*------------------------------------------------------------------------- * Function: H5D__get_chunk_info_by_coord_cb * * Purpose: Get the chunk info of the desired chunk, given its offset * coordinates. * * Return: Success: H5_ITER_CONT or H5_ITER_STOP * Failure: Negative (H5_ITER_ERROR) * * Programmer: Binh-Minh Ribler * June 2019 (HDFFV-10677) * *------------------------------------------------------------------------- */ static int H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_chunk_info_iter_ud_t *chunk_info = (H5D_chunk_info_iter_ud_t *)_udata; hbool_t different = FALSE; /* TRUE when a scaled value pair mismatch */ hsize_t ii; /* Local index value */ int ret_value = H5_ITER_CONT; /* Callback return value */ FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(chunk_rec); HDassert(chunk_info); /* Going through the scaled, stop when a mismatch is found */ for (ii = 0; ii < chunk_info->ndims && !different; ii++) if (chunk_info->scaled[ii] != chunk_rec->scaled[ii]) different = TRUE; /* Same scaled coords means the chunk is found, copy the chunk info */ if (!different) { chunk_info->nbytes = chunk_rec->nbytes; chunk_info->filter_mask = chunk_rec->filter_mask; chunk_info->chunk_addr = chunk_rec->chunk_addr; chunk_info->found = TRUE; /* Stop iterating */ ret_value = H5_ITER_STOP; } FUNC_LEAVE_NOAPI(ret_value) } /* H5D__get_chunk_info_by_coord_cb() */ /*------------------------------------------------------------------------- * Function: H5D__get_chunk_info_by_coord * * Purpose: Iterate over the chunks in the dataset to get the info * of the desired chunk, given by its offset coordinates. * * Return: Success: Non-negative * Failure: Negative * * Programmer: Binh-Minh Ribler * June 2019 (HDFFV-10677) * *------------------------------------------------------------------------- */ herr_t H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size) { const H5O_layout_t * layout = NULL; /* Dataset layout */ const H5D_rdcc_t * rdcc = NULL; /* Raw data chunk cache */ H5D_rdcc_ent_t * ent; /* Cache entry index */ H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_chunk_info_iter_ud_t udata; /* User data for callback */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) /* Check args */ HDassert(dset); HDassert(dset->shared); HDassert(offset); /* Get dataset layout and raw data chunk cache */ layout = &(dset->shared->layout); rdcc = &(dset->shared->cache.chunk); HDassert(layout); HDassert(rdcc); HDassert(H5D_CHUNKED == layout->type); /* 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, ent, FALSE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") /* Set addr & size for when dset is not written or queried chunk is not found */ if (addr) *addr = HADDR_UNDEF; if (size) *size = 0; /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; idx_info.pline = &dset->shared->dcpl_cache.pline; idx_info.layout = &dset->shared->layout.u.chunk; idx_info.storage = &dset->shared->layout.storage.u.chunk; /* If the dataset is not written, return without errors */ if (H5F_addr_defined(idx_info.storage->idx_addr)) { /* Calculate the scaled of this chunk */ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, udata.scaled); udata.scaled[dset->shared->ndims] = 0; /* Initialize before iteration */ udata.ndims = dset->shared->ndims; udata.nbytes = 0; udata.filter_mask = 0; udata.chunk_addr = HADDR_UNDEF; udata.found = FALSE; /* Iterate over the allocated chunks to find the requested chunk */ if ((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_chunk_info_by_coord_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve information of the chunk by its scaled coordinates") /* Obtain requested info if the chunk is found */ if (udata.found) { if (filter_mask) *filter_mask = udata.filter_mask; if (addr) *addr = udata.chunk_addr; if (size) *size = udata.nbytes; } /* end if */ } /* end if H5F_addr_defined */ done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__get_chunk_info_by_coord() */