diff options
| -rw-r--r-- | MANIFEST | 2 | ||||
| -rw-r--r-- | src/CMakeLists.txt | 2 | ||||
| -rw-r--r-- | src/H5B2.c | 36 | ||||
| -rw-r--r-- | src/H5B2private.h | 3 | ||||
| -rw-r--r-- | src/H5Dbtree2.c | 1491 | ||||
| -rw-r--r-- | src/H5Dchunk.c | 6 | ||||
| -rw-r--r-- | src/H5Dearray.c | 1740 | ||||
| -rw-r--r-- | src/H5Dint.c | 5 | ||||
| -rw-r--r-- | src/H5Dlayout.c | 140 | ||||
| -rw-r--r-- | src/H5Dpkg.h | 27 | ||||
| -rw-r--r-- | src/H5Dpublic.h | 4 | ||||
| -rw-r--r-- | src/H5Dtest.c | 41 | ||||
| -rw-r--r-- | src/H5EA.c | 88 | ||||
| -rw-r--r-- | src/H5EAprivate.h | 14 | ||||
| -rw-r--r-- | src/H5Olayout.c | 97 | ||||
| -rw-r--r-- | src/H5Oprivate.h | 47 | ||||
| -rw-r--r-- | src/H5VMprivate.h | 16 | ||||
| -rw-r--r-- | src/Makefile.am | 10 | ||||
| -rw-r--r-- | test/dsets.c | 25 |
19 files changed, 3773 insertions, 21 deletions
@@ -498,11 +498,13 @@ ./src/H5CSprivate.h ./src/H5D.c ./src/H5Dbtree.c +./src/H5Dbtree2.c ./src/H5Dchunk.c ./src/H5Dcompact.c ./src/H5Dcontig.c ./src/H5Ddbg.c ./src/H5Ddeprec.c +./src/H5Dearray.c ./src/H5Defl.c ./src/H5Dfill.c ./src/H5Dint.c diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 1e0061f..f65c77f 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -103,11 +103,13 @@ IDE_GENERATED_PROPERTIES ("H5CS" "${H5CS_HDRS}" "${H5CS_SRCS}" ) set (H5D_SRCS ${HDF5_SRC_DIR}/H5D.c ${HDF5_SRC_DIR}/H5Dbtree.c + ${HDF5_SRC_DIR}/H5Dbtree2.c ${HDF5_SRC_DIR}/H5Dchunk.c ${HDF5_SRC_DIR}/H5Dcompact.c ${HDF5_SRC_DIR}/H5Dcontig.c ${HDF5_SRC_DIR}/H5Ddbg.c ${HDF5_SRC_DIR}/H5Ddeprec.c + ${HDF5_SRC_DIR}/H5Dearray.c ${HDF5_SRC_DIR}/H5Defl.c ${HDF5_SRC_DIR}/H5Dfill.c ${HDF5_SRC_DIR}/H5Dint.c @@ -87,6 +87,8 @@ extern const H5B2_class_t H5G_BT2_CORDER[1]; extern const H5B2_class_t H5SM_INDEX[1]; extern const H5B2_class_t H5A_BT2_NAME[1]; extern const H5B2_class_t H5A_BT2_CORDER[1]; +extern const H5B2_class_t H5D_BT2[1]; +extern const H5B2_class_t H5D_BT2_FILT[1]; extern const H5B2_class_t H5B2_TEST2[1]; const H5B2_class_t *const H5B2_client_class_g[] = { @@ -100,7 +102,9 @@ const H5B2_class_t *const H5B2_client_class_g[] = { H5SM_INDEX, /* 7 - H5B2_SOHM_INDEX_ID */ H5A_BT2_NAME, /* 8 - H5B2_ATTR_DENSE_NAME_ID */ H5A_BT2_CORDER, /* 9 - H5B2_ATTR_DENSE_CORDER_ID */ - H5B2_TEST2, /* 10 - H5B2_TEST_ID */ + H5D_BT2, /* 10 - H5B2_CDSET_ID */ + H5D_BT2_FILT, /* 11 - H5B2_CDSET_FILT_ID */ + H5B2_TEST2 /* 12 - H5B2_TEST_ID */ }; @@ -1445,3 +1449,33 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5B2_delete() */ + +/*------------------------------------------------------------------------- + * Function: H5B2_patch_file + * + * Purpose: Patch the top-level file pointer contained in bt2 + * to point to idx_info->f if they are different. + * This is possible because the file pointer in bt2 can be + * closed out if bt2 remains open. + * + * Return: SUCCEED + * + *------------------------------------------------------------------------- + */ +herr_t +H5B2_patch_file(H5B2_t *bt2, H5F_t *f) +{ + FUNC_ENTER_NOAPI_NOINIT_NOERR + + /* + * Check arguments. + */ + HDassert(bt2); + HDassert(f); + + if(bt2->f != f || bt2->hdr->f != f) + bt2->f = bt2->hdr->f = f; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5B2_patch_file() */ + diff --git a/src/H5B2private.h b/src/H5B2private.h index b509869..3caf41f 100644 --- a/src/H5B2private.h +++ b/src/H5B2private.h @@ -54,6 +54,8 @@ typedef enum H5B2_subid_t { H5B2_SOHM_INDEX_ID, /* B-tree is an index for shared object header messages */ H5B2_ATTR_DENSE_NAME_ID, /* B-tree is for indexing 'name' field for "dense" attribute storage on objects */ H5B2_ATTR_DENSE_CORDER_ID, /* B-tree is for indexing 'creation order' field for "dense" attribute storage on objects */ + H5B2_CDSET_ID, /* B-tree is for non-filtered chunked dataset storage w/ >1 unlim dims */ + H5B2_CDSET_FILT_ID, /* B-tree is for filtered chunked dataset storage w/ >1 unlim dims */ H5B2_TEST2_ID, /* Another B-tree is for testing (do not use for actual data) */ H5B2_NUM_BTREE_ID /* Number of B-tree IDs (must be last) */ } H5B2_subid_t; @@ -151,6 +153,7 @@ H5_DLL herr_t H5B2_size(H5B2_t *bt2, hid_t dxpl_id, H5_DLL herr_t H5B2_close(H5B2_t *bt2, hid_t dxpl_id); H5_DLL herr_t H5B2_delete(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *ctx_udata, H5B2_remove_t op, void *op_data); +H5_DLL herr_t H5B2_patch_file(H5B2_t *fa, H5F_t *f); /* Statistics routines */ H5_DLL herr_t H5B2_stat_info(H5B2_t *bt2, H5B2_stat_t *info); diff --git a/src/H5Dbtree2.c b/src/H5Dbtree2.c new file mode 100644 index 0000000..9de609f --- /dev/null +++ b/src/H5Dbtree2.c @@ -0,0 +1,1491 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * + * Purpose: v2 B-tree indexing for chunked datasets with > 1 unlimited dimensions. + * Each dataset chunk in the b-tree is identified by its dimensional offset. + * + */ + +/****************/ +/* Module Setup */ +/****************/ + +#include "H5Dmodule.h" /* This source code file is part of the H5D module */ + + +/***********/ +/* Headers */ +/***********/ +#include "H5private.h" /* Generic Functions */ +#include "H5Dpkg.h" /* Datasets */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5MFprivate.h" /* File space management */ +#include "H5VMprivate.h" /* Vector and array functions */ + + +/****************/ +/* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ +/* User data for creating callback context */ +typedef struct H5D_bt2_ctx_ud_t { + const H5F_t *f; /* Pointer to file info */ + uint32_t chunk_size; /* Size of chunk (bytes; for filtered object) */ + unsigned ndims; /* Number of dimensions */ + uint32_t *dim; /* Size of chunk in elements */ +} H5D_bt2_ctx_ud_t; + +/* The callback context */ +typedef struct H5D_bt2_ctx_t { + uint32_t chunk_size; /* Size of chunk (bytes; constant for unfiltered object) */ + size_t sizeof_addr; /* Size of file addresses in the file (bytes) */ + size_t chunk_size_len; /* Size of chunk sizes in the file (bytes) */ + unsigned ndims; /* Number of dimensions in chunk */ + uint32_t *dim; /* Size of chunk in elements */ +} H5D_bt2_ctx_t; + +/* User data for the chunk's removal callback routine */ +typedef struct H5D_bt2_remove_ud_t { + H5F_t *f; /* File pointer for operation */ + hid_t dxpl_id; /* DXPL ID for operation */ +} H5D_bt2_remove_ud_t; + +/* Callback info for iteration over chunks in v2 B-tree */ +typedef struct H5D_bt2_it_ud_t { + H5D_chunk_cb_func_t cb; /* Callback routine for the chunk */ + void *udata; /* User data for the chunk's callback routine */ +} H5D_bt2_it_ud_t; + +/* User data for compare callback */ +typedef struct H5D_bt2_ud_t { + H5D_chunk_rec_t rec; /* The record to search for */ + unsigned ndims; /* Number of dimensions for the chunked dataset */ +} H5D_bt2_ud_t; + + +/********************/ +/* Local Prototypes */ +/********************/ + +/* Shared v2 B-tree methods for indexing filtered and non-filtered chunked datasets */ +static void *H5D__bt2_crt_context(void *udata); +static herr_t H5D__bt2_dst_context(void *ctx); +static herr_t H5D__bt2_store(void *native, const void *udata); +static herr_t H5D__bt2_compare(const void *rec1, const void *rec2, int *result); + +/* v2 B-tree class for indexing non-filtered chunked datasets */ +static herr_t H5D__bt2_unfilt_encode(uint8_t *raw, const void *native, void *ctx); +static herr_t H5D__bt2_unfilt_decode(const uint8_t *raw, void *native, void *ctx); +static herr_t H5D__bt2_unfilt_debug(FILE *stream, int indent, int fwidth, + const void *record, const void *u_ctx); + +/* v2 B-tree class for indexing filtered chunked datasets */ +static herr_t H5D__bt2_filt_encode(uint8_t *raw, const void *native, void *ctx); +static herr_t H5D__bt2_filt_decode(const uint8_t *raw, void *native, void *ctx); +static herr_t H5D__bt2_filt_debug(FILE *stream, int indent, int fwidth, + const void *record, const void *u_ctx); + +/* Helper routine */ +static herr_t H5D__bt2_idx_open(const H5D_chk_idx_info_t *idx_info); + +/* Callback for H5B2_iterate() which is called in H5D__bt2_idx_iterate() */ +static int H5D__bt2_idx_iterate_cb(const void *_record, void *_udata); + +/* Callback for H5B2_find() which is called in H5D__bt2_idx_get_addr() */ +static herr_t H5D__bt2_found_cb(const void *nrecord, void *op_data); + +/* + * Callback for H5B2_remove() and H5B2_delete() which is called + * in H5D__bt2_idx_remove() and H5D__bt2_idx_delete(). + */ +static herr_t H5D__bt2_remove_cb(const void *nrecord, void *_udata); + +/* Callback for H5B2_modify() which is called in H5D__bt2_idx_insert() */ +static herr_t H5D__bt2_mod_cb(void *_record, void *_op_data, hbool_t *changed); + +/* Chunked layout indexing callbacks for v2 B-tree indexing */ +static herr_t H5D__bt2_idx_init(const H5D_chk_idx_info_t *idx_info, + const H5S_t *space, haddr_t dset_ohdr_addr); +static herr_t H5D__bt2_idx_create(const H5D_chk_idx_info_t *idx_info); +static hbool_t H5D__bt2_idx_is_space_alloc(const H5O_storage_chunk_t *storage); +static herr_t H5D__bt2_idx_insert(const H5D_chk_idx_info_t *idx_info, + H5D_chunk_ud_t *udata, const H5D_t *dset); +static herr_t H5D__bt2_idx_get_addr(const H5D_chk_idx_info_t *idx_info, + H5D_chunk_ud_t *udata); +static int H5D__bt2_idx_iterate(const H5D_chk_idx_info_t *idx_info, + H5D_chunk_cb_func_t chunk_cb, void *chunk_udata); +static herr_t H5D__bt2_idx_remove(const H5D_chk_idx_info_t *idx_info, + H5D_chunk_common_ud_t *udata); +static herr_t H5D__bt2_idx_delete(const H5D_chk_idx_info_t *idx_info); +static herr_t H5D__bt2_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__bt2_idx_copy_shutdown(H5O_storage_chunk_t *storage_src, + H5O_storage_chunk_t *storage_dst, hid_t dxpl_id); +static herr_t H5D__bt2_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *size); +static herr_t H5D__bt2_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr); +static herr_t H5D__bt2_idx_dump(const H5O_storage_chunk_t *storage, + FILE *stream); +static herr_t H5D__bt2_idx_dest(const H5D_chk_idx_info_t *idx_info); + + +/*********************/ +/* Package Variables */ +/*********************/ + +/* Chunked dataset I/O ops for v2 B-tree indexing */ +const H5D_chunk_ops_t H5D_COPS_BT2[1] = {{ + H5D__bt2_idx_init, /* init */ + H5D__bt2_idx_create, /* create */ + H5D__bt2_idx_is_space_alloc, /* is_space_alloc */ + H5D__bt2_idx_insert, /* insert */ + H5D__bt2_idx_get_addr, /* get_addr */ + NULL, /* resize */ + H5D__bt2_idx_iterate, /* iterate */ + H5D__bt2_idx_remove, /* remove */ + H5D__bt2_idx_delete, /* delete */ + H5D__bt2_idx_copy_setup, /* copy_setup */ + H5D__bt2_idx_copy_shutdown, /* copy_shutdown */ + H5D__bt2_idx_size, /* size */ + H5D__bt2_idx_reset, /* reset */ + H5D__bt2_idx_dump, /* dump */ + H5D__bt2_idx_dest /* destroy */ +}}; + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + +/* v2 B-tree class for indexing non-filtered chunked datasets */ +const H5B2_class_t H5D_BT2[1] = {{ /* B-tree class information */ + H5B2_CDSET_ID, /* Type of B-tree */ + "H5B2_CDSET_ID", /* Name of B-tree class */ + sizeof(H5D_chunk_rec_t), /* Size of native record */ + H5D__bt2_crt_context, /* Create client callback context */ + H5D__bt2_dst_context, /* Destroy client callback context */ + H5D__bt2_store, /* Record storage callback */ + H5D__bt2_compare, /* Record comparison callback */ + H5D__bt2_unfilt_encode, /* Record encoding callback */ + H5D__bt2_unfilt_decode, /* Record decoding callback */ + H5D__bt2_unfilt_debug /* Record debugging callback */ +}}; + +/* v2 B-tree class for indexing filtered chunked datasets */ +const H5B2_class_t H5D_BT2_FILT[1] = {{ /* B-tree class information */ + H5B2_CDSET_FILT_ID, /* Type of B-tree */ + "H5B2_CDSET_FILT_ID", /* Name of B-tree class */ + sizeof(H5D_chunk_rec_t), /* Size of native record */ + H5D__bt2_crt_context, /* Create client callback context */ + H5D__bt2_dst_context, /* Destroy client callback context */ + H5D__bt2_store, /* Record storage callback */ + H5D__bt2_compare, /* Record comparison callback */ + H5D__bt2_filt_encode, /* Record encoding callback */ + H5D__bt2_filt_decode, /* Record decoding callback */ + H5D__bt2_filt_debug /* Record debugging callback */ +}}; + + +/*******************/ +/* Local Variables */ +/*******************/ + +/* Declare a free list to manage the H5D_bt2_ctx_t struct */ +H5FL_DEFINE_STATIC(H5D_bt2_ctx_t); +/* Declare a free list to manage the page elements */ +H5FL_BLK_DEFINE(chunk_dim); + + + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_crt_context + * + * Purpose: Create client callback context + * + * Return: Success: non-NULL + * Failure: NULL + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static void * +H5D__bt2_crt_context(void *_udata) +{ + H5D_bt2_ctx_ud_t *udata = (H5D_bt2_ctx_ud_t *)_udata; /* User data for building callback context */ + H5D_bt2_ctx_t *ctx; /* Callback context structure */ + uint32_t *my_dim = NULL; /* Pointer to copy of chunk dimension size */ + void *ret_value = NULL; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity check */ + HDassert(udata); + HDassert(udata->f); + HDassert(udata->ndims > 0 && udata->ndims < H5O_LAYOUT_NDIMS); + + /* Allocate callback context */ + if(NULL == (ctx = H5FL_MALLOC(H5D_bt2_ctx_t))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate callback context") + + /* Determine the size of addresses and set the chunk size and # of dimensions for the dataset */ + ctx->sizeof_addr = H5F_SIZEOF_ADDR(udata->f); + ctx->chunk_size = udata->chunk_size; + ctx->ndims = udata->ndims; + + /* Set up the "local" information for this dataset's chunk dimension sizes */ + if(NULL == (my_dim = (uint32_t *)H5FL_BLK_MALLOC(chunk_dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate chunk dims") + HDmemcpy(my_dim, udata->dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t)); + ctx->dim = my_dim; + + /* + * 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 + ((H5VM_log2_gen((uint64_t)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) +} /* H5D__bt2_crt_context() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_dst_context + * + * Purpose: Destroy client callback context + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_dst_context(void *_ctx) +{ + H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(ctx); + + /* Free array for chunk dimension sizes */ + if(ctx->dim) + (void)H5FL_BLK_FREE(chunk_dim, ctx->dim); + /* Release callback context */ + ctx = H5FL_FREE(H5D_bt2_ctx_t, ctx); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_dst_context() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_store + * + * Purpose: Store native information into record for v2 B-tree + * (non-filtered) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_store(void *record, const void *_udata) +{ + const H5D_bt2_ud_t *udata = (const H5D_bt2_ud_t *)_udata; /* User data */ + + FUNC_ENTER_STATIC_NOERR + + *(H5D_chunk_rec_t *)record = udata->rec; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_store() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_compare + * + * Purpose: Compare two native information records, according to some key + * (non-filtered) + * + * Return: <0 if rec1 < rec2 + * =0 if rec1 == rec2 + * >0 if rec1 > rec2 + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_compare(const void *_udata, const void *_rec2, int *result) +{ + const H5D_bt2_ud_t *udata = (const H5D_bt2_ud_t *)_udata; /* User data */ + const H5D_chunk_rec_t *rec1 = &(udata->rec); /* The search record */ + const H5D_chunk_rec_t *rec2 = (const H5D_chunk_rec_t *)_rec2; /* The native record */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity checks */ + HDassert(rec1); + HDassert(rec2); + + /* Compare the offsets but ignore the other fields */ + *result = H5VM_vector_cmp_u(udata->ndims, rec1->scaled, rec2->scaled); + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__bt2_compare() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_unfilt_encode + * + * Purpose: Encode native information into raw form for storing on disk + * (non-filtered) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_unfilt_encode(uint8_t *raw, const void *_record, void *_ctx) +{ + H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */ + const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */ + unsigned u; /* Local index varible */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(ctx); + + /* Encode the record's fields */ + H5F_addr_encode_len(ctx->sizeof_addr, &raw, record->chunk_addr); + /* (Don't encode the chunk size & filter mask for non-filtered B-tree records) */ + for(u = 0; u < ctx->ndims; u++) + UINT64ENCODE(raw, record->scaled[u]); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_unfilt_encode() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_unfilt_decode + * + * Purpose: Decode raw disk form of record into native form + * (non-filtered) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_unfilt_decode(const uint8_t *raw, void *_record, void *_ctx) +{ + H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */ + H5D_chunk_rec_t *record = (H5D_chunk_rec_t *)_record; /* The native record */ + unsigned u; /* Local index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(ctx); + + /* Decode the record's fields */ + H5F_addr_decode_len(ctx->sizeof_addr, &raw, &record->chunk_addr); + record->nbytes = ctx->chunk_size; + record->filter_mask = 0; + for(u = 0; u < ctx->ndims; u++) + UINT64DECODE(raw, record->scaled[u]); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_unfilt_decode() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_unfilt_debug + * + * Purpose: Debug native form of record (non-filtered) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_unfilt_debug(FILE *stream, int indent, int fwidth, + const void *_record, const void *_ctx) +{ + const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */ + const H5D_bt2_ctx_t *ctx = (const H5D_bt2_ctx_t *)_ctx; /* Callback context */ + unsigned u; /* Local index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity checks */ + HDassert(record); + HDassert(ctx->chunk_size == record->nbytes); + HDassert(0 == record->filter_mask); + + HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, "Chunk address:", record->chunk_addr); + + HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:"); + for(u = 0; u < ctx->ndims; u++) + HDfprintf(stream, "%s%Hd", u?", ":"", record->scaled[u] * ctx->dim[u]); + HDfputs("}\n", stream); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_unfilt_debug() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_filt_encode + * + * Purpose: Encode native information into raw form for storing on disk + * (filtered) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_filt_encode(uint8_t *raw, const void *_record, void *_ctx) +{ + H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */ + const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */ + unsigned u; /* Local index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(ctx); + HDassert(record); + HDassert(H5F_addr_defined(record->chunk_addr)); + HDassert(0 != record->nbytes); + + /* Encode the record's fields */ + H5F_addr_encode_len(ctx->sizeof_addr, &raw, record->chunk_addr); + UINT64ENCODE_VAR(raw, record->nbytes, ctx->chunk_size_len); + UINT32ENCODE(raw, record->filter_mask); + for(u = 0; u < ctx->ndims; u++) + UINT64ENCODE(raw, record->scaled[u]); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_filt_encode() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_filt_decode + * + * Purpose: Decode raw disk form of record into native form + * (filtered) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_filt_decode(const uint8_t *raw, void *_record, void *_ctx) +{ + H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */ + H5D_chunk_rec_t *record = (H5D_chunk_rec_t *)_record; /* The native record */ + unsigned u; /* Local index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(ctx); + HDassert(record); + + /* Decode the record's fields */ + H5F_addr_decode_len(ctx->sizeof_addr, &raw, &record->chunk_addr); + UINT64DECODE_VAR(raw, record->nbytes, ctx->chunk_size_len); + UINT32DECODE(raw, record->filter_mask); + for(u = 0; u < ctx->ndims; u++) + UINT64DECODE(raw, record->scaled[u]); + + /* Sanity checks */ + HDassert(H5F_addr_defined(record->chunk_addr)); + HDassert(0 != record->nbytes); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_filt_decode() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_filt_debug + * + * Purpose: Debug native form of record (filtered) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_filt_debug(FILE *stream, int indent, int fwidth, + const void *_record, const void *_ctx) +{ + const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */ + const H5D_bt2_ctx_t *ctx = (const H5D_bt2_ctx_t *)_ctx; /* Callback context */ + unsigned u; /* Local index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity checks */ + HDassert(record); + HDassert(H5F_addr_defined(record->chunk_addr)); + HDassert(0 != record->nbytes); + + HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, "Chunk address:", record->chunk_addr); + HDfprintf(stream, "%*s%-*s %u bytes\n", indent, "", fwidth, "Chunk size:", (unsigned)record->nbytes); + HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth, "Filter mask:", record->filter_mask); + + HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:"); + for(u = 0; u < ctx->ndims; u++) + HDfprintf(stream, "%s%Hd", u?", ":"", record->scaled[u] * ctx->dim[u]); + HDfputs("}\n", stream); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_filt_debug() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_init + * + * Purpose: Initialize the indexing information for a dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * Wednesday, May 23, 2012 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_init(const H5D_chk_idx_info_t H5_ATTR_UNUSED *idx_info, + const H5S_t H5_ATTR_UNUSED *space, haddr_t dset_ohdr_addr) +{ + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(H5F_addr_defined(dset_ohdr_addr)); + + idx_info->storage->u.btree2.dset_ohdr_addr = dset_ohdr_addr; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5D__bt2_idx_init() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_open() + * + * Purpose: Opens an existing v2 B-tree. + * + * Note: This information is passively initialized from each index + * operation callback because those abstract chunk index operations + * are designed to work with the v2 B-tree chunk indices also, + * which don't require an 'open' for the data structure. + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_open(const H5D_chk_idx_info_t *idx_info) +{ + H5D_bt2_ctx_ud_t u_ctx; /* user data for creating context */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Check args */ + HDassert(idx_info); + HDassert(idx_info->f); + HDassert(idx_info->pline); + HDassert(idx_info->layout); + HDassert(H5D_CHUNK_IDX_BT2 == idx_info->layout->idx_type); + HDassert(idx_info->storage); + HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); + HDassert(NULL == idx_info->storage->u.btree2.bt2); + + /* Set up the user data */ + u_ctx.f = idx_info->f; + u_ctx.ndims = idx_info->layout->ndims - 1; + u_ctx.chunk_size = idx_info->layout->size; + u_ctx.dim = idx_info->layout->dim; + + /* Open v2 B-tree for the chunk index */ + if(NULL == (idx_info->storage->u.btree2.bt2 = H5B2_open(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &u_ctx))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open v2 B-tree for tracking chunked dataset") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_open() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_create + * + * Purpose: Create the v2 B-tree for tracking dataset chunks + * + * Return: SUCCEED/FAIL + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_create(const H5D_chk_idx_info_t *idx_info) +{ + H5B2_create_t bt2_cparam; /* v2 B-tree creation parameters */ + H5D_bt2_ctx_ud_t u_ctx; /* data for context call */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* 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)); + + bt2_cparam.rrec_size = H5F_SIZEOF_ADDR(idx_info->f) /* Address of chunk */ + + (idx_info->layout->ndims - 1) * 8; /* # of dimensions x 64-bit chunk offsets */ + + /* 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 + ((H5VM_log2_gen((uint64_t)idx_info->layout->size) + 8) / 8); + if(chunk_size_len > 8) + chunk_size_len = 8; + + bt2_cparam.rrec_size += chunk_size_len + 4; /* Size of encoded chunk size & filter mask */ + bt2_cparam.cls = H5D_BT2_FILT; + } /* end if */ + else + bt2_cparam.cls = H5D_BT2; + + bt2_cparam.node_size = idx_info->layout->u.btree2.cparam.node_size; + bt2_cparam.split_percent = idx_info->layout->u.btree2.cparam.split_percent; + bt2_cparam.merge_percent = idx_info->layout->u.btree2.cparam.merge_percent; + + u_ctx.f = idx_info->f; + u_ctx.ndims = idx_info->layout->ndims - 1; + u_ctx.chunk_size = idx_info->layout->size; + u_ctx.dim = idx_info->layout->dim; + + /* Create the v2 B-tree for the chunked dataset */ + if(NULL == (idx_info->storage->u.btree2.bt2 = H5B2_create(idx_info->f, idx_info->dxpl_id, &bt2_cparam, &u_ctx))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create v2 B-tree for tracking chunked dataset") + + /* Retrieve the v2 B-tree's address in the file */ + if(H5B2_get_addr(idx_info->storage->u.btree2.bt2, &(idx_info->storage->idx_addr)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get v2 B-tree address for tracking chunked dataset") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_create() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_is_space_alloc + * + * Purpose: Query if space is allocated for index method + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static hbool_t +H5D__bt2_idx_is_space_alloc(const H5O_storage_chunk_t *storage) +{ + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(storage); + + FUNC_LEAVE_NOAPI((hbool_t)H5F_addr_defined(storage->idx_addr)) +} /* end H5D__bt2_idx_is_space_alloc() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_mod_cb + * + * Purpose: Modify record for dataset chunk when it is found in a v2 B-tree. + * This is the callback for H5B2_modify() which is called in + * H5D__bt2_idx_insert(). + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_mod_cb(void *_record, void *_op_data, hbool_t *changed) +{ + H5D_bt2_ud_t *op_data = (H5D_bt2_ud_t *)_op_data; /* User data for v2 B-tree calls */ + H5D_chunk_rec_t *record = (H5D_chunk_rec_t *)_record; /* Chunk record */ + + FUNC_ENTER_STATIC_NOERR + +/* Sanity check */ +#ifndef NDEBUG +{ + unsigned u; /* Local index variable */ + + for(u = 0; u < op_data->ndims; u++) + HDassert(record->scaled[u] == op_data->rec.scaled[u]); +} +#endif /* NDEBUG */ + + /* Modify record */ + *record = op_data->rec; + + /* Note that the record changed */ + *changed = TRUE; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5D__bt2_mod_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_insert + * + * Purpose: Insert chunk address into the indexing structure. + * A non-filtered chunk: + * Should not exist + * Allocate the chunk and pass chunk address back up + * A filtered chunk: + * If it was not found, create the chunk and pass chunk address back up + * If it was found but its size changed, reallocate the chunk and pass chunk address back up + * If it was found but its size was the same, pass chunk address back up + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata, + const H5D_t H5_ATTR_UNUSED *dset) +{ + H5B2_t *bt2; /* v2 B-tree handle for indexing chunks */ + H5D_bt2_ud_t bt2_udata; /* User data for v2 B-tree calls */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checks */ + 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); + HDassert(H5F_addr_defined(udata->chunk_block.offset)); + + /* Check if the v2 B-tree is open yet */ + if(NULL == idx_info->storage->u.btree2.bt2) { + /* Open existing v2 B-tree */ + if(H5D__bt2_idx_open(idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree") + } /* end if */ + else /* Patch the top level file pointer contained in bt2 if needed */ + if(H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch v2 B-tree file pointer") + + /* Set convenience pointer to v2 B-tree structure */ + bt2 = idx_info->storage->u.btree2.bt2; + + /* Set up callback info */ + bt2_udata.ndims = idx_info->layout->ndims - 1; + bt2_udata.rec.chunk_addr = udata->chunk_block.offset; + if(idx_info->pline->nused > 0) { /* filtered chunk */ + H5_CHECKED_ASSIGN(bt2_udata.rec.nbytes, uint32_t, udata->chunk_block.length, hsize_t); + bt2_udata.rec.filter_mask = udata->filter_mask; + } /* end if */ + else { /* non-filtered chunk */ + bt2_udata.rec.nbytes = idx_info->layout->size; + bt2_udata.rec.filter_mask = 0; + } /* end else */ + for(u = 0; u < (idx_info->layout->ndims - 1); u++) + bt2_udata.rec.scaled[u] = udata->common.scaled[u]; + + /* Update record for v2 B-tree (could be insert or modify) */ + if(H5B2_update(bt2, idx_info->dxpl_id, &bt2_udata, H5D__bt2_mod_cb, &bt2_udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTUPDATE, FAIL, "unable to update record in v2 B-tree") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__bt2_idx_insert() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_found_cb + * + * Purpose: Retrieve record for dataset chunk when it is found in a v2 B-tree. + * This is the callback for H5B2_find() which is called in + * H5D__bt2_idx_get_addr() and H5D__bt2_idx_insert(). + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_found_cb(const void *nrecord, void *op_data) +{ + FUNC_ENTER_STATIC_NOERR + + *(H5D_chunk_rec_t *)op_data = *(const H5D_chunk_rec_t *)nrecord; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5D__bt2_found_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_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: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata) +{ + H5B2_t *bt2; /* v2 B-tree handle for indexing chunks */ + H5D_bt2_ud_t bt2_udata; /* User data for v2 B-tree calls */ + H5D_chunk_rec_t found_rec; /* Record found from searching for object */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checks */ + HDassert(idx_info); + HDassert(idx_info->f); + HDassert(idx_info->pline); + HDassert(idx_info->layout); + HDassert(idx_info->layout->ndims > 0); + HDassert(idx_info->storage); + HDassert(H5F_addr_defined(idx_info->storage->idx_addr)); + HDassert(udata); + + /* Check if the v2 B-tree is open yet */ + if(NULL == idx_info->storage->u.btree2.bt2) { + /* Open existing v2 B-tree */ + if(H5D__bt2_idx_open(idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree") + } /* end if */ + else /* Patch the top level file pointer contained in bt2 if needed */ + if(H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch v2 B-tree file pointer") + + /* Set convenience pointer to v2 B-tree structure */ + bt2 = idx_info->storage->u.btree2.bt2; + + /* Clear the found record */ + found_rec.chunk_addr = HADDR_UNDEF; + found_rec.nbytes = 0; + found_rec.filter_mask = 0; + + /* Prepare user data for compare callback */ + bt2_udata.rec.chunk_addr = HADDR_UNDEF; + bt2_udata.ndims = idx_info->layout->ndims - 1; + + /* Set the chunk offset to be searched for */ + for(u = 0; u < (idx_info->layout->ndims - 1); u++) + bt2_udata.rec.scaled[u] = udata->common.scaled[u]; + + /* Go get chunk information from v2 B-tree */ + if(H5B2_find(bt2, idx_info->dxpl_id, &bt2_udata, H5D__bt2_found_cb, &found_rec) < 0) + HGOTO_ERROR(H5E_HEAP, H5E_NOTFOUND, FAIL, "can't find object in v2 B-tree") + + /* Set common info for the chunk */ + udata->chunk_block.offset = found_rec.chunk_addr; + + /* Check for setting other info */ + if(H5F_addr_defined(udata->chunk_block.offset)) { + /* Sanity check */ + HDassert(0 != found_rec.nbytes); + + /* Set other info for the chunk */ + if(idx_info->pline->nused > 0) { /* filtered chunk */ + udata->chunk_block.length = found_rec.nbytes; + udata->filter_mask = found_rec.filter_mask; + } /* end if */ + else { /* non-filtered chunk */ + udata->chunk_block.length = idx_info->layout->size; + udata->filter_mask = 0; + } /* end else */ + } /* end if */ + else { + udata->chunk_block.length = 0; + udata->filter_mask = 0; + } /* end else */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__bt2_idx_get_addr() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_iterate_cb + * + * Purpose: Translate the B-tree specific chunk record into a generic + * form and make the callback to the generic chunk callback + * routine. + * This is the callback for H5B2_iterate() which is called in + * H5D__bt2_idx_iterate(). + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static int +H5D__bt2_idx_iterate_cb(const void *_record, void *_udata) +{ + H5D_bt2_it_ud_t *udata = (H5D_bt2_it_ud_t *)_udata; /* User data */ + const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* Native record */ + int ret_value = -1; /* Return value */ + + FUNC_ENTER_STATIC_NOERR + + /* Make "generic chunk" callback */ + if((ret_value = (udata->cb)(record, udata->udata)) < 0) + HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback"); + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__bt2_idx_iterate_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_iterate + * + * Purpose: Iterate over the chunks in an index, making a callback + * for each one. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static int +H5D__bt2_idx_iterate(const H5D_chk_idx_info_t *idx_info, + H5D_chunk_cb_func_t chunk_cb, void *chunk_udata) +{ + H5B2_t *bt2; /* v2 B-tree handle for indexing chunks */ + H5D_bt2_it_ud_t udata; /* User data for B-tree iterator callback */ + int ret_value = FAIL; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checks */ + 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 v2 B-tree is open yet */ + if(NULL == idx_info->storage->u.btree2.bt2) { + /* Open existing v2 B-tree */ + if(H5D__bt2_idx_open(idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree") + } /* end if */ + else /* Patch the top level file pointer contained in bt2 if needed */ + if(H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch v2 B-tree file pointer") + + /* Set convenience pointer to v2 B-tree structure */ + bt2 = idx_info->storage->u.btree2.bt2; + + /* Prepare user data for iterate callback */ + udata.cb = chunk_cb; + udata.udata = chunk_udata; + + /* Iterate over the records in the v2 B-tree */ + if((ret_value = H5B2_iterate(bt2, idx_info->dxpl_id, H5D__bt2_idx_iterate_cb, &udata)) < 0) + HERROR(H5E_DATASET, H5E_BADITER, "unable to iterate over chunk v2 B-tree"); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_iterate() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_remove_cb() + * + * Purpose: Free space for 'dataset chunk' object as v2 B-tree + * is being deleted or v2 B-tree node is removed. + * This is the callback for H5B2_remove() and H5B2_delete() which + * which are called in H5D__bt2_idx_remove() and H5D__bt2_idx_delete(). + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_remove_cb(const void *_record, void *_udata) +{ + const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */ + H5D_bt2_remove_ud_t *udata = (H5D_bt2_remove_ud_t *)_udata; /* User data for removal callback */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checks */ + HDassert(udata); + HDassert(udata->f); + + /* Free the space in the file for the object being removed */ + H5_CHECK_OVERFLOW(record->nbytes, uint32_t, hsize_t); + if(H5MF_xfree(udata->f, H5FD_MEM_DRAW, udata->dxpl_id, record->chunk_addr, (hsize_t)record->nbytes) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__bt2_remove_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_remove + * + * Purpose: Remove chunk from index. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata) +{ + H5B2_t *bt2; /* v2 B-tree handle for indexing chunks */ + H5D_bt2_remove_ud_t remove_udata; /* User data for removal callback */ + H5D_bt2_ud_t bt2_udata; /* User data for v2 B-tree find call */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checks */ + 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 v2 B-tree is open yet */ + if(NULL == idx_info->storage->u.btree2.bt2) + /* Open existing v2 B-tree */ + if(H5D__bt2_idx_open(idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree") + + /* Set convenience pointer to v2 B-tree structure */ + bt2 = idx_info->storage->u.btree2.bt2; + + /* Initialize user data for removal callback */ + remove_udata.f = idx_info->f; + remove_udata.dxpl_id = idx_info->dxpl_id; + + /* Prepare user data for compare callback */ + bt2_udata.ndims = idx_info->layout->ndims - 1; + + /* Initialize the record to search for */ + for(u = 0; u < (idx_info->layout->ndims - 1); u++) + bt2_udata.rec.scaled[u] = udata->scaled[u]; + + /* Remove the record for the "dataset chunk" object from the v2 B-tree */ + /* (space in the file for the object is freed in the 'remove' callback) */ + if(H5B2_remove(bt2, idx_info->dxpl_id, &bt2_udata, H5D__bt2_remove_cb, &remove_udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "can't remove object from B-tree") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__bt2_idx_remove() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_delete + * + * Purpose: Delete index and raw data storage for entire dataset + * (i.e. all chunks) + * + * Return: Success: Non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + * Modifications: + * Vailin Choi; March 2011 + * Initialize size of an unfiltered chunk. + * This is a fix for for the assertion failure in: + * [src/H5FSsection.c:968: H5FS_sect_link_size: Assertion `bin < sinfo->nbins' failed.] + * which is uncovered by test_unlink_chunked_dataset() in test/unlink.c + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_delete(const H5D_chk_idx_info_t *idx_info) +{ + H5D_bt2_remove_ud_t remove_udata; /* User data for removal callback */ + H5B2_remove_t remove_op; /* The removal callback */ + H5D_bt2_ctx_ud_t u_ctx; /* data for context call */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* 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)) { + /* Set up user data for creating context */ + u_ctx.f = idx_info->f; + u_ctx.ndims = idx_info->layout->ndims - 1; + u_ctx.chunk_size = idx_info->layout->size; + u_ctx.dim = idx_info->layout->dim; + + /* Initialize user data for removal callback */ + remove_udata.f = idx_info->f; + remove_udata.dxpl_id = idx_info->dxpl_id; + + /* Set remove operation. */ + remove_op = H5D__bt2_remove_cb; + + /* Delete the v2 B-tree */ + /*(space in the file for each object is freed in the 'remove' callback) */ + if(H5B2_delete(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &u_ctx, remove_op, &remove_udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "can't delete v2 B-tree") + + idx_info->storage->idx_addr = HADDR_UNDEF; + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_delete() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_copy_setup + * + * Purpose: Set up any necessary information for copying chunks + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_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_STATIC + + /* Source file */ + HDassert(idx_info_src); + HDassert(idx_info_src->f); + HDassert(idx_info_src->pline); + HDassert(idx_info_src->layout); + HDassert(idx_info_src->storage); + + /* Destination file */ + 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 v2 B-tree is open yet */ + if(NULL == idx_info_src->storage->u.btree2.bt2) + if(H5D__bt2_idx_open(idx_info_src) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree") + + /* Set copied metadata tag */ + H5_BEGIN_TAG(idx_info_dst->dxpl_id, H5AC__COPIED_TAG, FAIL); + + /* Create v2 B-tree that describes the chunked dataset in the destination file */ + if(H5D__bt2_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)); + + /* Reset metadata tag */ + H5_END_TAG(FAIL); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_copy_setup() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_copy_shutdown + * + * Purpose: Shutdown any information from copying chunks + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_copy_shutdown(H5O_storage_chunk_t *storage_src, + H5O_storage_chunk_t *storage_dst, hid_t H5_ATTR_UNUSED dxpl_id) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Check args */ + HDassert(storage_src); + HDassert(storage_src->u.btree2.bt2); + HDassert(storage_dst); + HDassert(storage_dst->u.btree2.bt2); + + /* Close v2 B-tree for source file */ + if(H5B2_close(storage_src->u.btree2.bt2, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close v2 B-tree") + storage_src->u.btree2.bt2 = NULL; + + /* Close v2 B-tree for destination file */ + if(H5B2_close(storage_dst->u.btree2.bt2, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close v2 B-tree") + storage_dst->u.btree2.bt2 = NULL; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_copy_shutdown() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_size + * + * Purpose: Retrieve the amount of index storage for chunked dataset + * + * Return: Success: Non-negative + * Failure: negative + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size) +{ + H5B2_t *bt2_cdset = NULL; /* Pointer to v2 B-tree structure */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* 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 v2 B-tree */ + if(H5D__bt2_idx_open(idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree") + + /* Set convenience pointer to v2 B-tree structure */ + bt2_cdset = idx_info->storage->u.btree2.bt2; + + /* Get v2 B-tree size for indexing chunked dataset */ + if(H5B2_size(bt2_cdset, idx_info->dxpl_id, index_size) < 0) + HGOTO_ERROR(H5E_SYM, H5E_CANTGET, FAIL, "can't retrieve v2 B-tree storage info for chunked dataset") + +done: + /* Close v2 B-tree index */ + if(bt2_cdset && H5B2_close(bt2_cdset, idx_info->dxpl_id) < 0) + HDONE_ERROR(H5E_SYM, H5E_CLOSEERROR, FAIL, "can't close v2 B-tree for tracking chunked dataset") + idx_info->storage->u.btree2.bt2 = NULL; + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_size() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_reset + * + * Purpose: Reset indexing information. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr) +{ + FUNC_ENTER_STATIC_NOERR + + /* Sanity checks */ + HDassert(storage); + + /* Reset index info */ + if(reset_addr) + storage->idx_addr = HADDR_UNDEF; + storage->u.btree2.bt2 = NULL; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5D__bt2_idx_reset() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_dump + * + * Purpose: Dump indexing information to a stream. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_dump(const H5O_storage_chunk_t *storage, FILE *stream) +{ + FUNC_ENTER_STATIC_NOERR + + /* Sanity checks */ + HDassert(storage); + HDassert(stream); + + HDfprintf(stream, " Address: %a\n", storage->idx_addr); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5D__bt2_idx_dump() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__bt2_idx_dest + * + * Purpose: Release indexing information in memory. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; June 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__bt2_idx_dest(const H5D_chk_idx_info_t *idx_info) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Check args */ + HDassert(idx_info); + HDassert(idx_info->f); + HDassert(idx_info->storage); + + /* Check if the v2-btree is open */ + if(idx_info->storage->u.btree2.bt2) { + /* Close v2 B-tree */ + if(H5B2_close(idx_info->storage->u.btree2.bt2, idx_info->dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "can't close v2 B-tree") + idx_info->storage->u.btree2.bt2 = NULL; + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__bt2_idx_dest() */ + diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 4d0e2c3..4df493d 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -75,7 +75,9 @@ /* Sanity check on chunk index types: commonly used by a lot of routines in this file */ #define H5D_CHUNK_STORAGE_INDEX_CHK(storage) \ - HDassert((H5D_CHUNK_IDX_BTREE == storage->idx_type && H5D_COPS_BTREE == storage->ops)); + HDassert((H5D_CHUNK_IDX_EARRAY == storage->idx_type && H5D_COPS_EARRAY == storage->ops) || \ + (H5D_CHUNK_IDX_BT2 == storage->idx_type && H5D_COPS_BT2 == storage->ops) || \ + (H5D_CHUNK_IDX_BTREE == storage->idx_type && H5D_COPS_BTREE == storage->ops)); /* * Feature: If this constant is defined then every cache preemption and load @@ -6285,6 +6287,8 @@ H5D__chunk_file_alloc(const H5D_chk_idx_info_t *idx_info, const H5F_block_t *old /* Actually allocate space for the chunk in the file */ if(alloc_chunk) { switch(idx_info->storage->idx_type) { + case H5D_CHUNK_IDX_EARRAY: + case H5D_CHUNK_IDX_BT2: case H5D_CHUNK_IDX_BTREE: HDassert(new_chunk->length > 0); H5_CHECK_OVERFLOW(new_chunk->length, /*From: */uint32_t, /*To: */hsize_t); diff --git a/src/H5Dearray.c b/src/H5Dearray.c new file mode 100644 index 0000000..f24c69a --- /dev/null +++ b/src/H5Dearray.c @@ -0,0 +1,1740 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 */ +/****************/ + +#include "H5Dmodule.h" /* This source code file is part of the H5D module */ + + +/***********/ +/* 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 "H5VMprivate.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; + +/* Extensible Array callback info for iteration over chunks */ +typedef struct H5D_earray_it_ud_t { + H5D_chunk_common_ud_t common; /* Common info for Fixed Array user data (must be first) */ + H5D_chunk_rec_t chunk_rec; /* Generic chunk record for callback */ + hbool_t filtered; /* Whether the chunks are filtered */ + H5D_chunk_cb_func_t cb; /* Chunk callback routine */ + void *udata; /* User data for chunk callback routine */ +} H5D_earray_it_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 iterator callbacks */ +static int H5D__earray_idx_iterate_cb(hsize_t idx, const void *_elmt, void *_udata); +static int H5D__earray_idx_delete_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata); + +/* 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); +static void *H5D__earray_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr); +static herr_t H5D__earray_dst_dbg_context(void *dbg_ctx); + +/* 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, const H5D_t *dset); +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_dump(const H5O_storage_chunk_t *storage, + FILE *stream); +static herr_t H5D__earray_idx_dest(const H5D_chk_idx_info_t *idx_info); + +/* Generic extensible array routines */ +static herr_t H5D__earray_idx_open(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] = {{ + H5D__earray_idx_init, /* init */ + H5D__earray_idx_create, /* create */ + H5D__earray_idx_is_space_alloc, /* is_space_alloc */ + H5D__earray_idx_insert, /* insert */ + H5D__earray_idx_get_addr, /* get_addr */ + H5D__earray_idx_resize, /* resize */ + H5D__earray_idx_iterate, /* iterate */ + H5D__earray_idx_remove, /* remove */ + H5D__earray_idx_delete, /* delete */ + H5D__earray_idx_copy_setup, /* copy_setup */ + H5D__earray_idx_copy_shutdown, /* copy_shutdown */ + H5D__earray_idx_size, /* size */ + H5D__earray_idx_reset, /* reset */ + H5D__earray_idx_dump, /* dump */ + H5D__earray_idx_dest /* destroy */ +}}; + + +/*****************************/ +/* Library Private 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 */ + "Chunk w/o filters", /* Name of extensible array class */ + 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 */ + H5D__earray_crt_dbg_context, /* Create debugging context */ + H5D__earray_dst_dbg_context /* Destroy debugging context */ +}}; + +/* 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 */ + "Chunk w/filters", /* Name of extensible array class */ + 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 */ + H5D__earray_crt_dbg_context, /* Create debugging context */ + H5D__earray_dst_dbg_context /* Destroy debugging context */ +}}; + + +/*******************/ +/* Local Variables */ +/*******************/ + +/* Declare a free list to manage the H5D_earray_ctx_t struct */ +/* Declare a free list to manage the H5D_earray_ctx_ud_t struct */ +H5FL_DEFINE_STATIC(H5D_earray_ctx_t); +H5FL_DEFINE_STATIC(H5D_earray_ctx_ud_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 = NULL; /* Return value */ + + FUNC_ENTER_STATIC + + /* 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 + ((H5VM_log2_gen((uint64_t)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_STATIC_NOERR + + /* 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_STATIC_NOERR + + /* Sanity checks */ + HDassert(nat_blk); + HDassert(nelmts); + + H5VM_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_STATIC_NOERR + + /* 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_STATIC_NOERR + + /* 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_STATIC_NOERR + + /* 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_STATIC_NOERR + + /* Sanity checks */ + HDassert(nat_blk); + HDassert(nelmts); + HDassert(sizeof(fill_val) == H5EA_CLS_FILT_CHUNK->nat_elmt_size); + + H5VM_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_STATIC_NOERR + + /* 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_STATIC_NOERR + + /* 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_STATIC_NOERR + + /* 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_crt_dbg_context + * + * Purpose: Create context for debugging callback + * (get the layout message in the specified object header) + * + * Return: Success: non-NULL + * Failure: NULL + * + * Programmer: Vailin Choi; July 2010 + * + *------------------------------------------------------------------------- + */ +static void * +H5D__earray_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr) +{ + H5D_earray_ctx_ud_t *dbg_ctx = NULL; /* Context for fixed array callback */ + H5O_loc_t obj_loc; /* Pointer to an object's location */ + hbool_t obj_opened = FALSE; /* Flag to indicate that the object header was opened */ + H5O_layout_t layout; /* Layout message */ + void *ret_value = NULL; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checks */ + HDassert(f); + HDassert(H5F_addr_defined(obj_addr)); + + /* Allocate context for debugging callback */ + if(NULL == (dbg_ctx = H5FL_MALLOC(H5D_earray_ctx_ud_t))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate extensible array client callback context") + + /* Set up the object header location info */ + H5O_loc_reset(&obj_loc); + obj_loc.file = f; + obj_loc.addr = obj_addr; + + /* Open the object header where the layout message resides */ + if(H5O_open(&obj_loc) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "can't open object header") + obj_opened = TRUE; + + /* Read the layout message */ + if(NULL == H5O_msg_read(&obj_loc, H5O_LAYOUT_ID, &layout, dxpl_id)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get layout info") + + /* close the object header */ + if(H5O_close(&obj_loc) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, NULL, "can't close object header") + + /* Create user data */ + dbg_ctx->f = f; + dbg_ctx->chunk_size = layout.u.chunk.size; + + /* Set return value */ + ret_value = dbg_ctx; + +done: + /* Cleanup on error */ + if(ret_value == NULL) { + /* Release context structure */ + if(dbg_ctx) + dbg_ctx = H5FL_FREE(H5D_earray_ctx_ud_t, dbg_ctx); + + /* Close object header */ + if(obj_opened) { + if(H5O_close(&obj_loc) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, NULL, "can't close object header") + } /* end if */ + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__earray_crt_dbg_context() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__earray_dst_dbg_context + * + * Purpose: Destroy context for debugging callback + * (free the layout message from the specified object header) + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Vailin Choi; July 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__earray_dst_dbg_context(void *_dbg_ctx) +{ + H5D_earray_ctx_ud_t *dbg_ctx = (H5D_earray_ctx_ud_t *)_dbg_ctx; /* Context for extensible array callback */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity checks */ + HDassert(dbg_ctx); + + /* Release context structure */ + dbg_ctx = H5FL_FREE(H5D_earray_ctx_ud_t, dbg_ctx); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5D__earray_dst_dbg_context() */ + + +/*------------------------------------------------------------------------- + * 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_STATIC + + /* 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") + +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_STATIC + + /* 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_CHECKED_ASSIGN(ndims, unsigned, sndims, int); + + /* 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_STATIC + + /* 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 + ((H5VM_log2_gen((uint64_t)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") + +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) +{ + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(storage); + + FUNC_LEAVE_NOAPI((hbool_t)H5F_addr_defined(storage->idx_addr)) +} /* end H5D__earray_idx_is_space_alloc() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__earray_idx_insert + * + * Purpose: Insert chunk address into the indexing structure. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; May 2014 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata, + const H5D_t H5_ATTR_UNUSED *dset) +{ + H5EA_t *ea; /* Pointer to extensible array structure */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checks */ + 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") + } else /* Patch the top level file pointer contained in ea if needed */ + H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f); + + /* Set convenience pointer to extensible array structure */ + ea = idx_info->storage->u.earray.ea; + + if(!H5F_addr_defined(udata->chunk_block.offset)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "The chunk should have allocated already") + if(udata->chunk_idx != (udata->chunk_idx & 0xffffffff)) /* negative value */ + HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "chunk index must be less than 2^32") + + /* Check for filters on chunks */ + if(idx_info->pline->nused > 0) { + H5D_earray_filt_elmt_t elmt; /* Extensible array element */ + + elmt.addr = udata->chunk_block.offset; + H5_CHECKED_ASSIGN(elmt.nbytes, uint32_t, udata->chunk_block.length, hsize_t); + elmt.filter_mask = udata->filter_mask; + + /* Set the info for the chunk */ + if(H5EA_set(ea, idx_info->dxpl_id, udata->chunk_idx, &elmt) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk info") + } /* end if */ + else { + /* Set the address for the chunk */ + if(H5EA_set(ea, idx_info->dxpl_id, udata->chunk_idx, &udata->chunk_block.offset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk address") + } /* end else */ + +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_STATIC + + /* Sanity checks */ + 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") + } else /* Patch the top level file pointer contained in ea if needed */ + H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f); + + /* 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 */ + unsigned u; + + /* Compute coordinate offset from scaled offset */ + for(u = 0; u < ndims; u++) + swizzled_coords[u] = udata->common.scaled[u] * idx_info->layout->dim[u]; + + H5VM_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim); + + /* Calculate the index of this chunk */ + idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks); + } /* end if */ + else { + /* Calculate the index of this chunk */ + idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->down_chunks, udata->common.scaled); + } /* end else */ + + udata->chunk_idx = idx; + + /* 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->chunk_block.offset = elmt.addr; + udata->chunk_block.length = 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->chunk_block.offset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") + + /* Update the other (constant) information for the chunk */ + udata->chunk_block.length = idx_info->layout->size; + udata->filter_mask = 0; + } /* end else */ + + if(!H5F_addr_defined(udata->chunk_block.offset)) + udata->chunk_block.length = 0; + +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_STATIC + + /* Check args */ + HDassert(layout); + + /* "Swizzle" constant dimensions for this dataset */ + if(layout->u.earray.unlim_dim > 0) { + hsize_t swizzled_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of # of chunks in each dimension */ + + /* Get the swizzled chunk dimensions */ + HDmemcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0])); + H5VM_swizzle_coords(uint32_t, layout->u.earray.swizzled_dim, layout->u.earray.unlim_dim); + + /* Get the swizzled number of chunks in each dimension */ + HDmemcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0])); + H5VM_swizzle_coords(hsize_t, swizzled_chunks, layout->u.earray.unlim_dim); + + /* Get the swizzled "down" sizes for each dimension */ + if(H5VM_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_cb + * + * Purpose: Callback routine for extensible array element iteration. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; Feb 2015 + * + *------------------------------------------------------------------------- + */ +static int +H5D__earray_idx_iterate_cb(hsize_t H5_ATTR_UNUSED idx, const void *_elmt, void *_udata) +{ + H5D_earray_it_ud_t *udata = (H5D_earray_it_ud_t *)_udata; /* User data */ + unsigned ndims; /* Rank of chunk */ + int curr_dim; /* Current dimension */ + int ret_value = H5_ITER_CONT; /* Return value */ + + FUNC_ENTER_STATIC_NOERR + + /* Compose generic chunk record for callback */ + if(udata->filtered) { + const H5D_earray_filt_elmt_t *filt_elmt = (const H5D_earray_filt_elmt_t *)_elmt; + + udata->chunk_rec.chunk_addr = filt_elmt->addr; + udata->chunk_rec.nbytes = filt_elmt->nbytes; + udata->chunk_rec.filter_mask = filt_elmt->filter_mask; + } /* end if */ + else + udata->chunk_rec.chunk_addr = *(const haddr_t *)_elmt; + + /* Make "generic chunk" callback */ + if(H5F_addr_defined(udata->chunk_rec.chunk_addr)) + if((ret_value = (udata->cb)(&udata->chunk_rec, udata->udata)) < 0) + HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback"); + + /* Update coordinates of chunk in dataset */ + ndims = udata->common.layout->ndims - 1; + HDassert(ndims > 0); + curr_dim = (int)(ndims - 1); + while(curr_dim >= 0) { + /* Increment coordinate in current dimension */ + udata->chunk_rec.scaled[curr_dim]++; + + /* Check if we went off the end of the current dimension */ + if(udata->chunk_rec.scaled[curr_dim] >= udata->common.layout->chunks[curr_dim]) { + /* Reset coordinate & move to next faster dimension */ + udata->chunk_rec.scaled[curr_dim] = 0; + curr_dim--; + } /* end if */ + else + break; + } /* end while */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__earray_idx_iterate_cb() */ + + +/*------------------------------------------------------------------------- + * 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_STATIC + + /* Sanity checks */ + 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") + } else /* Patch the top level file pointer contained in ea if needed */ + H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f); + + /* 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") + + if(ea_stat.stored.max_idx_set > 0) { + H5D_earray_it_ud_t udata; /* User data for iteration callback */ + + /* Initialize userdata */ + HDmemset(&udata, 0, sizeof udata); + udata.common.layout = idx_info->layout; + udata.common.storage = idx_info->storage; + HDmemset(&udata.chunk_rec, 0, sizeof(udata.chunk_rec)); + udata.filtered = (idx_info->pline->nused > 0); + if(!udata.filtered) { + udata.chunk_rec.nbytes = idx_info->layout->size; + udata.chunk_rec.filter_mask = 0; + } /* end if */ + udata.cb = chunk_cb; + udata.udata = chunk_udata; + + /* Iterate over the extensible array elements */ + if((ret_value = H5EA_iterate(ea, idx_info->dxpl_id, H5D__earray_idx_iterate_cb, &udata)) < 0) + HERROR(H5E_DATASET, H5E_BADITER, "unable to iterate over fixed array chunk index"); + } /* 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_STATIC + + /* Sanity checks */ + 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") + + /* 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 */ + unsigned u; + + /* Compute coordinate offset from scaled offset */ + for(u = 0; u < ndims; u++) + swizzled_coords[u] = udata->scaled[u] * idx_info->layout->dim[u]; + + H5VM_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim); + + /* Calculate the index of this chunk */ + idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks); + } /* end if */ + else { + /* Calculate the index of this chunk */ + idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->down_chunks, udata->scaled); + } /* 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_STATIC + + /* 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_STATIC + + /* 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_STATIC + + /* 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") + + /* Set copied metadata tag */ + H5_BEGIN_TAG(idx_info_dst->dxpl_id, H5AC__COPIED_TAG, FAIL); + + /* 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)); + + /* Reset metadata tag */ + H5_END_TAG(FAIL); + +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_STATIC + + /* 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_STATIC + + /* 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 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__earray_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr) +{ + FUNC_ENTER_STATIC_NOERR + + /* 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_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_STATIC_NOERR + + /* 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_STATIC + + /* 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) { + /* 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() */ + diff --git a/src/H5Dint.c b/src/H5Dint.c index 6c1f24a..0355656 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -1222,6 +1222,11 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, if(H5D__layout_set_latest_version(&new_dset->shared->layout, new_dset->shared->space, &new_dset->shared->dcpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of layout") } /* end if */ + else if(new_dset->shared->layout.version >= H5O_LAYOUT_VERSION_4) { + /* Use latest indexing type for layout message version >= 4 */ + if(H5D__layout_set_latest_indexing(&new_dset->shared->layout, new_dset->shared->space, &new_dset->shared->dcpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest indexing") + } /* end if */ /* Check if this dataset is going into a parallel file and set space allocation time */ if(H5F_HAS_FEATURE(file, H5FD_FEAT_ALLOCATE_EARLY)) diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c index 7801632..c213140 100644 --- a/src/H5Dlayout.c +++ b/src/H5Dlayout.c @@ -96,8 +96,24 @@ H5D__layout_set_io_ops(const H5D_t *dataset) dataset->shared->layout.ops = H5D_LOPS_CHUNK; /* Set the chunk operations */ - /* (Only "B-tree" indexing type currently supported) */ - dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BTREE; + switch(dataset->shared->layout.u.chunk.idx_type) { + case H5D_CHUNK_IDX_BTREE: + dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BTREE; + break; + + case H5D_CHUNK_IDX_EARRAY: + dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_EARRAY; + break; + + case H5D_CHUNK_IDX_BT2: + dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BT2; + break; + + case H5D_CHUNK_IDX_NTYPES: + default: + HDassert(0 && "Unknown chunk index method!"); + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown chunk index method") + } /* end switch */ break; case H5D_COMPACT: @@ -190,8 +206,30 @@ H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t includ /* Dimension sizes */ ret_value += layout->u.chunk.ndims * layout->u.chunk.enc_bytes_per_dim; - /* B-tree address */ - ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */ + /* Type of chunk index */ + ret_value++; + + switch(layout->u.chunk.idx_type) { + case H5D_CHUNK_IDX_BTREE: + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, 0, "v1 B-tree index type found for layout message >v3") + + case H5D_CHUNK_IDX_EARRAY: + /* Extensible array creation parameters */ + ret_value += H5D_EARRAY_CREATE_PARAM_SIZE; + break; + + case H5D_CHUNK_IDX_BT2: + /* v2 B-tree creation parameters */ + ret_value += H5D_BT2_CREATE_PARAM_SIZE; + break; + + case H5D_CHUNK_IDX_NTYPES: + default: + HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, 0, "Invalid chunk index type") + } /* end switch */ + + /* Chunk index address */ + ret_value += H5F_SIZEOF_ADDR(f); } /* end else */ break; @@ -241,12 +279,106 @@ H5D__layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space, /* Set encoding of layout to latest version */ layout->version = H5O_LAYOUT_VERSION_LATEST; + /* Set the latest indexing type for the layout message */ + if(H5D__layout_set_latest_indexing(layout, space, dcpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest indexing type") + done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__layout_set_latest_version() */ /*------------------------------------------------------------------------- + * Function: H5D__layout_set_latest_indexing + * + * Purpose: Set the latest indexing type for a layout message + * This is moved from H5D_layout_set_latest_version(). + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, January 15, 2009 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__layout_set_latest_indexing(H5O_layout_t *layout, const H5S_t *space, + const H5D_dcpl_cache_t *dcpl_cache) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Sanity check */ + HDassert(layout); + HDassert(space); + HDassert(dcpl_cache); + + /* The indexing methods only apply to chunked datasets (currently) */ + if(layout->type == H5D_CHUNKED) { + int sndims; /* Rank of dataspace */ + unsigned ndims; /* Rank of dataspace */ + + /* Query the dimensionality of the dataspace */ + if((sndims = H5S_GET_EXTENT_NDIMS(space)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "invalid dataspace rank") + ndims = (unsigned)sndims; + + /* Avoid scalar/null dataspace */ + if(ndims > 0) { + hsize_t max_dims[H5O_LAYOUT_NDIMS]; /* Maximum dimension sizes */ + hsize_t cur_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */ + unsigned unlim_count = 0; /* Count of unlimited max. dimensions */ + unsigned u; /* Local index variable */ + + /* Query the dataspace's dimensions */ + if(H5S_get_simple_extent_dims(space, cur_dims, max_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace max. dimensions") + + /* Spin through the max. dimensions, looking for unlimited dimensions */ + for(u = 0; u < ndims; u++) + if(max_dims[u] == H5S_UNLIMITED) + unlim_count++; + + if(1 == unlim_count) { /* Chunked dataset with only 1 unlimited dimension */ + /* Set the chunk index type to an extensible array */ + layout->u.chunk.idx_type = H5D_CHUNK_IDX_EARRAY; + layout->storage.u.chunk.idx_type = H5D_CHUNK_IDX_EARRAY; + layout->storage.u.chunk.ops = H5D_COPS_EARRAY; + + /* Set the extensible array creation parameters */ + /* (use hard-coded defaults for now, until we give applications + * control over this with a property list - QAK) + */ + layout->u.chunk.u.earray.cparam.max_nelmts_bits = H5D_EARRAY_MAX_NELMTS_BITS; + layout->u.chunk.u.earray.cparam.idx_blk_elmts = H5D_EARRAY_IDX_BLK_ELMTS; + layout->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs = H5D_EARRAY_SUP_BLK_MIN_DATA_PTRS; + layout->u.chunk.u.earray.cparam.data_blk_min_elmts = H5D_EARRAY_DATA_BLK_MIN_ELMTS; + layout->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits = H5D_EARRAY_MAX_DBLOCK_PAGE_NELMTS_BITS; + } /* end if */ + else { + /* Set the chunk index type to v2 B-tree */ + layout->u.chunk.idx_type = H5D_CHUNK_IDX_BT2; + layout->storage.u.chunk.idx_type = H5D_CHUNK_IDX_BT2; + layout->storage.u.chunk.ops = H5D_COPS_BT2; + + /* Set the v2 B-tree creation parameters */ + /* (use hard-coded defaults for now, until we give applications + * control over this with a property list - QAK) + */ + layout->u.chunk.u.btree2.cparam.node_size = H5D_BT2_NODE_SIZE; + layout->u.chunk.u.btree2.cparam.split_percent = H5D_BT2_SPLIT_PERC; + layout->u.chunk.u.btree2.cparam.merge_percent = H5D_BT2_MERGE_PERC; + } /* end else */ + } /* end if */ + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__layout_set_latest_indexing() */ + + +/*------------------------------------------------------------------------- * Function: H5D__layout_oh_create * * Purpose: Create layout/pline/efl information for dataset diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 8fc5cac..bfd0601 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -33,6 +33,7 @@ /* Other private headers needed by this file */ #include "H5ACprivate.h" /* Metadata cache */ +#include "H5B2private.h" /* v2 B-trees */ #include "H5Fprivate.h" /* File access */ #include "H5Gprivate.h" /* Groups */ #include "H5SLprivate.h" /* Skip lists */ @@ -67,6 +68,23 @@ #define H5D_MARK_SPACE 0x01 #define H5D_MARK_LAYOUT 0x02 +/* Default creation parameters for chunk index data structures */ +/* See H5O_layout_chunk_t */ + +/* Extensible array creation values */ +#define H5D_EARRAY_CREATE_PARAM_SIZE 5 /* Size of the creation parameters in bytes */ +#define H5D_EARRAY_MAX_NELMTS_BITS 32 /* i.e. 4 giga-elements */ +#define H5D_EARRAY_IDX_BLK_ELMTS 4 +#define H5D_EARRAY_SUP_BLK_MIN_DATA_PTRS 4 +#define H5D_EARRAY_DATA_BLK_MIN_ELMTS 16 +#define H5D_EARRAY_MAX_DBLOCK_PAGE_NELMTS_BITS 10 /* i.e. 1024 elements per data block page */ + +/* v2 B-tree creation values for raw meta_size */ +#define H5D_BT2_CREATE_PARAM_SIZE 6 /* Size of the creation parameters in bytes */ +#define H5D_BT2_NODE_SIZE 2048 +#define H5D_BT2_SPLIT_PERC 100 +#define H5D_BT2_MERGE_PERC 40 + /****************************/ /* Package Private Typedefs */ @@ -519,6 +537,12 @@ H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1]; /* Chunked layout operations */ H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_BTREE[1]; +H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_EARRAY[1]; +H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_BT2[1]; + +/* The v2 B-tree class for indexing chunked datasets with >1 unlimited dimensions */ +H5_DLLVAR const H5B2_class_t H5D_BT2[1]; +H5_DLLVAR const H5B2_class_t H5D_BT2_FILT[1]; /******************************/ @@ -584,6 +608,8 @@ H5_DLL size_t H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t include_compact_data); H5_DLL herr_t H5D__layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space, const H5D_dcpl_cache_t *dcpl_cache); +H5_DLL herr_t H5D__layout_set_latest_indexing(H5O_layout_t *layout, + const H5S_t *space, const H5D_dcpl_cache_t *dcpl_cache); H5_DLL herr_t H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset, hid_t dapl_id); H5_DLL herr_t H5D__layout_oh_read(H5D_t *dset, hid_t dxpl_id, hid_t dapl_id, @@ -721,6 +747,7 @@ H5_DLL htri_t H5D__mpio_opt_possible(const H5D_io_info_t *io_info, #ifdef H5D_TESTING H5_DLL herr_t H5D__layout_version_test(hid_t did, unsigned *version); H5_DLL herr_t H5D__layout_contig_size_test(hid_t did, hsize_t *size); +H5_DLL herr_t H5D__layout_idx_type_test(hid_t did, H5D_chunk_index_t *idx_type); H5_DLL herr_t H5D__current_cache_size_test(hid_t did, size_t *nbytes_used, int *nused); #endif /* H5D_TESTING */ diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index 39e6aa7..a7bd981 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -61,7 +61,9 @@ typedef enum H5D_layout_t { /* Types of chunk index data structures */ typedef enum H5D_chunk_index_t { H5D_CHUNK_IDX_BTREE = 0, /* v1 B-tree index */ - H5D_CHUNK_IDX_NTYPES /* this one must be last! */ + H5D_CHUNK_IDX_EARRAY = 4, /* Extensible array (for 1 unlimited dim) */ + H5D_CHUNK_IDX_BT2 = 5, /* v2 B-tree index (for >1 unlimited dims) */ + H5D_CHUNK_IDX_NTYPES /*this one must be last! */ } H5D_chunk_index_t; /* Values for the space allocation time property */ diff --git a/src/H5Dtest.c b/src/H5Dtest.c index fd8ff71..c3b0b19 100644 --- a/src/H5Dtest.c +++ b/src/H5Dtest.c @@ -144,6 +144,47 @@ done: /*-------------------------------------------------------------------------- NAME + H5D__layout_idx_type_test + PURPOSE + Determine the storage layout index type for a dataset's layout information + USAGE + herr_t H5D__layout_idx_type_test(did, idx_type) + hid_t did; IN: Dataset to query + H5D_chunk_index_t *idx_type; OUT: Pointer to location to place index type info + RETURNS + Non-negative on success, negative on failure + DESCRIPTION + Checks the index type of the storage layout information for a dataset. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + DO NOT USE THIS FUNCTION FOR ANYTHING EXCEPT TESTING + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +herr_t +H5D__layout_idx_type_test(hid_t did, H5D_chunk_index_t *idx_type) +{ + H5D_t *dset; /* Pointer to dataset to query */ + herr_t ret_value = SUCCEED; /* return value */ + + FUNC_ENTER_PACKAGE + + /* Check args */ + if(NULL == (dset = (H5D_t *)H5I_object_verify(did, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + if(dset->shared->layout.type != H5D_CHUNKED) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not chunked") + + if(idx_type) + *idx_type = dset->shared->layout.u.chunk.idx_type; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__layout_idx_type_test() */ + + +/*-------------------------------------------------------------------------- + NAME H5D__current_cache_size_test PURPOSE Determine current the size of the dataset's chunk cache @@ -88,6 +88,8 @@ hbool_t H5_PKG_INIT_VAR = FALSE; * client class.. */ const H5EA_class_t *const H5EA_client_class_g[] = { + H5EA_CLS_CHUNK, /* 0 - H5EA_CLS_CHUNK_ID */ + H5EA_CLS_FILT_CHUNK, /* 1 - H5EA_CLS_FILT_CHUNK_ID */ H5EA_CLS_TEST, /* ? - H5EA_CLS_TEST_ID */ }; @@ -104,6 +106,8 @@ const H5EA_class_t *const H5EA_client_class_g[] = { /* Declare a free list to manage the H5EA_t struct */ H5FL_DEFINE_STATIC(H5EA_t); +/* Declare a PQ free list to manage the element */ +H5FL_BLK_DEFINE(ea_native_elmt); /*------------------------------------------------------------------------- @@ -1032,3 +1036,87 @@ CATCH END_FUNC(PRIV) /* end H5EA_delete() */ + +/*------------------------------------------------------------------------- + * Function: H5EA_iterate + * + * Purpose: Iterate over the elements of an extensible array + * (copied and modified from FA_iterate() in H5FA.c) + * + * Return: SUCCEED/FAIL + * + * Programmer: Vailin Choi; Feb 2015 + * + *------------------------------------------------------------------------- + */ +BEGIN_FUNC(PRIV, ERR, +herr_t, SUCCEED, FAIL, +H5EA_iterate(H5EA_t *ea, hid_t dxpl_id, H5EA_operator_t op, void *udata)) + + /* Local variables */ + uint8_t *elmt = NULL; + hsize_t u; + + /* + * Check arguments. + */ + HDassert(ea); + HDassert(op); + HDassert(udata); + + /* Allocate space for a native array element */ + if(NULL == (elmt = H5FL_BLK_MALLOC(ea_native_elmt, ea->hdr->cparam.cls->nat_elmt_size))) + H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array element") + + /* Iterate over all elements in array */ + for(u = 0; u < ea->hdr->stats.stored.max_idx_set; u++) { + int cb_ret; /* Return value from callback */ + + /* Get array element */ + if(H5EA_get(ea, dxpl_id, u, elmt) < 0) + H5E_THROW(H5E_CANTGET, "unable to delete fixed array") + + /* Make callback */ + if((cb_ret = (*op)(u, elmt, udata)) < 0) { + H5E_PRINTF(H5E_BADITER, "iterator function failed"); + H5_LEAVE(cb_ret) + } /* end if */ + } /* end for */ + +CATCH + + if(elmt) + elmt = H5FL_BLK_FREE(ea_native_elmt, elmt); + +END_FUNC(PRIV) /* end H5EA_iterate() */ + + +/*------------------------------------------------------------------------- + * Function: H5EA_patch_file + * + * Purpose: Patch the top-level file pointer contained in ea + * to point to idx_info->f if they are different. + * This is possible because the file pointer in ea can be + * closed out if ea remains open. + * + * Return: SUCCEED + * + *------------------------------------------------------------------------- + */ +BEGIN_FUNC(PRIV, NOERR, +herr_t, SUCCEED, -, +H5EA_patch_file(H5EA_t *ea, H5F_t *f)) + + /* Local variables */ + + /* + * Check arguments. + */ + HDassert(ea); + HDassert(f); + + if(ea->f != f || ea->hdr->f != f) + ea->f = ea->hdr->f = f; + +END_FUNC(PRIV) /* end H5EA_patch_file() */ + diff --git a/src/H5EAprivate.h b/src/H5EAprivate.h index 9147f39..0a1b945 100644 --- a/src/H5EAprivate.h +++ b/src/H5EAprivate.h @@ -49,6 +49,9 @@ /* Extensible array class IDs */ typedef enum H5EA_cls_id_t { + H5EA_CLS_CHUNK_ID = 0, /* Extensible array is for indexing dataset chunks w/o filters */ + H5EA_CLS_FILT_CHUNK_ID, /* Extensible array is for indexing dataset chunks w/filters */ + /* Start real class IDs at 0 -QAK */ /* (keep these last) */ H5EA_CLS_TEST_ID, /* Extensible array is for testing (do not use for actual data) */ @@ -112,11 +115,20 @@ typedef struct H5EA_stat_t { /* Extensible array info (forward decl - defined in H5EApkg.h) */ typedef struct H5EA_t H5EA_t; +/* Define the operator callback function pointer for H5EA_iterate() */ +typedef int (*H5EA_operator_t)(hsize_t idx, const void *_elmt, void *_udata); + /*****************************/ /* Library-private Variables */ /*****************************/ +/* The Extensible Array class for dataset chunks w/o filters*/ +H5_DLLVAR const H5EA_class_t H5EA_CLS_CHUNK[1]; + +/* The Extensible Array class for dataset chunks w/ filters*/ +H5_DLLVAR const H5EA_class_t H5EA_CLS_FILT_CHUNK[1]; + /***************************************/ /* Library-private Function Prototypes */ @@ -131,8 +143,10 @@ H5_DLL herr_t H5EA_get_addr(const H5EA_t *ea, haddr_t *addr); H5_DLL herr_t H5EA_set(const H5EA_t *ea, hid_t dxpl_id, hsize_t idx, const void *elmt); H5_DLL herr_t H5EA_get(const H5EA_t *ea, hid_t dxpl_id, hsize_t idx, void *elmt); H5_DLL herr_t H5EA_depend(H5AC_info_t *parent_entry, H5EA_t *ea); +H5_DLL herr_t H5EA_iterate(H5EA_t *fa, hid_t dxpl_id, H5EA_operator_t op, void *udata); H5_DLL herr_t H5EA_close(H5EA_t *ea, hid_t dxpl_id); H5_DLL herr_t H5EA_delete(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr, void *ctx_udata); +H5_DLL herr_t H5EA_patch_file(H5EA_t *fa, H5F_t *f); /* Statistics routines */ H5_DLL herr_t H5EA_get_stats(const H5EA_t *ea, H5EA_stat_t *stats); diff --git a/src/H5Olayout.c b/src/H5Olayout.c index f2af8ef..c19bbfc 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -287,9 +287,52 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED for(u = 1, mesg->u.chunk.size = mesg->u.chunk.dim[0]; u < mesg->u.chunk.ndims; u++) mesg->u.chunk.size *= mesg->u.chunk.dim[u]; - /* Set the chunk operations */ - mesg->storage.u.chunk.idx_type = H5D_CHUNK_IDX_BTREE; - mesg->storage.u.chunk.ops = H5D_COPS_BTREE; + /* Chunk index type */ + mesg->u.chunk.idx_type = (H5D_chunk_index_t)*p++; + if(mesg->u.chunk.idx_type >= H5D_CHUNK_IDX_NTYPES) + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "unknown chunk index type") + mesg->storage.u.chunk.idx_type = mesg->u.chunk.idx_type; + + switch(mesg->u.chunk.idx_type) { + case H5D_CHUNK_IDX_BTREE: + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "v1 B-tree index type should never be in a v4 layout message") + break; + + case H5D_CHUNK_IDX_EARRAY: + /* Extensible array creation parameters */ + mesg->u.chunk.u.earray.cparam.max_nelmts_bits = *p++; + if(0 == mesg->u.chunk.u.earray.cparam.max_nelmts_bits) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter") + mesg->u.chunk.u.earray.cparam.idx_blk_elmts = *p++; + if(0 == mesg->u.chunk.u.earray.cparam.idx_blk_elmts) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter") + mesg->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs = *p++; + if(0 == mesg->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter") + mesg->u.chunk.u.earray.cparam.data_blk_min_elmts = *p++; + if(0 == mesg->u.chunk.u.earray.cparam.data_blk_min_elmts) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter") + mesg->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits = *p++; + if(0 == mesg->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter") + + /* Set the chunk operations */ + mesg->storage.u.chunk.ops = H5D_COPS_EARRAY; + break; + + case H5D_CHUNK_IDX_BT2: /* v2 B-tree index */ + UINT32DECODE(p, mesg->u.chunk.u.btree2.cparam.node_size); + mesg->u.chunk.u.btree2.cparam.split_percent = *p++; + mesg->u.chunk.u.btree2.cparam.merge_percent = *p++; + + /* Set the chunk operations */ + mesg->storage.u.chunk.ops = H5D_COPS_BT2; + break; + + case H5D_CHUNK_IDX_NTYPES: + default: + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "Invalid chunk index type") + } /* end switch */ /* Chunk index address */ H5F_addr_decode(f, &p, &(mesg->storage.u.chunk.idx_addr)); @@ -557,6 +600,34 @@ H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, for(u = 0; u < mesg->u.chunk.ndims; u++) UINT64ENCODE_VAR(p, mesg->u.chunk.dim[u], mesg->u.chunk.enc_bytes_per_dim); + /* Chunk index type */ + *p++ = (uint8_t)mesg->u.chunk.idx_type; + + switch(mesg->u.chunk.idx_type) { + case H5D_CHUNK_IDX_BTREE: + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "v1 B-tree index type should never be in a v4 layout message") + break; + + case H5D_CHUNK_IDX_EARRAY: + /* Extensible array creation parameters */ + *p++ = mesg->u.chunk.u.earray.cparam.max_nelmts_bits; + *p++ = mesg->u.chunk.u.earray.cparam.idx_blk_elmts; + *p++ = mesg->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs; + *p++ = mesg->u.chunk.u.earray.cparam.data_blk_min_elmts; + *p++ = mesg->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits; + break; + + case H5D_CHUNK_IDX_BT2: /* v2 B-tree index */ + UINT32ENCODE(p, mesg->u.chunk.u.btree2.cparam.node_size); + *p++ = mesg->u.chunk.u.btree2.cparam.split_percent; + *p++ = mesg->u.chunk.u.btree2.cparam.merge_percent; + break; + + case H5D_CHUNK_IDX_NTYPES: + default: + HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "Invalid chunk index type") + } /* end switch */ + /* * Implicit index: Address of the chunks * Single chunk index: address of the single chunk @@ -1082,20 +1153,32 @@ H5O__layout_debug(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, const v HDfprintf(stream, "}\n"); /* Index information */ - switch(mesg->storage.u.chunk.idx_type) { + switch(mesg->u.chunk.idx_type) { case H5D_CHUNK_IDX_BTREE: HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, "Index Type:", "v1 B-tree"); - HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, - "B-tree address:", mesg->storage.u.chunk.idx_addr); + break; + + case H5D_CHUNK_IDX_EARRAY: + HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, + "Index Type:", "Extensible Array"); + /* (Should print the extensible array creation parameters) */ + break; + + case H5D_CHUNK_IDX_BT2: + HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, + "Index Type:", "v2 B-tree"); + /* (Should print the v2-Btree creation parameters) */ break; case H5D_CHUNK_IDX_NTYPES: default: HDfprintf(stream, "%*s%-*s %s (%u)\n", indent, "", fwidth, - "Index Type:", "Unknown", (unsigned)mesg->storage.u.chunk.idx_type); + "Index Type:", "Unknown", (unsigned)mesg->u.chunk.idx_type); break; } /* end switch */ + HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, + "Index address:", mesg->storage.u.chunk.idx_addr); break; case H5D_CONTIGUOUS: diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index 8175bd8..a5f07b2 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -416,12 +416,30 @@ typedef struct H5O_storage_chunk_btree_t { H5UC_t *shared; /* Ref-counted shared info for B-tree nodes */ } H5O_storage_chunk_btree_t; +/* Forward declaration of structs used below */ +struct H5EA_t; /* Defined in H5EAprivate.h */ + +typedef struct H5O_storage_chunk_earray_t { + haddr_t dset_ohdr_addr; /* File address dataset's object header */ + struct H5EA_t *ea; /* Pointer to extensible index array struct */ +} H5O_storage_chunk_earray_t; + +/* Forward declaration of structs used below */ +struct H5B2_t; /* Defined in H5B2pkg.h */ + +typedef struct H5O_storage_chunk_bt2_t { + haddr_t dset_ohdr_addr; /* File address dataset's object header */ + struct H5B2_t *bt2; /* Pointer to b-tree 2 struct */ +} H5O_storage_chunk_bt2_t; + typedef struct H5O_storage_chunk_t { H5D_chunk_index_t idx_type; /* Type of chunk index */ haddr_t idx_addr; /* File address of chunk index */ const struct H5D_chunk_ops_t *ops; /* Pointer to chunked storage operations */ union { H5O_storage_chunk_btree_t btree; /* Information for v1 B-tree index */ + H5O_storage_chunk_bt2_t btree2; /* Information for v2 B-tree index */ + H5O_storage_chunk_earray_t earray; /* Information for extensible array index */ } u; } H5O_storage_chunk_t; @@ -516,7 +534,32 @@ typedef struct H5O_storage_t { } u; } H5O_storage_t; +typedef struct H5O_layout_chunk_earray_t { + /* Creation parameters for extensible array data structure */ + struct { + uint8_t max_nelmts_bits; /* Log2(Max. # of elements in array) - i.e. # of bits needed to store max. # of elements */ + uint8_t idx_blk_elmts; /* # of elements to store in index block */ + uint8_t data_blk_min_elmts; /* Min. # of elements per data block */ + uint8_t sup_blk_min_data_ptrs; /* Min. # of data block pointers for a super block */ + uint8_t max_dblk_page_nelmts_bits; /* Log2(Max. # of elements in data block page) - i.e. # of bits needed to store max. # of elements in data block page */ + } cparam; + + unsigned unlim_dim; /* Rank of unlimited dimension for dataset */ + uint32_t swizzled_dim[H5O_LAYOUT_NDIMS]; /* swizzled chunk dimensions */ + hsize_t swizzled_down_chunks[H5O_LAYOUT_NDIMS]; /* swizzled "down" size of number of chunks in each dimension */ +} H5O_layout_chunk_earray_t; + +typedef struct H5O_layout_chunk_bt2_t { + /* Creation parameters for v2 B-tree data structure */ + struct { + uint32_t node_size; /* Size of each node (in bytes) */ + uint8_t split_percent; /* % full to split nodes */ + uint8_t merge_percent; /* % full to merge nodes */ + } cparam; +} H5O_layout_chunk_bt2_t; + typedef struct H5O_layout_chunk_t { + H5D_chunk_index_t idx_type; /* Type of chunk index */ uint8_t flags; /* Chunk layout flags */ unsigned ndims; /* Num dimensions in chunk */ uint32_t dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in elements */ @@ -528,6 +571,10 @@ typedef struct H5O_layout_chunk_t { hsize_t max_chunks[H5O_LAYOUT_NDIMS]; /* # of chunks in each dataset's max. dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ hsize_t max_down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each max dim */ + union { + H5O_layout_chunk_earray_t earray; /* Information for extensible array index */ + H5O_layout_chunk_bt2_t btree2; /* Information for v2 B-tree index */ + } u; } H5O_layout_chunk_t; typedef struct H5O_layout_t { diff --git a/src/H5VMprivate.h b/src/H5VMprivate.h index 7d3361b..f402b36 100644 --- a/src/H5VMprivate.h +++ b/src/H5VMprivate.h @@ -49,6 +49,22 @@ typedef herr_t (*H5VM_opvv_func_t)(hsize_t dst_off, hsize_t src_off, #define H5VM_vector_zero(N,DST) HDmemset(DST,0,(N)*sizeof(*(DST))) +/* Given a coordinate offset array (COORDS) of type TYPE, move the unlimited + * dimension (UNLIM_DIM) value to offset 0, sliding any intermediate values down + * one position. */ +#define H5VM_swizzle_coords(TYPE,COORDS,UNLIM_DIM) { \ + /* COORDS must be an array of type TYPE */ \ + HDassert(sizeof(COORDS[0]) == sizeof(TYPE)); \ + \ + /* Nothing to do when unlimited dimension is at position 0 */ \ + if(0 != (UNLIM_DIM)) { \ + TYPE _tmp = (COORDS)[UNLIM_DIM]; \ + \ + HDmemmove(&(COORDS)[1], &(COORDS)[0], sizeof(TYPE) * (UNLIM_DIM)); \ + (COORDS)[0] = _tmp; \ + } /* end if */ \ +} + /* A null pointer is equivalent to a zero vector */ #define H5VM_ZERO NULL diff --git a/src/Makefile.am b/src/Makefile.am index 9f748bf..ca9c4c3 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -47,8 +47,8 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ H5B2.c H5B2cache.c H5B2dbg.c H5B2hdr.c H5B2int.c H5B2stat.c H5B2test.c \ H5C.c \ H5CS.c \ - H5D.c H5Dbtree.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \ - H5Ddeprec.c H5Defl.c H5Dfill.c H5Dint.c \ + H5D.c H5Dbtree.c H5Dbtree2.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \ + H5Ddeprec.c H5Dearray.c H5Defl.c H5Dfill.c H5Dint.c \ H5Dio.c H5Dlayout.c \ H5Doh.c H5Dscatgath.c H5Dselect.c H5Dtest.c H5Dvirtual.c \ H5E.c H5Edeprec.c H5Eint.c \ @@ -84,8 +84,10 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ H5Olayout.c \ H5Olinfo.c H5Olink.c H5Omessage.c H5Omtime.c \ H5Oname.c H5Onull.c H5Opline.c H5Orefcount.c \ - H5Osdspace.c H5Oshared.c H5Ostab.c \ - H5Oshmesg.c H5Otest.c H5Ounknown.c \ + H5Osdspace.c H5Oshared.c \ + H5Oshmesg.c \ + H5Ostab.c \ + H5Otest.c H5Ounknown.c \ H5P.c H5Pacpl.c H5Pdapl.c H5Pdcpl.c \ H5Pdeprec.c H5Pdxpl.c H5Pencdec.c \ H5Pfapl.c H5Pfcpl.c H5Pfmpl.c \ diff --git a/test/dsets.c b/test/dsets.c index b3f11b8..5e92a6e 100644 --- a/test/dsets.c +++ b/test/dsets.c @@ -6462,15 +6462,24 @@ static herr_t test_zero_dims(hid_t file) { hid_t s = -1, d = -1, dcpl = -1; - hsize_t dsize = 0, dmax = H5S_UNLIMITED, csize = 5; + hsize_t dzero = 0, dmax = H5S_UNLIMITED, csize = 5; + hid_t fapl; /* File access property list */ + H5D_chunk_index_t idx_type; /* Dataset chunk index type */ + H5F_libver_t low; /* File format low bound */ herr_t ret; TESTING("I/O on datasets with zero-sized dims"); + /* Get the file's file access property list */ + if((fapl = H5Fget_access_plist(file)) < 0) FAIL_STACK_ERROR + + /* Get library format */ + if(H5Pget_libver_bounds(fapl, &low, NULL) < 0) FAIL_STACK_ERROR + /* * One-dimensional dataset */ - if((s = H5Screate_simple(1, &dsize, &dmax)) < 0) FAIL_STACK_ERROR + if((s = H5Screate_simple(1, &dzero, &dmax)) < 0) FAIL_STACK_ERROR /* Try creating chunked dataset with undefined chunk dimensions */ if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR @@ -6486,7 +6495,7 @@ test_zero_dims(hid_t file) /* Try creating chunked dataset with zero-sized chunk dimensions */ H5E_BEGIN_TRY { - ret = H5Pset_chunk(dcpl, 1, &dsize); + ret = H5Pset_chunk(dcpl, 1, &dzero); } H5E_END_TRY; if(ret > 0) FAIL_PUTS_ERROR("set zero-sized chunk dimensions") @@ -6498,6 +6507,16 @@ test_zero_dims(hid_t file) if(H5Pset_chunk(dcpl, 1, &csize) < 0) FAIL_STACK_ERROR if((d = H5Dcreate2(file, ZERODIM_DATASET, H5T_NATIVE_INT, s, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR + /* Get the chunk index type */ + if(H5D__layout_idx_type_test(d, &idx_type) < 0) FAIL_STACK_ERROR + + /* Verify index type */ + if(low == H5F_LIBVER_LATEST) { + if(idx_type != H5D_CHUNK_IDX_EARRAY) + FAIL_PUTS_ERROR("should be using extensible array as index"); + } else if(idx_type != H5D_CHUNK_IDX_BTREE) + FAIL_PUTS_ERROR("should be using v1 B-tree as index"); + /* Various no-op writes */ if(H5Dwrite(d, H5T_NATIVE_INT, s, s, H5P_DEFAULT, (void*)911) < 0) FAIL_STACK_ERROR if(H5Dwrite(d, H5T_NATIVE_INT, s, s, H5P_DEFAULT, NULL) < 0) FAIL_STACK_ERROR |