mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-11-21 01:04:10 +08:00
f859cb732b
* fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
465 lines
27 KiB
C
465 lines
27 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the COPYING file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* Programmer: Quincey Koziol
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* Tuesday, June 17, 2008
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*
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* Purpose: This file contains declarations which are visible only
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* within the H5EA package. Source files outside the H5EA
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* package should include H5EAprivate.h instead.
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*/
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#if !(defined(H5EA_FRIEND) | defined(H5EA_MODULE))
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#error "Do not include this file outside the H5EA package!"
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#endif
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#ifndef H5EApkg_H
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#define H5EApkg_H
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/* Get package's private header */
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#include "H5EAprivate.h"
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/* Other private headers needed by this file */
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#include "H5FLprivate.h" /* Free Lists */
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/**************************/
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/* Package Private Macros */
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/**************************/
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/* Fill value for extensible array test class */
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#ifdef H5EA_TESTING
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#define H5EA_TEST_FILL ((uint64_t)ULLONG_MAX)
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#endif /* H5EA_TESTING */
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/* Size of checksum information (on disk) */
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#define H5EA_SIZEOF_CHKSUM 4
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/* "Standard" size of prefix information for extensible array metadata */
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#define H5EA_METADATA_PREFIX_SIZE(c) \
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(H5_SIZEOF_MAGIC /* Signature */ \
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+ 1 /* Version */ \
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+ 1 /* Array type */ \
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+ ((c) ? H5EA_SIZEOF_CHKSUM : 0) /* Metadata checksum */ \
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)
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/* Size of the extensible array header on disk */
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#define H5EA_HEADER_SIZE(sizeof_addr, sizeof_size) \
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(/* General metadata fields */ \
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H5EA_METADATA_PREFIX_SIZE(TRUE) \
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\
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/* General array information */ \
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+ 1 /* Element Size */ \
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+ 1 /* Max. # of elements bits */ \
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+ 1 /* # of elements to store in index block */ \
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+ 1 /* Min. # elements per data block */ \
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+ 1 /* Min. # of data block pointers for a super block */ \
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+ 1 /* Log2(Max. # of elements in data block page) - i.e. # of bits needed to store max. # of elements \
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in data block page */ \
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\
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/* Extensible Array statistics fields */ \
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+ (sizeof_size) /* Number of super blocks created */ \
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+ (sizeof_size) /* Size of super blocks created */ \
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+ (sizeof_size) /* Number of data blocks created */ \
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+ (sizeof_size) /* Size of data blocks created */ \
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+ (sizeof_size) /* Max. index set */ \
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+ (sizeof_size) /* Number of elements 'realized' */ \
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\
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/* Extensible Array Header specific fields */ \
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+ (sizeof_addr) /* File address of index block */ \
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)
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/* Size of the extensible array header on disk (via file pointer) */
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#define H5EA_HEADER_SIZE_FILE(f) (H5EA_HEADER_SIZE(H5F_SIZEOF_ADDR(f), H5F_SIZEOF_SIZE(f)))
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/* Size of the extensible array header on disk (via extensible array header) */
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#define H5EA_HEADER_SIZE_HDR(h) (H5EA_HEADER_SIZE((h)->sizeof_addr, (h)->sizeof_size))
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/* Size of the extensible array index block on disk */
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#define H5EA_IBLOCK_SIZE(i) \
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(/* General metadata fields */ \
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H5EA_METADATA_PREFIX_SIZE(TRUE) \
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\
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/* Sanity-checking fields */ \
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+ (i)->hdr->sizeof_addr /* File address of array owning the block */ \
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\
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/* Extensible Array Index Block specific fields */ \
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+ ((size_t)(i)->hdr->cparam.idx_blk_elmts * \
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(size_t)(i)->hdr->cparam.raw_elmt_size) /* Elements in index block */ \
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+ ((i)->ndblk_addrs * (i)->hdr->sizeof_addr) /* Data block addresses in index block */ \
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+ ((i)->nsblk_addrs * (i)->hdr->sizeof_addr) /* Super block addresses in index block */ \
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)
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/* Size of the extensible array super block on disk */
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#define H5EA_SBLOCK_SIZE(s) \
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(/* General metadata fields */ \
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H5EA_METADATA_PREFIX_SIZE(TRUE) \
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\
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/* Sanity-checking fields */ \
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+ (s)->hdr->sizeof_addr /* File address of array owning the block */ \
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+ (s)->hdr->arr_off_size /* Offset of the block in the array */ \
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\
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/* Extensible Array Super Block specific fields */ \
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+ \
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((s)->ndblks * \
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(s)->dblk_page_init_size) /* Data block 'page init' bitmasks in super block (can be 0 if no pages) */ \
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+ ((s)->ndblks * (s)->hdr->sizeof_addr) /* Data block addresses in super block */ \
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)
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/* Size of the extensible array data block prefix on disk */
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#define H5EA_DBLOCK_PREFIX_SIZE(d) \
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(/* General metadata fields */ \
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H5EA_METADATA_PREFIX_SIZE(TRUE) \
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\
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/* Sanity-checking fields */ \
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+ (d)->hdr->sizeof_addr /* File address of array owning the block */ \
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+ (d)->hdr->arr_off_size /* Offset of the block in the array */ \
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)
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/* Size of the extensible array data block on disk */
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#define H5EA_DBLOCK_SIZE(d) \
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(/* Data block prefix size */ \
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H5EA_DBLOCK_PREFIX_SIZE(d) \
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\
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/* Extensible Array Data Block specific fields */ \
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+ ((d)->nelmts * (size_t)(d)->hdr->cparam.raw_elmt_size) /* Elements in data block */ \
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+ ((d)->npages * H5EA_SIZEOF_CHKSUM) /* Checksum for each page */ \
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)
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/* Size of the extensible array data block page on disk */
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#define H5EA_DBLK_PAGE_SIZE(h) \
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(+((h)->dblk_page_nelmts * (size_t)(h)->cparam.raw_elmt_size) /* Elements in data block page */ \
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+ H5EA_SIZEOF_CHKSUM /* Checksum for each page */ \
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)
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/* Compute the # of bytes required to store an offset into a given buffer size */
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#define H5EA_SIZEOF_OFFSET_BITS(b) (((b) + 7) / 8)
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/* Compute the first super block index that will hold a certain # of data block pointers */
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#define H5EA_SBLK_FIRST_IDX(m) (2 * H5VM_log2_of2((uint32_t)m))
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/****************************/
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/* Package Private Typedefs */
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/****************************/
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/* Information for each super block in extensible array */
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typedef struct H5EA_sblk_info_t {
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size_t ndblks; /* Number of data blocks for a super block */
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size_t dblk_nelmts; /* Number of elements in each data block for super block */
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hsize_t start_idx; /* Index of first element in super block */
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hsize_t start_dblk; /* Index of first data block in super block */
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} H5EA_sblk_info_t;
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/* The extensible array header information */
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/* (Each extensible array header has certain information that is shared across
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* all the blocks in that extensible array)
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*/
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typedef struct H5EA_hdr_t {
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/* Information for H5AC cache functions, _must_ be first field in structure */
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H5AC_info_t cache_info;
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/* Extensible array configuration/creation parameters (stored in header) */
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H5EA_create_t cparam; /* Creation parameters for extensible array */
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/* Index block information (stored in header) */
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haddr_t idx_blk_addr; /* Address of index block in header */
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/* Statistics for array (stored in index block, actually) */
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/* (header and index number/size fields not stored) */
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H5EA_stat_t stats; /* Statistics for extensible array */
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/* Data block element buffer factory info (not stored in header) */
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struct {
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size_t nalloc; /* Number of factories allocated */
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H5FL_fac_head_t **fac; /* Array of factories for data block element buffers */
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} elmt_fac;
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/* Computed/cached values (not stored in header) */
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size_t rc; /* Reference count of heap's components using heap header */
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haddr_t addr; /* Address of header in file */
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size_t size; /* Size of header in file */
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H5F_t * f; /* Pointer to file for extensible array */
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size_t file_rc; /* Reference count of files using array header */
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hbool_t pending_delete; /* Array is pending deletion */
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size_t sizeof_addr; /* Size of file addresses */
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size_t sizeof_size; /* Size of file sizes */
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unsigned char arr_off_size; /* Size of array offsets (in bytes) */
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/* Super block information (not stored) */
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size_t nsblks; /* Number of superblocks needed for array */
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H5EA_sblk_info_t *sblk_info; /* Array of information for each super block */
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/* Data block information (not stored) */
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size_t dblk_page_nelmts; /* # of elements per data block page */
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/* Client information (not stored) */
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void *cb_ctx; /* Callback context */
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/* SWMR / Flush dependency information (not stored) */
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hbool_t swmr_write; /* Flag indicating the file is opened with SWMR-write access */
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H5AC_proxy_entry_t *top_proxy; /* 'Top' proxy cache entry for all array entries */
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void * parent; /* Pointer to 'top' proxy flush dependency
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* parent, if it exists, otherwise NULL.
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* If the extensible array is being used
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* to index a chunked dataset and the
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* dataset metadata is modified by a
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* SWMR writer, this field will be set
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* equal to the object header proxy
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* that is the flush dependency parent
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* of the extensible array header.
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*
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* The field is used to avoid duplicate
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* setups of the flush dependency
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* relationship, and to allow the
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* extensible array header to destroy
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* the flush dependency on receipt of
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* an eviction notification from the
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* metadata cache.
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*/
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} H5EA_hdr_t;
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/* The extensible array index block information */
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typedef struct H5EA_iblock_t {
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/* Information for H5AC cache functions, _must_ be first field in structure */
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H5AC_info_t cache_info;
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/* Extensible array information (stored) */
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void * elmts; /* Buffer for elements stored in index block */
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haddr_t *dblk_addrs; /* Buffer for addresses of data blocks in index block */
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haddr_t *sblk_addrs; /* Buffer for addresses of super blocks in index block */
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/* Internal array information (not stored) */
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H5EA_hdr_t *hdr; /* Shared array header info */
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haddr_t addr; /* Address of this index block on disk */
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size_t size; /* Size of index block on disk */
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/* SWMR / Flush dependency information (not stored) */
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H5AC_proxy_entry_t *top_proxy; /* "Top" proxy cache entry for all array entries */
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/* Computed/cached values (not stored) */
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size_t nsblks; /* # of super blocks whose data block addresses are in index block */
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size_t ndblk_addrs; /* Number of pointers to data blocks in index block */
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size_t nsblk_addrs; /* Number of pointers to super blocks in index block */
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} H5EA_iblock_t;
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/* The extensible array super block information */
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typedef struct H5EA_sblock_t {
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/* Information for H5AC cache functions, _must_ be first field in structure */
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H5AC_info_t cache_info;
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/* Extensible array information (stored) */
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hsize_t block_off; /* Offset of the block within the array's address space */
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haddr_t *dblk_addrs; /* Addresses of data blocks in super block */
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uint8_t *page_init; /* Bitmap of whether a data block page is initialized */
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/* Internal array information (not stored) */
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H5EA_hdr_t *hdr; /* Shared array header info */
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haddr_t addr; /* Address of this index block on disk */
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size_t size; /* Size of index block on disk */
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/* SWMR / Flush dependency information (not stored) */
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hbool_t has_hdr_depend; /* Whether this object has a flush dependency on the header */
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H5AC_proxy_entry_t *top_proxy; /* "Top" proxy cache entry for all array entries */
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H5EA_iblock_t * parent; /* Parent object for super block (index block) */
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/* Computed/cached values (not stored) */
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unsigned idx; /* Super block index within the extensible array */
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size_t ndblks; /* # of data block addresses that are in super block */
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size_t dblk_nelmts; /* # of elements for data blocks reachable through this super block */
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size_t dblk_npages; /* # of pages in each data block */
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size_t dblk_page_init_size; /* Size of 'page init' bitmask for each data block */
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size_t dblk_page_size; /* Size of a data block page */
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} H5EA_sblock_t;
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/* The extensible array data block information */
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typedef struct H5EA_dblock_t {
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/* Information for H5AC cache functions, _must_ be first field in structure */
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H5AC_info_t cache_info;
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/* Extensible array information (stored) */
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hsize_t block_off; /* Offset of the block within the array's address space */
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void * elmts; /* Buffer for elements stored in data block */
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/* Internal array information (not stored) */
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H5EA_hdr_t *hdr; /* Shared array header info */
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haddr_t addr; /* Address of this data block on disk */
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size_t size; /* Size of data block on disk */
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/* SWMR / Flush dependency information (not stored) */
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hbool_t has_hdr_depend; /* Whether this object has a flush dependency on the header */
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H5AC_proxy_entry_t *top_proxy; /* 'Top' proxy cache entry for all array entries */
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void * parent; /* Parent object for data block (index or super block) */
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/* Computed/cached values (not stored) */
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size_t nelmts; /* Number of elements in block */
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size_t npages; /* Number of pages in a block (zero if not paged) */
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} H5EA_dblock_t;
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/* The extensible array data block page information */
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typedef struct H5EA_dbk_page_t {
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/* Information for H5AC cache functions, _must_ be first field in structure */
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H5AC_info_t cache_info;
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/* Extensible array information (stored) */
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void *elmts; /* Buffer for elements stored in data block page */
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/* Internal array information (not stored) */
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H5EA_hdr_t *hdr; /* Shared array header info */
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haddr_t addr; /* Address of this data block page on disk */
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size_t size; /* Size of data block page on disk */
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/* SWMR / Flush dependency information (not stored) */
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hbool_t has_hdr_depend; /* Whether this object has a flush dependency on the header */
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H5AC_proxy_entry_t *top_proxy; /* "Top" proxy cache entry for all array entries */
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H5EA_sblock_t * parent; /* Parent object for data block page (super block) */
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/* Computed/cached values (not stored) */
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/* <none> */
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} H5EA_dblk_page_t;
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/* Extensible array */
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struct H5EA_t {
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H5EA_hdr_t *hdr; /* Pointer to internal extensible array header info */
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H5F_t * f; /* Pointer to file for extensible array */
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};
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/* Metadata cache callback user data types */
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/* Info needed for loading header */
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typedef struct H5EA_hdr_cache_ud_t {
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H5F_t * f; /* Pointer to file for extensible array */
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haddr_t addr; /* Address of header on disk */
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void * ctx_udata; /* User context for class */
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} H5EA_hdr_cache_ud_t;
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/* Info needed for loading super block */
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typedef struct H5EA_sblock_cache_ud_t {
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H5EA_hdr_t * hdr; /* Shared extensible array information */
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H5EA_iblock_t *parent; /* Pointer to parent object for super block (index block) */
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unsigned sblk_idx; /* Index of super block */
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haddr_t sblk_addr; /* Address of super block */
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} H5EA_sblock_cache_ud_t;
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/* Info needed for loading data block */
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typedef struct H5EA_dblock_cache_ud_t {
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H5EA_hdr_t *hdr; /* Shared extensible array information */
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void * parent; /* Pointer to parent object for data block (index or super block) */
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size_t nelmts; /* Number of elements in data block */
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haddr_t dblk_addr; /* Address of data block */
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} H5EA_dblock_cache_ud_t;
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/* Info needed for loading data block page */
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typedef struct H5EA_dblk_page_cache_ud_t {
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H5EA_hdr_t * hdr; /* Shared extensible array information */
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H5EA_sblock_t *parent; /* Pointer to parent object for data block page (super block) */
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haddr_t dblk_page_addr; /* Address of data block page */
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} H5EA_dblk_page_cache_ud_t;
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#ifdef H5EA_TESTING
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typedef struct H5EA__ctx_cb_t {
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herr_t (*encode)(const void *elmt, size_t nelmts, void *udata); /* Perform action during encode step */
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void *udata; /* User data for encode action */
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} H5EA__ctx_cb_t;
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#endif /* H5EA_TESTING */
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/*****************************/
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/* Package Private Variables */
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/*****************************/
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/* Internal extensible array testing class */
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H5_DLLVAR const H5EA_class_t H5EA_CLS_TEST[1];
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/* Array of extensible array client ID -> client class mappings */
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H5_DLLVAR const H5EA_class_t *const H5EA_client_class_g[H5EA_NUM_CLS_ID];
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/******************************/
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/* Package Private Prototypes */
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/******************************/
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/* Generic routines */
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H5_DLL herr_t H5EA__create_flush_depend(H5AC_info_t *parent_entry, H5AC_info_t *child_entry);
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H5_DLL herr_t H5EA__destroy_flush_depend(H5AC_info_t *parent_entry, H5AC_info_t *child_entry);
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/* Header routines */
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H5_DLL H5EA_hdr_t *H5EA__hdr_alloc(H5F_t *f);
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H5_DLL herr_t H5EA__hdr_init(H5EA_hdr_t *hdr, void *ctx_udata);
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H5_DLL haddr_t H5EA__hdr_create(H5F_t *f, const H5EA_create_t *cparam, void *ctx_udata);
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H5_DLL void * H5EA__hdr_alloc_elmts(H5EA_hdr_t *hdr, size_t nelmts);
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H5_DLL herr_t H5EA__hdr_free_elmts(H5EA_hdr_t *hdr, size_t nelmts, void *elmts);
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H5_DLL herr_t H5EA__hdr_incr(H5EA_hdr_t *hdr);
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H5_DLL herr_t H5EA__hdr_decr(H5EA_hdr_t *hdr);
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H5_DLL herr_t H5EA__hdr_fuse_incr(H5EA_hdr_t *hdr);
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H5_DLL size_t H5EA__hdr_fuse_decr(H5EA_hdr_t *hdr);
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H5_DLL herr_t H5EA__hdr_modified(H5EA_hdr_t *hdr);
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H5_DLL H5EA_hdr_t *H5EA__hdr_protect(H5F_t *f, haddr_t ea_addr, void *ctx_udata, unsigned flags);
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H5_DLL herr_t H5EA__hdr_unprotect(H5EA_hdr_t *hdr, unsigned cache_flags);
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H5_DLL herr_t H5EA__hdr_delete(H5EA_hdr_t *hdr);
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H5_DLL herr_t H5EA__hdr_dest(H5EA_hdr_t *hdr);
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/* Index block routines */
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H5_DLL H5EA_iblock_t *H5EA__iblock_alloc(H5EA_hdr_t *hdr);
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H5_DLL haddr_t H5EA__iblock_create(H5EA_hdr_t *hdr, hbool_t *stats_changed);
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H5_DLL H5EA_iblock_t *H5EA__iblock_protect(H5EA_hdr_t *hdr, unsigned flags);
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H5_DLL herr_t H5EA__iblock_unprotect(H5EA_iblock_t *iblock, unsigned cache_flags);
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H5_DLL herr_t H5EA__iblock_delete(H5EA_hdr_t *hdr);
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H5_DLL herr_t H5EA__iblock_dest(H5EA_iblock_t *iblock);
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/* Super block routines */
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H5_DLL H5EA_sblock_t *H5EA__sblock_alloc(H5EA_hdr_t *hdr, H5EA_iblock_t *parent, unsigned sblk_idx);
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H5_DLL haddr_t H5EA__sblock_create(H5EA_hdr_t *hdr, H5EA_iblock_t *parent, hbool_t *stats_changed,
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unsigned sblk_idx);
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H5_DLL H5EA_sblock_t *H5EA__sblock_protect(H5EA_hdr_t *hdr, H5EA_iblock_t *parent, haddr_t sblk_addr,
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unsigned sblk_idx, unsigned flags);
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H5_DLL herr_t H5EA__sblock_unprotect(H5EA_sblock_t *sblock, unsigned cache_flags);
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H5_DLL herr_t H5EA__sblock_delete(H5EA_hdr_t *hdr, H5EA_iblock_t *parent, haddr_t sblk_addr,
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unsigned sblk_idx);
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H5_DLL herr_t H5EA__sblock_dest(H5EA_sblock_t *sblock);
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/* Data block routines */
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H5_DLL H5EA_dblock_t *H5EA__dblock_alloc(H5EA_hdr_t *hdr, void *parent, size_t nelmts);
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H5_DLL haddr_t H5EA__dblock_create(H5EA_hdr_t *hdr, void *parent, hbool_t *stats_changed, hsize_t dblk_off,
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size_t nelmts);
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H5_DLL unsigned H5EA__dblock_sblk_idx(const H5EA_hdr_t *hdr, hsize_t idx);
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H5_DLL H5EA_dblock_t *H5EA__dblock_protect(H5EA_hdr_t *hdr, void *parent, haddr_t dblk_addr,
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size_t dblk_nelmts, unsigned flags);
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H5_DLL herr_t H5EA__dblock_unprotect(H5EA_dblock_t *dblock, unsigned cache_flags);
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H5_DLL herr_t H5EA__dblock_delete(H5EA_hdr_t *hdr, void *parent, haddr_t dblk_addr, size_t dblk_nelmts);
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H5_DLL herr_t H5EA__dblock_dest(H5EA_dblock_t *dblock);
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/* Data block page routines */
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H5_DLL H5EA_dblk_page_t *H5EA__dblk_page_alloc(H5EA_hdr_t *hdr, H5EA_sblock_t *parent);
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H5_DLL herr_t H5EA__dblk_page_create(H5EA_hdr_t *hdr, H5EA_sblock_t *parent, haddr_t addr);
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H5_DLL H5EA_dblk_page_t *H5EA__dblk_page_protect(H5EA_hdr_t *hdr, H5EA_sblock_t *parent,
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haddr_t dblk_page_addr, unsigned flags);
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H5_DLL herr_t H5EA__dblk_page_unprotect(H5EA_dblk_page_t *dblk_page, unsigned cache_flags);
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H5_DLL herr_t H5EA__dblk_page_dest(H5EA_dblk_page_t *dblk_page);
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/* Debugging routines for dumping file structures */
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H5_DLL herr_t H5EA__hdr_debug(H5F_t *f, haddr_t addr, FILE *stream, int indent, int fwidth,
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const H5EA_class_t *cls, haddr_t obj_addr);
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H5_DLL herr_t H5EA__iblock_debug(H5F_t *f, haddr_t addr, FILE *stream, int indent, int fwidth,
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const H5EA_class_t *cls, haddr_t hdr_addr, haddr_t obj_addr);
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H5_DLL herr_t H5EA__sblock_debug(H5F_t *f, haddr_t addr, FILE *stream, int indent, int fwidth,
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const H5EA_class_t *cls, haddr_t hdr_addr, unsigned sblk_idx,
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haddr_t obj_addr);
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H5_DLL herr_t H5EA__dblock_debug(H5F_t *f, haddr_t addr, FILE *stream, int indent, int fwidth,
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const H5EA_class_t *cls, haddr_t hdr_addr, size_t dblk_nelmts,
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haddr_t obj_addr);
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/* Testing routines */
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#ifdef H5EA_TESTING
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H5_DLL herr_t H5EA__get_cparam_test(const H5EA_t *ea, H5EA_create_t *cparam);
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H5_DLL int H5EA__cmp_cparam_test(const H5EA_create_t *cparam1, const H5EA_create_t *cparam2);
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#endif /* H5EA_TESTING */
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#endif /* H5EApkg_H */
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