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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* 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.
*/
#ifndef H5D_PACKAGE
#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 "H5Gprivate.h" /* Groups */
#include "H5Oprivate.h" /* Object headers */
#include "H5Sprivate.h" /* Dataspaces */
#include "H5SLprivate.h" /* Skip lists */
#include "H5Tprivate.h" /* Datatypes */
/**************************/
/* Package Private Macros */
/**************************/
/* The number of reserved IDs in dataset ID group */
#define H5D_RESERVED_ATOMS 0
/* 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(io_info,ds,dxpl_c,dxpl_i,str) \
(io_info)->dset=ds; \
(io_info)->dxpl_cache=dxpl_c; \
(io_info)->dxpl_id=dxpl_i; \
(io_info)->store=str
/****************************/
/* Package Private Typedefs */
/****************************/
/*
* If there is no data type conversion then it might be possible to
* transfer data points between application memory and the file in one
* step without going through the data type conversion buffer.
*/
/* Read from file to application w/o intermediate scratch buffer */
struct H5D_io_info_t;
typedef herr_t (*H5D_io_read_func_t)(struct H5D_io_info_t *io_info,
size_t nelmts, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space, haddr_t addr,
void *buf/*out*/);
/* Write directly from app buffer to file */
typedef herr_t (*H5D_io_write_func_t)(struct H5D_io_info_t *io_info,
size_t nelmts, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space, haddr_t addr,
const void *buf);
/* Function pointers for I/O on particular types of dataset layouts */
typedef ssize_t (*H5D_io_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[],
void *buf);
typedef ssize_t (*H5D_io_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[],
const void *buf);
/* Typedef for raw data I/O framework info */
typedef struct H5D_io_ops_t {
H5D_io_read_func_t read; /* Direct I/O routine for reading */
H5D_io_write_func_t write; /* Direct I/O routine for writing */
H5D_io_readvv_func_t readvv; /* I/O routine for reading data */
H5D_io_writevv_func_t writevv; /* I/O routine for writing data */
} H5D_io_ops_t;
/* Typedef for raw data I/O operation info */
typedef struct H5D_io_info_t {
H5D_t *dset; /* Pointer to dataset being operated on */
#ifndef H5_HAVE_PARALLEL
const
#endif /* H5_HAVE_PARALLEL */
H5D_dxpl_cache_t *dxpl_cache; /* Pointer to cache DXPL info */
hid_t dxpl_id; /* Original DXPL ID */
#ifdef H5_HAVE_PARALLEL
MPI_Comm comm; /* MPI communicator for file */
hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */
hbool_t xfer_opt_mode_changed;
#endif /* H5_HAVE_PARALLEL */
const H5D_storage_t *store; /* Dataset storage info */
H5D_io_ops_t ops; /* I/O operation function pointers */
#ifdef H5S_DEBUG
H5S_iostats_t *stats; /* I/O statistics */
#endif /* H5S_DEBUG */
} H5D_io_info_t;
/* The raw data chunk cache */
typedef struct H5D_rdcc_t {
#ifdef H5D_ISTORE_DEBUG
unsigned ninits; /* Number of chunk creations */
unsigned nhits; /* Number of cache hits */
unsigned nmisses;/* Number of cache misses */
unsigned nflushes;/* Number of cache flushes */
#endif /* H5D_ISTORE_DEBUG */
size_t nbytes; /* Current cached raw data in bytes */
size_t nslots; /* Number of chunk slots allocated */
struct H5D_rdcc_ent_t *head; /* Head of doubly linked list */
struct H5D_rdcc_ent_t *tail; /* Tail of doubly linked list */
int nused; /* Number of chunk slots in use */
struct H5D_rdcc_ent_t **slot; /* Chunk slots, each points to a chunk*/
} 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) */
unsigned 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.
*/
typedef struct H5D_shared_t {
size_t fo_count; /* reference count */
hid_t type_id; /* ID for dataset's datatype */
H5T_t *type; /* datatype of 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 */
H5D_io_ops_t io_ops; /* I/O operations */
H5O_layout_t layout; /* data layout */
hbool_t checked_filters;/* TRUE if dataset passes can_apply check */
/* 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_shared_t;
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;
/* Structure holding information about a chunk's selection for mapping */
typedef struct H5D_chunk_info_t {
hsize_t index; /* "Index" of chunk in dataset */
size_t chunk_points; /* Number of elements selected in chunk */
H5S_t *fspace; /* Dataspace describing chunk & selection in it */
hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */
H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */
unsigned 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 fm_map {
H5SL_t *fsel; /* Skip list containing file dataspaces for all chunks */
hsize_t last_index; /* Index of last chunk operated on */
H5D_chunk_info_t *last_chunk_info; /* Pointer to last chunk's info */
const H5S_t *file_space; /* Pointer to the file dataspace */
const H5S_t *mem_space; /* Pointer to the memory dataspace */
unsigned mem_space_copy; /* Flag to indicate that the memory dataspace must be copied */
hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */
H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */
unsigned f_ndims; /* Number of dimensions for file dataspace */
H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
unsigned m_ndims; /* Number of dimensions for memory dataspace */
hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */
hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */
H5O_layout_t *layout; /* Dataset layout information*/
H5S_sel_type msel_type; /* Selection type in memory */
hsize_t total_chunks; /* Number of total chunks */
hbool_t *select_chunk; /* store the information about whether this chunk is selected or not */
} fm_map;
/* 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 */
} H5D_obj_create_t;
/* Typedef for filling a buffer with a fill value */
typedef struct {
hbool_t alloc_vl_during_refill; /* Whether to allocate VL-datatype fill buffer during refill */
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;
/*****************************/
/* Package Private Variables */
/*****************************/
extern H5D_dxpl_cache_t H5D_def_dxpl_cache;
/******************************/
/* 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 dxpl_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, hid_t dxpl_id);
H5_DLL herr_t H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset, H5D_time_alloc_t time_alloc,
hbool_t update_time, hbool_t full_overwrite);
/* Functions that perform serial I/O operations */
H5_DLL herr_t H5D_select_fscat (H5D_io_info_t *io_info,
const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts,
const void *_buf);
H5_DLL size_t H5D_select_fgath (H5D_io_info_t *io_info,
const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts,
void *buf);
H5_DLL herr_t H5D_select_mscat (const void *_tscat_buf,
const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
const H5D_dxpl_cache_t *dxpl_cache, void *_buf/*out*/);
H5_DLL size_t H5D_select_mgath (const void *_buf,
const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
const H5D_dxpl_cache_t *dxpl_cache, void *_tgath_buf/*out*/);
H5_DLL herr_t H5D_select_read(H5D_io_info_t *io_info,
size_t nelmts, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
haddr_t addr, void *buf/*out*/);
H5_DLL herr_t H5D_select_write(H5D_io_info_t *io_info,
size_t nelmts, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
haddr_t addr, const void *buf/*out*/);
/* Functions that operate on contiguous storage */
H5_DLL herr_t H5D_contig_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout);
H5_DLL herr_t H5D_contig_fill(H5D_t *dset, hid_t dxpl_id);
H5_DLL haddr_t H5D_contig_get_addr(const H5D_t *dset);
H5_DLL ssize_t H5D_contig_readvv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
void *buf);
H5_DLL ssize_t H5D_contig_writevv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
const void *buf);
H5_DLL herr_t H5D_contig_copy(H5F_t *f_src, const H5O_layout_t *layout_src, H5F_t *f_dst,
H5O_layout_t *layout_dst, H5T_t *src_dtype, H5O_copy_t *cpy_info, hid_t dxpl_id);
/* Functions that operate on compact dataset storage */
H5_DLL herr_t H5D_compact_fill(H5D_t *dset, hid_t dxpl_id);
H5_DLL ssize_t H5D_compact_readvv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
void *buf);
H5_DLL ssize_t H5D_compact_writevv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
const void *buf);
H5_DLL herr_t H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src,
H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *src_dtype, H5O_copy_t *cpy_info, hid_t dxpl_id);
/* Functions that operate on indexed storage */
/* forward reference for collective-chunk IO use */
struct H5D_istore_ud1_t; /*define in H5Distore.c*/
H5_DLL herr_t H5D_istore_init (const H5F_t *f, const H5D_t *dset);
H5_DLL herr_t H5D_istore_flush (H5D_t *dset, hid_t dxpl_id, unsigned flags);
H5_DLL herr_t H5D_istore_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout);
H5_DLL herr_t H5D_istore_dest (H5D_t *dset, hid_t dxpl_id);
H5_DLL herr_t H5D_istore_allocate (H5D_t *dset, hid_t dxpl_id,
hbool_t full_overwrite);
H5_DLL hsize_t H5D_istore_allocated(H5D_t *dset, hid_t dxpl_id);
H5_DLL herr_t H5D_istore_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout,
hsize_t *btree_size);
H5_DLL herr_t H5D_istore_prune_by_extent(const H5D_io_info_t *io_info,
const hsize_t *old_dims);
H5_DLL herr_t H5D_istore_initialize_by_extent(H5D_io_info_t *io_info);
H5_DLL herr_t H5D_istore_update_cache(H5D_t *dset, hid_t dxpl_id);
H5_DLL herr_t H5D_istore_dump_btree(H5F_t *f, hid_t dxpl_id, FILE *stream, unsigned ndims,
haddr_t addr);
H5_DLL herr_t H5D_istore_chunkmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],hsize_t down_chunks[] );
#ifdef H5D_ISTORE_DEBUG
H5_DLL herr_t H5D_istore_stats (H5D_t *dset, hbool_t headers);
#endif /* H5D_ISTORE_DEBUG */
H5_DLL ssize_t H5D_istore_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[], void *buf);
H5_DLL ssize_t H5D_istore_writevv(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[], const void *buf);
H5_DLL haddr_t H5D_istore_get_addr(const H5D_io_info_t *io_info,
struct H5D_istore_ud1_t *_udata);
H5_DLL herr_t H5D_istore_copy(H5F_t *f_src, H5O_layout_t *layout_src,
H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *src_dtype,
H5O_copy_t *cpy_info, H5O_pline_t *pline, hid_t dxpl_id);
/* Functions that operate on external file list (efl) storage */
H5_DLL ssize_t H5D_efl_readvv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
void *buf);
H5_DLL ssize_t H5D_efl_writevv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
const void *buf);
/* 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, hid_t dxpl_id);
H5_DLL herr_t H5D_fill_init(H5D_fill_buf_info_t *fb_info, void *caller_fill_buf,
hbool_t alloc_vl_during_refill,
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, hid_t dxpl_id);
H5_DLL herr_t H5D_fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts,
hid_t dxpl_id);
H5_DLL herr_t H5D_fill_release(H5D_fill_buf_info_t *fb_info);
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(H5D_io_info_t *io_info,
size_t nelmts, size_t elmt_size,
const struct H5S_t *file_space, const struct H5S_t *mem_space,
haddr_t addr,void *buf/*out*/);
/* MPI-IO function to read , it will select either regular or irregular read */
H5_DLL herr_t H5D_mpio_select_write(H5D_io_info_t *io_info,
size_t nelmts, size_t elmt_size,
const struct H5S_t *file_space, const struct H5S_t *mem_space,
haddr_t addr,const void *buf);
/* MPI-IO function to handle contiguous collective IO */
H5_DLL herr_t
H5D_contig_collective_io(H5D_io_info_t *io_info,
const H5S_t *file_space,const H5S_t *mem_space,
const void *_buf,hbool_t do_write);
/* MPI-IO function to handle chunked collective IO */
H5_DLL herr_t
H5D_chunk_collective_io(H5D_io_info_t * io_info,fm_map *fm, const void*buf,
hbool_t do_write);
/* 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 *mem_space,
const H5S_t *file_space, const H5T_path_t *tpath);
#ifndef H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS
H5_DLL herr_t H5D_mpio_chunk_adjust_iomode(H5D_io_info_t *io_info,const fm_map *fm);
#endif /* H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS */
#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);
#endif /* H5D_TESTING */
#endif /*_H5Dpkg_H*/
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