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-rw-r--r--src/H5Dchunk.c3047
1 files changed, 3011 insertions, 36 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index ba07725..711b91b 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -28,9 +28,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
-#ifdef H5_HAVE_PARALLEL
#include "H5MMprivate.h" /* Memory management */
-#endif /* H5_HAVE_PARALLEL */
#include "H5Vprivate.h" /* Vector and array functions */
@@ -39,24 +37,125 @@
/****************/
/* Default skip list height for storing list of chunks */
-#define H5D_DEFAULT_SKIPLIST_HEIGHT 8
+#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);
@@ -74,6 +173,8 @@ static ssize_t H5D_null_readvv(const H5D_io_info_t *io_info,
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);
@@ -93,6 +194,7 @@ static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims,
/* 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,
@@ -115,6 +217,7 @@ const H5D_layout_ops_t H5D_LOPS_NULL[1] = {{
NULL,
NULL,
NULL,
+ NULL,
#ifdef H5_HAVE_PARALLEL
NULL,
NULL,
@@ -124,9 +227,111 @@ const H5D_layout_ops_t H5D_LOPS_NULL[1] = {{
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() */
/*-------------------------------------------------------------------------
@@ -269,7 +474,7 @@ H5D_chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info
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_DEFAULT_SKIPLIST_HEIGHT)))
+ 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;
@@ -416,6 +621,7 @@ done:
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 */
@@ -424,6 +630,71 @@ done:
} /* 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
@@ -672,9 +943,9 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
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")
+ 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 */
@@ -1100,26 +1371,29 @@ H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr)
*-------------------------------------------------------------------------
*/
static hbool_t
-H5D_chunk_in_cache(const H5D_io_info_t *io_info)
+H5D_chunk_in_cache(const H5D_t *dset, const hsize_t *chunk_offset,
+ hsize_t chunk_idx)
{
- H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);/*raw data chunk cache*/
+ 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)
- HDassert(io_info);
+ /* 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(io_info->dset->shared, io_info->store->chunk.index); /* Cache entry index */
+ 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 < io_info->dset->shared->layout.u.chunk.ndims; u++) {
- if(io_info->store->chunk.offset[u] != ent->offset[u]) {
+ 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 */
@@ -1211,20 +1485,16 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
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_istore_ud1_t udata; /* B-tree pass-through */
+ 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);
- /* Pass in chunk's coordinates in a union. */
- io_info->store->chunk.offset = chunk_info->coords;
- io_info->store->chunk.index = chunk_info->index;
-
/* Get the address of the chunk in the file */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
+ 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)
+ 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;
@@ -1235,14 +1505,15 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
else {
/* Load the chunk into cache and lock it. */
if(H5D_chunk_cacheable(io_info, chunk_addr)) {
- size_t tmp_src_accessed_bytes; /* Total accessed size in a chunk */
+ /* 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 */
- tmp_src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
- H5_ASSIGN_OVERFLOW(src_accessed_bytes, tmp_src_accessed_bytes, size_t, uint32_t);
+ src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
/* Lock the chunk into the cache */
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint)))
+ 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 */
@@ -1272,7 +1543,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed")
/* Release the cache lock on the chunk. */
- if(chunk && H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, src_accessed_bytes) < 0)
+ 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 */
@@ -1342,25 +1613,23 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
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_istore_ud1_t udata; /* B-tree pass-through */
+ 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);
- /* Pass in chunk's coordinates in a union. */
- io_info->store->chunk.offset = chunk_info->coords;
- io_info->store->chunk.index = chunk_info->index;
-
/* Load the chunk into cache. But if the whole chunk is written,
* simply allocate space instead of load the chunk. */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
+ 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 */
- size_t tmp_dst_accessed_bytes; /* Total accessed size in a chunk */
+
+ /* 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 */
- tmp_dst_accessed_bytes = chunk_info->chunk_points * type_info->dst_type_size;
- H5_ASSIGN_OVERFLOW(dst_accessed_bytes, tmp_dst_accessed_bytes, size_t, uint32_t);
+ 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 ||
@@ -1368,7 +1637,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
entire_chunk = FALSE;
/* Lock the chunk into the cache */
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, entire_chunk, &idx_hint)))
+ 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 */
@@ -1397,7 +1666,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed")
/* Release the cache lock on the chunk. */
- if(chunk && H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, dst_accessed_bytes) < 0)
+ 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 */
@@ -1461,6 +1730,2712 @@ done:
/*-------------------------------------------------------------------------
+ * 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) */
+ bytes_accessed = 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)) < 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)) < 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)) < 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)) < 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) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID")
+ if(tid_src > 0)
+ if(H5I_dec_ref(tid_src) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+ if(tid_dst > 0)
+ if(H5I_dec_ref(tid_dst) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+ if(tid_mem > 0)
+ if(H5I_dec_ref(tid_mem) < 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