tcl.git - Tcl is a high-level, general-purpose, interpreted, dynamic programming language. It was designed with the goal of being very simple but powerful.

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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@hdfgroup.org> * Tuesday, January 27, 2009 * * Purpose: Extensible array indexed (chunked) I/O functions. The chunks * are given a single-dimensional index which is used as the * offset in an extensible array that maps a chunk coordinate to * a disk address. * */ /****************/ /* Module Setup */ /****************/ #define H5D_PACKAGE /*suppress error about including H5Dpkg */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #include "H5EAprivate.h" /* Extensible arrays */ #include "H5FLprivate.h" /* Free Lists */ #include "H5MFprivate.h" /* File space management */ #include "H5Vprivate.h" /* Vector functions */ /****************/ /* Local Macros */ /****************/ /* Value to fill unset array elements with */ #define H5D_EARRAY_FILL HADDR_UNDEF #define H5D_EARRAY_FILT_FILL {HADDR_UNDEF, 0, 0} /******************/ /* Local Typedefs */ /******************/ /* Extensible array create/open user data */ typedef struct H5D_earray_ctx_ud_t { const H5F_t *f; /* Pointer to file info */ uint32_t chunk_size; /* Size of chunk (bytes) */ } H5D_earray_ctx_ud_t; /* Extensible array callback context */ typedef struct H5D_earray_ctx_t { size_t file_addr_len; /* Size of addresses in the file (bytes) */ size_t chunk_size_len; /* Size of chunk sizes in the file (bytes) */ } H5D_earray_ctx_t; /* User data for chunk callbacks */ typedef struct H5D_earray_ud_t { H5F_t *f; /* File pointer for operation */ hid_t dxpl_id; /* DXPL ID for operation */ } H5D_earray_ud_t; /* Native extensible array element for chunks w/filters */ typedef struct H5D_earray_filt_elmt_t { haddr_t addr; /* Address of chunk */ uint32_t nbytes; /* Size of chunk (in file) */ uint32_t filter_mask; /* Excluded filters for chunk */ } H5D_earray_filt_elmt_t; /********************/ /* Local Prototypes */ /********************/ /* Extensible array class callbacks for chunks w/o filters */ static void *H5D_earray_crt_context(void *udata); static herr_t H5D_earray_dst_context(void *ctx); static herr_t H5D_earray_fill(void *nat_blk, size_t nelmts); static herr_t H5D_earray_encode(void *raw, const void *elmt, size_t nelmts, void *ctx); static herr_t H5D_earray_decode(const void *raw, void *elmt, size_t nelmts, void *ctx); static herr_t H5D_earray_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void *elmt); /* Extensible array class callbacks for chunks w/filters */ /* (some shared with callbacks for chunks w/o filters) */ static herr_t H5D_earray_filt_fill(void *nat_blk, size_t nelmts); static herr_t H5D_earray_filt_encode(void *raw, const void *elmt, size_t nelmts, void *ctx); static herr_t H5D_earray_filt_decode(const void *raw, void *elmt, size_t nelmts, void *ctx); static herr_t H5D_earray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void *elmt); /* Chunked layout indexing callbacks */ static herr_t H5D_earray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t *space, haddr_t dset_ohdr_addr); static herr_t H5D_earray_idx_create(const H5D_chk_idx_info_t *idx_info); static hbool_t H5D_earray_idx_is_space_alloc(const H5O_storage_chunk_t *storage); static herr_t H5D_earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata); static herr_t H5D_earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata); static herr_t H5D_earray_idx_resize(H5O_layout_chunk_t *layout); static int H5D_earray_idx_iterate(const H5D_chk_idx_info_t *idx_info, H5D_chunk_cb_func_t chunk_cb, void *chunk_udata); static herr_t H5D_earray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata); static herr_t H5D_earray_idx_delete(const H5D_chk_idx_info_t *idx_info); static herr_t H5D_earray_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src, const H5D_chk_idx_info_t *idx_info_dst); static herr_t H5D_earray_idx_copy_shutdown(H5O_storage_chunk_t *storage_src, H5O_storage_chunk_t *storage_dst, hid_t dxpl_id); static herr_t H5D_earray_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *size); static herr_t H5D_earray_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr); static herr_t H5D_earray_idx_support(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata, H5AC_info_t *child_entry); static herr_t H5D_earray_idx_unsupport(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata, H5AC_info_t *child_entry); static herr_t H5D_earray_idx_dump(const H5O_storage_chunk_t *storage, FILE *stream); static herr_t H5D_earray_idx_dest(const H5D_chk_idx_info_t *idx_info); /*********************/ /* Package Variables */ /*********************/ /* Extensible array indexed chunk I/O ops */ const H5D_chunk_ops_t H5D_COPS_EARRAY[1] = {{ TRUE, /* Extensible array indices support SWMR access */ H5D_earray_idx_init, H5D_earray_idx_create, H5D_earray_idx_is_space_alloc, H5D_earray_idx_insert, H5D_earray_idx_get_addr, H5D_earray_idx_resize, H5D_earray_idx_iterate, H5D_earray_idx_remove, H5D_earray_idx_delete, H5D_earray_idx_copy_setup, H5D_earray_idx_copy_shutdown, H5D_earray_idx_size, H5D_earray_idx_reset, H5D_earray_idx_support, H5D_earray_idx_unsupport, H5D_earray_idx_dump, H5D_earray_idx_dest }}; /*****************************/ /* Library Private Variables */ /*****************************/ /*******************/ /* Local Variables */ /*******************/ /* Extensible array class callbacks for dataset chunks w/o filters */ const H5EA_class_t H5EA_CLS_CHUNK[1]={{ H5EA_CLS_CHUNK_ID, /* Type of extensible array */ sizeof(haddr_t), /* Size of native element */ H5D_earray_crt_context, /* Create context */ H5D_earray_dst_context, /* Destroy context */ H5D_earray_fill, /* Fill block of missing elements callback */ H5D_earray_encode, /* Element encoding callback */ H5D_earray_decode, /* Element decoding callback */ H5D_earray_debug /* Element debugging callback */ }}; /* Extensible array class callbacks for dataset chunks w/filters */ const H5EA_class_t H5EA_CLS_FILT_CHUNK[1]={{ H5EA_CLS_FILT_CHUNK_ID, /* Type of extensible array */ sizeof(H5D_earray_filt_elmt_t), /* Size of native element */ H5D_earray_crt_context, /* Create context */ H5D_earray_dst_context, /* Destroy context */ H5D_earray_filt_fill, /* Fill block of missing elements callback */ H5D_earray_filt_encode, /* Element encoding callback */ H5D_earray_filt_decode, /* Element decoding callback */ H5D_earray_filt_debug /* Element debugging callback */ }}; /* Declare a free list to manage the H5D_earray_ctx_t struct */ H5FL_DEFINE_STATIC(H5D_earray_ctx_t); /*------------------------------------------------------------------------- * Function: H5D_earray_crt_context * * Purpose: Create context for callbacks * * Return: Success: non-NULL * Failure: NULL * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static void * H5D_earray_crt_context(void *_udata) { H5D_earray_ctx_t *ctx; /* Extensible array callback context */ H5D_earray_ctx_ud_t *udata = (H5D_earray_ctx_ud_t *)_udata; /* User data for extensible array context */ void *ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_crt_context) /* Sanity checks */ HDassert(udata); HDassert(udata->f); HDassert(udata->chunk_size > 0); /* Allocate new context structure */ if(NULL == (ctx = H5FL_MALLOC(H5D_earray_ctx_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate extensible array client callback context") /* Initialize the context */ ctx->file_addr_len = H5F_SIZEOF_ADDR(udata->f); /* Compute the size required for encoding the size of a chunk, allowing * for an extra byte, in case the filter makes the chunk larger. */ ctx->chunk_size_len = 1 + ((H5V_log2_gen(udata->chunk_size) + 8) / 8); if(ctx->chunk_size_len > 8) ctx->chunk_size_len = 8; /* Set return value */ ret_value = ctx; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_crt_context() */ /*------------------------------------------------------------------------- * Function: H5D_earray_dst_context * * Purpose: Destroy context for callbacks * * Return: Success: non-NULL * Failure: NULL * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_dst_context(void *_ctx) { H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_dst_context) /* Sanity checks */ HDassert(ctx); /* Release context structure */ ctx = H5FL_FREE(H5D_earray_ctx_t, ctx); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_dst_context() */ /*------------------------------------------------------------------------- * Function: H5D_earray_fill * * Purpose: Fill "missing elements" in block of elements * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Tuesday, January 27, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_fill(void *nat_blk, size_t nelmts) { haddr_t fill_val = H5D_EARRAY_FILL; /* Value to fill elements with */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_fill) /* Sanity checks */ HDassert(nat_blk); HDassert(nelmts); H5V_array_fill(nat_blk, &fill_val, H5EA_CLS_CHUNK->nat_elmt_size, nelmts); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_fill() */ /*------------------------------------------------------------------------- * Function: H5D_earray_encode * * Purpose: Encode an element from "native" to "raw" form * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Tuesday, January 27, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_encode(void *raw, const void *_elmt, size_t nelmts, void *_ctx) { H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */ const haddr_t *elmt = (const haddr_t *)_elmt; /* Convenience pointer to native elements */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_encode) /* Sanity checks */ HDassert(raw); HDassert(elmt); HDassert(nelmts); HDassert(ctx); /* Encode native elements into raw elements */ while(nelmts) { /* Encode element */ /* (advances 'raw' pointer) */ H5F_addr_encode_len(ctx->file_addr_len, (uint8_t **)&raw, *elmt); /* Advance native element pointer */ elmt++; /* Decrement # of elements to encode */ nelmts--; } /* end while */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_encode() */ /*------------------------------------------------------------------------- * Function: H5D_earray_decode * * Purpose: Decode an element from "raw" to "native" form * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_decode(const void *_raw, void *_elmt, size_t nelmts, void *_ctx) { H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */ haddr_t *elmt = (haddr_t *)_elmt; /* Convenience pointer to native elements */ const uint8_t *raw = (const uint8_t *)_raw; /* Convenience pointer to raw elements */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_decode) /* Sanity checks */ HDassert(raw); HDassert(elmt); HDassert(nelmts); /* Decode raw elements into native elements */ while(nelmts) { /* Decode element */ /* (advances 'raw' pointer) */ H5F_addr_decode_len(ctx->file_addr_len, &raw, elmt); /* Advance native element pointer */ elmt++; /* Decrement # of elements to decode */ nelmts--; } /* end while */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_decode() */ /*------------------------------------------------------------------------- * Function: H5D_earray_debug * * Purpose: Display an element for debugging * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void *elmt) { char temp_str[128]; /* Temporary string, for formatting */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_debug) /* Sanity checks */ HDassert(stream); HDassert(elmt); /* Print element */ sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, temp_str, *(const haddr_t *)elmt); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_debug() */ /*------------------------------------------------------------------------- * Function: H5D_earray_filt_fill * * Purpose: Fill "missing elements" in block of elements * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_filt_fill(void *nat_blk, size_t nelmts) { H5D_earray_filt_elmt_t fill_val = H5D_EARRAY_FILT_FILL; /* Value to fill elements with */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_filt_fill) /* Sanity checks */ HDassert(nat_blk); HDassert(nelmts); HDassert(sizeof(fill_val) == H5EA_CLS_FILT_CHUNK->nat_elmt_size); H5V_array_fill(nat_blk, &fill_val, H5EA_CLS_FILT_CHUNK->nat_elmt_size, nelmts); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_filt_fill() */ /*------------------------------------------------------------------------- * Function: H5D_earray_filt_encode * * Purpose: Encode an element from "native" to "raw" form * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_filt_encode(void *_raw, const void *_elmt, size_t nelmts, void *_ctx) { H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */ uint8_t *raw = (uint8_t *)_raw; /* Convenience pointer to raw elements */ const H5D_earray_filt_elmt_t *elmt = (const H5D_earray_filt_elmt_t *)_elmt; /* Convenience pointer to native elements */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_filt_encode) /* Sanity checks */ HDassert(raw); HDassert(elmt); HDassert(nelmts); HDassert(ctx); /* Encode native elements into raw elements */ while(nelmts) { /* Encode element */ /* (advances 'raw' pointer) */ H5F_addr_encode_len(ctx->file_addr_len, &raw, elmt->addr); UINT64ENCODE_VAR(raw, elmt->nbytes, ctx->chunk_size_len); UINT32ENCODE(raw, elmt->filter_mask); /* Advance native element pointer */ elmt++; /* Decrement # of elements to encode */ nelmts--; } /* end while */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_filt_encode() */ /*------------------------------------------------------------------------- * Function: H5D_earray_filt_decode * * Purpose: Decode an element from "raw" to "native" form * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_filt_decode(const void *_raw, void *_elmt, size_t nelmts, void *_ctx) { H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */ H5D_earray_filt_elmt_t *elmt = (H5D_earray_filt_elmt_t *)_elmt; /* Convenience pointer to native elements */ const uint8_t *raw = (const uint8_t *)_raw; /* Convenience pointer to raw elements */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_filt_decode) /* Sanity checks */ HDassert(raw); HDassert(elmt); HDassert(nelmts); /* Decode raw elements into native elements */ while(nelmts) { /* Decode element */ /* (advances 'raw' pointer) */ H5F_addr_decode_len(ctx->file_addr_len, &raw, &elmt->addr); UINT64DECODE_VAR(raw, elmt->nbytes, ctx->chunk_size_len); UINT32DECODE(raw, elmt->filter_mask); /* Advance native element pointer */ elmt++; /* Decrement # of elements to decode */ nelmts--; } /* end while */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_filt_decode() */ /*------------------------------------------------------------------------- * Function: H5D_earray_filt_debug * * Purpose: Display an element for debugging * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void *_elmt) { const H5D_earray_filt_elmt_t *elmt = (const H5D_earray_filt_elmt_t *)_elmt; /* Convenience pointer to native elements */ char temp_str[128]; /* Temporary string, for formatting */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_filt_debug) /* Sanity checks */ HDassert(stream); HDassert(elmt); /* Print element */ sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s {%a, %u, %0x}\n", indent, "", fwidth, temp_str, elmt->addr, elmt->nbytes, elmt->filter_mask); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_filt_debug() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_depend * * Purpose: Create flush dependency between extensible array and dataset's * object header. * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Tuesday, June 2, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_depend(const H5D_chk_idx_info_t *idx_info) { H5O_loc_t oloc; /* Temporary object header location for dataset */ H5O_t *oh = NULL; /* Dataset's object header */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_depend) /* Check args */ HDassert(idx_info); HDassert(idx_info->f); HDassert(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->layout->idx_type); HDassert(idx_info->storage); HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->storage->idx_type); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(idx_info->storage->u.earray.ea); /* Set up object header location for dataset */ H5O_loc_reset(&oloc); oloc.file = idx_info->f; oloc.addr = idx_info->storage->u.earray.dset_ohdr_addr; /* Pin the dataset's object header */ if(NULL == (oh = H5O_pin(&oloc, idx_info->dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Make the extensible array a child flush dependency of the dataset's object header */ if(H5EA_depend((H5AC_info_t *)oh, idx_info->storage->u.earray.ea) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL, "unable to create flush dependency on object header") done: /* Unpin the dataset's object header */ if(oh && H5O_unpin(&oloc, oh) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_depend() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_undepend * * Purpose: Remove flush dependency between extensible array and dataset's * object header. * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Tuesday, June 2, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_undepend(const H5D_chk_idx_info_t *idx_info) { H5O_loc_t oloc; /* Temporary object header location for dataset */ H5O_t *oh = NULL; /* Dataset's object header */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_undepend) /* Check args */ HDassert(idx_info); HDassert(idx_info->f); HDassert(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->layout->idx_type); HDassert(idx_info->storage); HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->storage->idx_type); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(idx_info->storage->u.earray.ea); /* Set up object header location for dataset */ H5O_loc_reset(&oloc); oloc.file = idx_info->f; oloc.addr = idx_info->storage->u.earray.dset_ohdr_addr; /* Pin the dataset's object header */ if(NULL == (oh = H5O_pin(&oloc, idx_info->dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Remove the extensible array as a child flush dependency of the dataset's object header */ if(H5EA_undepend((H5AC_info_t *)oh, idx_info->storage->u.earray.ea) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTUNDEPEND, FAIL, "unable to remove flush dependency on object header") done: /* Unpin the dataset's object header */ if(oh && H5O_unpin(&oloc, oh) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_undepend() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_open * * Purpose: Opens an existing extensible array. * * Note: This information is passively initialized from each index * operation callback because those abstract chunk index operations * are designed to work with the v1 B-tree chunk indices also, * which don't require an 'open' for the data structure. * * Return: Success: non-negative * Failure: negative * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_open(const H5D_chk_idx_info_t *idx_info) { H5D_earray_ctx_ud_t udata; /* User data for extensible array open call */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_open) /* Check args */ HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->layout->idx_type); HDassert(idx_info->storage); HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->storage->idx_type); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(NULL == idx_info->storage->u.earray.ea); /* Set up the user data */ udata.f = idx_info->f; udata.chunk_size = idx_info->layout->size; /* Open the extensible array for the chunk index */ if(NULL == (idx_info->storage->u.earray.ea = H5EA_open(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &udata))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open extensible array") /* Check for SWMR writes to the file */ if(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE) { if(H5D_earray_idx_depend(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL, "unable to create flush dependency on object header") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_open() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_init * * Purpose: Initialize the indexing information for a dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Wednesday, May 27, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t *space, haddr_t dset_ohdr_addr) { hsize_t max_dims[H5O_LAYOUT_NDIMS]; /* Max. size of dataset dimensions */ int unlim_dim; /* Rank of the dataset's unlimited dimension */ int sndims; /* Rank of dataspace */ unsigned ndims; /* Rank of dataspace */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_init) /* Check args */ HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(space); HDassert(H5F_addr_defined(dset_ohdr_addr)); /* Get the dim info for dataset */ if((sndims = H5S_get_simple_extent_dims(space, NULL, max_dims)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace dimensions") H5_ASSIGN_OVERFLOW(ndims, sndims, int, unsigned); /* Find the rank of the unlimited dimension */ unlim_dim = (-1); for(u = 0; u < ndims; u++) { /* Check for unlimited dimension */ if(H5S_UNLIMITED == max_dims[u]) { /* Check if we've already found an unlimited dimension */ if(unlim_dim >= 0) HGOTO_ERROR(H5E_DATASET, H5E_ALREADYINIT, FAIL, "already found unlimited dimension") /* Set the unlimited dimension */ unlim_dim = (int)u; } /* end if */ } /* end for */ /* Check if we didn't find an unlimited dimension */ if(unlim_dim < 0) HGOTO_ERROR(H5E_DATASET, H5E_UNINITIALIZED, FAIL, "didn't find unlimited dimension") /* Set the unlimited dimension for the layout's future use */ idx_info->layout->u.earray.unlim_dim = (unsigned)unlim_dim; /* Store the dataset's object header address for later */ idx_info->storage->u.earray.dset_ohdr_addr = dset_ohdr_addr; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_init() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_create * * Purpose: Creates a new indexed-storage extensible array and initializes * the layout struct with information about the storage. The * struct should be immediately written to the object header. * * This function must be called before passing LAYOUT to any of * the other indexed storage functions! * * Return: Non-negative on success (with the LAYOUT argument initialized * and ready to write to an object header). Negative on failure. * * Programmer: Quincey Koziol * Tuesday, January 27, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_create(const H5D_chk_idx_info_t *idx_info) { H5EA_create_t cparam; /* Extensible array creation parameters */ H5D_earray_ctx_ud_t udata; /* User data for extensible array create call */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_create) /* Check args */ HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(!H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(NULL == idx_info->storage->u.earray.ea); /* General parameters */ if(idx_info->pline->nused > 0) { unsigned chunk_size_len; /* Size of encoded chunk size */ /* Compute the size required for encoding the size of a chunk, allowing * for an extra byte, in case the filter makes the chunk larger. */ chunk_size_len = 1 + ((H5V_log2_gen(idx_info->layout->size) + 8) / 8); if(chunk_size_len > 8) chunk_size_len = 8; cparam.cls = H5EA_CLS_FILT_CHUNK; cparam.raw_elmt_size = (uint8_t)(H5F_SIZEOF_ADDR(idx_info->f) + chunk_size_len + 4); } /* end if */ else { cparam.cls = H5EA_CLS_CHUNK; cparam.raw_elmt_size = (uint8_t)H5F_SIZEOF_ADDR(idx_info->f); } /* end else */ cparam.max_nelmts_bits = idx_info->layout->u.earray.cparam.max_nelmts_bits; HDassert(cparam.max_nelmts_bits > 0); cparam.idx_blk_elmts = idx_info->layout->u.earray.cparam.idx_blk_elmts; HDassert(cparam.idx_blk_elmts > 0); cparam.sup_blk_min_data_ptrs = idx_info->layout->u.earray.cparam.sup_blk_min_data_ptrs; HDassert(cparam.sup_blk_min_data_ptrs > 0); cparam.data_blk_min_elmts = idx_info->layout->u.earray.cparam.data_blk_min_elmts; HDassert(cparam.data_blk_min_elmts > 0); cparam.max_dblk_page_nelmts_bits = idx_info->layout->u.earray.cparam.max_dblk_page_nelmts_bits; HDassert(cparam.max_dblk_page_nelmts_bits > 0); /* Set up the user data */ udata.f = idx_info->f; udata.chunk_size = idx_info->layout->size; /* Create the extensible array for the chunk index */ if(NULL == (idx_info->storage->u.earray.ea = H5EA_create(idx_info->f, idx_info->dxpl_id, &cparam, &udata))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create extensible array") /* Get the address of the extensible array in file */ if(H5EA_get_addr(idx_info->storage->u.earray.ea, &(idx_info->storage->idx_addr)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query extensible array address") /* Check for SWMR writes to the file */ if(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE) { if(H5D_earray_idx_depend(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL, "unable to create flush dependency on object header") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_create() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_is_space_alloc * * Purpose: Query if space is allocated for index method * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static hbool_t H5D_earray_idx_is_space_alloc(const H5O_storage_chunk_t *storage) { hbool_t ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_idx_is_space_alloc) /* Check args */ HDassert(storage); /* Set return value */ ret_value = (hbool_t)H5F_addr_defined(storage->idx_addr); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_is_space_alloc() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_insert * * Purpose: Create the chunk it if it doesn't exist, or reallocate the * chunk if its size changed. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata) { H5EA_t *ea; /* Pointer to extensible array structure */ hsize_t idx; /* Array index of chunk */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_insert) HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(udata); /* Check if the extensible array is open yet */ if(NULL == idx_info->storage->u.earray.ea) { /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") } /* end if */ /* Set convenience pointer to extensible array structure */ ea = idx_info->storage->u.earray.ea; /* Check for unlimited dim. not being the slowest-changing dim. */ if(idx_info->layout->u.earray.unlim_dim > 0) { hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ unsigned ndims = (idx_info->layout->ndims - 1); /* Number of dimensions */ /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->common.offset, ndims * sizeof(udata->common.offset[0])); H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { /* Calculate the index of this chunk */ if(H5V_chunk_index((idx_info->layout->ndims - 1), udata->common.offset, idx_info->layout->dim, idx_info->layout->down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end else */ /* Check for filters on chunks */ if(idx_info->pline->nused > 0) { H5D_earray_filt_elmt_t elmt; /* Extensible array element */ unsigned allow_chunk_size_len; /* Allowed size of encoded chunk size */ unsigned new_chunk_size_len; /* Size of encoded chunk size */ hbool_t alloc_chunk = FALSE; /* Whether to allocate chunk */ /* Compute the size required for encoding the size of a chunk, allowing * for an extra byte, in case the filter makes the chunk larger. */ allow_chunk_size_len = 1 + ((H5V_log2_gen(idx_info->layout->size) + 8) / 8); if(allow_chunk_size_len > 8) allow_chunk_size_len = 8; /* Compute encoded size of chunk */ new_chunk_size_len = (H5V_log2_gen(udata->nbytes) + 8) / 8; if(new_chunk_size_len > 8) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "encoded chunk size is more than 8 bytes?!?") /* Check if the chunk became too large to be encoded */ if(new_chunk_size_len > allow_chunk_size_len) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk size can't be encoded") /* Get the information for the chunk */ if(H5EA_get(ea, idx_info->dxpl_id, idx, &elmt) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info") /* Check for previous chunk */ if(H5F_addr_defined(elmt.addr)) { /* Sanity check */ HDassert(!H5F_addr_defined(udata->addr) || H5F_addr_eq(udata->addr, elmt.addr)); /* Check for chunk being same size */ if(udata->nbytes != elmt.nbytes) { /* Release previous chunk */ H5_CHECK_OVERFLOW(elmt.nbytes, uint32_t, hsize_t); if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, elmt.addr, (hsize_t)elmt.nbytes) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk") elmt.addr = HADDR_UNDEF; alloc_chunk = TRUE; } /* end if */ else { /* Don't need to reallocate chunk, but send its address back up */ if(!H5F_addr_defined(udata->addr)) udata->addr = elmt.addr; } /* end else */ } /* end if */ else alloc_chunk = TRUE; /* Check if we need to allocate the chunk */ if(alloc_chunk) { H5_CHECK_OVERFLOW(udata->nbytes, uint32_t, hsize_t); udata->addr = H5MF_alloc(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, (hsize_t)udata->nbytes); if(!H5F_addr_defined(udata->addr)) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") /* Update the element information */ elmt.addr = udata->addr; elmt.nbytes = udata->nbytes; elmt.filter_mask = udata->filter_mask; /* Set the info for the chunk */ if(H5EA_set(ea, idx_info->dxpl_id, idx, &elmt) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk info") } /* end if */ } /* end if */ else { HDassert(!H5F_addr_defined(udata->addr)); HDassert(udata->nbytes == idx_info->layout->size); #ifndef NDEBUG { haddr_t addr = HADDR_UNDEF; /* Address of chunk in file */ /* Get the address for the chunk */ if(H5EA_get(ea, idx_info->dxpl_id, idx, &addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") HDassert(!H5F_addr_defined(addr)); } #endif /* NDEBUG */ /* * Allocate storage for the new chunk */ H5_CHECK_OVERFLOW(udata->nbytes, /*From: */uint32_t, /*To: */hsize_t); udata->addr = H5MF_alloc(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, (hsize_t)udata->nbytes); if(!H5F_addr_defined(udata->addr)) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "file allocation failed") /* Set the address for the chunk */ if(H5EA_set(ea, idx_info->dxpl_id, idx, &udata->addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk address") } /* end else */ HDassert(H5F_addr_defined(udata->addr)); done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_earray_idx_insert() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_get_addr * * Purpose: Get the file address of a chunk if file space has been * assigned. Save the retrieved information in the udata * supplied. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata) { H5EA_t *ea; /* Pointer to extensible array structure */ hsize_t idx; /* Array index of chunk */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_get_addr) HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(udata); /* Check if the extensible array is open yet */ if(NULL == idx_info->storage->u.earray.ea) { /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") } /* end if */ /* Set convenience pointer to extensible array structure */ ea = idx_info->storage->u.earray.ea; /* Check for unlimited dim. not being the slowest-changing dim. */ if(idx_info->layout->u.earray.unlim_dim > 0) { hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ unsigned ndims = (idx_info->layout->ndims - 1); /* Number of dimensions */ /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->common.offset, ndims * sizeof(udata->common.offset[0])); H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { /* Calculate the index of this chunk */ if(H5V_chunk_index((idx_info->layout->ndims - 1), udata->common.offset, idx_info->layout->dim, idx_info->layout->down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end else */ /* Check for filters on chunks */ if(idx_info->pline->nused > 0) { H5D_earray_filt_elmt_t elmt; /* Extensible array element */ /* Get the information for the chunk */ if(H5EA_get(ea, idx_info->dxpl_id, idx, &elmt) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info") /* Set the info for the chunk */ udata->addr = elmt.addr; udata->nbytes = elmt.nbytes; udata->filter_mask = elmt.filter_mask; } /* end if */ else { /* Get the address for the chunk */ if(H5EA_get(ea, idx_info->dxpl_id, idx, &udata->addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") /* Update the other (constant) information for the chunk */ udata->nbytes = idx_info->layout->size; udata->filter_mask = 0; } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_earray_idx_get_addr() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_resize * * Purpose: Calculate/setup the swizzled down chunk array, used for chunk * index calculations. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, July 23, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_resize(H5O_layout_chunk_t *layout) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_resize) /* Check args */ HDassert(layout); /* Set up the swizzled "down" chunk information */ if(layout->u.earray.unlim_dim > 0) { hsize_t swizzled_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of # of chunks in each dimension */ HDmemcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0])); H5V_swizzle_coords(swizzled_chunks, layout->u.earray.unlim_dim); /* Get the swizzled "down" sizes for each dimension */ if(H5V_array_down((layout->ndims - 1), swizzled_chunks, layout->u.earray.swizzled_down_chunks) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute swizzled 'down' chunk size value") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_resize() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_iterate * * Purpose: Iterate over the chunks in an index, making a callback * for each one. * * Note: This implementation is slow, particularly for sparse * extensible arrays, replace it with call to H5EA_iterate() * when that's available. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static int H5D_earray_idx_iterate(const H5D_chk_idx_info_t *idx_info, H5D_chunk_cb_func_t chunk_cb, void *chunk_udata) { H5EA_t *ea; /* Pointer to extensible array structure */ H5EA_stat_t ea_stat; /* Extensible array statistics */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_iterate) HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(chunk_cb); HDassert(chunk_udata); /* Check if the extensible array is open yet */ if(NULL == idx_info->storage->u.earray.ea) { /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") } /* end if */ /* Set convenience pointer to extensible array structure */ ea = idx_info->storage->u.earray.ea; /* Get the extensible array statistics */ if(H5EA_get_stats(ea, &ea_stat) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query extensible array statistics") /* Check if there are any array elements */ if(ea_stat.stored.max_idx_set > 0) { H5D_chunk_rec_t chunk_rec; /* Generic chunk record for callback */ hsize_t u; /* Local index variable */ /* Check for filters on chunks */ if(idx_info->pline->nused > 0) { /* Prepare common fields of chunk record for callback */ HDmemset(&chunk_rec, 0, sizeof(chunk_rec)); /* Loop over array elements */ /* (Note: this may be too simple for datasets with >1 dimension) */ for(u = 0; u < ea_stat.stored.max_idx_set; u++, chunk_rec.offset[0] += idx_info->layout->dim[0]) { H5D_earray_filt_elmt_t elmt; /* Extensible array element */ /* Get the info about the chunk for the index */ if(H5EA_get(ea, idx_info->dxpl_id, u, &elmt) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info") /* Check if chunk exists */ if(H5F_addr_defined(elmt.addr)) { /* Set chunk info for callback record */ chunk_rec.chunk_addr = elmt.addr; chunk_rec.nbytes = elmt.nbytes; chunk_rec.filter_mask = elmt.filter_mask; /* Make chunk callback */ if((ret_value = (*chunk_cb)(&chunk_rec, chunk_udata)) < 0) HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback"); } /* end if */ } /* end for */ } /* end if */ else { /* Prepare common fields of chunk record for callback */ HDmemset(&chunk_rec, 0, sizeof(chunk_rec)); chunk_rec.nbytes = idx_info->layout->size; chunk_rec.filter_mask = 0; /* Loop over array elements */ /* (Note: this may be too simple for datasets with >1 dimension) */ for(u = 0; u < ea_stat.stored.max_idx_set; u++, chunk_rec.offset[0] += idx_info->layout->dim[0]) { haddr_t addr; /* Chunk address */ /* Get the address of the chunk for the index */ if(H5EA_get(ea, idx_info->dxpl_id, u, &addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") /* Check if chunk exists */ if(H5F_addr_defined(addr)) { /* Set chunk address for callback record */ chunk_rec.chunk_addr = addr; /* Make chunk callback */ if((ret_value = (*chunk_cb)(&chunk_rec, chunk_udata)) < 0) HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback"); } /* end if */ } /* end for */ } /* end else */ } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_iterate() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_remove * * Purpose: Remove chunk from index. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata) { H5EA_t *ea; /* Pointer to extensible array structure */ hsize_t idx; /* Array index of chunk */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_remove) HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(udata); /* Check if the extensible array is open yet */ if(NULL == idx_info->storage->u.earray.ea) { /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") } /* end if */ /* Set convenience pointer to extensible array structure */ ea = idx_info->storage->u.earray.ea; /* Check for unlimited dim. not being the slowest-changing dim. */ if(idx_info->layout->u.earray.unlim_dim > 0) { hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ unsigned ndims = (idx_info->layout->ndims - 1); /* Number of dimensions */ /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->offset, ndims * sizeof(udata->offset[0])); H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { /* Calculate the index of this chunk */ if(H5V_chunk_index((idx_info->layout->ndims - 1), udata->offset, idx_info->layout->dim, idx_info->layout->down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end else */ /* Check for filters on chunks */ if(idx_info->pline->nused > 0) { H5D_earray_filt_elmt_t elmt; /* Extensible array element */ /* Get the info about the chunk for the index */ if(H5EA_get(ea, idx_info->dxpl_id, idx, &elmt) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info") /* Remove raw data chunk from file */ HDassert(H5F_addr_defined(elmt.addr)); H5_CHECK_OVERFLOW(elmt.nbytes, /*From: */uint32_t, /*To: */hsize_t); if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, elmt.addr, (hsize_t)elmt.nbytes) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk") /* Reset the info about the chunk for the index */ elmt.addr = HADDR_UNDEF; elmt.nbytes = 0; elmt.filter_mask = 0; if(H5EA_set(ea, idx_info->dxpl_id, idx, &elmt) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to reset chunk info") } /* end if */ else { haddr_t addr = HADDR_UNDEF; /* Chunk address */ /* Get the address of the chunk for the index */ if(H5EA_get(ea, idx_info->dxpl_id, idx, &addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") /* Remove raw data chunk from file */ HDassert(H5F_addr_defined(addr)); H5_CHECK_OVERFLOW(idx_info->layout->size, /*From: */uint32_t, /*To: */hsize_t); if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, addr, (hsize_t)idx_info->layout->size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk") /* Reset the address of the chunk for the index */ addr = HADDR_UNDEF; if(H5EA_set(ea, idx_info->dxpl_id, idx, &addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to reset chunk address") } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_earray_idx_remove() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_delete_cb * * Purpose: Delete space for chunk in file * * Return: Success: Non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static int H5D_earray_idx_delete_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { H5D_earray_ud_t *udata = (H5D_earray_ud_t *)_udata; /* User data for callback */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_delete_cb) /* Sanity checks */ HDassert(chunk_rec); HDassert(H5F_addr_defined(chunk_rec->chunk_addr)); HDassert(chunk_rec->nbytes > 0); HDassert(udata); HDassert(udata->f); /* Remove raw data chunk from file */ H5_CHECK_OVERFLOW(chunk_rec->nbytes, /*From: */uint32_t, /*To: */hsize_t); if(H5MF_xfree(udata->f, H5FD_MEM_DRAW, udata->dxpl_id, chunk_rec->chunk_addr, (hsize_t)chunk_rec->nbytes) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "unable to free chunk") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_delete_cb() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_delete * * Purpose: Delete index and raw data storage for entire dataset * (i.e. all chunks) * * Note: This implementation is slow, particularly for sparse * extensible arrays, replace it with call to H5EA_iterate() * when that's available. * * Return: Success: Non-negative * Failure: negative * * Programmer: Quincey Koziol * Thursday, January 29, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_delete(const H5D_chk_idx_info_t *idx_info) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_delete) /* Sanity checks */ HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); /* Check if the index data structure has been allocated */ if(H5F_addr_defined(idx_info->storage->idx_addr)) { H5D_earray_ud_t udata; /* User data for callback */ H5D_earray_ctx_ud_t ctx_udata; /* User data for extensible array open call */ /* Initialize user data for callback */ udata.f = idx_info->f; udata.dxpl_id = idx_info->dxpl_id; /* Iterate over the chunk addresses in the extensible array, deleting each chunk */ if(H5D_earray_idx_iterate(idx_info, H5D_earray_idx_delete_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk addresses") /* Close extensible array */ if(H5EA_close(idx_info->storage->u.earray.ea, idx_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array") idx_info->storage->u.earray.ea = NULL; /* Set up the context user data */ ctx_udata.f = idx_info->f; ctx_udata.chunk_size = idx_info->layout->size; /* Delete extensible array */ if(H5EA_delete(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &ctx_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk extensible array") idx_info->storage->idx_addr = HADDR_UNDEF; } /* end if */ else HDassert(NULL == idx_info->storage->u.earray.ea); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_delete() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_copy_setup * * Purpose: Set up any necessary information for copying chunks * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src, const H5D_chk_idx_info_t *idx_info_dst) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_copy_setup) /* Check args */ HDassert(idx_info_src); HDassert(idx_info_src->f); HDassert(idx_info_src->pline); HDassert(idx_info_src->layout); HDassert(idx_info_src->storage); HDassert(idx_info_dst); HDassert(idx_info_dst->f); HDassert(idx_info_dst->pline); HDassert(idx_info_dst->layout); HDassert(idx_info_dst->storage); HDassert(!H5F_addr_defined(idx_info_dst->storage->idx_addr)); /* Check if the source extensible array is open yet */ if(NULL == idx_info_src->storage->u.earray.ea) { /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info_src) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") } /* end if */ /* Create the extensible array that describes chunked storage in the dest. file */ if(H5D_earray_idx_create(idx_info_dst) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") HDassert(H5F_addr_defined(idx_info_dst->storage->idx_addr)); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_copy_setup() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_copy_shutdown * * Purpose: Shutdown any information from copying chunks * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_copy_shutdown(H5O_storage_chunk_t *storage_src, H5O_storage_chunk_t *storage_dst, hid_t dxpl_id) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_copy_shutdown) /* Check args */ HDassert(storage_src); HDassert(storage_src->u.earray.ea); HDassert(storage_dst); HDassert(storage_dst->u.earray.ea); /* Close extensible arrays */ if(H5EA_close(storage_src->u.earray.ea, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array") storage_src->u.earray.ea = NULL; if(H5EA_close(storage_dst->u.earray.ea, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array") storage_dst->u.earray.ea = NULL; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_copy_shutdown() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_size * * Purpose: Retrieve the amount of index storage for chunked dataset * * Return: Success: Non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size) { H5EA_t *ea; /* Pointer to extensible array structure */ H5EA_stat_t ea_stat; /* Extensible array statistics */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_earray_idx_size, FAIL) /* Check args */ HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->pline); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); HDassert(index_size); /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") /* Set convenience pointer to extensible array structure */ ea = idx_info->storage->u.earray.ea; /* Get the extensible array statistics */ if(H5EA_get_stats(ea, &ea_stat) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query extensible array statistics") /* Set the size of the extensible array */ *index_size = ea_stat.computed.hdr_size + ea_stat.computed.index_blk_size + ea_stat.stored.super_blk_size + ea_stat.stored.data_blk_size; done: if(idx_info->storage->u.earray.ea) { if(H5EA_close(idx_info->storage->u.earray.ea, idx_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array") idx_info->storage->u.earray.ea = NULL; } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_size() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_reset * * Purpose: Reset indexing information. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * * Modifications: * Vailin Choi; April 2009 * Reset address of the chunked storage index if RESET_ADDR is set * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr) { FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_idx_reset) /* Check args */ HDassert(storage); /* Reset index info */ if(reset_addr) { storage->idx_addr = HADDR_UNDEF; storage->u.earray.dset_ohdr_addr = HADDR_UNDEF; } /* end if */ storage->u.earray.ea = NULL; FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_idx_reset() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_support * * Purpose: Create a dependency between a chunk [proxy] and the index * metadata that contains the record for the chunk. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, May 21, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_support(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata, H5AC_info_t *child_entry) { H5EA_t *ea; /* Pointer to extensible array structure */ hsize_t idx; /* Array index of chunk */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_support) /* Check args */ HDassert(idx_info); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(udata); HDassert(child_entry); /* Check if the extensible array is open yet */ if(NULL == idx_info->storage->u.earray.ea) { /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") } /* end if */ /* Set convenience pointer to extensible array structure */ ea = idx_info->storage->u.earray.ea; /* Check for unlimited dim. not being the slowest-changing dim. */ if(idx_info->layout->u.earray.unlim_dim > 0) { hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ unsigned ndims = (idx_info->layout->ndims - 1); /* Number of dimensions */ /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->offset, ndims * sizeof(udata->offset[0])); H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { /* Calculate the index of this chunk */ if(H5V_chunk_index((idx_info->layout->ndims - 1), udata->offset, idx_info->layout->dim, idx_info->layout->down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end else */ /* Create flush dependency between the child_entry and the piece of metadata * in the extensible array that contains the entry for this chunk. */ if(H5EA_support(ea, idx_info->dxpl_id, idx, child_entry) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL, "unable to create flush dependency on extensible array metadata") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_support() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_unsupport * * Purpose: Remove a dependency between a chunk [proxy] and the index * metadata that contains the record for the chunk. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, May 21, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_unsupport(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata, H5AC_info_t *child_entry) { H5EA_t *ea; /* Pointer to extensible array structure */ hsize_t idx; /* Array index of chunk */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_unsupport) /* Check args */ HDassert(idx_info); HDassert(idx_info->layout); HDassert(idx_info->storage); HDassert(udata); HDassert(child_entry); /* Check if the extensible array is open yet */ if(NULL == idx_info->storage->u.earray.ea) { /* Open the extensible array in file */ if(H5D_earray_idx_open(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array") } /* end if */ /* Set convenience pointer to extensible array structure */ ea = idx_info->storage->u.earray.ea; /* Check for unlimited dim. not being the slowest-changing dim. */ if(idx_info->layout->u.earray.unlim_dim > 0) { hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ unsigned ndims = (idx_info->layout->ndims - 1); /* Number of dimensions */ /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->offset, ndims * sizeof(udata->offset[0])); H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { /* Calculate the index of this chunk */ if(H5V_chunk_index((idx_info->layout->ndims - 1), udata->offset, idx_info->layout->dim, idx_info->layout->down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end else */ /* Remove flush dependency between the child_entry and the piece of metadata * in the extensible array that contains the entry for this chunk. */ if(H5EA_unsupport(ea, idx_info->dxpl_id, idx, child_entry) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTUNDEPEND, FAIL, "unable to remove flush dependency on extensible array metadata") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_unsupport() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_dump * * Purpose: Dump indexing information to a stream. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_dump(const H5O_storage_chunk_t *storage, FILE *stream) { FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_idx_dump) /* Check args */ HDassert(storage); HDassert(stream); HDfprintf(stream, " Address: %a\n", storage->idx_addr); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_earray_idx_dump() */ /*------------------------------------------------------------------------- * Function: H5D_earray_idx_dest * * Purpose: Release indexing information in memory. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Saturday, January 31, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D_earray_idx_dest(const H5D_chk_idx_info_t *idx_info) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_dest) /* Check args */ HDassert(idx_info); HDassert(idx_info->f); HDassert(idx_info->storage); /* Check if the extensible array is open */ if(idx_info->storage->u.earray.ea) { /* Check for SWMR writes to the file */ if(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE) { /* Sanity check */ HDassert(H5F_addr_defined(idx_info->storage->u.earray.dset_ohdr_addr)); /* Remove flush dependency between extensible array and dataset' object header */ if(H5D_earray_idx_undepend(idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTUNDEPEND, FAIL, "unable to remove flush dependency on object header") } /* end if */ /* Close extensible array */ if(H5EA_close(idx_info->storage->u.earray.ea, idx_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array") idx_info->storage->u.earray.ea = NULL; } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_dest() */


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