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cf4e78b3c9d1f1ed6687b24bbd738a63b9812a9e
hdf5/src/H5Dearray.c
Dana Robinson 127d1cfdf0 Minor changes from normalization with 1.10
2020-07-09 08:34:01 -07:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Quincey Koziol
* 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 "H5MMprivate.h" /* Memory 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;
/* 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, 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);
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);
static herr_t H5D__earray_idx_depend(const H5D_chk_idx_info_t *idx_info);
/*********************/
/* Package Variables */
/*********************/
/* Extensible array indexed chunk I/O ops */
const H5D_chunk_ops_t H5D_COPS_EARRAY[1] = {{
TRUE, /* Extensible array indices support SWMR access */
H5D__earray_idx_init, /* 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 */
HDsprintf(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 */
HDsprintf(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, 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))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get layout info")
/* close the object header */
if(H5O_close(&obj_loc, NULL) < 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, NULL) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, NULL, "can't close object header")
} /* 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_depend
*
* Purpose: Create flush dependency between extensible array and dataset's
* object header.
*
* Return: Success: non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Tuesday, June 2, 2009
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__earray_idx_depend(const H5D_chk_idx_info_t *idx_info)
{
H5O_t *oh = NULL; /* Object header */
H5O_loc_t oloc; /* Temporary object header location for dataset */
H5AC_proxy_entry_t *oh_proxy; /* Dataset's object header proxy */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Check args */
HDassert(idx_info);
HDassert(idx_info->f);
HDassert(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE);
HDassert(idx_info->pline);
HDassert(idx_info->layout);
HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->layout->idx_type);
HDassert(idx_info->storage);
HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->storage->idx_type);
HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
HDassert(idx_info->storage->u.earray.ea);
/* Set up object header location for dataset */
H5O_loc_reset(&oloc);
oloc.file = idx_info->f;
oloc.addr = idx_info->storage->u.earray.dset_ohdr_addr;
/* Get header */
if(NULL == (oh = H5O_protect(&oloc, H5AC__READ_ONLY_FLAG, TRUE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect object header")
/* Retrieve the dataset's object header proxy */
if(NULL == (oh_proxy = H5O_get_proxy(oh)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get dataset object header proxy")
/* Make the extensible array a child flush dependency of the dataset's object header */
if(H5EA_depend(idx_info->storage->u.earray.ea, oh_proxy) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL, "unable to create flush dependency on object header proxy")
done:
/* Release the object header from the cache */
if(oh && H5O_unprotect(&oloc, oh, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to release object header")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__earray_idx_depend() */
/*-------------------------------------------------------------------------
* 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->storage->idx_addr, &udata)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open extensible array")
/* Check for SWMR writes to the file */
if(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE)
if(H5D__earray_idx_depend(idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL, "unable to create flush dependency on object header")
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, &cparam, &udata)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create extensible array")
/* Get the address of the extensible array in file */
if(H5EA_get_addr(idx_info->storage->u.earray.ea, &(idx_info->storage->idx_addr)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query extensible array address")
/* Check for SWMR writes to the file */
if(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE)
if(H5D__earray_idx_depend(idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL, "unable to create flush dependency on object header")
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, 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, 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_max_down_chunks);
} /* end if */
else {
/* Calculate the index of this chunk */
idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->max_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, &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, &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 */
hsize_t swizzled_max_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of max # of chunks in each dimension */
/* Get the swizzled chunk dimensions */
H5MM_memcpy(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 */
H5MM_memcpy(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")
/* Get the swizzled max number of chunks in each dimension */
H5MM_memcpy(swizzled_max_chunks, layout->max_chunks, (layout->ndims - 1) * sizeof(swizzled_max_chunks[0]));
H5VM_swizzle_coords(hsize_t, swizzled_max_chunks, layout->u.earray.unlim_dim);
/* Get the swizzled max "down" sizes for each dimension */
if(H5VM_array_down((layout->ndims - 1), swizzled_max_chunks, layout->u.earray.swizzled_max_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->max_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, 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")
} else /* Patch the top level file pointer contained in ea if needed */
if(H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch earray file pointer")
/* 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_max_down_chunks);
} /* end if */
else {
/* Calculate the index of this chunk */
idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->max_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, &elmt) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info")
/* Remove raw data chunk from file if not doing SWMR writes */
HDassert(H5F_addr_defined(elmt.addr));
if(!(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE)) {
H5_CHECK_OVERFLOW(elmt.nbytes, /*From: */uint32_t, /*To: */hsize_t);
if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, elmt.addr, (hsize_t)elmt.nbytes) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk")
} /* end if */
/* 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, &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, &addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address")
/* Remove raw data chunk from file if not doing SWMR writes */
HDassert(H5F_addr_defined(addr));
if(!(H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE)) {
H5_CHECK_OVERFLOW(idx_info->layout->size, /*From: */uint32_t, /*To: */hsize_t);
if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, addr, (hsize_t)idx_info->layout->size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk")
} /* end if */
/* Reset the address of the chunk for the index */
addr = HADDR_UNDEF;
if(H5EA_set(ea, 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)
{
H5F_t *f = (H5F_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(f);
/* Remove raw data chunk from file */
H5_CHECK_OVERFLOW(chunk_rec->nbytes, /*From: */uint32_t, /*To: */hsize_t);
if(H5MF_xfree(f, H5FD_MEM_DRAW, 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_ctx_ud_t ctx_udata; /* User data for extensible array open call */
/* Iterate over the chunk addresses in the extensible array, deleting each chunk */
if(H5D__earray_idx_iterate(idx_info, H5D__earray_idx_delete_cb, idx_info->f) < 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) < 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->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(H5AC__COPIED_TAG);
/* 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
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)
{
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) < 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) < 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) < 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) {
/* Patch the top level file pointer contained in ea if needed */
if(H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch earray file pointer")
/* Close extensible array */
if(H5EA_close(idx_info->storage->u.earray.ea) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array")
idx_info->storage->u.earray.ea = NULL;
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__earray_idx_dest() */
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