mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2025-02-23 16:20:57 +08:00
Code Issues Packages Projects Releases Wiki Activity
5385f032dd
hdf5/src/H5Dpkg.h

765 lines
40 KiB
C
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Monday, April 14, 2003
*
* Purpose: This file contains declarations which are visible only within
* the H5D package. Source files outside the H5D package should
* include H5Dprivate.h instead.
*/
#if !(defined H5D_FRIEND || defined H5D_MODULE)
#error "Do not include this file outside the H5D package!"
#endif
#ifndef _H5Dpkg_H
#define _H5Dpkg_H
/* Get package's private header */
#include "H5Dprivate.h"
/* Other private headers needed by this file */
#include "H5ACprivate.h" /* Metadata cache */
#include "H5B2private.h" /* v2 B-trees */
#include "H5Fprivate.h" /* File access */
#include "H5Gprivate.h" /* Groups */
#include "H5SLprivate.h" /* Skip lists */
#include "H5Tprivate.h" /* Datatypes */
/**************************/
/* Package Private Macros */
/**************************/
/* Set the minimum object header size to create objects with */
#define H5D_MINHDR_SIZE 256
/* [Simple] Macro to construct a H5D_io_info_t from it's components */
#define H5D_BUILD_IO_INFO_WRT(io_info, ds, str, buf) \
(io_info)->dset = ds; \
(io_info)->store = str; \
(io_info)->op_type = H5D_IO_OP_WRITE; \
(io_info)->u.wbuf = buf
#define H5D_BUILD_IO_INFO_RD(io_info, ds, str, buf) \
(io_info)->dset = ds; \
(io_info)->store = str; \
(io_info)->op_type = H5D_IO_OP_READ; \
(io_info)->u.rbuf = buf
/* Flags for marking aspects of a dataset dirty */
#define H5D_MARK_SPACE 0x01
#define H5D_MARK_LAYOUT 0x02
/* Default creation parameters for chunk index data structures */
/* See H5O_layout_chunk_t */
/* Fixed array creation values */
#define H5D_FARRAY_CREATE_PARAM_SIZE 1 /* Size of the creation parameters in bytes */
#define H5D_FARRAY_MAX_DBLK_PAGE_NELMTS_BITS 10 /* i.e. 1024 elements per data block page */
/* Extensible array creation values */
#define H5D_EARRAY_CREATE_PARAM_SIZE 5 /* Size of the creation parameters in bytes */
#define H5D_EARRAY_MAX_NELMTS_BITS 32 /* i.e. 4 giga-elements */
#define H5D_EARRAY_IDX_BLK_ELMTS 4
#define H5D_EARRAY_SUP_BLK_MIN_DATA_PTRS 4
#define H5D_EARRAY_DATA_BLK_MIN_ELMTS 16
#define H5D_EARRAY_MAX_DBLOCK_PAGE_NELMTS_BITS 10 /* i.e. 1024 elements per data block page */
/* v2 B-tree creation values for raw meta_size */
#define H5D_BT2_CREATE_PARAM_SIZE 6 /* Size of the creation parameters in bytes */
#define H5D_BT2_NODE_SIZE 2048
#define H5D_BT2_SPLIT_PERC 100
#define H5D_BT2_MERGE_PERC 40
/****************************/
/* Package Private Typedefs */
/****************************/
/* Typedef for datatype information for raw data I/O operation */
typedef struct H5D_type_info_t {
/* Initial values */
const H5T_t *mem_type; /* Pointer to memory datatype */
const H5T_t *dset_type; /* Pointer to dataset datatype */
H5T_path_t *tpath; /* Datatype conversion path */
hid_t src_type_id; /* Source datatype ID */
hid_t dst_type_id; /* Destination datatype ID */
/* Computed/derived values */
size_t src_type_size; /* Size of source type */
size_t dst_type_size; /* Size of destination type */
size_t max_type_size; /* Size of largest source/destination type */
hbool_t is_conv_noop; /* Whether the type conversion is a NOOP */
hbool_t is_xform_noop; /* Whether the data transform is a NOOP */
const H5T_subset_info_t *cmpd_subset; /* Info related to the compound subset conversion functions */
H5T_bkg_t need_bkg; /* Type of background buf needed */
size_t request_nelmts; /* Requested strip mine */
uint8_t *tconv_buf; /* Datatype conv buffer */
hbool_t tconv_buf_allocated; /* Whether the type conversion buffer was allocated */
uint8_t *bkg_buf; /* Background buffer */
hbool_t bkg_buf_allocated; /* Whether the background buffer was allocated */
} H5D_type_info_t;
/* Forward declaration of structs used below */
struct H5D_io_info_t;
struct H5D_chunk_map_t;
typedef struct H5D_shared_t H5D_shared_t;
/* Function pointers for I/O on particular types of dataset layouts */
typedef herr_t (*H5D_layout_construct_func_t)(H5F_t *f, H5D_t *dset);
typedef herr_t (*H5D_layout_init_func_t)(H5F_t *f, const H5D_t *dset,
hid_t dapl_id);
typedef hbool_t (*H5D_layout_is_space_alloc_func_t)(const H5O_storage_t *storage);
typedef hbool_t (*H5D_layout_is_data_cached_func_t)(const H5D_shared_t *shared_dset);
typedef herr_t (*H5D_layout_io_init_func_t)(const struct 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,
struct H5D_chunk_map_t *cm);
typedef herr_t (*H5D_layout_read_func_t)(struct 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, struct H5D_chunk_map_t *fm);
typedef herr_t (*H5D_layout_write_func_t)(struct 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, struct H5D_chunk_map_t *fm);
typedef ssize_t (*H5D_layout_readvv_func_t)(const struct H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
typedef ssize_t (*H5D_layout_writevv_func_t)(const struct H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
typedef herr_t (*H5D_layout_flush_func_t)(H5D_t *dataset);
typedef herr_t (*H5D_layout_io_term_func_t)(const struct H5D_chunk_map_t *cm);
typedef herr_t (*H5D_layout_dest_func_t)(H5D_t *dataset);
/* Typedef for grouping layout I/O routines */
typedef struct H5D_layout_ops_t {
H5D_layout_construct_func_t construct; /* Layout constructor for new datasets */
H5D_layout_init_func_t init; /* Layout initializer for dataset */
H5D_layout_is_space_alloc_func_t is_space_alloc; /* Query routine to determine if storage is allocated */
H5D_layout_is_data_cached_func_t is_data_cached; /* Query routine to determine if any raw data is cached. If routine is not present then the layout type never caches raw data. */
H5D_layout_io_init_func_t io_init; /* I/O initialization routine */
H5D_layout_read_func_t ser_read; /* High-level I/O routine for reading data in serial */
H5D_layout_write_func_t ser_write; /* High-level I/O routine for writing data in serial */
#ifdef H5_HAVE_PARALLEL
H5D_layout_read_func_t par_read; /* High-level I/O routine for reading data in parallel */
H5D_layout_write_func_t par_write; /* High-level I/O routine for writing data in parallel */
#endif /* H5_HAVE_PARALLEL */
H5D_layout_readvv_func_t readvv; /* Low-level I/O routine for reading data */
H5D_layout_writevv_func_t writevv; /* Low-level I/O routine for writing data */
H5D_layout_flush_func_t flush; /* Low-level I/O routine for flushing raw data */
H5D_layout_io_term_func_t io_term; /* I/O shutdown routine */
H5D_layout_dest_func_t dest; /* Destroy layout info */
} H5D_layout_ops_t;
/* Function pointers for either multiple or single block I/O access */
typedef herr_t (*H5D_io_single_read_func_t)(const struct 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);
typedef herr_t (*H5D_io_single_write_func_t)(const struct 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);
/* Typedef for raw data I/O framework info */
typedef struct H5D_io_ops_t {
H5D_layout_read_func_t multi_read; /* High-level I/O routine for reading data */
H5D_layout_write_func_t multi_write; /* High-level I/O routine for writing data */
H5D_io_single_read_func_t single_read; /* I/O routine for reading single block */
H5D_io_single_write_func_t single_write; /* I/O routine for writing single block */
} H5D_io_ops_t;
/* Typedefs for dataset storage information */
typedef struct {
haddr_t dset_addr; /* Address of dataset in file */
hsize_t dset_size; /* Total size of dataset in file */
} H5D_contig_storage_t;
typedef struct {
hsize_t *scaled; /* Scaled coordinates for a chunk */
} H5D_chunk_storage_t;
typedef struct {
void *buf; /* Buffer for compact dataset */
hbool_t *dirty; /* Pointer to dirty flag to mark */
} H5D_compact_storage_t;
typedef union H5D_storage_t {
H5D_contig_storage_t contig; /* Contiguous information for dataset */
H5D_chunk_storage_t chunk; /* Chunk information for dataset */
H5D_compact_storage_t compact; /* Compact information for dataset */
H5O_efl_t efl; /* External file list information for dataset */
} H5D_storage_t;
/* Typedef for raw data I/O operation info */
typedef enum H5D_io_op_type_t {
H5D_IO_OP_READ, /* Read operation */
H5D_IO_OP_WRITE /* Write operation */
} H5D_io_op_type_t;
typedef struct H5D_io_info_t {
const H5D_t *dset; /* Pointer to dataset being operated on */
#ifdef H5_HAVE_PARALLEL
MPI_Comm comm; /* MPI communicator for file */
hbool_t using_mpi_vfd; /* Whether the file is using an MPI-based VFD */
#endif /* H5_HAVE_PARALLEL */
H5D_storage_t *store; /* Dataset storage info */
H5D_layout_ops_t layout_ops; /* Dataset layout I/O operation function pointers */
H5D_io_ops_t io_ops; /* I/O operation function pointers */
H5D_io_op_type_t op_type;
union {
void *rbuf; /* Pointer to buffer for read */
const void *wbuf; /* Pointer to buffer to write */
} u;
} H5D_io_info_t;
/******************/
/* Chunk typedefs */
/******************/
/* Typedef for chunked dataset index operation info */
typedef struct H5D_chk_idx_info_t {
H5F_t *f; /* File pointer for operation */
const H5O_pline_t *pline; /* I/O pipeline info */
H5O_layout_chunk_t *layout; /* Chunk layout description */
H5O_storage_chunk_t *storage; /* Chunk storage description */
} H5D_chk_idx_info_t;
/*
* "Generic" chunk record. Each chunk is keyed by the minimum logical
* N-dimensional coordinates and the datatype size of the chunk.
* The fastest-varying dimension is assumed to reference individual bytes of
* the array, so a 100-element 1-D array of 4-byte integers would really be a
* 2-D array with the slow varying dimension of size 100 and the fast varying
* dimension of size 4 (the storage dimensionality has very little to do with
* the real dimensionality).
*
* The chunk's file address, filter mask and size on disk are not key values.
*/
typedef struct H5D_chunk_rec_t {
hsize_t scaled[H5O_LAYOUT_NDIMS]; /* Logical offset to start */
uint32_t nbytes; /* Size of stored data */
uint32_t filter_mask; /* Excluded filters */
haddr_t chunk_addr; /* Address of chunk in file */
} H5D_chunk_rec_t;
/*
* Common data exchange structure for indexed storage nodes. This structure is
* passed through the indexing layer to the methods for the objects
* to which the index points.
*/
typedef struct H5D_chunk_common_ud_t {
const H5O_layout_chunk_t *layout; /* Chunk layout description */
const H5O_storage_chunk_t *storage; /* Chunk storage description */
const hsize_t *scaled; /* Scaled coordinates for a chunk */
} H5D_chunk_common_ud_t;
/* B-tree callback info for various operations */
typedef struct H5D_chunk_ud_t {
/* Downward */
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
/* Upward */
unsigned idx_hint; /* Index of chunk in cache, if present */
H5F_block_t chunk_block; /* Offset/length of chunk in file */
unsigned filter_mask; /* Excluded filters */
hbool_t new_unfilt_chunk; /* Whether the chunk just became unfiltered */
hsize_t chunk_idx; /* Chunk index for EA, FA indexing */
} H5D_chunk_ud_t;
/* Typedef for "generic" chunk callbacks */
typedef int (*H5D_chunk_cb_func_t)(const H5D_chunk_rec_t *chunk_rec,
void *udata);
/* Typedefs for chunk operations */
typedef herr_t (*H5D_chunk_init_func_t)(const H5D_chk_idx_info_t *idx_info,
const H5S_t *space, haddr_t dset_ohdr_addr);
typedef herr_t (*H5D_chunk_create_func_t)(const H5D_chk_idx_info_t *idx_info);
typedef hbool_t (*H5D_chunk_is_space_alloc_func_t)(const H5O_storage_chunk_t *storage);
typedef herr_t (*H5D_chunk_insert_func_t)(const H5D_chk_idx_info_t *idx_info,
H5D_chunk_ud_t *udata, const H5D_t *dset);
typedef herr_t (*H5D_chunk_get_addr_func_t)(const H5D_chk_idx_info_t *idx_info,
H5D_chunk_ud_t *udata);
typedef herr_t (*H5D_chunk_resize_func_t)(H5O_layout_chunk_t *layout);
typedef int (*H5D_chunk_iterate_func_t)(const H5D_chk_idx_info_t *idx_info,
H5D_chunk_cb_func_t chunk_cb, void *chunk_udata);
typedef herr_t (*H5D_chunk_remove_func_t)(const H5D_chk_idx_info_t *idx_info,
H5D_chunk_common_ud_t *udata);
typedef herr_t (*H5D_chunk_delete_func_t)(const H5D_chk_idx_info_t *idx_info);
typedef herr_t (*H5D_chunk_copy_setup_func_t)(const H5D_chk_idx_info_t *idx_info_src,
const H5D_chk_idx_info_t *idx_info_dst);
typedef herr_t (*H5D_chunk_copy_shutdown_func_t)(H5O_storage_chunk_t *storage_src,
H5O_storage_chunk_t *storage_dst);
typedef herr_t (*H5D_chunk_size_func_t)(const H5D_chk_idx_info_t *idx_info,
hsize_t *idx_size);
typedef herr_t (*H5D_chunk_reset_func_t)(H5O_storage_chunk_t *storage, hbool_t reset_addr);
typedef herr_t (*H5D_chunk_dump_func_t)(const H5O_storage_chunk_t *storage,
FILE *stream);
typedef herr_t (*H5D_chunk_dest_func_t)(const H5D_chk_idx_info_t *idx_info);
/* Typedef for grouping chunk I/O routines */
typedef struct H5D_chunk_ops_t {
hbool_t can_swim; /* Flag to indicate that the index supports SWMR access */
H5D_chunk_init_func_t init; /* Routine to initialize indexing information in memory */
H5D_chunk_create_func_t create; /* Routine to create chunk index */
H5D_chunk_is_space_alloc_func_t is_space_alloc; /* Query routine to determine if storage/index is allocated */
H5D_chunk_insert_func_t insert; /* Routine to insert a chunk into an index */
H5D_chunk_get_addr_func_t get_addr; /* Routine to retrieve address of chunk in file */
H5D_chunk_resize_func_t resize; /* Routine to update chunk index info after resizing dataset */
H5D_chunk_iterate_func_t iterate; /* Routine to iterate over chunks */
H5D_chunk_remove_func_t remove; /* Routine to remove a chunk from an index */
H5D_chunk_delete_func_t idx_delete; /* Routine to delete index & all chunks from file*/
H5D_chunk_copy_setup_func_t copy_setup; /* Routine to perform any necessary setup for copying chunks */
H5D_chunk_copy_shutdown_func_t copy_shutdown; /* Routine to perform any necessary shutdown for copying chunks */
H5D_chunk_size_func_t size; /* Routine to get size of indexing information */
H5D_chunk_reset_func_t reset; /* Routine to reset indexing information */
H5D_chunk_dump_func_t dump; /* Routine to dump indexing information */
H5D_chunk_dest_func_t dest; /* Routine to destroy indexing information in memory */
} H5D_chunk_ops_t;
/* Structure holding information about a chunk's selection for mapping */
typedef struct H5D_chunk_info_t {
hsize_t index; /* "Index" of chunk in dataset */
uint32_t chunk_points; /* Number of elements selected in chunk */
hsize_t scaled[H5O_LAYOUT_NDIMS]; /* Scaled coordinates of chunk (in file dataset's dataspace) */
H5S_t *fspace; /* Dataspace describing chunk & selection in it */
hbool_t fspace_shared; /* Indicate that the file space for a chunk is shared and shouldn't be freed */
H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */
hbool_t mspace_shared; /* Indicate that the memory space for a chunk is shared and shouldn't be freed */
} H5D_chunk_info_t;
/* Main structure holding the mapping between file chunks and memory */
typedef struct H5D_chunk_map_t {
H5O_layout_t *layout; /* Dataset layout information*/
hsize_t nelmts; /* Number of elements selected in file & memory dataspaces */
const H5S_t *file_space; /* Pointer to the file dataspace */
unsigned f_ndims; /* Number of dimensions for file dataspace */
const H5S_t *mem_space; /* Pointer to the memory dataspace */
H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */
H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
unsigned m_ndims; /* Number of dimensions for memory dataspace */
H5S_sel_type msel_type; /* Selection type in memory */
H5S_sel_type fsel_type; /* Selection type in file */
H5SL_t *sel_chunks; /* Skip list containing information for each chunk selected */
H5S_t *single_space; /* Dataspace for single chunk */
H5D_chunk_info_t *single_chunk_info; /* Pointer to single chunk's info */
hbool_t use_single; /* Whether I/O is on a single element */
hsize_t last_index; /* Index of last chunk operated on */
H5D_chunk_info_t *last_chunk_info; /* Pointer to last chunk's info */
hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */
#ifdef H5_HAVE_PARALLEL
H5D_chunk_info_t **select_chunk; /* Store the information about whether this chunk is selected or not */
#endif /* H5_HAVE_PARALLEL */
} H5D_chunk_map_t;
/* Cached information about a particular chunk */
typedef struct H5D_chunk_cached_t {
hbool_t valid; /*whether cache info is valid*/
hsize_t scaled[H5O_LAYOUT_NDIMS]; /*scaled offset of chunk*/
haddr_t addr; /*file address of chunk */
uint32_t nbytes; /*size of stored data */
hsize_t chunk_idx; /*index of chunk in dataset */
unsigned filter_mask; /*excluded filters */
} H5D_chunk_cached_t;
/****************************/
/* Virtual dataset typedefs */
/****************************/
/* List of files held open during refresh operations */
typedef struct H5D_virtual_held_file_t {
H5F_t *file; /* Pointer to file held open */
struct H5D_virtual_held_file_t *next; /* Pointer to next node in list */
} H5D_virtual_held_file_t;
/* The raw data chunk cache */
struct H5D_rdcc_ent_t; /* Forward declaration of struct used below */
typedef struct H5D_rdcc_t {
struct {
unsigned ninits; /* Number of chunk creations */
unsigned nhits; /* Number of cache hits */
unsigned nmisses; /* Number of cache misses */
unsigned nflushes; /* Number of cache flushes */
} stats;
size_t nbytes_max; /* Maximum cached raw data in bytes */
size_t nslots; /* Number of chunk slots allocated */
double w0; /* Chunk preemption policy */
struct H5D_rdcc_ent_t *head; /* Head of doubly linked list */
struct H5D_rdcc_ent_t *tail; /* Tail of doubly linked list */
struct H5D_rdcc_ent_t *tmp_head; /* Head of temporary doubly linked list. Chunks on this list are not in the hash table (slot). The head entry is a sentinel (does not refer to an actual chunk). */
size_t nbytes_used; /* Current cached raw data in bytes */
int nused; /* Number of chunk slots in use */
H5D_chunk_cached_t last; /* Cached copy of last chunk information */
struct H5D_rdcc_ent_t **slot; /* Chunk slots, each points to a chunk*/
H5SL_t *sel_chunks; /* Skip list containing information for each chunk selected */
H5S_t *single_space; /* Dataspace for single element I/O on chunks */
H5D_chunk_info_t *single_chunk_info; /* Pointer to single chunk's info */
/* Cached information about scaled dataspace dimensions */
hsize_t scaled_dims[H5S_MAX_RANK]; /* The scaled dim sizes */
hsize_t scaled_power2up[H5S_MAX_RANK]; /* The scaled dim sizes, rounded up to next power of 2 */
unsigned scaled_encode_bits[H5S_MAX_RANK]; /* The number of bits needed to encode the scaled dim sizes */
} H5D_rdcc_t;
/* The raw data contiguous data cache */
typedef struct H5D_rdcdc_t {
unsigned char *sieve_buf; /* Buffer to hold data sieve buffer */
haddr_t sieve_loc; /* File location (offset) of the data sieve buffer */
size_t sieve_size; /* Size of the data sieve buffer used (in bytes) */
size_t sieve_buf_size; /* Size of the data sieve buffer allocated (in bytes) */
hbool_t sieve_dirty; /* Flag to indicate that the data sieve buffer is dirty */
} H5D_rdcdc_t;
/*
* A dataset is made of two layers, an H5D_t struct that is unique to
* each instance of an opened datset, and a shared struct that is only
* created once for a given dataset. Thus, if a dataset is opened twice,
* there will be two IDs and two H5D_t structs, both sharing one H5D_shared_t.
*/
struct H5D_shared_t {
size_t fo_count; /* Reference count */
hbool_t closing; /* Flag to indicate dataset is closing */
hid_t type_id; /* ID for dataset's datatype */
H5T_t *type; /* Datatype for this dataset */
H5S_t *space; /* Dataspace of this dataset */
hid_t dcpl_id; /* Dataset creation property id */
H5D_dcpl_cache_t dcpl_cache; /* Cached DCPL values */
H5O_layout_t layout; /* Data layout */
hbool_t checked_filters;/* TRUE if dataset passes can_apply check */
/* Cached dataspace info */
unsigned ndims; /* The dataset's dataspace rank */
hsize_t curr_dims[H5S_MAX_RANK]; /* The curr. size of dataset dimensions */
hsize_t curr_power2up[H5S_MAX_RANK]; /* The curr. dim sizes, rounded up to next power of 2 */
hsize_t max_dims[H5S_MAX_RANK]; /* The max. size of dataset dimensions */
/* Buffered/cached information for types of raw data storage*/
struct {
H5D_rdcdc_t contig; /* Information about contiguous data */
/* (Note that the "contig" cache
* information can be used by a chunked
* dataset in certain circumstances)
*/
H5D_rdcc_t chunk; /* Information about chunked data */
} cache;
H5D_append_flush_t append_flush; /* Append flush property information */
char *extfile_prefix; /* expanded external file prefix */
char *vds_prefix; /* expanded vds prefix */
};
struct H5D_t {
H5O_loc_t oloc; /* Object header location */
H5G_name_t path; /* Group hierarchy path */
H5D_shared_t *shared; /* cached information from file */
};
/* Enumerated type for allocating dataset's storage */
typedef enum {
H5D_ALLOC_CREATE, /* Dataset is being created */
H5D_ALLOC_OPEN, /* Dataset is being opened */
H5D_ALLOC_EXTEND, /* Dataset's dataspace is being extended */
H5D_ALLOC_WRITE /* Dataset is being extended */
} H5D_time_alloc_t;
/* Typedef for dataset creation operation */
typedef struct {
hid_t type_id; /* Datatype for dataset */
const H5S_t *space; /* Dataspace for dataset */
hid_t dcpl_id; /* Dataset creation property list */
hid_t dapl_id; /* Dataset access property list */
} H5D_obj_create_t;
/* Typedef for filling a buffer with a fill value */
typedef struct H5D_fill_buf_info_t {
H5MM_allocate_t fill_alloc_func; /* Routine to call for allocating fill buffer */
void *fill_alloc_info; /* Extra info for allocation routine */
H5MM_free_t fill_free_func; /* Routine to call for freeing fill buffer */
void *fill_free_info; /* Extra info for free routine */
H5T_path_t *fill_to_mem_tpath; /* Datatype conversion path for converting the fill value to the memory buffer */
H5T_path_t *mem_to_dset_tpath; /* Datatype conversion path for converting the memory buffer to the dataset elements */
const H5O_fill_t *fill; /* Pointer to fill value */
void *fill_buf; /* Fill buffer */
size_t fill_buf_size; /* Size of fill buffer */
hbool_t use_caller_fill_buf; /* Whether the caller provided the fill buffer */
void *bkg_buf; /* Background conversion buffer */
size_t bkg_buf_size; /* Size of background buffer */
H5T_t *mem_type; /* Pointer to memory datatype */
const H5T_t *file_type; /* Pointer to file datatype */
hid_t mem_tid; /* ID for memory version of disk datatype */
hid_t file_tid; /* ID for disk datatype */
size_t mem_elmt_size, file_elmt_size; /* Size of element in memory and on disk */
size_t max_elmt_size; /* Max. size of memory or file datatype */
size_t elmts_per_buf; /* # of elements that fit into a buffer */
hbool_t has_vlen_fill_type; /* Whether the datatype for the fill value has a variable-length component */
} H5D_fill_buf_info_t;
/* Internal data structure for computing variable-length dataset's total size */
typedef struct {
H5VL_object_t *dset_vol_obj; /* VOL object for the dataset */
hid_t fspace_id; /* File dataspace ID of the dataset we are working on */
hid_t mspace_id; /* Memory dataspace ID of the dataset we are working on */
void *fl_tbuf; /* Ptr to the temporary buffer we are using for fixed-length data */
void *vl_tbuf; /* Ptr to the temporary buffer we are using for VL data */
hsize_t size; /* Accumulated number of bytes for the selection */
} H5D_vlen_bufsize_t;
/*****************************/
/* Package Private Variables */
/*****************************/
/* Storage layout class I/O operations */
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_CONTIG[1];
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_EFL[1];
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_COMPACT[1];
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_CHUNK[1];
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1];
/* Chunked layout operations */
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_BTREE[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_NONE[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_SINGLE[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_EARRAY[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_FARRAY[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_BT2[1];
/* The v2 B-tree class for indexing chunked datasets with >1 unlimited dimensions */
H5_DLLVAR const H5B2_class_t H5D_BT2[1];
H5_DLLVAR const H5B2_class_t H5D_BT2_FILT[1];
/* Array of versions for Layout */
H5_DLLVAR const unsigned H5O_layout_ver_bounds[H5F_LIBVER_NBOUNDS];
/******************************/
/* Package Private Prototypes */
/******************************/
H5_DLL H5D_t *H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space,
hid_t dcpl_id, hid_t dapl_id);
H5_DLL H5D_t *H5D__create_named(const H5G_loc_t *loc, const char *name,
hid_t type_id, const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id,
hid_t dapl_id);
H5_DLL H5D_t *H5D__open_name(const H5G_loc_t *loc, const char *name, hid_t dapl_id);
H5_DLL hid_t H5D__get_space(const H5D_t *dset);
H5_DLL hid_t H5D__get_type(const H5D_t *dset);
H5_DLL herr_t H5D__get_space_status(const H5D_t *dset, H5D_space_status_t *allocation);
H5_DLL herr_t H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, hbool_t full_overwrite, hsize_t old_dim[]);
H5_DLL herr_t H5D__get_storage_size(const H5D_t *dset, hsize_t *storage_size);
H5_DLL herr_t H5D__get_chunk_storage_size(H5D_t *dset, const hsize_t *offset, hsize_t *storage_size);
H5_DLL haddr_t H5D__get_offset(const H5D_t *dset);
H5_DLL void *H5D__vlen_get_buf_size_alloc(size_t size, void *info);
H5_DLL herr_t H5D__vlen_get_buf_size(void *elem, hid_t type_id, unsigned ndim, const hsize_t *point, void *op_data);
H5_DLL herr_t H5D__check_filters(H5D_t *dataset);
H5_DLL herr_t H5D__set_extent(H5D_t *dataset, const hsize_t *size);
H5_DLL herr_t H5D__flush_sieve_buf(H5D_t *dataset);
H5_DLL herr_t H5D__flush_real(H5D_t *dataset);
H5_DLL herr_t H5D__flush(H5D_t *dset, hid_t dset_id);
H5_DLL herr_t H5D__mark(const H5D_t *dataset, unsigned flags);
H5_DLL herr_t H5D__refresh(hid_t dset_id, H5D_t *dataset);
/* To convert a dataset's chunk indexing type to v1 B-tree */
H5_DLL herr_t H5D__format_convert(H5D_t *dataset);
/* Internal I/O routines */
H5_DLL herr_t H5D__read(H5D_t *dataset, hid_t mem_type_id,
const H5S_t *mem_space, const H5S_t *file_space, void *buf/*out*/);
H5_DLL herr_t H5D__write(H5D_t *dataset, hid_t mem_type_id,
const H5S_t *mem_space, const H5S_t *file_space, const void *buf);
/* Functions that perform direct serial I/O operations */
H5_DLL herr_t H5D__select_read(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);
H5_DLL herr_t H5D__select_write(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);
/* Functions that perform scatter-gather serial I/O operations */
H5_DLL herr_t H5D__scatter_mem(const void *_tscat_buf, H5S_sel_iter_t *iter,
size_t nelmts, void *_buf);
H5_DLL size_t H5D__gather_mem(const void *_buf, H5S_sel_iter_t *iter,
size_t nelmts, void *_tgath_buf/*out*/);
H5_DLL herr_t H5D__scatgath_read(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);
H5_DLL herr_t H5D__scatgath_write(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);
/* Functions that operate on dataset's layout information */
H5_DLL herr_t H5D__layout_set_io_ops(const H5D_t *dataset);
H5_DLL size_t H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout,
hbool_t include_compact_data);
H5_DLL herr_t H5D__layout_set_version(H5F_t *f, H5O_layout_t *layout);
H5_DLL herr_t H5D__layout_set_latest_indexing(H5O_layout_t *layout,
const H5S_t *space, const H5D_dcpl_cache_t *dcpl_cache);
H5_DLL herr_t H5D__layout_oh_create(H5F_t *file, H5O_t *oh, H5D_t *dset,
hid_t dapl_id);
H5_DLL herr_t H5D__layout_oh_read(H5D_t *dset, hid_t dapl_id,
H5P_genplist_t *plist);
H5_DLL herr_t H5D__layout_oh_write(const H5D_t *dataset, H5O_t *oh, unsigned update_flags);
/* Functions that operate on contiguous storage */
H5_DLL herr_t H5D__contig_alloc(H5F_t *f, H5O_storage_contig_t *storage);
H5_DLL hbool_t H5D__contig_is_space_alloc(const H5O_storage_t *storage);
H5_DLL hbool_t H5D__contig_is_data_cached(const H5D_shared_t *shared_dset);
H5_DLL herr_t H5D__contig_fill(const H5D_io_info_t *io_info);
H5_DLL herr_t H5D__contig_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);
H5_DLL herr_t H5D__contig_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);
H5_DLL herr_t H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src,
H5F_t *f_dst, H5O_storage_contig_t *storage_dst, H5T_t *src_dtype,
H5O_copy_t *cpy_info);
H5_DLL herr_t H5D__contig_delete(H5F_t *f, const H5O_storage_t *store);
/* Functions that operate on chunked dataset storage */
H5_DLL htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr,
hbool_t write_op);
H5_DLL herr_t H5D__chunk_create(const H5D_t *dset /*in,out*/);
H5_DLL herr_t H5D__chunk_set_info(const H5D_t *dset);
H5_DLL hbool_t H5D__chunk_is_space_alloc(const H5O_storage_t *storage);
H5_DLL hbool_t H5D__chunk_is_data_cached(const H5D_shared_t *shared_dset);
H5_DLL herr_t H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled,
H5D_chunk_ud_t *udata);
H5_DLL herr_t H5D__chunk_allocated(const H5D_t *dset, hsize_t *nbytes);
H5_DLL herr_t H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_t old_dim[]);
H5_DLL 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, hsize_t scaled[]);
H5_DLL herr_t H5D__chunk_update_old_edge_chunks(H5D_t *dset, hsize_t old_dim[]);
H5_DLL herr_t H5D__chunk_prune_by_extent(H5D_t *dset, const hsize_t *old_dim);
H5_DLL herr_t H5D__chunk_set_sizes(H5D_t *dset);
#ifdef H5_HAVE_PARALLEL
H5_DLL herr_t H5D__chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[]);
#endif /* H5_HAVE_PARALLEL */
H5_DLL herr_t H5D__chunk_update_cache(H5D_t *dset);
H5_DLL 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);
H5_DLL herr_t H5D__chunk_bh_info(const H5O_loc_t *loc, H5O_t *oh,
H5O_layout_t *layout, hsize_t *btree_size);
H5_DLL herr_t H5D__chunk_dump_index(H5D_t *dset, FILE *stream);
H5_DLL herr_t H5D__chunk_delete(H5F_t *f, H5O_t *oh, H5O_storage_t *store);
H5_DLL herr_t H5D__get_offset_copy(const H5D_t *dset, const hsize_t *offset, hsize_t *offset_copy);
H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters,
hsize_t *offset, uint32_t data_size, const void *buf);
H5_DLL herr_t H5D__chunk_direct_read(const H5D_t *dset, hsize_t *offset,
uint32_t *filters, void *buf);
#ifdef H5D_CHUNK_DEBUG
H5_DLL herr_t H5D__chunk_stats(const H5D_t *dset, hbool_t headers);
#endif /* H5D_CHUNK_DEBUG */
/* format convert */
H5_DLL herr_t H5D__chunk_format_convert(H5D_t *dset, H5D_chk_idx_info_t *idx_info, H5D_chk_idx_info_t *new_idx_info);
/* Functions that operate on compact dataset storage */
H5_DLL herr_t H5D__compact_fill(const H5D_t *dset);
H5_DLL herr_t H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src,
H5F_t *f_dst, H5O_storage_compact_t *storage_dst, H5T_t *src_dtype,
H5O_copy_t *cpy_info);
/* Functions that operate on virtual dataset storage */
H5_DLL herr_t H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout);
H5_DLL herr_t H5D__virtual_copy_layout(H5O_layout_t *layout);
H5_DLL herr_t H5D__virtual_set_extent_unlim(const H5D_t *dset);
H5_DLL herr_t H5D__virtual_reset_layout(H5O_layout_t *layout);
H5_DLL herr_t H5D__virtual_delete(H5F_t *f, H5O_storage_t *storage);
H5_DLL herr_t H5D__virtual_copy(H5F_t *f_src, H5O_layout_t *layout_dst);
H5_DLL herr_t H5D__virtual_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id);
H5_DLL hbool_t H5D__virtual_is_space_alloc(const H5O_storage_t *storage);
H5_DLL herr_t H5D__virtual_hold_source_dset_files(const H5D_t *dset,
H5D_virtual_held_file_t **head);
H5_DLL herr_t H5D__virtual_refresh_source_dsets(H5D_t *dset);
H5_DLL herr_t H5D__virtual_release_source_dset_files(H5D_virtual_held_file_t *head);
/* Functions that operate on EFL (External File List)*/
H5_DLL hbool_t H5D__efl_is_space_alloc(const H5O_storage_t *storage);
H5_DLL herr_t H5D__efl_bh_info(H5F_t *f, H5O_efl_t *efl, hsize_t *heap_size);
/* Functions that perform fill value operations on datasets */
H5_DLL herr_t H5D__fill(const void *fill, const H5T_t *fill_type, void *buf,
const H5T_t *buf_type, const H5S_t *space);
H5_DLL herr_t H5D__fill_init(H5D_fill_buf_info_t *fb_info, void *caller_fill_buf,
H5MM_allocate_t alloc_func, void *alloc_info,
H5MM_free_t free_func, void *free_info,
const H5O_fill_t *fill, const H5T_t *dset_type, hid_t dset_type_id,
size_t nelmts, size_t min_buf_size);
H5_DLL herr_t H5D__fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts);
H5_DLL herr_t H5D__fill_term(H5D_fill_buf_info_t *fb_info);
#ifdef H5_HAVE_PARALLEL
#ifdef H5S_DEBUG
#ifndef H5Dmpio_DEBUG
#define H5Dmpio_DEBUG
#endif /*H5Dmpio_DEBUG*/
#endif/*H5S_DEBUG*/
/* MPI-IO function to read, it will select either regular or irregular read */
H5_DLL herr_t H5D__mpio_select_read(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);
/* MPI-IO function to write, it will select either regular or irregular read */
H5_DLL herr_t H5D__mpio_select_write(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);
/* MPI-IO functions to handle contiguous collective IO */
H5_DLL herr_t H5D__contig_collective_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);
H5_DLL herr_t H5D__contig_collective_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);
/* MPI-IO functions to handle chunked collective IO */
H5_DLL herr_t H5D__chunk_collective_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);
H5_DLL herr_t H5D__chunk_collective_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);
/* MPI-IO function to check if a direct I/O transfer is possible between
* memory and the file */
H5_DLL htri_t H5D__mpio_opt_possible(const H5D_io_info_t *io_info,
const H5S_t *file_space, const H5S_t *mem_space,
const H5D_type_info_t *type_info);
#endif /* H5_HAVE_PARALLEL */
/* Testing functions */
#ifdef H5D_TESTING
H5_DLL herr_t H5D__layout_version_test(hid_t did, unsigned *version);
H5_DLL herr_t H5D__layout_contig_size_test(hid_t did, hsize_t *size);
H5_DLL herr_t H5D__layout_compact_dirty_test(hid_t did, hbool_t *dirty);
H5_DLL herr_t H5D__layout_idx_type_test(hid_t did, H5D_chunk_index_t *idx_type);
H5_DLL herr_t H5D__layout_type_test(hid_t did, H5D_layout_t *layout_type);
H5_DLL herr_t H5D__current_cache_size_test(hid_t did, size_t *nbytes_used, int *nused);
#endif /* H5D_TESTING */
#endif /*_H5Dpkg_H*/
Reference in New Issue View Git Blame Copy Permalink