/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/****************/
/* Module Setup */
/****************/
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Vprivate.h" /* Vector and array functions */
/****************/
/* Local Macros */
/****************/
/* Default skip list height for storing list of chunks */
#define H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT 8
/* Macros for iterating over chunks to operate on */
#define H5D_CHUNK_GET_FIRST_NODE(map) (map->use_single ? (H5SL_node_t *)(1) : H5SL_first(map->sel_chunks))
#define H5D_CHUNK_GET_NODE_INFO(map, node) (map->use_single ? map->single_chunk_info : (H5D_chunk_info_t *)H5SL_item(node))
#define H5D_CHUNK_GET_NEXT_NODE(map, node) (map->use_single ? (H5SL_node_t *)NULL : H5SL_next(node))
/*
* Feature: If this constant is defined then every cache preemption and load
* causes a character to be printed on the standard error stream:
*
* `.': Entry was preempted because it has been completely read or
* completely written but not partially read and not partially
* written. This is often a good reason for preemption because such
* a chunk will be unlikely to be referenced in the near future.
*
* `:': Entry was preempted because it hasn't been used recently.
*
* `#': Entry was preempted because another chunk collided with it. This
* is usually a relatively bad thing. If there are too many of
* these then the number of entries in the cache can be increased.
*
* c: Entry was preempted because the file is closing.
*
* w: A chunk read operation was eliminated because the library is
* about to write new values to the entire chunk. This is a good
* thing, especially on files where the chunk size is the same as
* the disk block size, chunks are aligned on disk block boundaries,
* and the operating system can also eliminate a read operation.
*/
/*#define H5D_CHUNK_DEBUG */
/******************/
/* Local Typedefs */
/******************/
/* Callback info for iteration to prune chunks */
typedef struct H5D_chunk_it_ud1_t {
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
const H5D_chk_idx_info_t *idx_info; /* Chunked index info */
const H5D_io_info_t *io_info; /* I/O info for dataset operation */
const hsize_t *dims; /* New dataset dimensions */
const hsize_t *down_chunks; /* "down" size of number of chunks in each dimension */
H5SL_t *outside; /* Skip list to hold chunks outside the new dimensions */
H5S_t *chunk_space; /* Dataspace for a chunk */
uint32_t elmts_per_chunk;/* Elements in chunk */
hsize_t *hyper_start; /* Starting location of hyperslab */
H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
hbool_t fb_info_init; /* Whether the fill value buffer has been initialized */
} H5D_chunk_it_ud1_t;
/* Skip list node for storing chunks to remove during a "prune" iteration */
typedef struct H5D_chunk_sl_ck_t {
hsize_t index; /* Index of chunk to remove (must be first) */
H5D_chunk_rec_t rec; /* Chunk record */
} H5D_chunk_sl_ck_t;
/* Skip list callback info when destroying list & removing chunks during "prune" */
typedef struct H5D_chunk_sl_rm_t {
const H5D_chk_idx_info_t *idx_info; /* I/O info for dataset operation */
const H5O_layout_t *mesg; /* Layout message */
} H5D_chunk_sl_rm_t;
/* Callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */
typedef struct H5D_chunk_id_ud2_t {
/* down */
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
const hsize_t *down_chunks; /* "down chunk" element counts for chunks */
/* up */
haddr_t *chunk_addr; /* Array of chunk addresses to fill in */
} H5D_chunk_it_ud2_t;
/* Callback info for iteration to copy data */
typedef struct H5D_chunk_it_ud3_t {
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
H5F_t *file_src; /* Source file for copy */
H5D_chk_idx_info_t *idx_info_dst; /* Dest. chunk index info object */
void *buf; /* Buffer to hold chunk data for read/write */
void *bkg; /* Buffer for background information during type conversion */
size_t buf_size; /* Buffer size */
hbool_t do_convert; /* Whether to perform type conversions */
/* needed for converting variable-length data */
hid_t tid_src; /* Datatype ID for source datatype */
hid_t tid_dst; /* Datatype ID for destination datatype */
hid_t tid_mem; /* Datatype ID for memory datatype */
H5T_t *dt_src; /* Source datatype */
H5T_path_t *tpath_src_mem; /* Datatype conversion path from source file to memory */
H5T_path_t *tpath_mem_dst; /* Datatype conversion path from memory to dest. file */
void *reclaim_buf; /* Buffer for reclaiming data */
size_t reclaim_buf_size; /* Reclaim buffer size */
uint32_t nelmts; /* Number of elements in buffer */
H5S_t *buf_space; /* Dataspace describing buffer */
/* needed for compressed variable-length data */
H5O_pline_t *pline; /* Filter pipeline */
/* needed for copy object pointed by refs */
H5O_copy_t *cpy_info; /* Copy options */
} H5D_chunk_it_ud3_t;
/* Callback info for iteration to dump index */
typedef struct H5D_chunk_it_ud4_t {
FILE *stream; /* Output stream */
hbool_t header_displayed; /* Node's header is displayed? */
unsigned ndims; /* Number of dimensions for chunk/dataset */
} H5D_chunk_it_ud4_t;
/********************/
/* Local Prototypes */
/********************/
/* Chunked layout operation callbacks */
static herr_t H5D_chunk_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset,
const H5P_genplist_t *dc_plist);
static herr_t H5D_chunk_io_init(const H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space,
const H5S_t *mem_space, H5D_chunk_map_t *fm);
static herr_t H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm);
static herr_t H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm);
static herr_t H5D_chunk_io_term(const H5D_chunk_map_t *fm);
/* "Null" layout operation callbacks */
static ssize_t H5D_null_readvv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
/* Helper routines */
static void *H5D_chunk_alloc(size_t size, const H5O_pline_t *pline);
static void *H5D_chunk_xfree(void *chk, const H5O_pline_t *pline);
static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata);
static herr_t H5D_create_chunk_map_single(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm);
static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, unsigned ndims,
const hsize_t *coords, void *fm);
static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims,
const hsize_t *coords, void *fm);
/*********************/
/* Package Variables */
/*********************/
/* Compact storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{
H5D_chunk_new,
H5D_chunk_io_init,
H5D_chunk_read,
H5D_chunk_write,
#ifdef H5_HAVE_PARALLEL
H5D_chunk_collective_read,
H5D_chunk_collective_write,
#endif /* H5_HAVE_PARALLEL */
NULL,
NULL,
H5D_chunk_io_term
}};
/*******************/
/* Local Variables */
/*******************/
/* "null" storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_NULL[1] = {{
NULL,
NULL,
NULL,
NULL,
#ifdef H5_HAVE_PARALLEL
NULL,
NULL,
#endif /* H5_HAVE_PARALLEL */
H5D_null_readvv,
NULL,
NULL
}};
/* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */
H5FL_SEQ_DEFINE_STATIC(H5D_rdcc_ent_ptr_t);
/* Declare a free list to manage H5F_rdcc_ent_t objects */
H5FL_DEFINE_STATIC(H5D_rdcc_ent_t);
/* Declare a free list to manage the H5D_chunk_info_t struct */
H5FL_DEFINE(H5D_chunk_info_t);
/* Declare a free list to manage the chunk sequence information */
H5FL_BLK_DEFINE_STATIC(chunk);
/* Declare a free list to manage H5D_chunk_sl_ck_t objects */
H5FL_DEFINE_STATIC(H5D_chunk_sl_ck_t);
/*-------------------------------------------------------------------------
* Function: H5D_chunk_new
*
* Purpose: Constructs new chunked layout information for dataset
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 22, 2008
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset,
const H5P_genplist_t *dc_plist)
{
const H5T_t *type = dset->shared->type; /* Convenience pointer to dataset's datatype */
hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
uint64_t chunk_size; /* Size of chunk in bytes */
unsigned chunk_ndims = 0; /* Dimensionality of chunk */
int ndims; /* Rank of dataspace */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_new)
/* Sanity checks */
HDassert(f);
HDassert(dset);
HDassert(dc_plist);
/* Retrieve rank of chunks from property list */
if(H5P_get(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve chunk dimensions")
/* Set up layout information */
if((ndims = H5S_GET_EXTENT_NDIMS(dset->shared->space)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get rank")
dset->shared->layout.u.chunk.ndims = (unsigned)ndims + 1;
HDassert((unsigned)(dset->shared->layout.u.chunk.ndims) <= NELMTS(dset->shared->layout.u.chunk.dim));
/* Initialize to no address */
dset->shared->layout.u.chunk.addr = HADDR_UNDEF;
/*
* Chunked storage allows any type of data space extension, so we
* don't even bother checking.
*/
if(chunk_ndims != (unsigned)ndims)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dimensionality of chunks doesn't match the data space")
if(dset->shared->dcpl_cache.efl.nused > 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "external storage not supported with chunked layout")
/*
* The chunk size of a dimension with a fixed size cannot exceed
* the maximum dimension size
*/
if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, dset->shared->layout.u.chunk.dim) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve chunk size")
dset->shared->layout.u.chunk.dim[dset->shared->layout.u.chunk.ndims - 1] = H5T_get_size(type);
/* Sanity check dimensions */
if(H5S_get_simple_extent_dims(dset->shared->space, NULL, max_dim) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to query maximum dimensions")
for(u = 0; u < dset->shared->layout.u.chunk.ndims - 1; u++)
if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < dset->shared->layout.u.chunk.dim[u])
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be <= maximum dimension size for fixed-sized dimensions")
/* Compute the total size of a chunk */
/* (Use 64-bit value to ensure that we can detect >4GB chunks) */
for(u = 1, chunk_size = (uint64_t)dset->shared->layout.u.chunk.dim[0]; u < dset->shared->layout.u.chunk.ndims; u++)
chunk_size *= (uint64_t)dset->shared->layout.u.chunk.dim[u];
/* Check for chunk larger than can be represented in 32-bits */
/* (Chunk size is encoded in 32-bit value in v1 B-tree records) */
if(chunk_size > (uint64_t)0xffffffff)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be < 4GB")
/* Retain computed chunk size */
H5_ASSIGN_OVERFLOW(dset->shared->layout.u.chunk.size, chunk_size, uint64_t, uint32_t);
/* Initialize the chunk cache for the dataset */
if(H5D_chunk_init(f, dxpl_id, dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_new() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_io_init
*
* Purpose: Performs initialization before any sort of I/O on the raw data
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, March 20, 2008
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm)
{
H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */
const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */
H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */
htri_t file_space_normalized = FALSE; /* File dataspace was normalized */
hid_t f_tid = (-1); /* Temporary copy of file datatype for iteration */
hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */
unsigned f_ndims; /* The number of dimensions of the file's dataspace */
int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */
H5SL_node_t *curr_node; /* Current node in skip list */
H5S_sel_type fsel_type; /* Selection type on disk */
char bogus; /* "bogus" buffer to pass to selection iterator */
unsigned u; /* Local index variable */
hbool_t sel_hyper_flag;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_io_init)
/* Get layout for dataset */
fm->layout = &(dataset->shared->layout);
fm->nelmts = nelmts;
/* Check if the memory space is scalar & make equivalent memory space */
if((sm_ndims = H5S_GET_EXTENT_NDIMS(mem_space)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number")
/* Set the number of dimensions for the memory dataspace */
H5_ASSIGN_OVERFLOW(fm->m_ndims, sm_ndims, int, unsigned);
/* Get dim number and dimensionality for each dataspace */
fm->f_ndims = f_ndims = dataset->shared->layout.u.chunk.ndims - 1;
if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
/* Normalize hyperslab selections by adjusting them by the offset */
/* (It might be worthwhile to normalize both the file and memory dataspaces
* before any (contiguous, chunked, etc) file I/O operation, in order to
* speed up hyperslab calculations by removing the extra checks and/or
* additions involving the offset and the hyperslab selection -QAK)
*/
if((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
/* Decide the number of chunks in each dimension*/
for(u = 0; u < f_ndims; u++) {
/* Keep the size of the chunk dimensions as hsize_t for various routines */
fm->chunk_dim[u] = fm->layout->u.chunk.dim[u];
/* Round up to the next integer # of chunks, to accomodate partial chunks */
fm->chunks[u] = ((fm->f_dims[u] + dataset->shared->layout.u.chunk.dim[u]) - 1) / dataset->shared->layout.u.chunk.dim[u];
} /* end for */
/* Compute the "down" size of 'chunks' information */
if(H5V_array_down(f_ndims, fm->chunks, fm->down_chunks) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
#ifdef H5_HAVE_PARALLEL
/* Calculate total chunk in file map*/
fm->select_chunk = NULL;
fm->total_chunks = 1;
for(u = 0; u < fm->f_ndims; u++)
fm->total_chunks = fm->total_chunks * fm->chunks[u];
if(io_info->using_mpi_vfd) {
H5_CHECK_OVERFLOW(fm->total_chunks, hsize_t, size_t);
if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->total_chunks * sizeof(H5D_chunk_info_t *))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
#endif /* H5_HAVE_PARALLEL */
/* Initialize "last chunk" information */
fm->last_index = (hsize_t)-1;
fm->last_chunk_info = NULL;
/* Point at the dataspaces */
fm->file_space = file_space;
fm->mem_space = mem_space;
/* Special case for only one element in selection */
/* (usually appending a record) */
if(nelmts == 1
#ifdef H5_HAVE_PARALLEL
&& !(io_info->using_mpi_vfd)
#endif /* H5_HAVE_PARALLEL */
) {
/* Initialize skip list for chunk selections */
fm->sel_chunks = NULL;
fm->use_single = TRUE;
/* Initialize single chunk dataspace */
if(NULL == dataset->shared->cache.chunk.single_space) {
/* Make a copy of the dataspace for the dataset */
if((dataset->shared->cache.chunk.single_space = H5S_copy(file_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
/* Resize chunk's dataspace dimensions to size of chunk */
if(H5S_set_extent_real(dataset->shared->cache.chunk.single_space, fm->chunk_dim) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "can't adjust chunk dimensions")
/* Set the single chunk dataspace to 'all' selection */
if(H5S_select_all(dataset->shared->cache.chunk.single_space, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to set all selection")
} /* end if */
fm->single_space = dataset->shared->cache.chunk.single_space;
HDassert(fm->single_space);
/* Allocate the single chunk information */
if(NULL == dataset->shared->cache.chunk.single_chunk_info) {
if(NULL == (dataset->shared->cache.chunk.single_chunk_info = H5FL_MALLOC(H5D_chunk_info_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
fm->single_chunk_info = dataset->shared->cache.chunk.single_chunk_info;
HDassert(fm->single_chunk_info);
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
/* Set up chunk mapping for single element */
if(H5D_create_chunk_map_single(fm, io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element")
} /* end if */
else {
/* Initialize skip list for chunk selections */
if(NULL == dataset->shared->cache.chunk.sel_chunks) {
if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections")
} /* end if */
fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks;
HDassert(fm->sel_chunks);
/* We are not using single element mode */
fm->use_single = FALSE;
/* Get type of selection on disk & in memory */
if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
if((fm->msel_type = H5S_GET_SELECT_TYPE(mem_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
/* If the selection is NONE or POINTS, set the flag to FALSE */
if(fsel_type == H5S_SEL_POINTS || fsel_type == H5S_SEL_NONE)
sel_hyper_flag = FALSE;
else
sel_hyper_flag = TRUE;
/* Check if file selection is a not a hyperslab selection */
if(sel_hyper_flag) {
/* Build the file selection for each chunk */
if(H5D_create_chunk_file_map_hyper(fm, io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
/* Clean file chunks' hyperslab span "scratch" information */
curr_node = H5SL_first(fm->sel_chunks);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
HDassert(chunk_info);
/* Clean hyperslab span's "scratch" information */
if(H5S_hyper_reset_scratch(chunk_info->fspace) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
/* Get the next chunk node in the skip list */
curr_node = H5SL_next(curr_node);
} /* end while */
} /* end if */
else {
/* Create temporary datatypes for selection iteration */
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL), FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
/* Spaces might not be the same shape, iterate over the file selection directly */
if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_file_cb, fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
/* Reset "last chunk" info */
fm->last_index = (hsize_t)-1;
fm->last_chunk_info = NULL;
} /* end else */
/* Build the memory selection for each chunk */
if(sel_hyper_flag && H5S_select_shape_same(file_space, mem_space) == TRUE) {
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
/* If the selections are the same shape, use the file chunk information
* to generate the memory chunk information quickly.
*/
if(H5D_create_chunk_mem_map_hyper(fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
} /* end if */
else {
size_t elmt_size; /* Memory datatype size */
/* Make a copy of equivalent memory space */
if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* De-select the mem space copy */
if(H5S_select_none(tmp_mspace) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space")
/* Save chunk template information */
fm->mchunk_tmpl = tmp_mspace;
/* Create temporary datatypes for selection iteration */
if(f_tid < 0) {
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL), FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
} /* end if */
/* Create selection iterator for memory selection */
if(0 == (elmt_size = H5T_get_size(mem_type)))
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init = TRUE; /* Selection iteration info has been initialized */
/* Spaces aren't the same shape, iterate over the memory selection directly */
if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
/* Clean up hyperslab stuff, if necessary */
if(fm->msel_type != H5S_SEL_POINTS) {
/* Clean memory chunks' hyperslab span "scratch" information */
curr_node = H5SL_first(fm->sel_chunks);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
HDassert(chunk_info);
/* Clean hyperslab span's "scratch" information */
if(H5S_hyper_reset_scratch(chunk_info->mspace) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
/* Get the next chunk node in the skip list */
curr_node = H5SL_next(curr_node);
} /* end while */
} /* end if */
} /* end else */
} /* end else */
done:
/* Release the [potentially partially built] chunk mapping information if an error occurs */
if(ret_value < 0) {
if(tmp_mspace && !fm->mchunk_tmpl) {
if(H5S_close(tmp_mspace) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
} /* end if */
if(H5D_chunk_io_term(fm) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping")
} /* end if */
/* Reset the global dataspace info */
fm->file_space = NULL;
fm->mem_space = NULL;
if(iter_init) {
if(H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
} /* end if */
if(f_tid!=(-1)) {
if(H5I_dec_ref(f_tid, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
if(file_space_normalized) {
/* (Casting away const OK -QAK) */
if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_io_init() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_alloc
*
* Purpose: Allocate space for a chunk in memory. This routine allocates
* memory space for non-filtered chunks from a block free list
* and uses malloc()/free() for filtered chunks.
*
* Return: Pointer to memory for chunk on success/NULL on failure
*
* Programmer: Quincey Koziol
* April 22, 2004
*
*-------------------------------------------------------------------------
*/
static void *
H5D_chunk_alloc(size_t size, const H5O_pline_t *pline)
{
void *ret_value = NULL; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_alloc)
HDassert(size);
HDassert(pline);
if(pline->nused > 0)
ret_value = H5MM_malloc(size);
else
ret_value = H5FL_BLK_MALLOC(chunk, size);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_xfree
*
* Purpose: Free space for a chunk in memory. This routine allocates
* memory space for non-filtered chunks from a block free list
* and uses malloc()/free() for filtered chunks.
*
* Return: NULL (never fails)
*
* Programmer: Quincey Koziol
* April 22, 2004
*
*-------------------------------------------------------------------------
*/
static void *
H5D_chunk_xfree(void *chk, const H5O_pline_t *pline)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_xfree)
HDassert(pline);
if(chk) {
if(pline->nused > 0)
H5MM_xfree(chk);
else
(void)H5FL_BLK_FREE(chunk, chk);
} /* end if */
FUNC_LEAVE_NOAPI(NULL)
} /* H5D_chunk_xfree() */
/*--------------------------------------------------------------------------
NAME
H5D_free_chunk_info
PURPOSE
Internal routine to destroy a chunk info node
USAGE
void H5D_free_chunk_info(chunk_info)
void *chunk_info; IN: Pointer to chunk info to destroy
RETURNS
No return value
DESCRIPTION
Releases all the memory for a chunk info node. Called by H5SL_free
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5D_free_chunk_info(void *item, void UNUSED *key, void UNUSED *opdata)
{
H5D_chunk_info_t *chunk_info = (H5D_chunk_info_t *)item;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_free_chunk_info)
HDassert(chunk_info);
/* Close the chunk's file dataspace, if it's not shared */
if(!chunk_info->fspace_shared)
(void)H5S_close(chunk_info->fspace);
else
H5S_select_all(chunk_info->fspace, TRUE);
/* Close the chunk's memory dataspace, if it's not shared */
if(!chunk_info->mspace_shared)
(void)H5S_close(chunk_info->mspace);
/* Free the actual chunk info */
H5FL_FREE(H5D_chunk_info_t, chunk_info);
FUNC_LEAVE_NOAPI(0)
} /* H5D_free_chunk_info() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_map_single
*
* Purpose: Create chunk selections when appending a single record
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 20, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t
#ifndef H5_HAVE_PARALLEL
UNUSED
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
H5D_chunk_info_t *chunk_info; /* Chunk information to insert into skip list */
hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map_single)
/* Sanity check */
HDassert(fm->f_ndims > 0);
/* Get coordinate for selection */
if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Initialize the 'single chunk' file & memory chunk information */
chunk_info = fm->single_chunk_info;
chunk_info->chunk_points = 1;
/* Set chunk location & hyperslab size */
for(u = 0; u < fm->f_ndims; u++) {
HDassert(sel_start[u] == sel_end[u]);
chunk_info->coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u];
} /* end for */
chunk_info->coords[fm->f_ndims] = 0;
/* Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_info->index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Copy selection for file's dataspace into chunk dataspace */
if(H5S_select_copy(fm->single_space, fm->file_space, FALSE) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file selection")
/* Move selection back to have correct offset in chunk */
if(H5S_SELECT_ADJUST_U(fm->single_space, chunk_info->coords) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
#ifdef H5_HAVE_PARALLEL
/* store chunk selection information */
if(io_info->using_mpi_vfd)
fm->select_chunk[chunk_info->index] = chunk_info;
#endif /* H5_HAVE_PARALLEL */
/* Set the file dataspace for the chunk to the shared 'single' dataspace */
chunk_info->fspace = fm->single_space;
/* Indicate that the chunk's file dataspace is shared */
chunk_info->fspace_shared = TRUE;
/* Just point at the memory dataspace & selection */
/* (Casting away const OK -QAK) */
chunk_info->mspace = (H5S_t *)fm->mem_space;
/* Indicate that the chunk's memory dataspace is shared */
chunk_info->mspace_shared = TRUE;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_map_single() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_file_map_hyper
*
* Purpose: Create all chunk selections in file.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 29, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
#ifndef H5_HAVE_PARALLEL
UNUSED
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hsize_t sel_points; /* Number of elements in file selection */
hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t chunk_index; /* Index of chunk */
int curr_dim; /* Current dimension to increment */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_file_map_hyper)
/* Sanity check */
assert(fm->f_ndims>0);
/* Get number of elements selected in file */
sel_points = fm->nelmts;
/* Get bounding box for selection (to reduce the number of chunks to iterate over) */
if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Set initial chunk location & hyperslab size */
for(u = 0; u < fm->f_ndims; u++) {
start_coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u];
coords[u] = start_coords[u];
end[u] = (coords[u] + fm->chunk_dim[u]) - 1;
} /* end for */
/* Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Iterate through each chunk in the dataset */
while(sel_points) {
/* Check for intersection of temporary chunk and file selection */
/* (Casting away const OK - QAK) */
if(H5S_hyper_intersect_block((H5S_t *)fm->file_space,coords,end)==TRUE) {
H5S_t *tmp_fchunk; /* Temporary file dataspace */
H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */
hssize_t schunk_points; /* Number of elements in chunk selection */
/* Create "temporary" chunk for selection operations (copy file space) */
if((tmp_fchunk = H5S_copy(fm->file_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */
if(H5S_hyper_convert(tmp_fchunk) < 0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
} /* end if */
/* "AND" temporary chunk and current chunk */
if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL) < 0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection")
} /* end if */
/* Resize chunk's dataspace dimensions to size of chunk */
if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim) < 0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions")
} /* end if */
/* Move selection back to have correct offset in chunk */
if(H5S_SELECT_ADJUST_U(tmp_fchunk, coords) < 0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
} /* end if */
/* Add temporary chunk to the list of chunks */
/* Allocate the file & memory chunk information */
if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
/* Initialize the chunk information */
/* Set the chunk index */
new_chunk_info->index=chunk_index;
#ifdef H5_HAVE_PARALLEL
/* store chunk selection information */
if(io_info->using_mpi_vfd)
fm->select_chunk[chunk_index] = new_chunk_info;
#endif /* H5_HAVE_PARALLEL */
/* Set the file chunk dataspace */
new_chunk_info->fspace = tmp_fchunk;
new_chunk_info->fspace_shared = FALSE;
/* Set the memory chunk dataspace */
new_chunk_info->mspace=NULL;
new_chunk_info->mspace_shared = FALSE;
/* Copy the chunk's coordinates */
for(u=0; u<fm->f_ndims; u++)
new_chunk_info->coords[u]=coords[u];
new_chunk_info->coords[fm->f_ndims]=0;
/* Insert the new chunk into the skip list */
if(H5SL_insert(fm->sel_chunks, new_chunk_info, &new_chunk_info->index) < 0) {
H5D_free_chunk_info(new_chunk_info, NULL, NULL);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert chunk into skip list")
} /* end if */
/* Get number of elements selected in chunk */
if((schunk_points = H5S_GET_SELECT_NPOINTS(tmp_fchunk)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points, schunk_points, hssize_t, uint32_t);
/* Decrement # of points left in file selection */
sel_points -= (hsize_t)schunk_points;
/* Leave if we are done */
if(sel_points == 0)
HGOTO_DONE(SUCCEED)
} /* end if */
/* Increment chunk index */
chunk_index++;
/* Set current increment dimension */
curr_dim=(int)fm->f_ndims-1;
/* Increment chunk location in fastest changing dimension */
H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t);
coords[curr_dim]+=fm->chunk_dim[curr_dim];
end[curr_dim]+=fm->chunk_dim[curr_dim];
/* Bring chunk location back into bounds, if necessary */
if(coords[curr_dim]>sel_end[curr_dim]) {
do {
/* Reset current dimension's location to 0 */
coords[curr_dim]=start_coords[curr_dim]; /*lint !e771 The start_coords will always be initialized */
end[curr_dim]=(coords[curr_dim]+(hssize_t)fm->chunk_dim[curr_dim])-1;
/* Decrement current dimension */
curr_dim--;
/* Increment chunk location in current dimension */
coords[curr_dim]+=fm->chunk_dim[curr_dim];
end[curr_dim]=(coords[curr_dim]+fm->chunk_dim[curr_dim])-1;
} while(coords[curr_dim]>sel_end[curr_dim]);
/* Re-Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
} /* end if */
} /* end while */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_file_map_hyper() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_mem_map_hyper
*
* Purpose: Create all chunk selections in memory by copying the file
* chunk selections and adjusting their offsets to be correct
* for the memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 29, 2003
*
* Assumptions: That the file and memory selections are the same shape.
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
{
H5SL_node_t *curr_node; /* Current node in skip list */
hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */
hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_mem_map_hyper)
/* Sanity check */
assert(fm->f_ndims>0);
/* Check for all I/O going to a single chunk */
if(H5SL_count(fm->sel_chunks)==1) {
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get the node */
curr_node=H5SL_first(fm->sel_chunks);
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
assert(chunk_info);
/* Just point at the memory dataspace & selection */
/* (Casting away const OK -QAK) */
chunk_info->mspace=(H5S_t *)fm->mem_space;
/* Indicate that the chunk's memory space is shared */
chunk_info->mspace_shared = TRUE;
} /* end if */
else {
/* Get bounding box for file selection */
if(H5S_SELECT_BOUNDS(fm->file_space, file_sel_start, file_sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Get bounding box for memory selection */
if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Calculate the adjustment for memory selection from file selection */
assert(fm->m_ndims==fm->f_ndims);
for(u=0; u<fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(file_sel_start[u],hsize_t,hssize_t);
H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t);
adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u];
} /* end for */
/* Iterate over each chunk in the chunk list */
curr_node=H5SL_first(fm->sel_chunks);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
assert(chunk_info);
/* Copy the information */
/* Copy the memory dataspace */
if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Release the current selection */
if(H5S_SELECT_RELEASE(chunk_info->mspace) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection")
/* Copy the file chunk's selection */
if(H5S_select_copy(chunk_info->mspace,chunk_info->fspace,FALSE) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection")
/* Compensate for the chunk offset */
for(u=0; u<fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(chunk_info->coords[u],hsize_t,hssize_t);
chunk_adjust[u]=adjust[u]-(hssize_t)chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */
} /* end for */
/* Adjust the selection */
if(H5S_hyper_adjust_s(chunk_info->mspace,chunk_adjust) < 0) /*lint !e772 The chunk_adjust array will always be initialized */
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
/* Get the next chunk node in the skip list */
curr_node=H5SL_next(curr_node);
} /* end while */
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_mem_map_hyper() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_file_cb
*
* Purpose: Callback routine for file selection iterator. Used when
* creating selections in file for each point selected.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Wednesday, July 23, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm)
{
H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */
H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */
hsize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */
hsize_t chunk_index; /* Chunk index */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb)
/* Calculate the index of this chunk */
if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory skip list */
if(chunk_index==fm->last_index) {
/* If the chunk index is the same as the last chunk index we used,
* get the cached info to operate on.
*/
chunk_info=fm->last_chunk_info;
} /* end if */
else {
/* If the chunk index is not the same as the last chunk index we used,
* find the chunk in the skip list.
*/
/* Get the chunk node from the skip list */
if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index))) {
H5S_t *fspace; /* Memory chunk's dataspace */
/* Allocate the file & memory chunk information */
if (NULL==(chunk_info = H5FL_MALLOC (H5D_chunk_info_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
/* Initialize the chunk information */
/* Set the chunk index */
chunk_info->index=chunk_index;
/* Create a dataspace for the chunk */
if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) {
H5FL_FREE(H5D_chunk_info_t,chunk_info);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk")
} /* end if */
/* De-select the chunk space */
if(H5S_select_none(fspace) < 0) {
(void)H5S_close(fspace);
H5FL_FREE(H5D_chunk_info_t,chunk_info);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select dataspace")
} /* end if */
/* Set the file chunk dataspace */
chunk_info->fspace = fspace;
chunk_info->fspace_shared = FALSE;
/* Set the memory chunk dataspace */
chunk_info->mspace = NULL;
chunk_info->mspace_shared = FALSE;
/* Set the number of selected elements in chunk to zero */
chunk_info->chunk_points = 0;
/* Compute the chunk's coordinates */
for(u = 0; u < fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u], hsize_t, hssize_t);
chunk_info->coords[u] = (coords[u] / (hssize_t)fm->layout->u.chunk.dim[u]) * (hssize_t)fm->layout->u.chunk.dim[u];
} /* end for */
chunk_info->coords[fm->f_ndims] = 0;
/* Insert the new chunk into the skip list */
if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) {
H5D_free_chunk_info(chunk_info,NULL,NULL);
HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list")
} /* end if */
} /* end if */
/* Update the "last chunk seen" information */
fm->last_index=chunk_index;
fm->last_chunk_info=chunk_info;
} /* end else */
/* Get the coordinates of the element in the chunk */
for(u = 0; u < fm->f_ndims; u++)
coords_in_chunk[u] = coords[u] % fm->layout->u.chunk.dim[u];
/* Add point to file selection for chunk */
if(H5S_select_elements(chunk_info->fspace, H5S_SELECT_APPEND, (size_t)1, coords_in_chunk) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
/* Increment the number of elemented selected in chunk */
chunk_info->chunk_points++;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_file_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_mem_cb
*
* Purpose: Callback routine for file selection iterator. Used when
* creating selections in memory for each chunk.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm)
{
H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */
H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */
hsize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */
hsize_t chunk_index; /* Chunk index */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb)
/* Calculate the index of this chunk */
if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory skip list */
if(chunk_index==fm->last_index) {
/* If the chunk index is the same as the last chunk index we used,
* get the cached spaces to operate on.
*/
chunk_info=fm->last_chunk_info;
} /* end if */
else {
/* If the chunk index is not the same as the last chunk index we used,
* find the chunk in the skip list.
*/
/* Get the chunk node from the skip list */
if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index)))
HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list")
/* Check if the chunk already has a memory space */
if(chunk_info->mspace==NULL) {
/* Copy the template memory chunk dataspace */
if((chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
} /* end else */
/* Update the "last chunk seen" information */
fm->last_index=chunk_index;
fm->last_chunk_info=chunk_info;
} /* end else */
/* Get coordinates of selection iterator for memory */
if(H5S_SELECT_ITER_COORDS(&fm->mem_iter,coords_in_mem) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates")
/* Add point to memory selection for chunk */
if(fm->msel_type==H5S_SEL_POINTS) {
if(H5S_select_elements(chunk_info->mspace, H5S_SELECT_APPEND, (size_t)1, coords_in_mem) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
} /* end if */
else {
if(H5S_hyper_add_span_element(chunk_info->mspace, fm->m_ndims, coords_in_mem) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
} /* end else */
/* Move memory selection iterator to next element in selection */
if(H5S_SELECT_ITER_NEXT(&fm->mem_iter, (size_t)1) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL, "unable to move to next iterator location")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_mem_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cacheable
*
* Purpose: A small internal function to if it's possible to load the
* chunk into cache.
*
* Return: TRUE or FALSE
*
* Programmer: Raymond Lu
* 17 July 2007
*
*-------------------------------------------------------------------------
*/
hbool_t
H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr)
{
const H5D_t *dataset = io_info->dset;
hbool_t ret_value;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cacheable)
HDassert(io_info);
HDassert(dataset);
/* Must bring the whole chunk in if there are any filters */
if(dataset->shared->dcpl_cache.pline.nused > 0)
ret_value = TRUE;
else {
#ifdef H5_HAVE_PARALLEL
/* If MPI based VFD is used and the file is opened for write access, must
* bypass the chunk-cache scheme because other MPI processes could
* be writing to other elements in the same chunk. Do a direct
* write-through of only the elements requested.
*/
if(io_info->using_mpi_vfd && (H5F_ACC_RDWR & H5F_INTENT(dataset->oloc.file)))
ret_value = FALSE;
else {
#endif /* H5_HAVE_PARALLEL */
/* If the chunk is too large to keep in the cache and if the address
* for the chunk has been defined, then don't load the chunk into the
* cache, just write the data to it directly.
*/
H5_CHECK_OVERFLOW(dataset->shared->layout.u.chunk.size, uint32_t, size_t);
if((size_t)dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes
&& H5F_addr_defined(caddr))
ret_value = FALSE;
else
ret_value = TRUE;
#ifdef H5_HAVE_PARALLEL
} /* end else */
#endif /* H5_HAVE_PARALLEL */
} /* end else */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_cacheable() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_in_cache
*
* Purpose: Check if a chunk is in the cache.
*
* Return: TRUE or FALSE
*
* Programmer: Quincey Koziol
* 1 April 2008
*
*-------------------------------------------------------------------------
*/
static hbool_t
H5D_chunk_in_cache(const H5D_t *dset, const hsize_t *chunk_offset,
hsize_t chunk_idx)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/
hbool_t found = FALSE; /*already in cache? */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_in_cache)
/* Sanity checks */
HDassert(dset);
HDassert(chunk_offset);
/* Check if the chunk is in the cache (but hasn't been written to disk yet) */
if(rdcc->nslots > 0) {
unsigned idx = H5D_CHUNK_HASH(dset->shared, chunk_idx); /* Cache entry index */
H5D_rdcc_ent_t *ent = rdcc->slot[idx]; /* Cache entry */
/* Potential match... */
if(ent) {
size_t u; /* Local index variable */
for(u = 0, found = TRUE; u < dset->shared->layout.u.chunk.ndims; u++) {
if(chunk_offset[u] != ent->offset[u]) {
found = FALSE;
break;
} /* end if */
} /* end for */
} /* end if */
} /* end if */
FUNC_LEAVE_NOAPI(found)
} /* end H5D_chunk_in_cache() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_read
*
* Purpose: Read from a chunked dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t UNUSED nelmts, const H5S_t UNUSED *file_space, const H5S_t UNUSED *mem_space,
H5D_chunk_map_t *fm)
{
H5SL_node_t *chunk_node; /* Current node in chunk skip list */
H5D_io_info_t nul_io_info; /* "null" I/O info object */
H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */
H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */
H5D_io_info_t cpt_io_info; /* Compact I/O info object */
H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */
hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */
uint32_t src_accessed_bytes = 0; /* Total accessed size in a chunk */
hbool_t skip_missing_chunks = FALSE; /* Whether to skip missing chunks */
unsigned idx_hint = 0; /* Cache index hint */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read)
/* Sanity check */
HDassert(io_info);
HDassert(io_info->u.rbuf);
HDassert(type_info);
HDassert(fm);
/* Set up "null" I/O info object */
HDmemcpy(&nul_io_info, io_info, sizeof(nul_io_info));
nul_io_info.layout_ops = *H5D_LOPS_NULL;
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
/* Initialize temporary contiguous storage info */
H5_ASSIGN_OVERFLOW(ctg_store.contig.dset_size, io_info->dset->shared->layout.u.chunk.size, uint32_t, hsize_t);
/* Set up compact I/O info object */
HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
cpt_io_info.store = &cpt_store;
cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
/* Initialize temporary compact storage info */
cpt_store.compact.dirty = &cpt_dirty;
{
const H5O_fill_t *fill = &(io_info->dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status; /* Fill value status */
/* Check the fill value status */
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If we are never to return fill values, or if we would return them
* but they aren't set, set the flag to skip missing chunks.
*/
if(fill->fill_time == H5D_FILL_TIME_NEVER ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status != H5D_FILL_VALUE_USER_DEFINED))
skip_missing_chunks = TRUE;
}
/* Iterate through nodes in chunk skip list */
chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* Chunk information */
H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
void *chunk; /* Pointer to locked chunk buffer */
haddr_t chunk_addr; /* Chunk address on disk */
H5D_chunk_ud_t udata; /* B-tree pass-through */
/* Get the actual chunk information from the skip list node */
chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
/* Get the address of the chunk in the file */
chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata);
/* Check for non-existant chunk & skip it if appropriate */
if(!H5F_addr_defined(chunk_addr) && !H5D_chunk_in_cache(io_info->dset, chunk_info->coords, chunk_info->index)
&& skip_missing_chunks) {
/* No chunk cached */
chunk = NULL;
/* Point I/O info at "null" I/O info for this chunk */
chk_io_info = &nul_io_info;
} /* end if */
else {
/* Load the chunk into cache and lock it. */
if(H5D_chunk_cacheable(io_info, chunk_addr)) {
/* Pass in chunk's coordinates in a union. */
io_info->store->chunk.offset = chunk_info->coords;
io_info->store->chunk.index = chunk_info->index;
/* Compute # of bytes accessed in chunk */
src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
/* Lock the chunk into the cache */
if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;
/* Point I/O info at contiguous I/O info for this chunk */
chk_io_info = &cpt_io_info;
} /* end if */
else {
/* Sanity check */
HDassert(H5F_addr_defined(chunk_addr));
/* Set up the storage address information for this chunk */
ctg_store.contig.dset_addr = chunk_addr;
/* No chunk cached */
chunk = NULL;
/* Point I/O info at temporary I/O info for this chunk */
chk_io_info = &ctg_io_info;
} /* end else */
} /* end else */
/* Perform the actual read operation */
if((io_info->io_ops.single_read)(chk_io_info, type_info,
(hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed")
/* Release the cache lock on the chunk. */
if(chunk && H5D_chunk_unlock(io_info, FALSE, idx_hint, chunk, src_accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
/* Advance to next chunk in list */
chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
} /* end while */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_read() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_write
*
* Purpose: Writes to a chunked dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t UNUSED nelmts, const H5S_t UNUSED *file_space, const H5S_t UNUSED *mem_space,
H5D_chunk_map_t *fm)
{
H5SL_node_t *chunk_node; /* Current node in chunk skip list */
H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */
H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */
H5D_io_info_t cpt_io_info; /* Compact I/O info object */
H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */
hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */
uint32_t dst_accessed_bytes = 0; /* Total accessed size in a chunk */
unsigned idx_hint = 0; /* Cache index hint */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write)
/* Sanity check */
HDassert(io_info);
HDassert(io_info->u.wbuf);
HDassert(type_info);
HDassert(fm);
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
/* Initialize temporary contiguous storage info */
H5_ASSIGN_OVERFLOW(ctg_store.contig.dset_size, io_info->dset->shared->layout.u.chunk.size, uint32_t, hsize_t);
/* Set up compact I/O info object */
HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
cpt_io_info.store = &cpt_store;
cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
/* Initialize temporary compact storage info */
cpt_store.compact.dirty = &cpt_dirty;
/* Iterate through nodes in chunk skip list */
chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* Chunk information */
H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
void *chunk; /* Pointer to locked chunk buffer */
haddr_t chunk_addr; /* Chunk address on disk */
H5D_chunk_ud_t udata; /* B-tree pass-through */
/* Get the actual chunk information from the skip list node */
chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
/* Load the chunk into cache. But if the whole chunk is written,
* simply allocate space instead of load the chunk. */
chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata);
if(H5D_chunk_cacheable(io_info, chunk_addr)) {
hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */
/* Pass in chunk's coordinates in a union. */
io_info->store->chunk.offset = chunk_info->coords;
io_info->store->chunk.index = chunk_info->index;
/* Compute # of bytes accessed in chunk */
dst_accessed_bytes = chunk_info->chunk_points * type_info->dst_type_size;
/* Determine if we will access all the data in the chunk */
if(dst_accessed_bytes != ctg_store.contig.dset_size ||
(chunk_info->chunk_points * type_info->src_type_size) != ctg_store.contig.dset_size)
entire_chunk = FALSE;
/* Lock the chunk into the cache */
if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, entire_chunk, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;
/* Point I/O info at main I/O info for this chunk */
chk_io_info = &cpt_io_info;
} /* end if */
else {
/* Sanity check */
HDassert(H5F_addr_defined(chunk_addr));
/* Set up the storage address information for this chunk */
ctg_store.contig.dset_addr = chunk_addr;
/* No chunk cached */
chunk = NULL;
/* Point I/O info at temporary I/O info for this chunk */
chk_io_info = &ctg_io_info;
} /* end else */
/* Perform the actual write operation */
if((io_info->io_ops.single_write)(chk_io_info, type_info,
(hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed")
/* Release the cache lock on the chunk. */
if(chunk && H5D_chunk_unlock(io_info, TRUE, idx_hint, chunk, dst_accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
/* Advance to next chunk in list */
chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
} /* end while */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_write() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_io_term
*
* Purpose: Destroy I/O operation information.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Saturday, May 17, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_io_term(const H5D_chunk_map_t *fm)
{
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_io_term)
/* Single element I/O vs. multiple element I/O cleanup */
if(fm->use_single) {
/* Sanity checks */
HDassert(fm->sel_chunks == NULL);
HDassert(fm->single_chunk_info);
HDassert(fm->single_chunk_info->fspace_shared);
HDassert(fm->single_chunk_info->mspace_shared);
/* Reset the selection for the single element I/O */
H5S_select_all(fm->single_space, TRUE);
} /* end if */
else {
/* Release the nodes on the list of selected chunks */
if(fm->sel_chunks)
if(H5SL_free(fm->sel_chunks, H5D_free_chunk_info, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTNEXT, FAIL, "can't iterate over chunks")
} /* end else */
/* Free the memory chunk dataspace template */
if(fm->mchunk_tmpl)
if(H5S_close(fm->mchunk_tmpl) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
#ifdef H5_HAVE_PARALLEL
if(fm->select_chunk)
H5MM_xfree(fm->select_chunk);
#endif /* H5_HAVE_PARALLEL */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_io_term() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_init
*
* Purpose: Initialize the raw data chunk cache for a dataset. This is
* called when the dataset is initialized.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Monday, May 18, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Convenience pointer to dataset's chunk cache */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_init, FAIL)
/* Sanity check */
HDassert(f);
HDassert(dset);
if(H5F_RDCC_NBYTES(f) > 0 && H5F_RDCC_NELMTS(f) > 0) {
rdcc->nbytes = H5F_RDCC_NBYTES(f);
rdcc->nslots = H5F_RDCC_NELMTS(f);
rdcc->slot = H5FL_SEQ_CALLOC(H5D_rdcc_ent_ptr_t, rdcc->nslots);
if(NULL == rdcc->slot)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Reset any cached chunk info for this dataset */
H5D_chunk_cinfo_cache_reset(&(rdcc->last));
} /* end if */
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Allocate any indexing structures */
if((dset->shared->layout.u.chunk.ops->init)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_init() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cinfo_cache_reset
*
* Purpose: Reset the cached chunk info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* November 27, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_cinfo_cache_reset(H5D_chunk_cached_t *last)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_reset)
/* Sanity check */
HDassert(last);
/* Indicate that the cached info is not valid */
last->valid = FALSE;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5D_chunk_cinfo_cache_reset() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cinfo_cache_update
*
* Purpose: Update the cached chunk info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* November 27, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *udata)
{
unsigned u; /* Local index variable */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_update)
/* Sanity check */
HDassert(last);
HDassert(udata);
HDassert(udata->common.mesg);
HDassert(udata->common.offset);
/* Stored the information to cache */
for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
last->offset[u] = udata->common.offset[u];
last->nbytes = udata->nbytes;
last->filter_mask = udata->filter_mask;
last->addr = udata->addr;
/* Indicate that the cached info is valid */
last->valid = TRUE;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5D_chunk_cinfo_cache_update() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cinfo_cache_found
*
* Purpose: Look for chunk info in cache
*
* Return: TRUE/FALSE/FAIL
*
* Programmer: Quincey Koziol
* November 27, 2007
*
*-------------------------------------------------------------------------
*/
static hbool_t
H5D_chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *udata)
{
hbool_t ret_value = FALSE; /* Return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_found)
/* Sanity check */
HDassert(last);
HDassert(udata);
HDassert(udata->common.mesg);
HDassert(udata->common.offset);
/* Check if the cached information is what is desired */
if(last->valid) {
unsigned u; /* Local index variable */
/* Check that the offset is the same */
for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
if(last->offset[u] != udata->common.offset[u])
HGOTO_DONE(FALSE)
/* Retrieve the information from the cache */
udata->nbytes = last->nbytes;
udata->filter_mask = last->filter_mask;
udata->addr = last->addr;
/* Indicate that the data was found */
HGOTO_DONE(TRUE)
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_cinfo_cache_found() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_create
*
* Purpose: Creates a new chunked storage index and initializes the
* layout information with information about the storage. The
* layout info should be immediately written to the object header.
*
* Return: Non-negative on success (with the layout information initialized
* and ready to write to an object header). Negative on failure.
*
* Programmer: Quincey Koziol
* Thursday, May 22, 2008
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_create, FAIL)
/* Check args */
HDassert(dset);
HDassert(H5D_CHUNKED == dset->shared->layout.type);
HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
#ifndef NDEBUG
{
unsigned u; /* Local index variable */
for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
HDassert(dset->shared->layout.u.chunk.dim[u] > 0);
}
#endif
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Create the index for the chunks */
if((dset->shared->layout.u.chunk.ops->create)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_create() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_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: Albert Cheng
* June 27, 1998
*
*-------------------------------------------------------------------------
*/
haddr_t
H5D_chunk_get_addr(const H5D_t *dset, hid_t dxpl_id, const hsize_t *chunk_offset,
H5D_chunk_ud_t *_udata)
{
H5D_chunk_ud_t tmp_udata; /* Information about a chunk */
H5D_chunk_ud_t *udata; /* Pointer to information about a chunk */
haddr_t ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_get_addr)
HDassert(dset);
HDassert(dset->shared->layout.u.chunk.ndims > 0);
HDassert(chunk_offset);
/* Check for udata struct to return */
udata = (_udata != NULL ? _udata : &tmp_udata);
/* Initialize the information about the chunk we are looking for */
udata->common.mesg = &(dset->shared->layout);
udata->common.offset = chunk_offset;
udata->nbytes = 0;
udata->filter_mask = 0;
udata->addr = HADDR_UNDEF;
/* Check for cached information */
if(!H5D_chunk_cinfo_cache_found(&dset->shared->cache.chunk.last, udata)) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Go get the chunk information */
if(!H5F_addr_defined((dset->shared->layout.u.chunk.ops->get_addr)(&idx_info, udata))) {
/* Cache the fact that the chunk is not in the B-tree */
H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata);
HGOTO_DONE(HADDR_UNDEF)
} /* end if */
/* Cache the information retrieved */
HDassert(H5F_addr_defined(udata->addr));
H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata);
} /* end if */
/* Success! Set the return value */
ret_value = udata->addr;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_get_addr() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_flush_entry
*
* Purpose: Writes a chunk to disk. If RESET is non-zero then the
* entry is cleared -- it's slightly faster to flush a chunk if
* the RESET flag is turned on because it results in one fewer
* memory copy.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache,
H5D_rdcc_ent_t *ent, hbool_t reset)
{
void *buf = NULL; /* Temporary buffer */
hbool_t point_of_no_return = FALSE;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_flush_entry)
HDassert(dset);
HDassert(dxpl_cache);
HDassert(ent);
HDassert(!ent->locked);
buf = ent->chunk;
if(ent->dirty) {
H5D_chunk_ud_t udata; /* pass through B-tree */
hbool_t must_insert = FALSE; /* Whether the chunk must go through the "insert" method */
/* Set up user data for index callbacks */
udata.common.mesg = &dset->shared->layout;
udata.common.offset = ent->offset;
udata.filter_mask = 0;
udata.nbytes = ent->chunk_size;
udata.addr = ent->chunk_addr;
/* Should the chunk be filtered before writing it to disk? */
if(dset->shared->dcpl_cache.pline.nused) {
size_t alloc = ent->alloc_size; /* Bytes allocated for BUF */
size_t nbytes; /* Chunk size (in bytes) */
if(!reset) {
/*
* Copy the chunk to a new buffer before running it through
* the pipeline because we'll want to save the original buffer
* for later.
*/
H5_ASSIGN_OVERFLOW(alloc, ent->chunk_size, uint32_t, size_t);
if(NULL == (buf = H5MM_malloc(alloc)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline")
HDmemcpy(buf, ent->chunk, ent->chunk_size);
} /* end if */
else {
/*
* If we are reseting and something goes wrong after this
* point then it's too late to recover because we may have
* destroyed the original data by calling H5Z_pipeline().
* The only safe option is to continue with the reset
* even if we can't write the data to disk.
*/
point_of_no_return = TRUE;
ent->chunk = NULL;
} /* end else */
H5_ASSIGN_OVERFLOW(nbytes, udata.nbytes, uint32_t, size_t);
if(H5Z_pipeline(&(dset->shared->dcpl_cache.pline), 0, &(udata.filter_mask), dxpl_cache->err_detect,
dxpl_cache->filter_cb, &nbytes, &alloc, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed")
H5_ASSIGN_OVERFLOW(udata.nbytes, nbytes, size_t, uint32_t);
/* Indicate that the chunk must go through 'insert' method */
must_insert = TRUE;
} /* end if */
else if(!H5F_addr_defined(udata.addr))
/* Indicate that the chunk must go through 'insert' method */
must_insert = TRUE;
/* Check if the chunk needs to be 'inserted' (could exist already and
* the 'insert' operation could resize it)
*/
if(must_insert) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Create the chunk it if it doesn't exist, or reallocate the chunk
* if its size changed.
*/
if((dset->shared->layout.u.chunk.ops->insert)(&idx_info, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk")
/* Update the chunk entry's address, in case it was allocated or relocated */
ent->chunk_addr = udata.addr;
} /* end if */
/* Write the data to the file */
HDassert(H5F_addr_defined(udata.addr));
if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.nbytes, dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
/* Cache the chunk's info, in case it's accessed again shortly */
H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata);
/* Mark cache entry as clean */
ent->dirty = FALSE;
/* Increment # of flushed entries */
dset->shared->cache.chunk.stats.nflushes++;
} /* end if */
/* Reset, but do not free or removed from list */
if(reset) {
point_of_no_return = FALSE;
if(buf == ent->chunk)
buf = NULL;
if(ent->chunk != NULL)
ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
} /* end if */
done:
/* Free the temp buffer only if it's different than the entry chunk */
if(buf != ent->chunk)
H5MM_xfree(buf);
/*
* If we reached the point of no return then we have no choice but to
* reset the entry. This can only happen if RESET is true but the
* output pipeline failed. Do not free the entry or remove it from the
* list.
*/
if(ret_value < 0 && point_of_no_return) {
if(ent->chunk)
ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_flush_entry() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cache_evict
*
* Purpose: Preempts the specified entry from the cache, flushing it to
* disk if necessary.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache,
H5D_rdcc_ent_t *ent, hbool_t flush)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_evict)
HDassert(dset);
HDassert(dxpl_cache);
HDassert(ent);
HDassert(!ent->locked);
HDassert(ent->idx < rdcc->nslots);
if(flush) {
/* Flush */
if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end if */
else {
/* Don't flush, just free chunk */
if(ent->chunk != NULL)
ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
} /* end else */
/* Unlink from list */
if(ent->prev)
ent->prev->next = ent->next;
else
rdcc->head = ent->next;
if(ent->next)
ent->next->prev = ent->prev;
else
rdcc->tail = ent->prev;
ent->prev = ent->next = NULL;
/* Remove from cache */
rdcc->slot[ent->idx] = NULL;
ent->idx = UINT_MAX;
rdcc->nbytes -= ent->chunk_size;
--rdcc->nused;
/* Free */
H5FL_FREE(H5D_rdcc_ent_t, ent);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_cache_evict() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cache_prune
*
* Purpose: Prune the cache by preempting some things until the cache has
* room for something which is SIZE bytes. Only unlocked
* entries are considered for preemption.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_cache_prune(const H5D_t *dset, hid_t dxpl_id,
const H5D_dxpl_cache_t *dxpl_cache, size_t size)
{
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
size_t total = rdcc->nbytes;
const int nmeth = 2; /*number of methods */
int w[1]; /*weighting as an interval */
H5D_rdcc_ent_t *p[2], *cur; /*list pointers */
H5D_rdcc_ent_t *n[2]; /*list next pointers */
int nerrors = 0; /* Accumulated error count during preemptions */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_prune)
/*
* Preemption is accomplished by having multiple pointers (currently two)
* slide down the list beginning at the head. Pointer p(N+1) will start
* traversing the list when pointer pN reaches wN percent of the original
* list. In other words, preemption method N gets to consider entries in
* approximate least recently used order w0 percent before method N+1
* where 100% means tha method N will run to completion before method N+1
* begins. The pointers participating in the list traversal are each
* given a chance at preemption before any of the pointers are advanced.
*/
w[0] = (int)(rdcc->nused * H5F_RDCC_W0(dset->oloc.file));
p[0] = rdcc->head;
p[1] = NULL;
while((p[0] || p[1]) && (rdcc->nbytes + size) > total) {
int i; /* Local index variable */
/* Introduce new pointers */
for(i = 0; i < nmeth - 1; i++)
if(0 == w[i])
p[i + 1] = rdcc->head;
/* Compute next value for each pointer */
for(i = 0; i < nmeth; i++)
n[i] = p[i] ? p[i]->next : NULL;
/* Give each method a chance */
for(i = 0; i < nmeth && (rdcc->nbytes + size) > total; i++) {
if(0 == i && p[0] && !p[0]->locked &&
((0 == p[0]->rd_count && 0 == p[0]->wr_count) ||
(0 == p[0]->rd_count && p[0]->chunk_size == p[0]->wr_count) ||
(p[0]->chunk_size == p[0]->rd_count && 0 == p[0]->wr_count))) {
/*
* Method 0: Preempt entries that have been completely written
* and/or completely read but not entries that are partially
* written or partially read.
*/
cur = p[0];
} else if(1 == i && p[1] && !p[1]->locked) {
/*
* Method 1: Preempt the entry without regard to
* considerations other than being locked. This is the last
* resort preemption.
*/
cur = p[1];
} else {
/* Nothing to preempt at this point */
cur = NULL;
}
if(cur) {
int j; /* Local index variable */
for(j = 0; j < nmeth; j++) {
if(p[j] == cur)
p[j] = NULL;
if(n[j] == cur)
n[j] = cur->next;
} /* end for */
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, cur, TRUE) < 0)
nerrors++;
} /* end if */
} /* end for */
/* Advance pointers */
for(i = 0; i < nmeth; i++)
p[i] = n[i];
for(i = 0; i < nmeth - 1; i++)
w[i] -= 1;
} /* end while */
if(nerrors)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to preempt one or more raw data cache entry")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_cache_prune() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_lock
*
* Purpose: Return a pointer to a dataset chunk. The pointer points
* directly into the chunk cache and should not be freed
* by the caller but will be valid until it is unlocked. The
* input value IDX_HINT is used to speed up cache lookups and
* it's output value should be given to H5F_chunk_unlock().
* IDX_HINT is ignored if it is out of range, and if it points
* to the wrong entry then we fall back to the normal search
* method.
*
* If RELAX is non-zero and the chunk isn't in the cache then
* don't try to read it from the file, but just allocate an
* uninitialized buffer to hold the result. This is intended
* for output functions that are about to overwrite the entire
* chunk.
*
* Return: Success: Ptr to a file chunk.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
void *
H5D_chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
hbool_t relax, unsigned *idx_hint/*in,out*/)
{
H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache*/
H5D_rdcc_ent_t *ent = NULL; /*cache entry */
unsigned idx = 0; /*hash index number */
hbool_t found = FALSE; /*already in cache? */
haddr_t chunk_addr = HADDR_UNDEF; /* Address of chunk on disk */
size_t chunk_size; /*size of a chunk */
void *chunk = NULL; /*the file chunk */
unsigned u; /*counters */
void *ret_value; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_lock)
HDassert(io_info);
HDassert(dset);
HDassert(io_info->dxpl_cache);
HDassert(io_info->store);
HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER));
/* Get the chunk's size */
HDassert(layout->u.chunk.size > 0);
H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
/* Search for the chunk in the cache */
if(rdcc->nslots > 0) {
idx = H5D_CHUNK_HASH(dset->shared, io_info->store->chunk.index);
ent = rdcc->slot[idx];
if(ent)
for(u = 0, found = TRUE; u < layout->u.chunk.ndims; u++)
if(io_info->store->chunk.offset[u] != ent->offset[u]) {
found = FALSE;
break;
} /* end if */
} /* end if */
if(found) {
/*
* Already in the cache. Count a hit.
*/
rdcc->stats.nhits++;
} /* end if */
else if(relax) {
/*
* Not in the cache, but we're about to overwrite the whole thing
* anyway, so just allocate a buffer for it but don't initialize that
* buffer with the file contents. Count this as a hit instead of a
* miss because we saved ourselves lots of work.
*/
rdcc->stats.nhits++;
if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
/* In the case that some dataset functions look through this data,
* clear it to all 0s. */
HDmemset(chunk, 0, chunk_size);
} /* end if */
else {
H5D_chunk_ud_t tmp_udata; /*B-tree pass-through */
if(udata != NULL)
chunk_addr = udata->addr;
else {
/* Point at temporary storage for B-tree pass through */
udata = &tmp_udata;
/*
* Not in the cache. Read it from the file and count this as a miss
* if it's in the file or an init if it isn't.
*/
chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, io_info->store->chunk.offset, udata);
} /* end else */
/* Check if the chunk exists on disk */
if(H5F_addr_defined(chunk_addr)) {
size_t chunk_alloc = 0; /*allocated chunk size */
/* Chunk size on disk isn't [likely] the same size as the final chunk
* size in memory, so allocate memory big enough. */
H5_ASSIGN_OVERFLOW(chunk_alloc, udata->nbytes, uint32_t, size_t);
if(NULL == (chunk = H5D_chunk_alloc(chunk_alloc, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, chunk_addr, chunk_alloc, io_info->dxpl_id, chunk) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk")
if(pline->nused) {
if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &(udata->filter_mask), io_info->dxpl_cache->err_detect,
io_info->dxpl_cache->filter_cb, &chunk_alloc, &chunk_alloc, &chunk) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, NULL, "data pipeline read failed")
H5_ASSIGN_OVERFLOW(udata->nbytes, chunk_alloc, size_t, uint32_t);
} /* end if */
/* Increment # of cache misses */
rdcc->stats.nmisses++;
} /* end if */
else {
H5D_fill_value_t fill_status;
#ifdef OLD_WAY
/* Clear the error stack from not finding the chunk on disk */
H5E_clear_stack(NULL);
#endif /* OLD_WAY */
/* Chunk size on disk isn't [likely] the same size as the final chunk
* size in memory, so allocate memory big enough. */
if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined")
if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
/*
* The chunk doesn't exist in the file. Replicate the fill
* value throughout the chunk, if the fill value is defined.
*/
/* Initialize the fill value buffer */
/* (use the compact dataset storage buffer as the fill value buffer) */
if(H5D_fill_init(&fb_info, chunk, FALSE,
NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, chunk_size, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize fill buffer info")
fb_info_init = TRUE;
/* Check for VL datatype & non-default fill value */
if(fb_info.has_vlen_fill_type)
/* Fill the buffer with VL datatype fill values */
if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, NULL, "can't refill fill value buffer")
} /* end if */
else
HDmemset(chunk, 0, chunk_size);
/* Increment # of creations */
rdcc->stats.ninits++;
} /* end else */
} /* end else */
HDassert(found || chunk_size > 0);
if(!found && rdcc->nslots > 0 && chunk_size <= rdcc->nbytes &&
(!ent || !ent->locked)) {
/*
* Add the chunk to the cache only if the slot is not already locked.
* Preempt enough things from the cache to make room.
*/
if(ent) {
if(H5D_chunk_cache_evict(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk from cache")
} /* end if */
if(H5D_chunk_cache_prune(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, chunk_size) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk(s) from cache")
/* Create a new entry */
ent = H5FL_MALLOC(H5D_rdcc_ent_t);
ent->locked = 0;
ent->dirty = FALSE;
ent->chunk_addr = chunk_addr;
H5_ASSIGN_OVERFLOW(ent->chunk_size, chunk_size, size_t, uint32_t);
ent->alloc_size = chunk_size;
for(u = 0; u < layout->u.chunk.ndims; u++)
ent->offset[u] = io_info->store->chunk.offset[u];
H5_ASSIGN_OVERFLOW(ent->rd_count, chunk_size, size_t, uint32_t);
H5_ASSIGN_OVERFLOW(ent->wr_count, chunk_size, size_t, uint32_t);
ent->chunk = (uint8_t *)chunk;
/* Add it to the cache */
HDassert(NULL == rdcc->slot[idx]);
rdcc->slot[idx] = ent;
ent->idx = idx;
rdcc->nbytes += chunk_size;
rdcc->nused++;
/* Add it to the linked list */
ent->next = NULL;
if(rdcc->tail) {
rdcc->tail->next = ent;
ent->prev = rdcc->tail;
rdcc->tail = ent;
} /* end if */
else {
rdcc->head = rdcc->tail = ent;
ent->prev = NULL;
} /* end else */
found = TRUE;
} else if(!found) {
/*
* The chunk is larger than the entire cache so we don't cache it.
* This is the reason all those arguments have to be repeated for the
* unlock function.
*/
ent = NULL;
idx = UINT_MAX;
} else {
/*
* The chunk is not at the beginning of the cache; move it backward
* by one slot. This is how we implement the LRU preemption
* algorithm.
*/
HDassert(ent);
if(ent->next) {
if(ent->next->next)
ent->next->next->prev = ent;
else
rdcc->tail = ent;
ent->next->prev = ent->prev;
if(ent->prev)
ent->prev->next = ent->next;
else
rdcc->head = ent->next;
ent->prev = ent->next;
ent->next = ent->next->next;
ent->prev->next = ent;
} /* end if */
} /* end else */
/* Lock the chunk into the cache */
if(ent) {
HDassert(!ent->locked);
ent->locked = TRUE;
chunk = ent->chunk;
} /* end if */
if(idx_hint)
*idx_hint = idx;
/* Set return value */
ret_value = chunk;
done:
/* Release the fill buffer info, if it's been initialized */
if(fb_info_init && H5D_fill_term(&fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "Can't release fill buffer info")
/* Release the chunk allocated, on error */
if(!ret_value)
if(chunk)
chunk = H5D_chunk_xfree(chunk, pline);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_lock() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_unlock
*
* Purpose: Unlocks a previously locked chunk. The LAYOUT, COMP, and
* OFFSET arguments should be the same as for H5D_chunk_lock().
* The DIRTY argument should be set to non-zero if the chunk has
* been modified since it was locked. The IDX_HINT argument is
* the returned index hint from the lock operation and BUF is
* the return value from the lock.
*
* The NACCESSED argument should be the number of bytes accessed
* for reading or writing (depending on the value of DIRTY).
* It's only purpose is to provide additional information to the
* preemption policy.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_unlock(const H5D_io_info_t *io_info, hbool_t dirty, unsigned idx_hint,
void *chunk, uint32_t naccessed)
{
const H5O_layout_t *layout = &(io_info->dset->shared->layout); /* Dataset layout */
const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);
H5D_rdcc_ent_t *ent = NULL;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_unlock)
HDassert(io_info);
if(UINT_MAX == idx_hint) {
/*
* It's not in the cache, probably because it's too big. If it's
* dirty then flush it to disk. In any case, free the chunk.
* Note: we have to copy the layout and filter messages so we
* don't discard the `const' qualifier.
*/
if(dirty) {
H5D_rdcc_ent_t x;
HDmemset(&x, 0, sizeof(x));
x.dirty = TRUE;
HDmemcpy(x.offset, io_info->store->chunk.offset, layout->u.chunk.ndims * sizeof(x.offset[0]));
HDassert(layout->u.chunk.size > 0);
x.chunk_addr = HADDR_UNDEF;
x.chunk_size = layout->u.chunk.size;
H5_ASSIGN_OVERFLOW(x.alloc_size, x.chunk_size, uint32_t, size_t);
x.chunk = (uint8_t *)chunk;
if(H5D_chunk_flush_entry(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, &x, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end if */
else {
if(chunk)
chunk = H5D_chunk_xfree(chunk, &(io_info->dset->shared->dcpl_cache.pline));
} /* end else */
} /* end if */
else {
/* Sanity check */
HDassert(idx_hint < rdcc->nslots);
HDassert(rdcc->slot[idx_hint]);
HDassert(rdcc->slot[idx_hint]->chunk == chunk);
/*
* It's in the cache so unlock it.
*/
ent = rdcc->slot[idx_hint];
HDassert(ent->locked);
if(dirty) {
ent->dirty = TRUE;
ent->wr_count -= MIN(ent->wr_count, naccessed);
} /* end if */
else
ent->rd_count -= MIN(ent->rd_count, naccessed);
ent->locked = FALSE;
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_unlock() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_flush
*
* Purpose: Writes all dirty chunks to disk and optionally preempts them
* from the cache.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags)
{
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
unsigned nerrors = 0;
H5D_rdcc_ent_t *ent, *next;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_flush, FAIL)
/* Fill the DXPL cache values for later use */
if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Loop over all entries in the chunk cache */
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
if((flags & H5F_FLUSH_INVALIDATE)) {
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
nerrors++;
} else {
if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
nerrors++;
}
} /* end for */
if(nerrors)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_flush() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_allocated_cb
*
* Purpose: Simply counts the number of chunks for a dataset.
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static int
H5D_chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
hsize_t *nbytes = (hsize_t *)_udata;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_allocated_cb)
*(hsize_t *)nbytes += chunk_rec->nbytes;
FUNC_LEAVE_NOAPI(H5_ITER_CONT)
} /* H5D_chunk_allocated_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_allocated
*
* Purpose: Return the number of bytes allocated in the file for storage
* of raw data in the chunked dataset
*
* Return: Success: Number of bytes stored in all chunks.
* Failure: 0
*
* Programmer: Quincey Koziol
* Tuesday, May 20, 2008
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
hsize_t chunk_bytes = 0; /* Number of bytes allocated for chunks */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_allocated, FAIL)
HDassert(dset);
/* Fill the DXPL cache values for later use */
if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Search for cached chunks that haven't been written out */
for(ent = rdcc->head; ent; ent = ent->next) {
/* Flush the chunk out to disk, to make certain the size is correct later */
if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end for */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Call the index-specific "get all the allocated chunks sizes" routine */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_allocated_cb, &chunk_bytes) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
/* Set number of bytes for caller */
*nbytes = chunk_bytes;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_allocated() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_allocate
*
* Purpose: Allocate file space for all chunks that are not allocated yet.
* Return SUCCEED if all needed allocation succeed, otherwise
* FAIL.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Albert Cheng
* June 26, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
const H5D_chunk_ops_t *ops = dset->shared->layout.u.chunk.ops; /* Chunk operations */
hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
size_t orig_chunk_size; /* Original size of chunk in bytes */
unsigned filter_mask = 0; /* Filter mask for chunks that have them */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status; /* The fill value status */
hbool_t should_fill = FALSE; /* Whether fill values should be written */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
#ifdef H5_HAVE_PARALLEL
MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank = (-1); /* This process's rank */
int mpi_code; /* MPI return code */
hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */
hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
#endif /* H5_HAVE_PARALLEL */
hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
int space_ndims; /* Dataset's space rank */
hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
hid_t data_dxpl_id; /* DXPL ID to use for raw data I/O operations */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_allocate, FAIL)
/* Check args */
HDassert(dset && H5D_CHUNKED == layout->type);
HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
HDassert(H5F_addr_defined(layout->u.chunk.addr));
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
/* Retrieve the dataset dimensions */
if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info")
space_dim[space_ndims] = layout->u.chunk.dim[space_ndims];
#ifdef H5_HAVE_PARALLEL
/* Retrieve MPI parameters */
if(IS_H5FD_MPI(dset->oloc.file)) {
/* Get the MPI communicator */
if(MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file)))
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator")
/* Get the MPI rank */
if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file)) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank")
/* Set the MPI-capable file driver flag */
using_mpi = TRUE;
/* Use the internal "independent" DXPL */
data_dxpl_id = H5AC_ind_dxpl_id;
} /* end if */
else {
#endif /* H5_HAVE_PARALLEL */
/* Use the DXPL we were given */
data_dxpl_id = dxpl_id;
#ifdef H5_HAVE_PARALLEL
} /* end else */
#endif /* H5_HAVE_PARALLEL */
/* Fill the DXPL cache values for later use */
if(H5D_get_dxpl_cache(data_dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Get original chunk size */
H5_ASSIGN_OVERFLOW(orig_chunk_size, layout->u.chunk.size, uint32_t, size_t);
/* Check the dataset's fill-value status */
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If we are filling the dataset on allocation or "if set" and
* the fill value _is_ set, _and_ we are not overwriting the new blocks,
* or if there are any pipeline filters defined,
* set the "should fill" flag
*/
if((!full_overwrite && (fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)))
|| pline->nused > 0)
should_fill = TRUE;
/* Check if fill values should be written to chunks */
if(should_fill) {
/* Initialize the fill value buffer */
/* (delay allocating fill buffer for VL datatypes until refilling) */
/* (casting away const OK - QAK) */
if(H5D_fill_init(&fb_info, NULL, (hbool_t)(pline->nused > 0),
(H5MM_allocate_t)H5D_chunk_alloc, (void *)pline,
(H5MM_free_t)H5D_chunk_xfree, (void *)pline,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, orig_chunk_size, data_dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
fb_info_init = TRUE;
/* Check if there are filters which need to be applied to the chunk */
/* (only do this in advance when the chunk info can be re-used (i.e.
* it doesn't contain any non-default VL datatype fill values)
*/
if(!fb_info.has_vlen_fill_type && pline->nused > 0) {
size_t buf_size = orig_chunk_size;
/* Push the chunk through the filters */
if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
} /* end if */
} /* end if */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Reset the chunk offset indices */
HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0])));
/* Loop over all chunks */
carry = FALSE;
while(!carry) {
haddr_t chunk_addr; /* Address of chunk */
int i; /* Local index variable */
/* Get the chunk's address */
chunk_addr = H5D_chunk_get_addr(dset, dxpl_id, chunk_offset, NULL);
/* Check if the chunk exists yet on disk */
if(!H5F_addr_defined(chunk_addr)) {
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry */
hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */
unsigned u; /* Local index variable */
/* Didn't find the chunk on disk */
chunk_exists = FALSE;
/* Look for chunk in cache */
for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
/* Assume a match */
chunk_exists = TRUE;
for(u = 0; u < layout->u.chunk.ndims; u++)
if(ent->offset[u] != chunk_offset[u]) {
chunk_exists = FALSE; /* Reset if no match */
break;
} /* end if */
} /* end for */
/* Chunk wasn't in cache either, create it now */
if(!chunk_exists) {
H5D_chunk_ud_t udata; /* B-tree pass-through for creating chunk */
size_t chunk_size; /* Size of chunk in bytes, possibly filtered */
/* Check for VL datatype & non-default fill value */
if(fb_info_init && fb_info.has_vlen_fill_type) {
/* Sanity check */
HDassert(should_fill);
/* Fill the buffer with VL datatype fill values */
if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
/* Check if there are filters which need to be applied to the chunk */
if(pline->nused > 0) {
size_t buf_size = orig_chunk_size;
size_t nbytes = fb_info.fill_buf_size;
/* Push the chunk through the filters */
if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
/* Keep the number of bytes the chunk turned in to */
chunk_size = nbytes;
} /* end if */
else
H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
} /* end if */
else
chunk_size = orig_chunk_size;
/* Initialize the chunk information */
udata.common.mesg = layout;
udata.common.offset = chunk_offset;
H5_ASSIGN_OVERFLOW(udata.nbytes, chunk_size, size_t, uint32_t);
udata.filter_mask = filter_mask;
udata.addr = HADDR_UNDEF;
/* Allocate the chunk with all processes */
if((ops->insert)(&idx_info, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert record into chunk index")
HDassert(H5F_addr_defined(udata.addr));
/* Check if fill values should be written to chunks */
if(should_fill) {
/* Sanity check */
HDassert(fb_info_init);
HDassert(udata.nbytes == chunk_size);
#ifdef H5_HAVE_PARALLEL
/* Check if this file is accessed with an MPI-capable file driver */
if(using_mpi) {
/* Write the chunks out from only one process */
/* !! Use the internal "independent" DXPL!! -QAK */
if(H5_PAR_META_WRITE == mpi_rank)
if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
/* Indicate that blocks are being written */
blocks_written = TRUE;
} /* end if */
else {
#endif /* H5_HAVE_PARALLEL */
if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
#ifdef H5_HAVE_PARALLEL
} /* end else */
#endif /* H5_HAVE_PARALLEL */
} /* end if */
/* Release the fill buffer if we need to re-allocate it each time */
if(fb_info_init && fb_info.has_vlen_fill_type && pline->nused > 0)
H5D_fill_release(&fb_info);
} /* end if */
} /* end if */
/* Increment indices */
carry = TRUE;
for(i = (int)(space_ndims - 1); i >= 0; --i) {
chunk_offset[i] += layout->u.chunk.dim[i];
if(chunk_offset[i] >= space_dim[i])
chunk_offset[i] = 0;
else {
carry = FALSE;
break;
} /* end else */
} /* end for */
} /* end while */
#ifdef H5_HAVE_PARALLEL
/* Only need to block at the barrier if we actually initialized a chunk */
/* using an MPI-capable file driver */
if(using_mpi && blocks_written) {
/* Wait at barrier to avoid race conditions where some processes are
* still writing out chunks and other processes race ahead to read
* them in, getting bogus data.
*/
if(MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
} /* end if */
#endif /* H5_HAVE_PARALLEL */
/* Reset any cached chunk info for this dataset */
H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last);
done:
/* Release the fill buffer info, if it's been initialized */
if(fb_info_init && H5D_fill_term(&fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_allocate() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_prune_cb
*
* Purpose: Search for chunks that are no longer inside the pruned
* dataset's extent
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* March 26, 2002
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static int
H5D_chunk_prune_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud1_t *udata = (H5D_chunk_it_ud1_t *)_udata; /* User data */
H5D_chunk_sl_ck_t *sl_node = NULL; /* Skip list node for chunk to remove */
unsigned rank; /* Current # of dimensions */
hbool_t should_delete = FALSE; /* Whether the chunk should be deleted */
hbool_t needs_fill = FALSE; /* Whether the chunk overlaps the new extent and needs fill valiues */
unsigned u; /* Local index variable */
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_cb)
/* Figure out what chunks are no longer in use for the specified extent and release them */
rank = udata->common.mesg->u.chunk.ndims - 1;
for(u = 0; u < rank; u++)
/* The chunk record points to a chunk of storage that contains the
* beginning of the logical address space represented by UDATA.
*/
if(chunk_rec->offset[u] >= udata->dims[u]) {
/* Indicate that the chunk will be deleted */
should_delete = TRUE;
/* Break out of loop, we know the chunk is outside the current dimensions */
break;
} /* end if */
/* Check for chunk that overlaps new extent and will need fill values */
else if((chunk_rec->offset[u] + udata->common.mesg->u.chunk.dim[u]) > udata->dims[u])
/* Indicate that the chunk needs filling */
/* (but continue in loop, since it could be outside the extent in
* another dimension -QAK)
*/
needs_fill = TRUE;
/* Check for chunk to delete */
if(should_delete) {
/* Allocate space for the shared structure */
if(NULL == (sl_node = H5FL_MALLOC(H5D_chunk_sl_ck_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for shared B-tree info")
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &sl_node->index) < 0)
HGOTO_ERROR(H5E_IO, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index")
/* Store the key for the chunk */
sl_node->rec = *chunk_rec;
/* Insert the chunk description in the skip list */
if(H5SL_insert(udata->outside, sl_node, &sl_node->index) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINSERT, H5_ITER_ERROR, "can't insert chunk into skip list")
} /* end if */
/* Check for chunk that overlaps the new dataset dimensions and needs filling */
else if(needs_fill) {
const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */
H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */
H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */
hssize_t sel_nelmts; /* Number of elements in selection */
hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */
void *chunk; /* The file chunk */
unsigned idx_hint; /* Which chunk we're dealing with */
H5D_chunk_ud_t chk_udata; /* User data for locking chunk */
uint32_t bytes_accessed; /* Bytes accessed in chunk */
/* Initialize the fill value buffer, if necessary */
if(!udata->fb_info_init) {
H5_CHECK_OVERFLOW(udata->elmts_per_chunk, uint32_t, size_t);
if(H5D_fill_init(&udata->fb_info, NULL, FALSE, NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill,
dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk,
io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't initialize fill buffer info")
udata->fb_info_init = TRUE;
} /* end if */
/* Compute the # of elements to leave with existing value, in each dimension */
for(u = 0; u < rank; u++) {
count[u] = MIN(layout->u.chunk.dim[u], (udata->dims[u] - chunk_rec->offset[u]));
HDassert(count[u] > 0);
} /* end for */
/* Select all elements in chunk, to begin with */
if(H5S_select_all(udata->chunk_space, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select space")
/* "Subtract out" the elements to keep */
if(H5S_select_hyperslab(udata->chunk_space, H5S_SELECT_NOTB, udata->hyper_start, NULL, count, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select hyperslab")
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, udata->down_chunks, &io_info->store->chunk.index) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't get chunk index")
/* Lock the chunk into the cache, to get a pointer to the chunk buffer */
/* (Casting away const OK -QAK) */
io_info->store->chunk.offset = (hsize_t *)chunk_rec->offset;
chk_udata.common.mesg = layout;
chk_udata.common.offset = chunk_rec->offset;
chk_udata.nbytes = chunk_rec->nbytes;
chk_udata.filter_mask = chunk_rec->filter_mask;
chk_udata.addr = chunk_rec->chunk_addr;
if(NULL == (chunk = (void *)H5D_chunk_lock(udata->io_info, &chk_udata, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "unable to lock raw data chunk")
/* Fill the selection in the memory buffer */
/* Use the size of the elements in the chunk directly instead of */
/* relying on the fill.size, which might be set to 0 if there is */
/* no fill-value defined for the dataset -QAK */
/* Get the number of elements in the selection */
sel_nelmts = H5S_GET_SELECT_NPOINTS(udata->chunk_space);
HDassert(sel_nelmts >= 0);
H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, size_t);
/* Check for VL datatype & non-default fill value */
if(udata->fb_info.has_vlen_fill_type)
/* Re-fill the buffer to use for this I/O operation */
if(H5D_fill_refill_vl(&udata->fb_info, (size_t)sel_nelmts, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, H5_ITER_ERROR, "can't refill fill value buffer")
/* Create a selection iterator for scattering the elements to memory buffer */
if(H5S_select_iter_init(&chunk_iter, udata->chunk_space, layout->u.chunk.dim[rank]) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "unable to initialize chunk selection information")
/* Scatter the data into memory */
if(H5D_scatter_mem(udata->fb_info.fill_buf, udata->chunk_space, &chunk_iter, (size_t)sel_nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) {
H5S_SELECT_ITER_RELEASE(&chunk_iter);
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "scatter failed")
} /* end if */
/* Release the selection iterator */
if(H5S_SELECT_ITER_RELEASE(&chunk_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "Can't release selection iterator")
/* The number of bytes accessed in the chunk */
/* (i.e. the bytes replaced with fill values) */
H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, uint32_t);
bytes_accessed = (uint32_t)sel_nelmts * layout->u.chunk.dim[rank];
/* Release lock on chunk */
if(H5D_chunk_unlock(io_info, TRUE, idx_hint, chunk, bytes_accessed) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5_ITER_ERROR, "unable to unlock raw data chunk")
} /* end else-if */
done:
if(ret_value != H5_ITER_CONT && sl_node)
H5FL_FREE(H5D_chunk_sl_ck_t, sl_node);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_prune_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_prune_sl_rm_cb
*
* Purpose: Destroy a skip list node for "pruning" chunks, also removes
* the chunk from the index.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol, koziol@hdfgroup.org
* May 3, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_prune_sl_rm_cb(void *item, void UNUSED *key, void *op_data)
{
H5D_chunk_sl_ck_t *sl_node = (H5D_chunk_sl_ck_t *)item; /* Temporary pointer to chunk to remove */
H5D_chunk_sl_rm_t *rm_info = (H5D_chunk_sl_rm_t *)op_data; /* Information needed for removing chunk from B-tree */
H5D_chunk_common_ud_t idx_udata; /* User data for index removal routine */
herr_t ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_sl_rm_cb)
/* Sanity checks */
HDassert(sl_node);
HDassert(rm_info);
/* Initialize the user data for the index callback */
idx_udata.mesg = rm_info->mesg;
idx_udata.offset = sl_node->rec.offset;
/* Remove */
if((rm_info->idx_info->layout->u.chunk.ops->remove)(rm_info->idx_info, &idx_udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, H5_ITER_ERROR, "unable to remove chunk entry from index")
done:
H5FL_FREE(H5D_chunk_sl_ck_t, sl_node);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_prune_sl_rm_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_prune_by_extent
*
* Purpose: This function searches for chunks that are no longer necessary
* both in the raw data cache and in the chunk index.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* Algorithm: Robb Matzke
* March 27, 2002
*
* The algorithm is:
*
* For chunks that are no longer necessary:
*
* 1. Search in the raw data cache for each chunk
* 2. If found then preempt it from the cache
* 3. Search in the B-tree for each chunk
* 4. If found then remove it from the B-tree and deallocate file storage for the chunk
*
* This example shows a 2d dataset of 90x90 with a chunk size of 20x20.
*
*
* 0 20 40 60 80 90 100
* 0 +---------+---------+---------+---------+-----+...+
* |:::::X:::::::::::::: : : | :
* |:::::::X:::::::::::: : : | : Key
* |::::::::::X::::::::: : : | : --------
* |::::::::::::X::::::: : : | : +-+ Dataset
* 20+::::::::::::::::::::.........:.........:.....+...: | | Extent
* | :::::X::::: : : | : +-+
* | ::::::::::: : : | :
* | ::::::::::: : : | : ... Chunk
* | :::::::X::: : : | : : : Boundary
* 40+.........:::::::::::.........:.........:.....+...: :.:
* | : : : : | :
* | : : : : | : ... Allocated
* | : : : : | : ::: & Filled
* | : : : : | : ::: Chunk
* 60+.........:.........:.........:.........:.....+...:
* | : :::::::X::: : | : X Element
* | : ::::::::::: : | : Written
* | : ::::::::::: : | :
* | : ::::::::::: : | :
* 80+.........:.........:::::::::::.........:.....+...: O Fill Val
* | : : ::::::::::: | : Explicitly
* | : : ::::::X:::: | : Written
* 90+---------+---------+---------+---------+-----+ :
* : : : ::::::::::: :
* 100:.........:.........:.........:::::::::::.........:
*
*
* We have 25 total chunks for this dataset, 5 of which have space
* allocated in the file because they were written to one or more
* elements. These five chunks (and only these five) also have entries in
* the storage B-tree for this dataset.
*
* Now lets say we want to shrink the dataset down to 70x70:
*
*
* 0 20 40 60 70 80 90 100
* 0 +---------+---------+---------+----+----+-----+...+
* |:::::X:::::::::::::: : | : | :
* |:::::::X:::::::::::: : | : | : Key
* |::::::::::X::::::::: : | : | : --------
* |::::::::::::X::::::: : | : | : +-+ Dataset
* 20+::::::::::::::::::::.........:....+....:.....|...: | | Extent
* | :::::X::::: : | : | : +-+
* | ::::::::::: : | : | :
* | ::::::::::: : | : | : ... Chunk
* | :::::::X::: : | : | : : : Boundary
* 40+.........:::::::::::.........:....+....:.....|...: :.:
* | : : : | : | :
* | : : : | : | : ... Allocated
* | : : : | : | : ::: & Filled
* | : : : | : | : ::: Chunk
* 60+.........:.........:.........:....+....:.....|...:
* | : :::::::X::: | : | : X Element
* | : ::::::::::: | : | : Written
* +---------+---------+---------+----+ : | :
* | : ::::::::::: : | :
* 80+.........:.........:::::::::X:.........:.....|...: O Fill Val
* | : : ::::::::::: | : Explicitly
* | : : ::::::X:::: | : Written
* 90+---------+---------+---------+---------+-----+ :
* : : : ::::::::::: :
* 100:.........:.........:.........:::::::::::.........:
*
*
* That means that the nine chunks along the bottom and right side should
* no longer exist. Of those nine chunks, (0,80), (20,80), (40,80),
* (60,80), (80,80), (80,60), (80,40), (80,20), and (80,0), one is actually allocated
* that needs to be released.
* To release the chunks, we traverse the B-tree to obtain a list of unused
* allocated chunks, and then call H5B_remove() for each chunk.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_io_info_t chk_io_info; /* Chunked I/O info object */
H5D_storage_t chk_store; /* Chunk storage information */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Cache entries */
hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dataspace dimensions */
H5D_chunk_it_ud1_t udata; /* Chunk index iterator user data */
hbool_t udata_init = FALSE; /* Whether the chunk index iterator user data has been initialized */
H5D_chunk_sl_rm_t rm_info; /* User data for skip list destroy callback */
H5S_t *chunk_space = NULL; /* Dataspace for a chunk */
hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */
hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Current number of chunks in each dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */
uint32_t elmts_per_chunk; /* Elements in chunk */
unsigned rank; /* Current # of dimensions */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_prune_by_extent, FAIL)
/* Check args */
HDassert(dset && H5D_CHUNKED == layout->type);
HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
HDassert(H5F_addr_defined(layout->u.chunk.addr));
HDassert(dxpl_cache);
/* Fill the DXPL cache values for later use */
if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Go get the rank & dimensions (including the element size) */
rank = layout->u.chunk.ndims - 1;
if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
curr_dims[rank] = layout->u.chunk.dim[rank];
/*-------------------------------------------------------------------------
* Figure out what chunks are no longer in use for the specified extent
* and release them from the linked list raw data cache
*-------------------------------------------------------------------------
*/
for(ent = rdcc->head; ent; ent = next) {
/* Get pointer to next extry in cache, in case this one is evicted */
next = ent->next;
/* Check for chunk offset outside of new dimensions */
for(u = 0; u < rank; u++)
if((hsize_t)ent->offset[u] > curr_dims[u]) {
/* Evict the entry from the cache, but do not flush it to disk */
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
/* Break out of loop, chunk is evicted */
break;
} /* end if */
} /* end for */
/* Round up to the next integer # of chunks, to accomodate partial chunks */
/* (also compute the number of elements per chunk) */
/* (also copy the chunk dimensions into 'hsize_t' array for creating dataspace) */
elmts_per_chunk = 1;
for(u = 0; u < rank; u++) {
chunks[u] = ((old_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u];
elmts_per_chunk *= layout->u.chunk.dim[u];
chunk_dims[u] = layout->u.chunk.dim[u];
} /* end for */
/* Get the "down" sizes for each dimension */
if(H5V_array_down(rank, chunks, down_chunks) < 0)
HGOTO_ERROR(H5E_IO, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
/* Create a data space for a chunk & set the extent */
if(NULL == (chunk_space = H5S_create_simple(rank, chunk_dims, NULL)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
/* Reset hyperslab start array */
/* (hyperslabs will always start from origin) */
HDmemset(hyper_start, 0, sizeof(hyper_start));
/* Set up chunked I/O info object, for operations on chunks (in callback) */
/* (Casting away const OK -QAK) */
H5D_BUILD_IO_INFO_RD(&chk_io_info, dset, dxpl_cache, dxpl_id, &chk_store, NULL);
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Initialize the user data for the iteration */
HDmemset(&udata, 0, sizeof udata);
udata.common.mesg = layout;
udata.io_info = &chk_io_info;
udata.idx_info = &idx_info;
udata.dims = curr_dims;
udata.down_chunks = down_chunks;
udata.elmts_per_chunk = elmts_per_chunk;
udata.chunk_space = chunk_space;
udata.hyper_start = hyper_start;
udata_init = TRUE;
/* Initialize the skip list that will hold the chunks outside the dimensions */
if(NULL == (udata.outside = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT)))
HGOTO_ERROR(H5E_IO, H5E_CANTCREATE, FAIL, "can't create skip list for chunks outside new dimensions")
/* Iterate over the chunks */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_prune_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve prune chunks from index")
/* Set up user data for skip list callback */
rm_info.idx_info = &idx_info;
rm_info.mesg = layout;
/* Destroy the skip list, deleting the chunks in the callback */
H5SL_destroy(udata.outside, H5D_chunk_prune_sl_rm_cb, &rm_info);
/* Reset any cached chunk info for this dataset */
H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last);
done:
/* Release resources */
if(chunk_space && H5S_close(chunk_space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
if(udata_init) {
if(udata.fb_info_init && H5D_fill_term(&udata.fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_prune_by_extent() */
#ifdef H5_HAVE_PARALLEL
/*-------------------------------------------------------------------------
* Function: H5D_chunk_addrmap_cb
*
* Purpose: Callback when obtaining the chunk addresses for all existing chunks
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Kent Yang
* Tuesday, November 15, 2005
*
*-------------------------------------------------------------------------
*/
static int
H5D_chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud2_t *udata = (H5D_chunk_it_ud2_t *)_udata; /* User data for callback */
unsigned rank = udata->common.mesg->u.chunk.ndims - 1; /* # of dimensions of dataset */
hsize_t chunk_index;
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_addrmap_cb)
/* Compute the index for this chunk */
if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index")
/* Set it in the userdata to return */
udata->chunk_addr[chunk_index] = chunk_rec->chunk_addr;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_addrmap_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_addrmap
*
* Purpose: Obtain the chunk addresses for all existing chunks
*
* Return: Success: Non-negative on succeed.
* Failure: negative value
*
* Programmer: Kent Yang
* November 15, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],
const hsize_t down_chunks[])
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_t *dset = io_info->dset; /* Local pointer to dataset info */
H5D_chunk_it_ud2_t udata; /* User data for iteration callback */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_addrmap, FAIL)
HDassert(dset);
HDassert(chunk_addr);
HDassert(down_chunks);
/* Set up user data for B-tree callback */
HDmemset(&udata, 0, sizeof(udata));
udata.common.mesg = &dset->shared->layout;
udata.down_chunks = down_chunks;
udata.chunk_addr = chunk_addr;
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = io_info->dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Iterate over chunks to build mapping of chunk addresses */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_addrmap_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to iterate over chunk index to build address map")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_addrmap() */
#endif /* H5_HAVE_PARALLEL */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_delete
*
* Purpose: Delete raw data storage for entire dataset (i.e. all chunks)
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Thursday, March 20, 2003
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_delete, FAIL)
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = layout;
/* Check if the index has been created in the file */
if(H5F_addr_defined(layout->u.chunk.addr)) {
/* Delete the chunked storage information in the file */
if((layout->u.chunk.ops->delete)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk index")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_delete() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_update_cache
*
* Purpose: Update any cached chunks index values after the dataspace
* size has changed
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Saturday, May 29, 2004
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
H5D_rdcc_ent_t *ent, *next; /*cache entry */
H5D_rdcc_ent_t *old_ent; /* Old cache entry */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
unsigned rank; /*current # of dimensions */
hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */
hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
unsigned u; /*counters */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_update_cache, FAIL)
/* Check args */
HDassert(dset && H5D_CHUNKED == dset->shared->layout.type);
HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
/* Get the rank */
rank = dset->shared->layout.u.chunk.ndims-1;
HDassert(rank > 0);
/* 1-D dataset's chunks can't have their index change */
if(rank == 1)
HGOTO_DONE(SUCCEED)
/* Go get the dimensions */
if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
/* Round up to the next integer # of chunks, to accomodate partial chunks */
for(u = 0; u < rank; u++)
chunks[u] = ((curr_dims[u] + dset->shared->layout.u.chunk.dim[u]) - 1) / dset->shared->layout.u.chunk.dim[u];
/* Get the "down" sizes for each dimension */
if(H5V_array_down(rank, chunks, down_chunks) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
/* Fill the DXPL cache values for later use */
if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Recompute the index for each cached chunk that is in a dataset */
for(ent = rdcc->head; ent; ent = next) {
hsize_t idx; /* Chunk index */
unsigned old_idx; /* Previous index number */
/* Get the pointer to the next cache entry */
next = ent->next;
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank, ent->offset, dset->shared->layout.u.chunk.dim, down_chunks, &idx) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Compute the index for the chunk entry */
old_idx = ent->idx; /* Save for later */
ent->idx = H5D_CHUNK_HASH(dset->shared, idx);
if(old_idx != ent->idx) {
/* Check if there is already a chunk at this chunk's new location */
old_ent = rdcc->slot[ent->idx];
if(old_ent != NULL) {
HDassert(old_ent->locked == 0);
/* Check if we are removing the entry we would walk to next */
if(old_ent == next)
next = old_ent->next;
/* Remove the old entry from the cache */
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, old_ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
} /* end if */
/* Insert this chunk into correct location in hash table */
rdcc->slot[ent->idx] = ent;
/* Null out previous location */
rdcc->slot[old_idx] = NULL;
} /* end if */
} /* end for */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_update_cache() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_copy_cb
*
* Purpose: Copy chunked raw data from source file and insert to the
* index in the destination file
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* August 20, 2005
*
*-------------------------------------------------------------------------
*/
static int
H5D_chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud3_t *udata = (H5D_chunk_it_ud3_t *)_udata; /* User data for callback */
H5D_chunk_ud_t udata_dst; /* User data about new destination chunk */
hbool_t is_vlen = FALSE; /* Whether datatype is variable-length */
hbool_t fix_ref = FALSE; /* Whether to fix up references in the dest. file */
/* General information about chunk copy */
void *bkg = udata->bkg; /* Background buffer for datatype conversion */
void *buf = udata->buf; /* Chunk buffer for I/O & datatype conversions */
size_t buf_size = udata->buf_size; /* Size of chunk buffer */
H5O_pline_t *pline = udata->pline; /* I/O pipeline for applying filters */
/* needed for commpressed variable length data */
hbool_t has_filters = FALSE; /* Whether chunk has filters */
size_t nbytes; /* Size of chunk in file (in bytes) */
H5Z_cb_t cb_struct; /* Filter failure callback struct */
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_copy_cb)
/* Get 'size_t' local value for number of bytes in chunk */
H5_ASSIGN_OVERFLOW(nbytes, chunk_rec->nbytes, uint32_t, size_t);
/* Check parameter for type conversion */
if(udata->do_convert) {
if(H5T_detect_class(udata->dt_src, H5T_VLEN) > 0)
is_vlen = TRUE;
else if((H5T_get_class(udata->dt_src, FALSE) == H5T_REFERENCE) && (udata->file_src != udata->idx_info_dst->f))
fix_ref = TRUE;
else
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements")
} /* end if */
/* Check for filtered chunks */
if(pline && pline->nused) {
has_filters = TRUE;
cb_struct.func = NULL; /* no callback function when failed */
} /* end if */
/* Resize the buf if it is too small to hold the data */
if(nbytes > buf_size) {
void *new_buf; /* New buffer for data */
/* Re-allocate memory for copying the chunk */
if(NULL == (new_buf = H5MM_realloc(udata->buf, nbytes)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
udata->buf = new_buf;
if(udata->bkg) {
if(NULL == (new_buf = H5MM_realloc(udata->bkg, nbytes)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
udata->bkg = new_buf;
if(!udata->cpy_info->expand_ref)
HDmemset((uint8_t *)udata->bkg + buf_size, 0, (size_t)(nbytes - buf_size));
bkg = udata->bkg;
} /* end if */
buf = udata->buf;
udata->buf_size = buf_size = nbytes;
} /* end if */
/* read chunk data from the source file */
if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
/* Need to uncompress variable-length & reference data elements */
if(has_filters && (is_vlen || fix_ref)) {
unsigned filter_mask = chunk_rec->filter_mask;
if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "data pipeline read failed")
} /* end if */
/* Perform datatype conversion, if necessary */
if(is_vlen) {
H5T_path_t *tpath_src_mem = udata->tpath_src_mem;
H5T_path_t *tpath_mem_dst = udata->tpath_mem_dst;
H5S_t *buf_space = udata->buf_space;
hid_t tid_src = udata->tid_src;
hid_t tid_dst = udata->tid_dst;
hid_t tid_mem = udata->tid_mem;
void *reclaim_buf = udata->reclaim_buf;
size_t reclaim_buf_size = udata->reclaim_buf_size;
/* Convert from source file to memory */
H5_CHECK_OVERFLOW(udata->nelmts, uint32_t, size_t);
if(H5T_convert(tpath_src_mem, tid_src, tid_mem, (size_t)udata->nelmts, (size_t)0, (size_t)0, buf, NULL, udata->idx_info_dst->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
/* Copy into another buffer, to reclaim memory later */
HDmemcpy(reclaim_buf, buf, reclaim_buf_size);
/* Set background buffer to all zeros */
HDmemset(bkg, 0, buf_size);
/* Convert from memory to destination file */
if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, udata->nelmts, (size_t)0, (size_t)0, buf, bkg, udata->idx_info_dst->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
/* Reclaim space from variable length data */
if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, H5_ITER_ERROR, "unable to reclaim variable-length data")
} /* end if */
else if(fix_ref) {
/* Check for expanding references */
/* (background buffer has already been zeroed out, if not expanding) */
if(udata->cpy_info->expand_ref) {
size_t ref_count;
/* Determine # of reference elements to copy */
ref_count = nbytes / H5T_get_size(udata->dt_src);
/* Copy the reference elements */
if(H5O_copy_expand_ref(udata->file_src, buf, udata->idx_info_dst->dxpl_id, udata->idx_info_dst->f, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute")
} /* end if */
/* After fix ref, copy the new reference elements to the buffer to write out */
HDmemcpy(buf, bkg, buf_size);
} /* end if */
/* Set up destination chunk callback information for insertion */
udata_dst.common.mesg = udata->idx_info_dst->layout;
udata_dst.common.offset = chunk_rec->offset;
udata_dst.nbytes = chunk_rec->nbytes;
udata_dst.filter_mask = chunk_rec->filter_mask;
udata_dst.addr = HADDR_UNDEF;
/* Need to compress variable-length & reference data elements before writing to file */
if(has_filters && (is_vlen || fix_ref) ) {
if(H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed")
H5_ASSIGN_OVERFLOW(udata_dst.nbytes, nbytes, size_t, uint32_t);
udata->buf = buf;
udata->buf_size = buf_size;
} /* end if */
/* Insert chunk into the destination index */
if((udata->idx_info_dst->layout->u.chunk.ops->insert)(udata->idx_info_dst, &udata_dst) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk into index")
/* Write chunk data to destination file */
HDassert(H5F_addr_defined(udata_dst.addr));
if(H5F_block_write(udata->idx_info_dst->f, H5FD_MEM_DRAW, udata_dst.addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_copy_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_copy
*
* Purpose: Copy chunked storage from SRC file to DST file.
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Peter Cao
* August 20, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst,
H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info,
H5O_pline_t *pline, hid_t dxpl_id)
{
H5D_chunk_it_ud3_t udata; /* User data for iteration callback */
H5D_chk_idx_info_t idx_info_dst; /* Dest. chunked index info */
H5D_chk_idx_info_t idx_info_src; /* Source chunked index info */
H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */
hid_t tid_src = -1; /* Datatype ID for source datatype */
hid_t tid_dst = -1; /* Datatype ID for destination datatype */
hid_t tid_mem = -1; /* Datatype ID for memory datatype */
size_t buf_size; /* Size of copy buffer */
size_t reclaim_buf_size; /* Size of reclaim buffer */
void *buf = NULL; /* Buffer for copying data */
void *bkg = NULL; /* Buffer for background during type conversion */
void *reclaim_buf = NULL; /* Buffer for reclaiming data */
H5S_t *buf_space = NULL; /* Dataspace describing buffer */
hid_t sid_buf = -1; /* ID for buffer dataspace */
uint32_t nelmts = 0; /* Number of elements in buffer */
hbool_t do_convert = FALSE; /* Indicate that type conversions should be performed */
hbool_t copy_setup_done = FALSE; /* Indicate that 'copy setup' is done */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_copy, FAIL)
/* Check args */
HDassert(f_src);
HDassert(f_dst);
HDassert(layout_src && H5D_CHUNKED == layout_src->type);
HDassert(layout_dst && H5D_CHUNKED == layout_dst->type);
HDassert(dt_src);
/* Compose source & dest chunked index info structs */
idx_info_src.f = f_src;
idx_info_src.dxpl_id = dxpl_id;
idx_info_src.layout = layout_src;
idx_info_dst.f = f_dst;
idx_info_dst.dxpl_id = dxpl_id;
idx_info_dst.layout = layout_dst;
/* Call the index-specific "copy setup" routine */
if((layout_src->u.chunk.ops->copy_setup)(&idx_info_src, &idx_info_dst) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up index-specific chunk copying information")
HDassert(H5F_addr_defined(layout_dst->u.chunk.addr));
copy_setup_done = TRUE;
/* Create datatype ID for src datatype */
if((tid_src = H5I_register(H5I_DATATYPE, dt_src, FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
/* If there's a VLEN source datatype, set up type conversion information */
if(H5T_detect_class(dt_src, H5T_VLEN) > 0) {
H5T_t *dt_dst; /* Destination datatype */
H5T_t *dt_mem; /* Memory datatype */
size_t mem_dt_size; /* Memory datatype size */
size_t tmp_dt_size; /* Temp. datatype size */
size_t max_dt_size; /* Max atatype size */
hsize_t buf_dim; /* Dimension for buffer */
unsigned u;
/* create a memory copy of the variable-length datatype */
if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
/* create variable-length datatype at the destinaton file */
if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst, FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
/* Set up the conversion functions */
if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
/* Determine largest datatype size */
if(0 == (max_dt_size = H5T_get_size(dt_src)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
if(0 == (mem_dt_size = H5T_get_size(dt_mem)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
max_dt_size = MAX(max_dt_size, mem_dt_size);
if(0 == (tmp_dt_size = H5T_get_size(dt_dst)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
max_dt_size = MAX(max_dt_size, tmp_dt_size);
/* Compute the number of elements per chunk */
nelmts = 1;
for(u = 0; u < (layout_src->u.chunk.ndims - 1); u++)
nelmts *= layout_src->u.chunk.dim[u];
/* Create the space and set the initial extent */
buf_dim = nelmts;
if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
/* Atomize */
if((sid_buf = H5I_register(H5I_DATASPACE, buf_space, FALSE)) < 0) {
H5S_close(buf_space);
HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
} /* end if */
/* Set initial buffer sizes */
buf_size = nelmts * max_dt_size;
reclaim_buf_size = nelmts * mem_dt_size;
/* Allocate memory for reclaim buf */
if(NULL == (reclaim_buf = H5MM_malloc(reclaim_buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
/* Indicate that type conversion should be performed */
do_convert = TRUE;
} /* end if */
else {
if(H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) {
/* Indicate that type conversion should be performed */
do_convert = TRUE;
} /* end if */
H5_ASSIGN_OVERFLOW(buf_size, layout_src->u.chunk.size, uint32_t, size_t);
reclaim_buf_size = 0;
} /* end else */
/* Set up conversion buffer, if appropriate */
if(do_convert) {
/* Allocate background memory for converting the chunk */
if(NULL == (bkg = H5MM_malloc(buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
/* Check for reference datatype and no expanding references & clear background buffer */
if(!cpy_info->expand_ref &&
((H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) && (f_src != f_dst)))
/* Reset value to zero */
HDmemset(bkg, 0, buf_size);
} /* end if */
/* Allocate memory for copying the chunk */
if(NULL == (buf = H5MM_malloc(buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
/* Initialize the callback structure for the source */
HDmemset(&udata, 0, sizeof udata);
udata.common.mesg = layout_src;
udata.file_src = f_src;
udata.idx_info_dst = &idx_info_dst;
udata.buf = buf;
udata.bkg = bkg;
udata.buf_size = buf_size;
udata.tid_src = tid_src;
udata.tid_mem = tid_mem;
udata.tid_dst = tid_dst;
udata.dt_src = dt_src;
udata.do_convert = do_convert;
udata.tpath_src_mem = tpath_src_mem;
udata.tpath_mem_dst = tpath_mem_dst;
udata.reclaim_buf = reclaim_buf;
udata.reclaim_buf_size = reclaim_buf_size;
udata.buf_space = buf_space;
udata.nelmts = nelmts;
udata.pline = pline;
udata.cpy_info = cpy_info;
/* Iterate over chunks to copy data */
if((layout_src->u.chunk.ops->iterate)(&idx_info_src, H5D_chunk_copy_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to copy data")
/* I/O buffers may have been re-allocated */
buf = udata.buf;
bkg = udata.bkg;
done:
if(sid_buf > 0)
if(H5I_dec_ref(sid_buf, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID")
if(tid_src > 0)
if(H5I_dec_ref(tid_src, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(tid_dst > 0)
if(H5I_dec_ref(tid_dst, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(tid_mem > 0)
if(H5I_dec_ref(tid_mem, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(buf)
H5MM_xfree(buf);
if(bkg)
H5MM_xfree(bkg);
if(reclaim_buf)
H5MM_xfree(reclaim_buf);
/* Clean up any index information */
if(copy_setup_done)
if((layout_src->u.chunk.ops->copy_shutdown)(layout_src, layout_dst) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to shut down index copying info")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_copy() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_bh_size
*
* Purpose: Retrieve the amount of index storage for chunked dataset
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Vailin Choi
* June 8, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout,
hsize_t *index_size)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_bh_info, FAIL)
/* Check args */
HDassert(f);
HDassert(layout);
HDassert(index_size);
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = layout;
/* Get size of index structure */
if((layout->u.chunk.ops->size)(&idx_info, index_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve chunk index info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_bh_info() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_iter_dump
*
* Purpose: If the UDATA.STREAM member is non-null then debugging
* information is written to that stream.
*
* Return: Success: Non-negative
*
* Failure: Negative
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static int
H5D_chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud4_t *udata = (H5D_chunk_it_ud4_t *)_udata; /* User data from caller */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_dump_index_cb)
if(udata->stream) {
unsigned u; /* Local index variable */
/* Print header if not already displayed */
if(!udata->header_displayed) {
HDfprintf(udata->stream, " Flags Bytes Address Logical Offset\n");
HDfprintf(udata->stream, " ========== ======== ========== ==============================\n");
/* Set flag that the headers has been printed */
udata->header_displayed = TRUE;
} /* end if */
/* Print information about this chunk */
HDfprintf(udata->stream, " 0x%08x %8Zu %10a [", chunk_rec->filter_mask, chunk_rec->nbytes, chunk_rec->chunk_addr);
for(u = 0; u < udata->ndims; u++)
HDfprintf(udata->stream, "%s%Hd", (u ? ", " : ""), chunk_rec->offset[u]);
HDfputs("]\n", udata->stream);
} /* end if */
FUNC_LEAVE_NOAPI(H5_ITER_CONT)
} /* H5D_chunk_dump_index_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_dump_index
*
* Purpose: Prints information about the storage index to the specified
* stream.
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Robb Matzke
* Wednesday, April 28, 1999
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream)
{
H5D_chunk_it_ud4_t udata; /* User data for callback */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_dump_index, FAIL)
/* Sanity check */
HDassert(dset);
/* Only display info if stream is defined */
if(stream) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
/* Display address of index */
HDfprintf(stream, " Address: %a\n", dset->shared->layout.u.chunk.addr);
/* Set up user data for callback */
udata.stream = stream;
udata.header_displayed = FALSE;
udata.ndims = dset->shared->layout.u.chunk.ndims;
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Iterate over index and dump chunk info */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_dump_index_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to dump chunk info")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_dump_index() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_dest
*
* Purpose: Destroy the entire chunk cache by flushing dirty entries,
* preempting all entries, and freeing the cache itself.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Dataset's chunk cache */
H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Pointer to current & next cache entries */
int nerrors = 0; /* Accumulated count of errors */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_dest, FAIL)
HDassert(f);
HDassert(dset);
/* Fill the DXPL cache values for later use */
if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Flush all the cached chunks */
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
nerrors++;
} /* end for */
if(nerrors)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
/* Release cache structures */
if(rdcc->slot)
H5FL_SEQ_FREE(H5D_rdcc_ent_ptr_t, rdcc->slot);
HDmemset(rdcc, 0, sizeof(H5D_rdcc_t));
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Free any index structures */
if((dset->shared->layout.u.chunk.ops->dest)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_dest() */
#ifdef H5D_CHUNK_DEBUG
/*-------------------------------------------------------------------------
* Function: H5D_chunk_stats
*
* Purpose: Print raw data cache statistics to the debug stream. If
* HEADERS is non-zero then print table column headers,
* otherwise assume that the H5AC layer has already printed them.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_stats(const H5D_t *dset, hbool_t headers)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
double miss_rate;
char ascii[32];
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_stats, FAIL)
if (!H5DEBUG(AC))
HGOTO_DONE(SUCCEED)
if (headers) {
fprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n");
fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n",
"Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes");
fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n",
"-----", "----", "------", "--------", "-----", "-------");
}
#ifdef H5AC_DEBUG
if (H5DEBUG(AC)) headers = TRUE;
#endif
if (headers) {
if (rdcc->nhits>0 || rdcc->nmisses>0) {
miss_rate = 100.0 * rdcc->nmisses /
(rdcc->nhits + rdcc->nmisses);
} else {
miss_rate = 0.0;
}
if (miss_rate > 100) {
sprintf(ascii, "%7d%%", (int) (miss_rate + 0.5));
} else {
sprintf(ascii, "%7.2f%%", miss_rate);
}
fprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n",
"raw data chunks", rdcc->nhits, rdcc->nmisses, ascii,
rdcc->ninits, (long)(rdcc->nflushes)-(long)(rdcc->ninits));
}
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_stats() */
#endif /* H5D_CHUNK_DEBUG */
/*-------------------------------------------------------------------------
* Function: H5D_null_readvv
*
* Purpose: Performs "no-op" I/O operation, advancing through two I/O
* vectors, until one runs out.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, April 1, 2008
*
*-------------------------------------------------------------------------
*/
static ssize_t
H5D_null_readvv(const H5D_io_info_t UNUSED *io_info,
size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[])
{
size_t u, v; /* Local index variables */
size_t size; /* Size of sequence in bytes */
ssize_t bytes_processed = 0; /* Eventual return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_null_readvv)
/* Check args */
HDassert(chunk_len_arr);
HDassert(chunk_offset_arr);
HDassert(mem_len_arr);
HDassert(mem_offset_arr);
/* Work through all the sequences */
for(u = *mem_curr_seq, v = *chunk_curr_seq; u < mem_max_nseq && v < chunk_max_nseq; ) {
/* Choose smallest buffer to write */
if(chunk_len_arr[v] < mem_len_arr[u])
size = chunk_len_arr[v];
else
size = mem_len_arr[u];
/* Update source information */
chunk_len_arr[v] -= size;
chunk_offset_arr[v] += size;
if(chunk_len_arr[v] == 0)
v++;
/* Update destination information */
mem_len_arr[u] -= size;
mem_offset_arr[u] += size;
if(mem_len_arr[u] == 0)
u++;
/* Increment number of bytes copied */
bytes_processed += (ssize_t)size;
} /* end for */
/* Update current sequence vectors */
*mem_curr_seq = u;
*chunk_curr_seq = v;
FUNC_LEAVE_NOAPI(bytes_processed)
} /* H5D_null_readvv() */