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|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Robb Matzke <matzke@llnl.gov>
* Wednesday, October 8, 1997
*
* Purpose: Indexed (chunked) I/O functions. The logical
* multi-dimensional data space is regularly partitioned into
* same-sized "chunks", the first of which is aligned with the
* logical origin. The chunks are given a multi-dimensional
* index which is used as a lookup key in a B-tree that maps
* chunk index to disk address. Each chunk can be compressed
* independently and the chunks may move around in the file as
* their storage requirements change.
*
* Cache: Disk I/O is performed in units of chunks and H5MF_alloc()
* contains code to optionally align chunks on disk block
* boundaries for performance.
*
* The chunk cache is an extendible hash indexed by a function
* of storage B-tree address and chunk N-dimensional offset
* within the dataset. Collisions are not resolved -- one of
* the two chunks competing for the hash slot must be preempted
* from the cache. All entries in the hash also participate in
* a doubly-linked list and entries are penalized by moving them
* toward the front of the list. When a new chunk is about to
* be added to the cache the heap is pruned by preempting
* entries near the front of the list to make room for the new
* entry which is added to the end of the list.
*/
#define H5B_PACKAGE /*suppress error about including H5Bpkg */
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
/* Pablo information */
/* (Put before include files to avoid problems with inline functions) */
#define PABLO_MASK H5Distore_mask
#include "H5private.h" /* Generic Functions */
#include "H5Bpkg.h" /* B-link trees */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* Files */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MFprivate.h" /* File space management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Oprivate.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
#include "H5Sprivate.h" /* Dataspaces */
#include "H5Vprivate.h" /* Vector and array functions */
/* MPIO, MPIPOSIX, & FPHDF5 drivers needed for special checks */
#include "H5FDfphdf5.h"
#include "H5FDmpio.h"
#include "H5FDmpiposix.h"
/*
* 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_ISTORE_DEBUG */
/* Interface initialization */
static int interface_initialize_g = 0;
#define INTERFACE_INIT NULL
/*
* Given a B-tree node return the dimensionality of the chunks pointed to by
* that node.
*/
#define H5D_ISTORE_NDIMS(X) ((int)(((X)->sizeof_rkey-8)/8))
/* Raw data chunks are cached. Each entry in the cache is: */
typedef struct H5D_rdcc_ent_t {
hbool_t locked; /*entry is locked in cache */
hbool_t dirty; /*needs to be written to disk? */
hssize_t offset[H5O_LAYOUT_NDIMS]; /*chunk name */
size_t rd_count; /*bytes remaining to be read */
size_t wr_count; /*bytes remaining to be written */
size_t chunk_size; /*size of a chunk */
size_t alloc_size; /*amount allocated for the chunk */
uint8_t *chunk; /*the unfiltered chunk data */
unsigned idx; /*index in hash table */
struct H5D_rdcc_ent_t *next;/*next item in doubly-linked list */
struct H5D_rdcc_ent_t *prev;/*previous item in doubly-linked list */
} H5D_rdcc_ent_t;
typedef H5D_rdcc_ent_t *H5D_rdcc_ent_ptr_t; /* For free lists */
/*
* B-tree key. A key contains the minimum logical N-dimensional address and
* the logical size of the chunk to which this key refers. The
* fastest-varying dimension is assumed to reference individual bytes of the
* array, so a 100-element 1-d array of 4-byte integers would really be a 2-d
* array with the slow varying dimension of size 100 and the fast varying
* dimension of size 4 (the storage dimensionality has very little to do with
* the real dimensionality).
*
* Only the first few values of the OFFSET and SIZE fields are actually
* stored on disk, depending on the dimensionality.
*
* The chunk's file address is part of the B-tree and not part of the key.
*/
typedef struct H5D_istore_key_t {
size_t nbytes; /*size of stored data */
hssize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
unsigned filter_mask; /*excluded filters */
} H5D_istore_key_t;
typedef struct H5D_istore_ud1_t {
H5D_istore_key_t key; /*key values */
haddr_t addr; /*file address of chunk */
const H5O_layout_t *mesg; /*layout message */
hsize_t total_storage; /*output from iterator */
FILE *stream; /*debug output stream */
hsize_t *dims; /*dataset dimensions */
} H5D_istore_ud1_t;
#define H5D_HASH(D,ADDR) H5F_addr_hash(ADDR,(D)->cache.chunk.nslots)
/* Private prototypes */
static haddr_t H5D_istore_get_addr(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
const hssize_t offset[], H5D_istore_ud1_t *_udata);
static void *H5D_istore_chunk_alloc(size_t size, const H5O_pline_t *pline);
static void *H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline);
static herr_t H5D_istore_shared_free (void *page);
/* B-tree iterator callbacks */
static int H5D_istore_iter_allocated(H5F_t *f, hid_t dxpl_id, void *left_key, haddr_t addr,
void *right_key, void *_udata);
static int H5D_istore_iter_dump(H5F_t *f, hid_t dxpl_id, void *left_key, haddr_t addr,
void *right_key, void *_udata);
static int H5D_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t addr,
void *_rt_key, void *_udata);
/* B-tree callbacks */
static size_t H5D_istore_sizeof_rkey(H5F_t *f, const void *_udata);
static H5RC_t *H5D_istore_get_shared(H5F_t *f, const void *_udata);
static herr_t H5D_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t, void *_lt_key,
void *_udata, void *_rt_key,
haddr_t *addr_p /*out*/);
static int H5D_istore_cmp2(H5F_t *f, hid_t dxpl_id, void *_lt_key, void *_udata,
void *_rt_key);
static int H5D_istore_cmp3(H5F_t *f, hid_t dxpl_id, void *_lt_key, void *_udata,
void *_rt_key);
static herr_t H5D_istore_found(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void *_lt_key,
void *_udata, const void *_rt_key);
static H5B_ins_t H5D_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key,
hbool_t *lt_key_changed, void *_md_key,
void *_udata, void *_rt_key,
hbool_t *rt_key_changed,
haddr_t *new_node/*out*/);
static H5B_ins_t H5D_istore_remove( H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key,
hbool_t *lt_key_changed, void *_udata, void *_rt_key,
hbool_t *rt_key_changed);
static herr_t H5D_istore_decode_key(H5F_t *f, H5B_t *bt, uint8_t *raw,
void *_key);
static herr_t H5D_istore_encode_key(H5F_t *f, H5B_t *bt, uint8_t *raw,
void *_key);
static herr_t H5D_istore_debug_key(FILE *stream, H5F_t *f, hid_t dxpl_id,
int indent, int fwidth, const void *key,
const void *udata);
/* inherits B-tree like properties from H5B */
H5B_class_t H5B_ISTORE[1] = {{
H5B_ISTORE_ID, /*id */
sizeof(H5D_istore_key_t), /*sizeof_nkey */
H5D_istore_sizeof_rkey, /*get_sizeof_rkey */
H5D_istore_get_shared, /*get_shared */
H5D_istore_new_node, /*new */
H5D_istore_cmp2, /*cmp2 */
H5D_istore_cmp3, /*cmp3 */
H5D_istore_found, /*found */
H5D_istore_insert, /*insert */
FALSE, /*follow min branch? */
FALSE, /*follow max branch? */
H5D_istore_remove, /*remove */
H5D_istore_decode_key, /*decode */
H5D_istore_encode_key, /*encode */
H5D_istore_debug_key, /*debug */
}};
/* Declare a free list to manage the H5B_shared_t struct */
H5FL_EXTERN(H5B_shared_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 H5F_rdcc_ent_ptr_t sequence information */
H5FL_SEQ_DEFINE_STATIC(H5D_rdcc_ent_ptr_t);
/* Declare a free list to manage the chunk sequence information */
H5FL_BLK_DEFINE_STATIC(chunk);
/* Declare a free list to manage the native key offset sequence information */
H5FL_SEQ_DEFINE_STATIC(size_t);
/* Declare a free list to manage the raw page information */
H5FL_BLK_DEFINE_STATIC(chunk_page);
/*-------------------------------------------------------------------------
* Function: H5D_istore_sizeof_rkey
*
* Purpose: Returns the size of a raw key for the specified UDATA. The
* size of the key is dependent on the number of dimensions for
* the object to which this B-tree points. The dimensionality
* of the UDATA is the only portion that's referenced here.
*
* Return: Success: Size of raw key in bytes.
*
* Failure: abort()
*
* Programmer: Robb Matzke
* Wednesday, October 8, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
H5D_istore_sizeof_rkey(H5F_t UNUSED *f, const void *_udata)
{
const H5D_istore_ud1_t *udata = (const H5D_istore_ud1_t *) _udata;
size_t nbytes;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_sizeof_rkey);
assert(udata);
assert(udata->mesg->u.chunk.ndims > 0 && udata->mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
nbytes = 4 + /*storage size */
4 + /*filter mask */
udata->mesg->u.chunk.ndims*8; /*dimension indices */
FUNC_LEAVE_NOAPI(nbytes);
} /* end H5D_istore_sizeof_rkey() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_get_shared
*
* Purpose: Returns the shared B-tree info for the specified UDATA.
*
* Return: Success: Pointer to the raw B-tree page for this dataset
*
* Failure: Can't fail
*
* Programmer: Quincey Koziol
* Monday, July 5, 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static H5RC_t *
H5D_istore_get_shared(H5F_t UNUSED *f, const void *_udata)
{
const H5D_istore_ud1_t *udata = (const H5D_istore_ud1_t *) _udata;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_get_shared);
assert(udata);
assert(udata->mesg);
assert(udata->mesg->u.chunk.btree_shared);
/* Increment reference count on B-tree info */
H5RC_INC(udata->mesg->u.chunk.btree_shared);
/* Return the pointer to the ref-count object */
FUNC_LEAVE_NOAPI(udata->mesg->u.chunk.btree_shared);
} /* end H5D_istore_get_shared() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_decode_key
*
* Purpose: Decodes a raw key into a native key for the B-tree
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Friday, October 10, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_decode_key(H5F_t UNUSED *f, H5B_t *bt, uint8_t *raw, void *_key)
{
H5D_istore_key_t *key = (H5D_istore_key_t *) _key;
H5B_shared_t *shared; /* Pointer to shared B-tree info */
unsigned u;
unsigned ndims;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_decode_key);
/* check args */
assert(f);
assert(bt);
shared=H5RC_GET_OBJ(bt->rc_shared);
HDassert(shared);
assert(raw);
assert(key);
ndims = H5D_ISTORE_NDIMS(shared);
assert(ndims<=H5O_LAYOUT_NDIMS);
/* decode */
UINT32DECODE(raw, key->nbytes);
UINT32DECODE(raw, key->filter_mask);
for (u=0; u<ndims; u++)
UINT64DECODE(raw, key->offset[u]);
FUNC_LEAVE_NOAPI(SUCCEED);
} /* end H5D_istore_decode_key() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_encode_key
*
* Purpose: Encode a key from native format to raw format.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Friday, October 10, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_encode_key(H5F_t UNUSED *f, H5B_t *bt, uint8_t *raw, void *_key)
{
H5D_istore_key_t *key = (H5D_istore_key_t *) _key;
H5B_shared_t *shared; /* Pointer to shared B-tree info */
unsigned ndims;
unsigned u;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_encode_key);
/* check args */
assert(f);
assert(bt);
shared=H5RC_GET_OBJ(bt->rc_shared);
HDassert(shared);
assert(raw);
assert(key);
ndims = H5D_ISTORE_NDIMS(shared);
assert(ndims<=H5O_LAYOUT_NDIMS);
/* encode */
UINT32ENCODE(raw, key->nbytes);
UINT32ENCODE(raw, key->filter_mask);
for (u=0; u<ndims; u++)
UINT64ENCODE(raw, key->offset[u]);
FUNC_LEAVE_NOAPI(SUCCEED);
} /* end H5D_istore_encode_key() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_debug_key
*
* Purpose: Prints a key.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_debug_key (FILE *stream, H5F_t UNUSED *f, hid_t UNUSED dxpl_id, int indent, int fwidth,
const void *_key, const void *_udata)
{
const H5D_istore_key_t *key = (const H5D_istore_key_t *)_key;
const H5D_istore_ud1_t *udata = (const H5D_istore_ud1_t *)_udata;
unsigned u;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_debug_key);
assert (key);
HDfprintf(stream, "%*s%-*s %Zd bytes\n", indent, "", fwidth,
"Chunk size:", key->nbytes);
HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth,
"Filter mask:", key->filter_mask);
HDfprintf(stream, "%*s%-*s {", indent, "", fwidth,
"Logical offset:");
for (u=0; u<udata->mesg->u.chunk.ndims; u++)
HDfprintf (stream, "%s%Hd", u?", ":"", key->offset[u]);
HDfputs ("}\n", stream);
FUNC_LEAVE_NOAPI(SUCCEED);
} /* end H5D_istore_debug_key() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_cmp2
*
* Purpose: Compares two keys sort of like strcmp(). The UDATA pointer
* is only to supply extra information not carried in the keys
* (in this case, the dimensionality) and is not compared
* against the keys.
*
* Return: Success: -1 if LT_KEY is less than RT_KEY;
* 1 if LT_KEY is greater than RT_KEY;
* 0 if LT_KEY and RT_KEY are equal.
*
* Failure: FAIL (same as LT_KEY<RT_KEY)
*
* Programmer: Robb Matzke
* Thursday, November 6, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
H5D_istore_cmp2(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_udata,
void *_rt_key)
{
H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key;
H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key;
H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata;
int ret_value;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_cmp2);
assert(lt_key);
assert(rt_key);
assert(udata);
assert(udata->mesg->u.chunk.ndims > 0 && udata->mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
/* Compare the offsets but ignore the other fields */
ret_value = H5V_vector_cmp_s(udata->mesg->u.chunk.ndims, lt_key->offset, rt_key->offset);
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_cmp2() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_cmp3
*
* Purpose: Compare the requested datum UDATA with the left and right
* keys of the B-tree.
*
* Return: Success: negative if the min_corner of UDATA is less
* than the min_corner of LT_KEY.
*
* positive if the min_corner of UDATA is
* greater than or equal the min_corner of
* RT_KEY.
*
* zero otherwise. The min_corner of UDATA is
* not necessarily contained within the address
* space represented by LT_KEY, but a key that
* would describe the UDATA min_corner address
* would fall lexicographically between LT_KEY
* and RT_KEY.
*
* Failure: FAIL (same as UDATA < LT_KEY)
*
* Programmer: Robb Matzke
* Wednesday, October 8, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
H5D_istore_cmp3(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_udata,
void *_rt_key)
{
H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key;
H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key;
H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata;
int ret_value = 0;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_cmp3);
assert(lt_key);
assert(rt_key);
assert(udata);
assert(udata->mesg->u.chunk.ndims > 0 && udata->mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
/* Special case for faster checks on 1-D chunks */
/* (Checking for ndims==2 because last dimension is the datatype size) */
/* The additional checking for the right key is necessary due to the */
/* slightly odd way the library initializes the right-most node in the */
/* indexed storage B-tree... */
/* (Dump the B-tree with h5debug to look at it) -QAK */
if(udata->mesg->u.chunk.ndims==2) {
if(udata->key.offset[0]>rt_key->offset[0])
ret_value=1;
else if(udata->key.offset[0]==rt_key->offset[0] &&
udata->key.offset[1]>=rt_key->offset[1])
ret_value=1;
else if(udata->key.offset[0]<lt_key->offset[0])
ret_value=(-1);
} /* end if */
else {
if (H5V_vector_ge_s(udata->mesg->u.chunk.ndims, udata->key.offset,
rt_key->offset))
ret_value = 1;
else if (H5V_vector_lt_s(udata->mesg->u.chunk.ndims, udata->key.offset,
lt_key->offset))
ret_value = -1;
} /* end else */
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_cmp3() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_new_node
*
* Purpose: Adds a new entry to an i-storage B-tree. We can assume that
* the domain represented by UDATA doesn't intersect the domain
* already represented by the B-tree.
*
* Return: Success: Non-negative. The address of leaf is returned
* through the ADDR argument. It is also added
* to the UDATA.
*
* Failure: Negative
*
* Programmer: Robb Matzke
* Tuesday, October 14, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op,
void *_lt_key, void *_udata, void *_rt_key,
haddr_t *addr_p/*out*/)
{
H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key;
H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key;
H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata;
unsigned u;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_new_node);
/* check args */
assert(f);
assert(lt_key);
assert(rt_key);
assert(udata);
assert(udata->mesg->u.chunk.ndims > 0 && udata->mesg->u.chunk.ndims < H5O_LAYOUT_NDIMS);
assert(addr_p);
/* Allocate new storage */
assert (udata->key.nbytes > 0);
H5_CHECK_OVERFLOW( udata->key.nbytes ,size_t, hsize_t);
if (HADDR_UNDEF==(*addr_p=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, (hsize_t)udata->key.nbytes)))
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "couldn't allocate new file storage");
udata->addr = *addr_p;
/*
* The left key describes the storage of the UDATA chunk being
* inserted into the tree.
*/
lt_key->nbytes = udata->key.nbytes;
lt_key->filter_mask = udata->key.filter_mask;
for (u=0; u<udata->mesg->u.chunk.ndims; u++)
lt_key->offset[u] = udata->key.offset[u];
/*
* The right key might already be present. If not, then add a zero-width
* chunk.
*/
if (H5B_INS_LEFT != op) {
rt_key->nbytes = 0;
rt_key->filter_mask = 0;
for (u=0; u<udata->mesg->u.chunk.ndims; u++) {
assert (udata->key.offset[u]+(hssize_t)(udata->mesg->u.chunk.dim[u]) >
udata->key.offset[u]);
rt_key->offset[u] = udata->key.offset[u] +
(hssize_t)(udata->mesg->u.chunk.dim[u]);
}
}
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_new_node() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_found
*
* Purpose: This function is called when the B-tree search engine has
* found the leaf entry that points to a chunk of storage that
* contains the beginning of the logical address space
* represented by UDATA. The LT_KEY is the left key (the one
* that describes the chunk) and RT_KEY is the right key (the
* one that describes the next or last chunk).
*
* Note: It's possible that the chunk isn't really found. For
* instance, in a sparse dataset the requested chunk might fall
* between two stored chunks in which case this function is
* called with the maximum stored chunk indices less than the
* requested chunk indices.
*
* Return: Non-negative on success with information about the chunk
* returned through the UDATA argument. Negative on failure.
*
* Programmer: Robb Matzke
* Thursday, October 9, 1997
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value.
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void *_lt_key,
void *_udata, const void UNUSED *_rt_key)
{
H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata;
const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *) _lt_key;
unsigned u;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_found);
/* Check arguments */
assert(f);
assert(H5F_addr_defined(addr));
assert(udata);
assert(lt_key);
/* Is this *really* the requested chunk? */
for (u=0; u<udata->mesg->u.chunk.ndims; u++) {
if (udata->key.offset[u] >= lt_key->offset[u]+(hssize_t)(udata->mesg->u.chunk.dim[u]))
HGOTO_DONE(FAIL);
}
/* Initialize return values */
udata->addr = addr;
udata->key.nbytes = lt_key->nbytes;
udata->key.filter_mask = lt_key->filter_mask;
assert (lt_key->nbytes>0);
for (u = 0; u < udata->mesg->u.chunk.ndims; u++)
udata->key.offset[u] = lt_key->offset[u];
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_found() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_insert
*
* Purpose: This function is called when the B-tree insert engine finds
* the node to use to insert new data. The UDATA argument
* points to a struct that describes the logical addresses being
* added to the file. This function allocates space for the
* data and returns information through UDATA describing a
* file chunk to receive (part of) the data.
*
* The LT_KEY is always the key describing the chunk of file
* memory at address ADDR. On entry, UDATA describes the logical
* addresses for which storage is being requested (through the
* `offset' and `size' fields). On return, UDATA describes the
* logical addresses contained in a chunk on disk.
*
* Return: Success: An insertion command for the caller, one of
* the H5B_INS_* constants. The address of the
* new chunk is returned through the NEW_NODE
* argument.
*
* Failure: H5B_INS_ERROR
*
* Programmer: Robb Matzke
* Thursday, October 9, 1997
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value. The NEW_NODE argument
* is renamed NEW_NODE_P.
*-------------------------------------------------------------------------
*/
static H5B_ins_t
H5D_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key,
hbool_t *lt_key_changed,
void *_md_key, void *_udata, void *_rt_key,
hbool_t UNUSED *rt_key_changed,
haddr_t *new_node_p/*out*/)
{
H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key;
H5D_istore_key_t *md_key = (H5D_istore_key_t *) _md_key;
H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key;
H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata;
int cmp;
unsigned u;
H5B_ins_t ret_value;
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_insert);
/* check args */
assert(f);
assert(H5F_addr_defined(addr));
assert(lt_key);
assert(lt_key_changed);
assert(md_key);
assert(udata);
assert(rt_key);
assert(rt_key_changed);
assert(new_node_p);
cmp = H5D_istore_cmp3(f, dxpl_id, lt_key, udata, rt_key);
assert(cmp <= 0);
if (cmp < 0) {
/* Negative indices not supported yet */
assert("HDF5 INTERNAL ERROR -- see rpm" && 0);
HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error");
} else if (H5V_vector_eq_s (udata->mesg->u.chunk.ndims,
udata->key.offset, lt_key->offset) &&
lt_key->nbytes>0) {
/*
* Already exists. If the new size is not the same as the old size
* then we should reallocate storage.
*/
if (lt_key->nbytes != udata->key.nbytes) {
/* Currently, the old chunk data is "thrown away" after the space is reallocated,
* so avoid data copy in H5MF_realloc() call by just free'ing the space and
* allocating new space.
*
* This should keep the file smaller also, by freeing the space and then
* allocating new space, instead of vice versa (in H5MF_realloc).
*
* QAK - 11/19/2002
*/
#ifdef OLD_WAY
if (HADDR_UNDEF==(*new_node_p=H5MF_realloc(f, H5FD_MEM_DRAW, addr,
(hsize_t)lt_key->nbytes, (hsize_t)udata->key.nbytes)))
HGOTO_ERROR (H5E_STORAGE, H5E_NOSPACE, H5B_INS_ERROR, "unable to reallocate chunk storage");
#else /* OLD_WAY */
H5_CHECK_OVERFLOW( lt_key->nbytes ,size_t, hsize_t);
if (H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, addr, (hsize_t)lt_key->nbytes)<0)
HGOTO_ERROR(H5E_STORAGE, H5E_CANTFREE, H5B_INS_ERROR, "unable to free chunk");
H5_CHECK_OVERFLOW( udata->key.nbytes ,size_t, hsize_t);
if (HADDR_UNDEF==(*new_node_p=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, (hsize_t)udata->key.nbytes)))
HGOTO_ERROR(H5E_STORAGE, H5E_NOSPACE, H5B_INS_ERROR, "unable to reallocate chunk");
#endif /* OLD_WAY */
lt_key->nbytes = udata->key.nbytes;
lt_key->filter_mask = udata->key.filter_mask;
*lt_key_changed = TRUE;
udata->addr = *new_node_p;
ret_value = H5B_INS_CHANGE;
} else {
udata->addr = addr;
ret_value = H5B_INS_NOOP;
}
} else if (H5V_hyper_disjointp(udata->mesg->u.chunk.ndims,
lt_key->offset, udata->mesg->u.chunk.dim,
udata->key.offset, udata->mesg->u.chunk.dim)) {
assert(H5V_hyper_disjointp(udata->mesg->u.chunk.ndims,
rt_key->offset, udata->mesg->u.chunk.dim,
udata->key.offset, udata->mesg->u.chunk.dim));
/*
* Split this node, inserting the new new node to the right of the
* current node. The MD_KEY is where the split occurs.
*/
md_key->nbytes = udata->key.nbytes;
md_key->filter_mask = udata->key.filter_mask;
for (u=0; u<udata->mesg->u.chunk.ndims; u++) {
assert(0 == udata->key.offset[u] % udata->mesg->u.chunk.dim[u]);
md_key->offset[u] = udata->key.offset[u];
}
/*
* Allocate storage for the new chunk
*/
H5_CHECK_OVERFLOW( udata->key.nbytes ,size_t, hsize_t);
if (HADDR_UNDEF==(*new_node_p=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, (hsize_t)udata->key.nbytes)))
HGOTO_ERROR(H5E_STORAGE, H5E_NOSPACE, H5B_INS_ERROR, "file allocation failed");
udata->addr = *new_node_p;
ret_value = H5B_INS_RIGHT;
} else {
assert("HDF5 INTERNAL ERROR -- see rpm" && 0);
HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error");
}
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_insert() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_iter_allocated
*
* Purpose: Simply counts the number of chunks for a dataset.
*
* Return: Success: Non-negative
*
* Failure: Negative
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value.
*
* Quincey Koziol, 2002-04-22
* Changed to callback from H5B_iterate
*-------------------------------------------------------------------------
*/
static int
H5D_istore_iter_allocated (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, haddr_t UNUSED addr,
void UNUSED *_rt_key, void *_udata)
{
H5D_istore_ud1_t *bt_udata = (H5D_istore_ud1_t *)_udata;
H5D_istore_key_t *lt_key = (H5D_istore_key_t *)_lt_key;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_iter_allocated);
bt_udata->total_storage += lt_key->nbytes;
FUNC_LEAVE_NOAPI(H5B_ITER_CONT);
} /* H5D_istore_iter_allocated() */
/*-------------------------------------------------------------------------
* 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
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value.
*
* Quincey Koziol, 2002-04-22
* Changed to callback from H5B_iterate
*-------------------------------------------------------------------------
*/
static int
H5D_istore_iter_dump (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, haddr_t UNUSED addr,
void UNUSED *_rt_key, void *_udata)
{
H5D_istore_ud1_t *bt_udata = (H5D_istore_ud1_t *)_udata;
H5D_istore_key_t *lt_key = (H5D_istore_key_t *)_lt_key;
unsigned u;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_iter_dump);
if (bt_udata->stream) {
if (0==bt_udata->total_storage) {
fprintf(bt_udata->stream,
" Flags Bytes Address Logical Offset\n");
fprintf(bt_udata->stream,
" ========== ======== ========== "
"==============================\n");
}
HDfprintf(bt_udata->stream, " 0x%08x %8Zu %10a [",
lt_key->filter_mask, lt_key->nbytes, addr);
for (u=0; u<bt_udata->mesg->u.chunk.ndims; u++)
HDfprintf(bt_udata->stream, "%s%Hd", u?", ":"", lt_key->offset[u]);
HDfputs("]\n", bt_udata->stream);
/* Use "total storage" information as flag for printing headers */
bt_udata->total_storage++;
}
FUNC_LEAVE_NOAPI(H5B_ITER_CONT);
} /* H5D_istore_iter_dump() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_init (H5F_t *f, H5D_t *dset)
{
H5D_istore_ud1_t udata;
H5B_shared_t *shared; /* Shared B-tree node info */
size_t u; /* Local index variable */
H5D_rdcc_t *rdcc = &(dset->cache.chunk);
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_init, FAIL);
HDmemset (rdcc, 0, sizeof(H5D_rdcc_t));
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");
} /* end if */
/* Initialize "user" data for B-tree callbacks, etc. */
udata.mesg = &dset->layout;
/* Allocate space for the shared structure */
if(NULL==(shared=H5FL_MALLOC(H5B_shared_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
/* Set up the "global" information for this file's groups */
shared->type= H5B_ISTORE;
shared->two_k=2*H5F_KVALUE(f,H5B_ISTORE);
shared->sizeof_rkey = H5D_istore_sizeof_rkey(f, &udata);
assert(shared->sizeof_rkey);
shared->sizeof_rnode = H5B_nodesize(f, shared, &shared->sizeof_keys);
assert(shared->sizeof_rnode);
if(NULL==(shared->page=H5FL_BLK_MALLOC(chunk_page,shared->sizeof_rnode)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
if(NULL==(shared->nkey=H5FL_SEQ_MALLOC(size_t,(size_t)(2*H5F_KVALUE(f,H5B_ISTORE)+1))))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
/* Initialize the offsets into the native key buffer */
for(u=0; u<(2*H5F_KVALUE(f,H5B_ISTORE)+1); u++)
shared->nkey[u]=u*H5B_ISTORE->sizeof_nkey;
/* Make shared B-tree info reference counted */
if(NULL==(dset->layout.u.chunk.btree_shared=H5RC_create(shared,H5D_istore_shared_free)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_init() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_flush_entry(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache,
hid_t dxpl_id, H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset)
{
herr_t ret_value=SUCCEED; /*return value */
unsigned u; /*counters */
void *buf=NULL; /*temporary buffer */
size_t alloc; /*bytes allocated for BUF */
hbool_t point_of_no_return = FALSE;
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_flush_entry);
assert(f);
assert(ent);
assert(!ent->locked);
buf = ent->chunk;
if (ent->dirty) {
H5D_istore_ud1_t udata; /*pass through B-tree */
udata.mesg = &dset->layout;
udata.key.filter_mask = 0;
udata.addr = HADDR_UNDEF;
udata.key.nbytes = ent->chunk_size;
for (u=0; u<dset->layout.u.chunk.ndims; u++)
udata.key.offset[u] = ent->offset[u];
alloc = ent->alloc_size;
/* Should the chunk be filtered before writing it to disk? */
if (dset->dcpl_cache.pline.nused) {
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.
*/
alloc = ent->chunk_size;
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);
} 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;
}
if (H5Z_pipeline(&(dset->dcpl_cache.pline), 0, &(udata.key.filter_mask), dxpl_cache->err_detect,
dxpl_cache->filter_cb, &(udata.key.nbytes), &alloc, &buf)<0)
HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
}
/*
* Create the chunk it if it doesn't exist, or reallocate the chunk if
* its size changed. Then write the data into the file.
*/
if (H5B_insert(f, dxpl_id, H5B_ISTORE, dset->layout.u.chunk.addr, &udata)<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk");
if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, buf)<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file");
/* Mark cache entry as clean */
ent->dirty = FALSE;
dset->cache.chunk.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 = H5D_istore_chunk_xfree(ent->chunk,&(dset->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 = H5D_istore_chunk_xfree(ent->chunk,&(dset->dcpl_cache.pline));
} /* end if */
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_flush_entry() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_preempt
*
* 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
*
* Modifications:
* Pedro Vicente, March 28, 2002
* Added flush parameter that switches the call to H5F_istore_flush_entry
* The call with FALSE is used by the H5F_istore_prune_by_extent function
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_preempt(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
H5D_t *dset, H5D_rdcc_ent_t * ent, hbool_t flush)
{
H5D_rdcc_t *rdcc = &(dset->cache.chunk);
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_preempt);
assert(f);
assert(ent);
assert(!ent->locked);
assert(ent->idx < rdcc->nslots);
if(flush) {
/* Flush */
if(H5D_istore_flush_entry(f, dxpl_cache, dxpl_id, dset, ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer");
}
else {
/* Don't flush, just free chunk */
if(ent->chunk != NULL)
ent->chunk = H5D_istore_chunk_xfree(ent->chunk,&(dset->dcpl_cache.pline));
}
/* 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_istore_preempt() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
* Pedro Vicente, March 28, 2002
* Added TRUE parameter to the call to H5F_istore_preempt
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_flush (H5F_t *f, hid_t dxpl_id, H5D_t *dset, 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->cache.chunk);
int nerrors=0;
H5D_rdcc_ent_t *ent=NULL, *next=NULL;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_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")
for (ent=rdcc->head; ent; ent=next) {
next = ent->next;
if ((flags&H5F_FLUSH_CLEAR_ONLY)) {
/* Just mark cache entry as clean */
ent->dirty = FALSE;
} /* end if */
else if ((flags&H5F_FLUSH_INVALIDATE)) {
if (H5D_istore_preempt(f, dxpl_cache, dxpl_id, dset, ent, TRUE )<0)
nerrors++;
} else {
if (H5D_istore_flush_entry(f, dxpl_cache, dxpl_id, dset, 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_istore_flush() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
* Pedro Vicente, March 28, 2002
* Added TRUE parameter to the call to H5F_istore_preempt
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_dest (H5F_t *f, hid_t dxpl_id, H5D_t *dset)
{
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->cache.chunk);
int nerrors=0;
H5D_rdcc_ent_t *ent=NULL, *next=NULL;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_dest, 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")
/* Flush all the cached chunks */
for (ent=rdcc->head; ent; ent=next) {
#ifdef H5D_ISTORE_DEBUG
HDfputc('c', stderr);
HDfflush(stderr);
#endif
next = ent->next;
if (H5D_istore_preempt(f, dxpl_cache, dxpl_id, dset, ent, TRUE )<0)
nerrors++;
}
if (nerrors)
HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks");
H5FL_SEQ_FREE (H5D_rdcc_ent_ptr_t,rdcc->slot);
HDmemset (rdcc, 0, sizeof(H5D_rdcc_t));
/* Free the raw B-tree node buffer */
if(H5RC_DEC(dset->layout.u.chunk.btree_shared)<0)
HGOTO_ERROR (H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page");
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_dest() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_shared_free
*
* Purpose: Free B-tree shared info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, July 8, 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_shared_free (void *_shared)
{
H5B_shared_t *shared = (H5B_shared_t *)_shared;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_shared_free)
/* Free the raw B-tree node buffer */
H5FL_BLK_FREE(chunk_page,shared->page);
/* Free the B-tree native key offsets buffer */
H5FL_SEQ_FREE(size_t,shared->nkey);
/* Free the shared B-tree info */
H5FL_FREE(H5B_shared_t,shared);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5D_istore_shared_free() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
* Pedro Vicente, March 28, 2002
* TRUE parameter to the call to H5F_istore_preempt
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_prune (H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, H5D_t *dset,
size_t size)
{
int i, j, nerrors=0;
H5D_rdcc_t *rdcc = &(dset->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 */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_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(f));
p[0] = rdcc->head;
p[1] = NULL;
while ((p[0] || p[1]) && rdcc->nbytes+size>total) {
/* 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];
#ifdef H5D_ISTORE_DEBUG
HDputc('.', stderr);
HDfflush(stderr);
#endif
} 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];
#ifdef H5D_ISTORE_DEBUG
HDputc(':', stderr);
HDfflush(stderr);
#endif
} else {
/* Nothing to preempt at this point */
cur= NULL;
}
if (cur) {
for (j=0; j<nmeth; j++) {
if (p[j]==cur)
p[j] = NULL;
if (n[j]==cur)
n[j] = cur->next;
}
if (H5D_istore_preempt(f, dxpl_cache, dxpl_id, dset, cur, TRUE)<0)
nerrors++;
}
}
/* Advance pointers */
for (i=0; i<nmeth; i++)
p[i] = n[i];
for (i=0; i<nmeth-1; i++)
w[i] -= 1;
}
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_istore_prune() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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_istore_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
*
* Modifications:
* Robb Matzke, 1999-08-02
* The split ratios are passed in as part of the data transfer
* property list.
*
* Pedro Vicente, March 28, 2002
* TRUE parameter to the call to H5F_istore_preempt
*-------------------------------------------------------------------------
*/
static void *
H5D_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
H5D_t *dset, const H5D_storage_t *store,
H5D_istore_ud1_t *udata, hbool_t relax, unsigned *idx_hint/*in,out*/)
{
unsigned idx=0; /*hash index number */
hbool_t found = FALSE; /*already in cache? */
const H5O_pline_t *pline=&(dset->dcpl_cache.pline); /* I/O pipeline info */
const H5O_layout_t *layout=&(dset->layout); /* Dataset layout */
const H5O_fill_t *fill=&(dset->dcpl_cache.fill); /* Fill value info */
H5D_fill_time_t fill_time=dset->dcpl_cache.fill_time; /* Fill time */
H5D_rdcc_t *rdcc = &(dset->cache.chunk);/*raw data chunk cache*/
H5D_rdcc_ent_t *ent = NULL; /*cache entry */
unsigned u; /*counters */
size_t chunk_size=0; /*size of a chunk */
void *chunk=NULL; /*the file chunk */
void *ret_value; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_lock);
assert(f);
assert(dset);
assert(store);
assert(dxpl_cache);
assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));
/* Get the chunk's size */
assert(layout->u.chunk.size>0);
H5_ASSIGN_OVERFLOW(chunk_size,layout->u.chunk.size,hsize_t,size_t);
/* Search for the chunk in the cache */
if (rdcc->nslots>0) {
idx=H5D_HASH(dset,store->chunk.index);
ent = rdcc->slot[idx];
if (ent) {
for (u=0, found=TRUE; u<dset->layout.u.chunk.ndims; u++) {
if (store->chunk.offset[u]!=ent->offset[u]) {
found = FALSE;
break;
} /* end if */
} /* end for */
} /* end if */
} /* end if */
if (found) {
/*
* Already in the cache. Count a hit.
*/
rdcc->nhits++;
} else if (!found && 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.
*/
#ifdef H5D_ISTORE_DEBUG
HDputc('w', stderr);
HDfflush(stderr);
#endif
rdcc->nhits++;
if (NULL==(chunk=H5D_istore_chunk_alloc (chunk_size,pline)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk");
} else {
H5D_istore_ud1_t tmp_udata; /*B-tree pass-through */
haddr_t chunk_addr; /* Address of chunk on disk */
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_istore_get_addr(f, dxpl_id, layout, store->chunk.offset, udata);
} /* end else */
if (H5F_addr_defined(chunk_addr)) {
size_t chunk_alloc=0; /*allocated chunk size */
/*
* The chunk exists on disk.
*/
/* Chunk size on disk isn't [likely] the same size as the final chunk
* size in memory, so allocate memory big enough. */
chunk_alloc = udata->key.nbytes;
if (NULL==(chunk = H5D_istore_chunk_alloc (chunk_alloc,pline)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk");
if (H5F_block_read(f, H5FD_MEM_DRAW, chunk_addr, udata->key.nbytes, 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->key.filter_mask), dxpl_cache->err_detect,
dxpl_cache->filter_cb, &(udata->key.nbytes), &chunk_alloc, &chunk)<0) {
HGOTO_ERROR(H5E_PLINE, H5E_READERROR, NULL, "data pipeline read failed");
}
rdcc->nmisses++;
} else {
H5D_fill_value_t fill_status;
#ifdef OLD_WAY
/* Clear the error stack from not finding the chunk on disk */
H5E_clear();
#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_istore_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_time==H5D_FILL_TIME_ALLOC ||
(fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_USER_DEFINED)) {
if (fill && fill->buf) {
/*
* The chunk doesn't exist in the file. Replicate the fill
* value throughout the chunk.
*/
assert(0==chunk_size % fill->size);
H5V_array_fill(chunk, fill->buf, fill->size, chunk_size/fill->size);
} else {
/*
* The chunk doesn't exist in the file and no fill value was
* specified. Assume all zeros.
*/
HDmemset (chunk, 0, chunk_size);
} /* end else */
} /* end if */
rdcc->ninits++;
} /* end else */
}
assert (found || chunk_size>0);
if (!found && rdcc->nslots>0 && chunk_size<=dset->cache.chunk.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) {
#ifdef H5D_ISTORE_DEBUG
HDputc('#', stderr);
HDfflush(stderr);
#endif
if (H5D_istore_preempt(f, dxpl_cache, dxpl_id, dset, ent, TRUE)<0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk from cache");
}
if (H5D_istore_prune(f, dxpl_cache, dxpl_id, dset, 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_size = chunk_size;
ent->alloc_size = chunk_size;
for (u=0; u<layout->u.chunk.ndims; u++)
ent->offset[u] = store->chunk.offset[u];
ent->rd_count = chunk_size;
ent->wr_count = chunk_size;
ent->chunk = chunk;
/* Add it to the cache */
assert(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;
} else {
rdcc->head = rdcc->tail = ent;
ent->prev = NULL;
}
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 if (found) {
/*
* 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.
*/
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;
}
}
/* Lock the chunk into the cache */
if (ent) {
assert (!ent->locked);
ent->locked = TRUE;
chunk = ent->chunk;
}
if (idx_hint)
*idx_hint = idx;
/* Set return value */
ret_value = chunk;
done:
if (!ret_value)
if(chunk)
H5D_istore_chunk_xfree (chunk,pline);
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_lock() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_unlock
*
* Purpose: Unlocks a previously locked chunk. The LAYOUT, COMP, and
* OFFSET arguments should be the same as for H5F_rdcc_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
*
* Modifications:
* Robb Matzke, 1999-08-02
* The split_ratios are passed as part of the data transfer
* property list.
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
H5D_t *dset, const H5D_storage_t *store,
hbool_t dirty, unsigned idx_hint, uint8_t *chunk, size_t naccessed)
{
H5D_rdcc_t *rdcc = &(dset->cache.chunk);
H5D_rdcc_ent_t *ent = NULL;
int found = -1;
unsigned u;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_unlock);
if (UINT_MAX==idx_hint) {
/*not in cache*/
} else {
assert(idx_hint<rdcc->nslots);
assert(rdcc->slot[idx_hint]);
assert(rdcc->slot[idx_hint]->chunk==chunk);
found = idx_hint;
}
if (found<0) {
/*
* 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;
for (u=0; u<dset->layout.u.chunk.ndims; u++)
x.offset[u] = store->chunk.offset[u];
assert(dset->layout.u.chunk.size>0);
H5_ASSIGN_OVERFLOW(x.chunk_size,dset->layout.u.chunk.size,hsize_t,size_t);
x.alloc_size = x.chunk_size;
x.chunk = chunk;
H5D_istore_flush_entry (f, dxpl_cache, dxpl_id, dset, &x, TRUE);
} else {
if(chunk)
H5D_istore_chunk_xfree (chunk,&(dset->dcpl_cache.pline));
}
} else {
/*
* It's in the cache so unlock it.
*/
ent = rdcc->slot[found];
assert (ent->locked);
if (dirty) {
ent->dirty = TRUE;
ent->wr_count -= MIN (ent->wr_count, naccessed);
} else {
ent->rd_count -= MIN (ent->rd_count, naccessed);
}
ent->locked = FALSE;
}
FUNC_LEAVE_NOAPI(SUCCEED);
} /* end H5D_istore_unlock() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_readvv
*
* Purpose: Reads a multi-dimensional buffer from (part of) an indexed raw
* storage array.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Wednesday, May 7, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
ssize_t
H5D_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
H5D_t *dset, const H5D_storage_t *store,
size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
void *buf)
{
H5D_istore_ud1_t udata; /*B-tree pass-through */
haddr_t chunk_addr; /* Chunk address on disk */
#ifndef NDEBUG
size_t u; /* Local index variables */
#endif
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_readvv, FAIL);
/* Check args */
assert(f);
assert(dxpl_cache);
assert(dset && H5D_CHUNKED==dset->layout.type);
assert(dset->layout.u.chunk.ndims>0 && dset->layout.u.chunk.ndims<=H5O_LAYOUT_NDIMS);
assert(store);
assert(chunk_len_arr);
assert(chunk_offset_arr);
assert(mem_len_arr);
assert(mem_offset_arr);
assert(buf);
#ifndef NDEBUG
for (u=0; u<dset->layout.u.chunk.ndims; u++)
assert(store->chunk.offset[u]>=0); /*negative coordinates not supported (yet) */
#endif
/* Get the address of this chunk on disk */
#ifdef QAK
HDfprintf(stderr,"%s: chunk_coords={",FUNC);
for(u=0; u<dset->layout.u.chunk.ndims; u++)
HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(dset->layout.u.chunk.ndims-1) ? ", " : "}\n"));
#endif /* QAK */
chunk_addr=H5D_istore_get_addr(f, dxpl_id, &(dset->layout), store->chunk.offset, &udata);
#ifdef QAK
HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,dset->layout.u.chunk.size);
HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]);
HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]);
HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]);
HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_arr[*mem_curr_seq]);
#endif /* QAK */
/*
* If the chunk is too large to load into the cache and it has no
* filters in the pipeline (i.e. not compressed) and if the address
* for the chunk has been defined, then don't load the chunk into the
* cache, just write the data to it directly.
*/
if (dset->layout.u.chunk.size>dset->cache.chunk.nbytes && dset->dcpl_cache.pline.nused==0 &&
chunk_addr!=HADDR_UNDEF) {
if ((ret_value=H5D_contig_readvv(f, dxpl_id, dset, chunk_addr, (hsize_t)dset->layout.u.chunk.size, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, buf))<0)
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file");
} /* end if */
else {
uint8_t *chunk; /* Pointer to cached chunk in memory */
unsigned idx_hint=0; /* Cache index hint */
ssize_t naccessed; /* Number of bytes accessed in chunk */
/*
* Lock the chunk, copy from application to chunk, then unlock the
* chunk.
*/
if (NULL==(chunk=H5D_istore_lock(f, dxpl_cache, dxpl_id, dset, store,
&udata, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk");
/* Use the vectorized memory copy routine to do actual work */
if((naccessed=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_len_arr,mem_offset_arr,chunk,chunk_max_nseq,chunk_curr_seq,chunk_len_arr,chunk_offset_arr))<0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "vectorized memcpy failed");
H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
if (H5D_istore_unlock(f, dxpl_cache, dxpl_id, dset, store,
FALSE, idx_hint, chunk, (size_t)naccessed)<0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk");
/* Set return value */
ret_value=naccessed;
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* H5D_istore_readvv() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_writevv
*
* Purpose: Writes a multi-dimensional buffer to (part of) an indexed raw
* storage array.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Friday, May 2, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
ssize_t
H5D_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
hid_t dxpl_id, H5D_t *dset, const H5D_storage_t *store,
size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
const void *buf)
{
H5D_istore_ud1_t udata; /*B-tree pass-through */
haddr_t chunk_addr; /* Chunk address on disk */
#ifndef NDEBUG
size_t u; /* Local index variables */
#endif
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_writevv, FAIL);
/* Check args */
assert(f);
assert(dxpl_cache);
assert(dset && H5D_CHUNKED==dset->layout.type);
assert(dset->layout.u.chunk.ndims>0 && dset->layout.u.chunk.ndims<=H5O_LAYOUT_NDIMS);
assert(store);
assert(chunk_len_arr);
assert(chunk_offset_arr);
assert(mem_len_arr);
assert(mem_offset_arr);
assert(buf);
#ifndef NDEBUG
for (u=0; u<dset->layout.u.chunk.ndims; u++)
assert(store->chunk.offset[u]>=0); /*negative coordinates not supported (yet) */
#endif
/* Get the address of this chunk on disk */
#ifdef QAK
HDfprintf(stderr,"%s: chunk_coords={",FUNC);
for(u=0; u<dset->layout.u.chunk.ndims; u++)
HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(dset->layout.u.chunk.ndims-1) ? ", " : "}\n"));
#endif /* QAK */
chunk_addr=H5D_istore_get_addr(f, dxpl_id, &(dset->layout), store->chunk.offset, &udata);
#ifdef QAK
HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,dset->layout.u.chunk.size);
HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]);
HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]);
HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]);
HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_arr[*mem_curr_seq]);
#endif /* QAK */
/*
* If the chunk is too large to load into the cache and it has no
* filters in the pipeline (i.e. not compressed) and if the address
* for the chunk has been defined, then don't load the chunk into the
* cache, just write the data to it directly.
*
* If MPI based VFD is used, must bypass the
* chunk-cache scheme because other MPI processes could be
* writing to other elements in the same chunk. Do a direct
* write-through of only the elements requested.
*/
if ((dset->layout.u.chunk.size>dset->cache.chunk.nbytes && dset->dcpl_cache.pline.nused==0 && chunk_addr!=HADDR_UNDEF)
|| (IS_H5FD_MPI(f) && (H5F_ACC_RDWR & H5F_get_intent(f)))) {
#ifdef H5_HAVE_PARALLEL
/* Additional sanity check when operating in parallel */
if (chunk_addr==HADDR_UNDEF || dset->dcpl_cache.pline.nused>0)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk");
#endif /* H5_HAVE_PARALLEL */
if ((ret_value=H5D_contig_writevv(f, dxpl_id, dset, chunk_addr, (hsize_t)dset->layout.u.chunk.size, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, buf))<0)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file");
} /* end if */
else {
uint8_t *chunk; /* Pointer to cached chunk in memory */
unsigned idx_hint=0; /* Cache index hint */
ssize_t naccessed; /* Number of bytes accessed in chunk */
hbool_t relax; /* Whether whole chunk is selected */
/*
* Lock the chunk, copy from application to chunk, then unlock the
* chunk.
*/
if(chunk_max_nseq==1 && chunk_len_arr[0] == dset->layout.u.chunk.size)
relax = TRUE;
else
relax = FALSE;
if (NULL==(chunk=H5D_istore_lock(f, dxpl_cache, dxpl_id, dset, store,
&udata, relax, &idx_hint)))
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk");
/* Use the vectorized memory copy routine to do actual work */
if((naccessed=H5V_memcpyvv(chunk,chunk_max_nseq,chunk_curr_seq,chunk_len_arr,chunk_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_len_arr,mem_offset_arr))<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed");
H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
if (H5D_istore_unlock(f, dxpl_cache, dxpl_id, dset, store,
TRUE, idx_hint, chunk, (size_t)naccessed)<0)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk");
/* Set return value */
ret_value=naccessed;
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* H5D_istore_writevv() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_create
*
* Purpose: Creates a new indexed-storage B-tree and initializes the
* istore struct with information about the storage. The
* struct should be immediately written to the object header.
*
* This function must be called before passing ISTORE to any of
* the other indexed storage functions!
*
* Return: Non-negative on success (with the ISTORE argument initialized
* and ready to write to an object header). Negative on failure.
*
* Programmer: Robb Matzke
* Tuesday, October 21, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */ )
{
H5D_istore_ud1_t udata;
#ifndef NDEBUG
unsigned u;
#endif
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_create, FAIL);
/* Check args */
assert(f);
assert(layout && H5D_CHUNKED == layout->type);
assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
#ifndef NDEBUG
for (u = 0; u < layout->u.chunk.ndims; u++)
assert(layout->u.chunk.dim[u] > 0);
#endif
/* Initialize "user" data for B-tree callbacks, etc. */
udata.mesg = layout;
if (H5B_create(f, dxpl_id, H5B_ISTORE, &udata, &(layout->u.chunk.addr)/*out*/) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't create B-tree");
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_create() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_allocated
*
* Purpose: Return the number of bytes allocated in the file for storage
* of raw data under the specified B-tree (ADDR is the address
* of the B-tree).
*
* Return: Success: Number of bytes stored in all chunks.
*
* Failure: 0
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value.
*-------------------------------------------------------------------------
*/
hsize_t
H5D_istore_allocated(H5F_t *f, hid_t dxpl_id, H5D_t *dset)
{
H5D_rdcc_t *rdcc = &(dset->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 */
H5D_istore_ud1_t udata;
hsize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_allocated, 0);
/* Fill the DXPL cache values for later use */
if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "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_istore_flush_entry(f, dxpl_cache, dxpl_id, dset, ent, FALSE)<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, 0, "cannot flush indexed storage buffer");
} /* end for */
HDmemset(&udata, 0, sizeof udata);
udata.mesg = &dset->layout;
if (H5B_iterate(f, dxpl_id, H5B_ISTORE, H5D_istore_iter_allocated, dset->layout.u.chunk.addr, &udata)<0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree");
/* Set return value */
ret_value=udata.total_storage;
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_allocated() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
* Modified to return the address instead of returning it through
* a parameter - QAK, 1/30/02
*
*-------------------------------------------------------------------------
*/
static haddr_t
H5D_istore_get_addr(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
const hssize_t offset[], H5D_istore_ud1_t *_udata)
{
H5D_istore_ud1_t tmp_udata; /* Information about a chunk */
H5D_istore_ud1_t *udata; /* Pointer to information about a chunk */
unsigned u;
haddr_t ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_get_addr);
assert(f);
assert(layout && (layout->u.chunk.ndims > 0));
assert(offset);
/* Check for udata struct to return */
udata = (_udata!=NULL ? _udata : &tmp_udata);
/* Initialize the information about the chunk we are looking for */
for (u=0; u<layout->u.chunk.ndims; u++)
udata->key.offset[u] = offset[u];
udata->mesg = layout;
udata->addr = HADDR_UNDEF;
/* Go get the chunk information */
if (H5B_find (f, dxpl_id, H5B_ISTORE, layout->u.chunk.addr, udata)<0) {
/* Note: don't push error on stack, leave that to next higher level,
* since many times the B-tree is searched in order to determine
* if a chunk exists in the B-tree or not. -QAK
*/
#ifdef OLD_WAY
H5E_clear();
HGOTO_ERROR(H5E_BTREE,H5E_NOTFOUND,HADDR_UNDEF,"Can't locate chunk info");
#else /* OLD_WAY */
HGOTO_DONE(HADDR_UNDEF)
#endif /* OLD_WAY */
} /* end if */
/* Success! Set the return value */
ret_value=udata->addr;
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* H5D_istore_get_addr() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5D_istore_chunk_alloc(size_t size, const H5O_pline_t *pline)
{
void *ret_value=NULL; /* Return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_chunk_alloc);
assert(size);
assert(pline);
if(pline->nused>0)
ret_value=H5MM_malloc(size);
else
ret_value=H5FL_BLK_MALLOC(chunk,size);
FUNC_LEAVE_NOAPI(ret_value);
} /* H5D_istore_chunk_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_chunk_xfree);
assert(pline);
if(chk) {
if(pline->nused>0)
H5MM_xfree(chk);
else
H5FL_BLK_FREE(chunk,chk);
} /* end if */
FUNC_LEAVE_NOAPI(NULL);
} /* H5D_istore_chunk_xfree() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Note: Current implementation relies on cache_size being 0,
* thus no chunk is cashed and written to disk immediately
* when a chunk is unlocked (via H5F_istore_unlock)
* This should be changed to do a direct flush independent
* of the cache value.
*
* This routine might be called before the dcpl_cache is set up
* correctly, so don't use those values.
*
* Programmer: Albert Cheng
* June 26, 1998
*
* Modifications:
* rky, 1998-09-23
* Added barrier to preclude racing with data writes.
*
* rky, 1998-12-07
* Added Wait-Signal wrapper around unlock-lock critical region
* to prevent race condition (unlock reads, lock writes the
* chunk).
*
* Robb Matzke, 1999-08-02
* The split_ratios are passed in as part of the data transfer
* property list.
*
* Quincey Koziol, 2002-05-16
* Rewrote algorithm to allocate & write blocks without using
* lock/unlock code.
*
* Quincey Koziol, 2002-05-17
* Added feature to avoid writing fill-values if user has indicated
* that they should never be written.
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5D_t *dset,
hbool_t full_overwrite)
{
hssize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
hsize_t chunk_size; /* Size of chunk in bytes */
H5O_pline_t pline; /* I/O pipeline information */
H5O_fill_t fill; /* Fill value information */
H5D_fill_time_t fill_time; /* When to write fill values */
H5D_fill_value_t fill_status; /* The fill value status */
unsigned should_fill=0; /* Whether fill values should be written */
H5D_istore_ud1_t udata; /* B-tree pass-through for creating chunk */
void *chunk=NULL; /* Chunk buffer for writing fill values */
H5P_genplist_t *dx_plist; /* Data xfer property list */
#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 */
unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */
unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
#endif /* H5_HAVE_PARALLEL */
int carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
unsigned chunk_exists; /* Flag to indicate whether a chunk exists already */
int i; /* Local index variable */
unsigned u; /* Local index variable */
H5Z_EDC_t edc; /* Decide whether to enable EDC for read */
H5Z_cb_t cb_struct;
H5P_genplist_t *dc_plist; /* Property list */
int space_ndims; /* Dataset's space rank */
hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_allocate, FAIL);
/* Check args */
assert(f);
assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));
assert(dset && H5D_CHUNKED==dset->layout.type);
assert(dset->layout.u.chunk.ndims>0 && dset->layout.u.chunk.ndims<=H5O_LAYOUT_NDIMS);
assert(H5F_addr_defined(dset->layout.u.chunk.addr));
/* Get dataset's creation property list */
if (NULL == (dc_plist = H5I_object(dset->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* We only handle simple data spaces so far */
if ((space_ndims=H5S_get_simple_extent_dims(dset->space, space_dim, NULL))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info")
space_dim[space_ndims] = dset->layout.u.chunk.dim[space_ndims];
/* Get necessary properties from dataset creation property list */
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get fill value");
if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get data pipeline");
if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time");
/* Get necessary properties from dataset transfer property list */
if (NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list");
if(H5P_get(dx_plist,H5D_XFER_EDC_NAME,&edc)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get edc information");
if(H5P_get(dx_plist,H5D_XFER_FILTER_CB_NAME,&cb_struct)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get filter callback struct");
#ifdef H5_HAVE_PARALLEL
/* Retrieve MPI parameters */
if(IS_H5FD_MPI(f)) {
/* Get the MPI communicator */
if (MPI_COMM_NULL == (mpi_comm=H5F_mpi_get_comm(f)))
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
/* Get the MPI rank */
if ((mpi_rank=H5F_mpi_get_rank(f))<0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
/* Set the MPI-capable file driver flag */
using_mpi=1;
} /* end if */
#endif /* H5_HAVE_PARALLEL */
/*
* Setup indice to go through all chunks. (Future improvement
* should allocate only chunks that have no file space assigned yet.
*/
for (u=0; u<dset->layout.u.chunk.ndims; u++)
chunk_offset[u] = 0;
chunk_size = dset->layout.u.chunk.size;
/* 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,
* set the "should fill" flag
*/
if(!full_overwrite && (fill_time==H5D_FILL_TIME_ALLOC ||
(fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_USER_DEFINED)))
should_fill=1;
/* Check if fill values should be written to blocks */
if(should_fill) {
/* Allocate chunk buffer for processes to use when writing fill values */
H5_CHECK_OVERFLOW(chunk_size,hsize_t,size_t);
if (NULL==(chunk = H5D_istore_chunk_alloc((size_t)chunk_size,&pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk");
/* Fill the chunk with the proper values */
if(fill.buf) {
/*
* Replicate the fill value throughout the chunk.
*/
assert(0==chunk_size % fill.size);
H5V_array_fill(chunk, fill.buf, fill.size, (size_t)chunk_size/fill.size);
} else {
/*
* No fill value was specified, assume all zeros.
*/
HDmemset (chunk, 0, (size_t)chunk_size);
} /* end else */
/* Check if there are filters which need to be applied to the chunk */
if (pline.nused>0) {
unsigned filter_mask=0;
size_t buf_size=(size_t)chunk_size;
size_t nbytes=(size_t)chunk_size;
/* Push the chunk through the filters */
if (H5Z_pipeline(&pline, 0, &filter_mask, edc, cb_struct, &nbytes, &buf_size, &chunk)<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 */
} /* end if */
/* Loop over all chunks */
carry=0;
while (carry==0) {
/* Check if the chunk exists yet on disk */
chunk_exists=1;
if(H5D_istore_get_addr(f,dxpl_id,&(dset->layout),chunk_offset, NULL)==HADDR_UNDEF) {
const H5D_rdcc_t *rdcc = &(dset->cache.chunk); /*raw data chunk cache */
H5D_rdcc_ent_t *ent = NULL; /*cache entry */
/* Didn't find the chunk on disk */
chunk_exists = 0;
/* Look for chunk in cache */
for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
/* Assume a match */
chunk_exists = 1;
for(u = 0; u < dset->layout.u.chunk.ndims && chunk_exists; u++) {
if(ent->offset[u] != chunk_offset[u])
chunk_exists = 0; /* Reset if no match */
} /* end for */
} /* end for */
} /* end if */
if(!chunk_exists) {
/* Initialize the chunk information */
udata.mesg = &dset->layout;
udata.key.filter_mask = 0;
udata.addr = HADDR_UNDEF;
H5_CHECK_OVERFLOW(chunk_size,hsize_t,size_t);
udata.key.nbytes = (size_t)chunk_size;
for (u=0; u<dset->layout.u.chunk.ndims; u++)
udata.key.offset[u] = chunk_offset[u];
/* Allocate the chunk with all processes */
if (H5B_insert(f, dxpl_id, H5B_ISTORE, dset->layout.u.chunk.addr, &udata)<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk");
/* Check if fill values should be written to blocks */
if(should_fill) {
#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(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, H5AC_ind_dxpl_id, chunk)<0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file");
} /* end if */
/* Indicate that blocks are being written */
blocks_written=1;
} /* end if */
else {
#endif /* H5_HAVE_PARALLEL */
if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, chunk)<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 */
} /* end if */
/* Increment indices */
for (i=dset->layout.u.chunk.ndims-1, carry=1; i>=0 && carry; --i) {
chunk_offset[i] += dset->layout.u.chunk.dim[i];
if (chunk_offset[i] >= (hssize_t)(space_dim[i]))
chunk_offset[i] = 0;
else
carry = 0;
} /* end for */
} /* end while */
#ifdef H5_HAVE_PARALLEL
/* Only need to block at the barrier if we actually allocated a chunk */
/* And if we are 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 */
done:
/* Free the chunk for fill values */
if(chunk!=NULL)
H5D_istore_chunk_xfree(chunk,&pline);
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_allocate() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_prune_by_extent
*
* Purpose: This function searches for chunks that are no longer necessary both in the
* raw data cache and in the B-tree.
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* Algorithm: Robb Matzke
*
* Date: 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_istore_prune_by_extent(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache,
hid_t dxpl_id, H5D_t *dset)
{
H5D_rdcc_t *rdcc = &(dset->cache.chunk); /*raw data chunk cache */
H5D_rdcc_ent_t *ent = NULL, *next = NULL; /*cache entry */
unsigned u; /*counters */
int found; /*remove this entry */
H5D_istore_ud1_t udata; /*B-tree pass-through */
hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_prune_by_extent, FAIL);
/* Check args */
assert(f);
assert(dxpl_cache);
assert(dset && H5D_CHUNKED == dset->layout.type);
assert(dset->layout.u.chunk.ndims > 0 && dset->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
assert(H5F_addr_defined(dset->layout.u.chunk.addr));
/* Go get the rank & dimensions */
if(H5S_get_simple_extent_dims(dset->space, curr_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
/*-------------------------------------------------------------------------
* Figure out what chunks are no longer in use for the specified extent
* and release them from the linked list raw data cache
*-------------------------------------------------------------------------
*/
found = 0;
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
for(u = 0; u < dset->layout.u.chunk.ndims - 1; u++) {
if((hsize_t)ent->offset[u] > curr_dims[u]) {
found = 1;
break;
} /* end if */
} /* end for */
if(found) {
#ifdef H5D_ISTORE_DEBUG
HDfputs("cache:remove:[", stderr);
for(u = 0; u < dset->layout.u.chunk.ndims - 1; u++)
HDfprintf(stderr, "%s%Hd", u ? ", " : "", ent->offset[u]);
HDfputs("]\n", stderr);
#endif
/* Preempt the entry from the cache, but do not flush it to disk */
if(H5D_istore_preempt(f, dxpl_cache, dxpl_id, dset, ent, FALSE) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to preempt chunk");
found=0;
}
}
/*-------------------------------------------------------------------------
* Check if there are any chunks on the B-tree
*-------------------------------------------------------------------------
*/
HDmemset(&udata, 0, sizeof udata);
udata.stream = stdout;
udata.mesg = &dset->layout;
udata.dims = curr_dims;
if(H5B_iterate(f, dxpl_id, H5B_ISTORE, H5D_istore_prune_extent, dset->layout.u.chunk.addr, &udata) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over B-tree");
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_prune_by_extent() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_prune_extent
*
* Purpose: Search for chunks that are no longer necessary in the B-tree.
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: March 26, 2002
*
* Comments: Called by H5D_prune_by_extent
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
H5D_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t UNUSED addr,
void UNUSED *_rt_key, void *_udata)
{
H5D_istore_ud1_t *bt_udata = (H5D_istore_ud1_t *)_udata;
H5D_istore_key_t *lt_key = (H5D_istore_key_t *)_lt_key;
unsigned u;
H5D_istore_ud1_t udata;
int ret_value=H5B_ITER_CONT; /* Return value */
/* The LT_KEY is the left key (the one that describes the chunk). It points to a chunk of
* storage that contains the beginning of the logical address space represented by UDATA.
*/
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_prune_extent);
/* Figure out what chunks are no longer in use for the specified extent and release them */
for(u = 0; u < bt_udata->mesg->u.chunk.ndims - 1; u++)
if((hsize_t)lt_key->offset[u] > bt_udata->dims[u]) {
#ifdef H5D_ISTORE_DEBUG
HDfputs("b-tree:remove:[", bt_udata->stream);
for(u = 0; u < bt_udata->mesg->u.chunk.ndims - 1; u++)
HDfprintf(bt_udata->stream, "%s%Hd", u ? ", " : "", lt_key->offset[u]);
HDfputs("]\n", bt_udata->stream);
#endif
HDmemset(&udata, 0, sizeof udata);
udata.key = *lt_key;
udata.mesg = bt_udata->mesg;
/* Remove */
if(H5B_remove(f, dxpl_id, H5B_ISTORE, bt_udata->mesg->u.chunk.addr, &udata) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, H5B_ITER_ERROR, "unable to remove entry");
break;
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_prune_extent() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_remove
*
* Purpose: Removes chunks that are no longer necessary in the B-tree.
*
* Return: Success: 0, Failure: -1
*
* Programmer: Robb Matzke
* Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: March 28, 2002
*
* Comments: Part of H5B_ISTORE
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static H5B_ins_t
H5D_istore_remove(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key /*in,out */ ,
hbool_t *lt_key_changed /*out */ ,
void UNUSED * _udata /*in,out */ ,
void UNUSED * _rt_key /*in,out */ ,
hbool_t *rt_key_changed /*out */ )
{
H5D_istore_key_t *lt_key = (H5D_istore_key_t *)_lt_key;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_remove);
/* Remove raw data chunk from file */
H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, addr, (hsize_t)lt_key->nbytes);
/* Mark keys as unchanged */
*lt_key_changed = FALSE;
*rt_key_changed = FALSE;
FUNC_LEAVE_NOAPI(H5B_INS_REMOVE);
} /* end H5D_istore_remove() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_initialize_by_extent
*
* Purpose: This function searches for chunks that have to be initialized with the fill
* value both in the raw data cache and in the B-tree.
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: April 4, 2002
*
* Comments:
*
* (See the example of H5D_istore_prune_by_extent)
* Next, there are seven chunks where the database extent boundary is
* within the chunk. We find those seven just like we did with the previous nine.
* Fot the ones that are allocated we initialize the part that lies outside the boundary
* with the fill value.
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
hid_t dxpl_id, H5D_t *dset)
{
uint8_t *chunk = NULL; /*the file chunk */
unsigned idx_hint = 0; /*input value for H5F_istore_lock */
hssize_t chunk_offset[H5O_LAYOUT_NDIMS]; /*logical location of the chunks */
hsize_t idx_cur[H5O_LAYOUT_NDIMS]; /*multi-dimensional counters */
hsize_t idx_max[H5O_LAYOUT_NDIMS];
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hsize_t naccessed; /*bytes accessed in chunk */
hsize_t end_chunk; /*chunk position counter */
hssize_t start[H5O_LAYOUT_NDIMS]; /*starting location of hyperslab */
hsize_t count[H5O_LAYOUT_NDIMS]; /*element count of hyperslab */
hsize_t size[H5O_LAYOUT_NDIMS]; /*current size of dimensions */
H5S_t *space_chunk = NULL; /*dataspace for a chunk */
hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /*current chunk 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 */
int srank; /*current # of dimensions (signed) */
unsigned rank; /*current # of dimensions */
int i, carry; /*counters */
unsigned u;
int found = 0; /*initialize this entry */
H5P_genplist_t *dc_plist; /* Property list */
H5O_pline_t pline; /* I/O pipeline information */
H5O_fill_t fill; /* Fill value information */
H5D_fill_time_t fill_time; /* Fill time information */
H5D_storage_t store; /* Dataset storage information */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_initialize_by_extent, FAIL);
/* Check args */
assert(f);
assert(dxpl_cache);
assert(dset && H5D_CHUNKED == dset->layout.type);
assert(dset->layout.u.chunk.ndims > 0 && dset->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
assert(H5F_addr_defined(dset->layout.u.chunk.addr));
/* Get dataset's creation property list */
if (NULL == (dc_plist = H5I_object(dset->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Get necessary properties from property list */
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value");
if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill time");
if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data pipeline");
/* Reset start & count arrays */
HDmemset(start, 0, sizeof(start));
HDmemset(count, 0, sizeof(count));
/* Go get the rank & dimensions */
if((srank = H5S_get_simple_extent_dims(dset->space, curr_dims, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned);
/* Copy current dimensions */
for(u = 0; u < rank; u++) {
size[u] = curr_dims[u];
/* Round up to the next integer # of chunks, to accomodate partial chunks */
chunks[u] = ((curr_dims[u]+dset->layout.u.chunk.dim[u])-1) / dset->layout.u.chunk.dim[u];
} /* end for */
size[u] = dset->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")
/* Create a data space for a chunk & set the extent */
for(u = 0; u < rank; u++)
chunk_dims[u] = dset->layout.u.chunk.dim[u];
if(NULL == (space_chunk = H5S_create_simple(rank,chunk_dims,NULL)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace");
/*
* Set up multi-dimensional counters (idx_max, and idx_cur) and
* loop through the chunks copying each chunk from the application to the
* chunk cache.
*/
for(u = 0; u < dset->layout.u.chunk.ndims; u++) {
idx_max[u] = (size[u] - 1) / dset->layout.u.chunk.dim[u] + 1;
idx_cur[u] = 0;
} /* end for */
/* Loop over all chunks */
carry=0;
while(carry==0) {
for(u = 0, naccessed = 1; u < dset->layout.u.chunk.ndims; u++) {
/* The location and size of the chunk being accessed */
chunk_offset[u] = idx_cur[u] * (hssize_t)(dset->layout.u.chunk.dim[u]);
sub_size[u] = MIN((idx_cur[u] + 1) * dset->layout.u.chunk.dim[u],
size[u]) - chunk_offset[u];
naccessed *= sub_size[u];
} /* end for */
/*
* Figure out what chunks have to be initialized. These are the chunks where the dataspace
* extent boundary is within the chunk
*/
for(u = 0, found = 0; u < dset->layout.u.chunk.ndims - 1; u++) {
end_chunk = chunk_offset[u] + dset->layout.u.chunk.dim[u];
if(end_chunk > size[u]) {
found = 1;
break;
}
} /* end for */
if(found) {
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank,chunk_offset,dset->layout.u.chunk.dim,down_chunks,&store.chunk.index)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
store.chunk.offset=chunk_offset;
if(NULL == (chunk = H5D_istore_lock(f, dxpl_cache, dxpl_id, dset,
&store, NULL, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk");
if(H5S_select_all(space_chunk,1) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select space");
for(u = 0; u < rank; u++)
count[u] = MIN((idx_cur[u] + 1) * dset->layout.u.chunk.dim[u], size[u] - chunk_offset[u]);
#ifdef H5D_ISTORE_DEBUG
HDfputs("cache:initialize:offset:[", stdout);
for(u = 0; u < dset->layout.u.chunk.ndims - 1; u++)
HDfprintf(stdout, "%s%Hd", u ? ", " : "", chunk_offset[u]);
HDfputs("]", stdout);
HDfputs(":count:[", stdout);
for(u = 0; u < dset->layout.u.chunk.ndims - 1; u++)
HDfprintf(stdout, "%s%Hd", u ? ", " : "", count[u]);
HDfputs("]\n", stdout);
#endif
if(H5S_select_hyperslab(space_chunk, H5S_SELECT_NOTB, start, NULL,
count, NULL) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select hyperslab");
/* 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 */
H5_CHECK_OVERFLOW(size[rank],hsize_t,size_t);
if(H5S_select_fill(fill.buf, (size_t)size[rank], space_chunk, chunk) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed");
if(H5D_istore_unlock(f, dxpl_cache, dxpl_id, dset, &store,
TRUE, idx_hint, chunk, (size_t)naccessed) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk");
} /*found */
/* Increment indices */
for(i = dset->layout.u.chunk.ndims - 1, carry = 1; i >= 0 && carry; --i) {
if(++idx_cur[i] >= idx_max[i])
idx_cur[i] = 0;
else
carry = 0;
} /* end for */
} /* end while */
done:
if(space_chunk)
H5S_close(space_chunk);
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_initialize_by_extent() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout)
{
H5D_istore_ud1_t udata; /* User data for B-tree iterator call */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_delete, FAIL);
/* Check if the B-tree has been created in the file */
if(H5F_addr_defined(layout->u.chunk.addr)) {
/* Set up user data for B-tree deletion */
HDmemset(&udata, 0, sizeof udata);
udata.mesg = layout;
/* Delete entire B-tree */
if(H5B_delete(f, dxpl_id, H5B_ISTORE, layout->u.chunk.addr, &udata)<0)
HGOTO_ERROR(H5E_IO, H5E_CANTDELETE, 0, "unable to delete chunk B-tree");
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_delete() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_update_cache(H5F_t *f, hid_t dxpl_id, H5D_t *dset)
{
H5D_rdcc_t *rdcc = &(dset->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 */
int srank; /*current # of dimensions (signed) */
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 */
hsize_t idx; /* Chunk index */
unsigned old_idx; /* Previous index number */
unsigned u; /*counters */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_update_cache, FAIL);
/* Check args */
assert(f);
assert(dset && H5D_CHUNKED == dset->layout.type);
assert(dset->layout.u.chunk.ndims > 0 && dset->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
/* Go get the rank & dimensions */
if((srank = H5S_get_simple_extent_dims(dset->space, curr_dims, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned);
/* Round up to the next integer # of chunks, to accomodate partial chunks */
for(u = 0; u < rank; u++)
chunks[u] = ((curr_dims[u]+dset->layout.u.chunk.dim[u])-1) / dset->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) {
next=ent->next;
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank,ent->offset,dset->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_HASH(dset,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) {
assert(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_istore_preempt(f, dxpl_cache, dxpl_id, dset, 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 H5F_istore_update_cache() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_dump_btree
*
* Purpose: Prints information about the storage B-tree to the specified
* stream.
*
* Return: Success: Non-negative
*
* Failure: negative
*
* Programmer: Robb Matzke
* Wednesday, April 28, 1999
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value.
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_dump_btree(H5F_t *f, hid_t dxpl_id, FILE *stream, unsigned ndims, haddr_t addr)
{
H5O_layout_t layout;
H5D_istore_ud1_t udata;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_dump_btree, FAIL);
HDmemset(&udata, 0, sizeof udata);
layout.u.chunk.ndims = ndims;
udata.mesg = &layout;
udata.stream = stream;
if(stream)
HDfprintf(stream, " Address: %a\n",addr);
if(H5B_iterate(f, dxpl_id, H5B_ISTORE, H5D_istore_iter_dump, addr, &udata)<0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree");
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_dump_btree() */
#ifdef H5D_ISTORE_DEBUG
/*-------------------------------------------------------------------------
* Function: H5D_istore_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
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_stats (H5D_t *dset, hbool_t headers)
{
H5D_rdcc_t *rdcc = &(dset->cache.chunk);
double miss_rate;
char ascii[32];
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_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_istore_stats() */
#endif /* H5D_ISTORE_DEBUG */
/*-------------------------------------------------------------------------
* Function: H5D_istore_debug
*
* Purpose: Debugs a B-tree node for indexed raw data storage.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value.
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent,
int fwidth, int ndims)
{
H5O_layout_t layout;
H5D_istore_ud1_t udata;
H5B_shared_t *shared; /* Shared B-tree node info */
size_t u; /* Local index variable */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_debug,FAIL);
HDmemset (&udata, 0, sizeof udata);
layout.u.chunk.ndims = ndims;
udata.mesg = &layout;
/* Allocate space for the shared structure */
if(NULL==(shared=H5FL_MALLOC(H5B_shared_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
/* Set up the "global" information for this file's groups */
shared->type= H5B_ISTORE;
shared->two_k=2*H5F_KVALUE(f,H5B_ISTORE);
shared->sizeof_rkey = H5D_istore_sizeof_rkey(f, &udata);
assert(shared->sizeof_rkey);
shared->sizeof_rnode = H5B_nodesize(f, shared, &shared->sizeof_keys);
assert(shared->sizeof_rnode);
if(NULL==(shared->page=H5FL_BLK_MALLOC(chunk_page,shared->sizeof_rnode)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
if(NULL==(shared->nkey=H5FL_SEQ_MALLOC(size_t,(size_t)(2*H5F_KVALUE(f,H5B_ISTORE)+1))))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
/* Initialize the offsets into the native key buffer */
for(u=0; u<(2*H5F_KVALUE(f,H5B_ISTORE)+1); u++)
shared->nkey[u]=u*H5B_ISTORE->sizeof_nkey;
/* Make shared B-tree info reference counted */
if(NULL==(layout.u.chunk.btree_shared=H5RC_create(shared,H5D_istore_shared_free)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
H5B_debug (f, dxpl_id, addr, stream, indent, fwidth, H5B_ISTORE, &udata);
/* Free the raw B-tree node buffer */
if(H5RC_DEC(layout.u.chunk.btree_shared)<0)
HGOTO_ERROR (H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page");
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_debug() */
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