/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Programmer: Quincey Koziol * 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 */ /* Cache some frequently accessed values from the DCPL */ H5O_efl_t efl; /* External file list information */ H5D_alloc_time_t alloc_time; /* Dataset allocation time */ H5D_fill_time_t fill_time; /* Dataset fill value writing time */ H5O_fill_t fill; /* Dataset fill value information */ /* 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; /*****************************/ /* Package Private Variables */ /*****************************/ extern H5D_dxpl_cache_t H5D_def_dxpl_cache; /******************************/ /* Package Private Prototypes */ /******************************/ 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 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_prune_by_extent(const H5D_io_info_t *io_info); 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); #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*/