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authorQuincey Koziol <koziol@hdfgroup.org>2008-06-03 20:34:58 (GMT)
committerQuincey Koziol <koziol@hdfgroup.org>2008-06-03 20:34:58 (GMT)
commit79380c228cb804bb7ed9bb1ac7b3f36706719c20 (patch)
tree24e7905fd80682e481e5ab9b342dd20862095f01 /src
parenta9fa9a4a3715b8bd0dce83911548b88f30329c62 (diff)
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[svn-r15132] Description:
Bring back revision 15131 from trunk: Finish omnibus chunked dataset I/O refactoring, to separate general actions on chunked datasets from actions that are specific to using the v1 B-tree index. Cleaned up a few bugs and added some additional tests also. Tested on: Mac OS X/32 10.5.3 (amazon) Linux/32 2.4 (chicago)
Diffstat (limited to 'src')
-rw-r--r--src/H5B.c469
-rw-r--r--src/H5Bcache.c13
-rw-r--r--src/H5Bpkg.h3
-rw-r--r--src/H5Bprivate.h50
-rw-r--r--src/H5Dchunk.c3047
-rw-r--r--src/H5Dcompact.c50
-rw-r--r--src/H5Dcontig.c70
-rw-r--r--src/H5Ddbg.c2
-rw-r--r--src/H5Ddeprec.c4
-rw-r--r--src/H5Defl.c74
-rw-r--r--src/H5Dint.c263
-rw-r--r--src/H5Dio.c20
-rw-r--r--src/H5Distore.c3210
-rw-r--r--src/H5Dmpio.c46
-rw-r--r--src/H5Doh.c2
-rw-r--r--src/H5Dpkg.h299
-rw-r--r--src/H5Dprivate.h5
-rw-r--r--src/H5Gname.c3
-rw-r--r--src/H5Gnode.c78
-rw-r--r--src/H5Gstab.c35
-rw-r--r--src/H5Olayout.c42
-rw-r--r--src/H5Oprivate.h6
-rw-r--r--src/H5Ostab.c2
-rw-r--r--src/H5Pint.c2
-rw-r--r--src/H5Pprivate.h2
-rw-r--r--src/H5S.c3
-rw-r--r--src/H5Sprivate.h2
27 files changed, 4287 insertions, 3515 deletions
diff --git a/src/H5B.c b/src/H5B.c
index 9847b7a..e463982 100644
--- a/src/H5B.c
+++ b/src/H5B.c
@@ -128,6 +128,13 @@
/* Local Typedefs */
/******************/
+/* "user data" for iterating over B-tree (collects B-tree metadata size) */
+typedef struct H5B_iter_ud_t {
+ H5B_info_t *bt_info; /* Information about B-tree */
+ void *udata; /* Node type's 'udata' for loading & iterator callback */
+} H5B_info_ud_t;
+
+
/********************/
/* Local Prototypes */
/********************/
@@ -168,13 +175,20 @@ H5FL_DEFINE(H5B_t);
/* Library Private Variables */
/*****************************/
-/* Declare a free list to manage the H5B_shared_t struct */
-H5FL_DEFINE(H5B_shared_t);
-
/*******************/
/* Local Variables */
/*******************/
+/* Declare a free list to manage the H5B_shared_t struct */
+H5FL_DEFINE_STATIC(H5B_shared_t);
+
+/* Declare a free list to manage the raw page information */
+H5FL_BLK_DEFINE_STATIC(page);
+
+/* Declare a free list to manage the native key offset sequence information */
+H5FL_SEQ_DEFINE_STATIC(size_t);
+
+
/*-------------------------------------------------------------------------
* Function: H5B_create
@@ -1143,10 +1157,10 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5B_iterate
+ * Function: H5B_iterate_helper
*
* Purpose: Calls the list callback for each leaf node of the
- * B-tree, passing it the UDATA structure.
+ * B-tree, passing it the caller's UDATA structure.
*
* Return: Non-negative on success/Negative on failure
*
@@ -1154,106 +1168,167 @@ done:
* matzke@llnl.gov
* Jun 23 1997
*
- * Modifications:
- * Robb Matzke, 1999-04-21
- * The key values are passed to the function which is called.
- *
- * Robb Matzke, 1999-07-28
- * The ADDR argument is passed by value.
- *
- * Quincey Koziol, 2002-04-22
- * Changed callback to function pointer from static function
- *
- * John Mainzer, 6/10/05
- * Modified the function to use the new dirtied parameter of
- * of H5AC_unprotect() instead of modifying the is_dirty
- * field of the cache info.
- *
*-------------------------------------------------------------------------
*/
-herr_t
-H5B_iterate(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, H5B_operator_t op, haddr_t addr, void *udata)
+static herr_t
+H5B_iterate_helper(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
+ H5B_operator_t op, void *udata)
{
H5B_t *bt = NULL; /* Pointer to current B-tree node */
+ uint8_t *native = NULL; /* Array of keys in native format */
+ haddr_t *child = NULL; /* Array of child pointers */
herr_t ret_value; /* Return value */
- FUNC_ENTER_NOAPI(H5B_iterate, FAIL)
+ FUNC_ENTER_NOAPI_NOINIT(H5B_iterate_helper)
/*
* Check arguments.
*/
HDassert(f);
HDassert(type);
- HDassert(op);
HDassert(H5F_addr_defined(addr));
+ HDassert(op);
HDassert(udata);
/* Protect the initial/current node */
if(NULL == (bt = (H5B_t *)H5AC_protect(f, dxpl_id, H5AC_BT, addr, type, udata, H5AC_READ)))
- HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "unable to load B-tree node")
+ HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, H5_ITER_ERROR, "unable to load B-tree node")
if(bt->level > 0) {
+ haddr_t left_child = bt->child[0]; /* Address of left-most child in node */
+
+ /* Release current node */
+ if(H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_PROTECT, H5_ITER_ERROR, "unable to release B-tree node")
+ bt = NULL;
+
/* Keep following the left-most child until we reach a leaf node. */
- if((ret_value = H5B_iterate(f, dxpl_id, type, op, bt->child[0], udata)) < 0)
- HGOTO_ERROR(H5E_BTREE, H5E_CANTLIST, FAIL, "unable to list B-tree node")
+ if((ret_value = H5B_iterate_helper(f, dxpl_id, type, left_child, op, udata)) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_CANTLIST, H5_ITER_ERROR, "unable to list B-tree node")
} /* end if */
else {
+ H5B_shared_t *shared; /* Pointer to shared B-tree info */
+ unsigned nchildren; /* Number of child pointers */
+ haddr_t next_addr; /* Address of next node to the right */
+
+ /* Get the shared B-tree information */
+ shared = (H5B_shared_t *)H5RC_GET_OBJ(bt->rc_shared);
+ HDassert(shared);
+
+ /* Allocate space for a copy of the native records & child pointers */
+ if(NULL == (native = H5FL_BLK_MALLOC(native_block, shared->sizeof_keys)))
+ HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for shared B-tree native records")
+ if(NULL == (child = H5FL_SEQ_MALLOC(haddr_t, (size_t)shared->two_k)))
+ HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for shared B-tree child addresses")
+
+ /* Cache information from this node */
+ nchildren = bt->nchildren;
+ next_addr = bt->right;
+
+ /* Copy the native keys & child pointers into local arrays */
+ HDmemcpy(native, bt->native, shared->sizeof_keys);
+ HDmemcpy(child, bt->child, (nchildren * sizeof(haddr_t)));
+
+ /* Release current node */
+ if(H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_PROTECT, H5_ITER_ERROR, "unable to release B-tree node")
+ bt = NULL;
+
/*
* We've reached the left-most leaf. Now follow the right-sibling
* pointer from leaf to leaf until we've processed all leaves.
*/
ret_value = H5_ITER_CONT;
- while(bt && ret_value == H5_ITER_CONT) {
- haddr_t *child; /* Pointer to node's child addresses */
- uint8_t *key; /* Pointer to node's native keys */
+ while(ret_value == H5_ITER_CONT) {
+ haddr_t *curr_child; /* Pointer to node's child addresses */
+ uint8_t *curr_native; /* Pointer to node's native keys */
unsigned u; /* Local index variable */
/*
* Perform the iteration operator, which might invoke an
* application callback.
*/
- for(u = 0, child = bt->child, key = bt->native; u < bt->nchildren && ret_value == H5_ITER_CONT; u++, child++, key += type->sizeof_nkey) {
- ret_value = (*op)(f, dxpl_id, key, *child, key + type->sizeof_nkey, udata);
+ for(u = 0, curr_child = child, curr_native = native; u < nchildren && ret_value == H5_ITER_CONT; u++, curr_child++, curr_native += type->sizeof_nkey) {
+ ret_value = (*op)(f, dxpl_id, curr_native, *curr_child, curr_native + type->sizeof_nkey, udata);
if(ret_value < 0)
HERROR(H5E_BTREE, H5E_CANTLIST, "iterator function failed");
} /* end for */
/* Check for continuing iteration */
if(ret_value == H5_ITER_CONT) {
- H5B_t *next_bt; /* Pointer to next B-tree node */
- haddr_t next_addr; /* Address of next node to iterate over */
-
- /* Protect the next node to the right, if there is one */
- if(H5F_addr_defined(bt->right)) {
+ /* Check for another node */
+ if(H5F_addr_defined(next_addr)) {
+ /* Protect the next node to the right */
+ addr = next_addr;
+ if(NULL == (bt = (H5B_t *)H5AC_protect(f, dxpl_id, H5AC_BT, addr, type, udata, H5AC_READ)))
+ HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, H5_ITER_ERROR, "B-tree node")
+
+ /* Cache information from this node */
+ nchildren = bt->nchildren;
next_addr = bt->right;
- if(NULL == (next_bt = (H5B_t *)H5AC_protect(f, dxpl_id, H5AC_BT, next_addr, type, udata, H5AC_READ)))
- HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "B-tree node")
- } /* end if */
- else {
- next_addr = HADDR_UNDEF;
- next_bt = NULL;
- } /* end if */
- /* Unprotect this node */
- if(H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0) {
- if(next_bt) {
- HDassert(H5F_addr_defined(next_addr));
- if(H5AC_unprotect(f, dxpl_id, H5AC_BT, next_addr, next_bt, H5AC__NO_FLAGS_SET) < 0)
- HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree node")
- } /* end if */
- HGOTO_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree node")
- } /* end if */
+ /* Copy the native keys & child pointers into local arrays */
+ HDmemcpy(native, bt->native, shared->sizeof_keys);
+ HDmemcpy(child, bt->child, nchildren * sizeof(haddr_t));
- /* Advance to the next node */
- bt = next_bt;
- addr = next_addr;
+ /* Unprotect node */
+ if(H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_PROTECT, H5_ITER_ERROR, "unable to release B-tree node")
+ bt = NULL;
+ } /* end if */
+ else
+ /* Exit loop */
+ break;
} /* end if */
- } /* end for */
+ } /* end while */
} /* end else */
done:
if(bt && H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
- HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree node")
+ HDONE_ERROR(H5E_BTREE, H5E_PROTECT, H5_ITER_ERROR, "unable to release B-tree node")
+ if(native)
+ (void)H5FL_BLK_FREE(native_block, native);
+ if(child)
+ (void)H5FL_SEQ_FREE(haddr_t, child);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5B_iterate_helper() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5B_iterate
+ *
+ * Purpose: Calls the list callback for each leaf node of the
+ * B-tree, passing it the UDATA structure.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * matzke@llnl.gov
+ * Jun 23 1997
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5B_iterate(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
+ H5B_operator_t op, void *udata)
+{
+ herr_t ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5B_iterate, FAIL)
+
+ /*
+ * Check arguments.
+ */
+ HDassert(f);
+ HDassert(type);
+ HDassert(H5F_addr_defined(addr));
+ HDassert(op);
+ HDassert(udata);
+
+ /* Iterate over the B-tree records */
+ if((ret_value = H5B_iterate_helper(f, dxpl_id, type, addr, op, udata)) < 0)
+ HERROR(H5E_BTREE, H5E_BADITER, "B-tree iteration failed");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5B_iterate() */
@@ -1704,59 +1779,99 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5B_nodesize
- *
- * Purpose: Returns the number of bytes needed for this type of
- * B-tree node. The size is the size of the header plus
- * enough space for 2t child pointers and 2t+1 keys.
+ * Function: H5B_shared_new
*
- * If TOTAL_NKEY_SIZE is non-null, what it points to will
- * be initialized with the total number of bytes required to
- * hold all the key values in native order.
+ * Purpose: Allocates & constructs a shared v1 B-tree struct for client.
*
- * Return: Success: Size of node in file.
+ * Return: Success: non-NULL pointer to struct allocated
+ * Failure: NULL
*
- * Failure: 0
- *
- * Programmer: Robb Matzke
- * matzke@llnl.gov
- * Jul 3 1997
- *
- * Modifications:
+ * Programmer: Quincey Koziol
+ * koziol@hdfgroup.org
+ * May 27 2008
*
*-------------------------------------------------------------------------
*/
-size_t
-H5B_nodesize(const H5F_t *f, const H5B_shared_t *shared,
- size_t *total_nkey_size/*out*/)
+H5B_shared_t *
+H5B_shared_new(const H5F_t *f, const H5B_class_t *type, size_t sizeof_rkey)
{
- size_t size;
+ H5B_shared_t *shared; /* New shared B-tree struct */
+ size_t u; /* Local index variable */
+ H5B_shared_t *ret_value; /* Return value */
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5B_nodesize)
+ FUNC_ENTER_NOAPI(H5B_shared_new, NULL)
/*
* Check arguments.
*/
- assert(f);
- assert(shared);
- assert(shared->two_k > 0);
- assert(shared->sizeof_rkey > 0);
-
- /*
- * Total native key size.
- */
- if (total_nkey_size)
- *total_nkey_size = (shared->two_k + 1) * shared->type->sizeof_nkey;
+ HDassert(type);
- /*
- * Total node size.
- */
- size = (H5B_SIZEOF_HDR(f) + /*node header */
+ /* Allocate space for the shared structure */
+ if(NULL == (shared = H5FL_MALLOC(H5B_shared_t)))
+ HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, NULL, "memory allocation failed for shared B-tree info")
+
+ /* Set up the "global" information for this file's groups */
+ shared->type = type;
+ shared->two_k = 2 * H5F_KVALUE(f, type);
+ shared->sizeof_rkey = sizeof_rkey;
+ HDassert(shared->sizeof_rkey);
+ shared->sizeof_keys = (shared->two_k + 1) * type->sizeof_nkey;
+ shared->sizeof_rnode = (H5B_SIZEOF_HDR(f) + /*node header */
shared->two_k * H5F_SIZEOF_ADDR(f) + /*child pointers */
(shared->two_k + 1) * shared->sizeof_rkey); /*keys */
+ HDassert(shared->sizeof_rnode);
- FUNC_LEAVE_NOAPI(size)
-}
+ /* Allocate shared buffers */
+ if(NULL == (shared->page = H5FL_BLK_MALLOC(page, shared->sizeof_rnode)))
+ HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, NULL, "memory allocation failed for B-tree page")
+#ifdef H5_CLEAR_MEMORY
+HDmemset(shared->page, 0, shared->sizeof_rnode);
+#endif /* H5_CLEAR_MEMORY */
+ if(NULL == (shared->nkey = H5FL_SEQ_MALLOC(size_t, (size_t)(2 * H5F_KVALUE(f, type) + 1))))
+ HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, NULL, "memory allocation failed for B-tree page")
+
+ /* Initialize the offsets into the native key buffer */
+ for(u = 0; u < (2 * H5F_KVALUE(f, type) + 1); u++)
+ shared->nkey[u] = u * type->sizeof_nkey;
+
+ /* Set return value */
+ ret_value = shared;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5B_shared_new() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5B_shared_free
+ *
+ * Purpose: Free B-tree shared info
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, May 27, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5B_shared_free(void *_shared)
+{
+ H5B_shared_t *shared = (H5B_shared_t *)_shared;
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5B_shared_free)
+
+ /* Free the raw B-tree node buffer */
+ (void)H5FL_BLK_FREE(page, shared->page);
+
+ /* Free the B-tree native key offsets buffer */
+ (void)H5FL_SEQ_FREE(size_t, shared->nkey);
+
+ /* Free the shared B-tree info */
+ (void)H5FL_FREE(H5B_shared_t, shared);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5B_shared_free() */
/*-------------------------------------------------------------------------
@@ -1827,29 +1942,31 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5B_iterate_size
+ * Function: H5B_get_info_helper
*
- * Purpose: Return the amount of storage used for the btree.
- * Keep following the left-most child until reaching the leaf node.
- * For each level, gather storage for all the nodes on that level.
- * For 0 level, also gather storage for the SNODs.
+ * Purpose: Walks the B-tree nodes, getting information for all of them.
*
- * Return: Non-negative on success/Negative on failure
+ * Return: Non-negative on success/Negative on failure
*
- * Programmer: Vailin Choi
- * June 19, 2007
+ * Programmer: Quincey Koziol
+ * koziol@hdfgroup.org
+ * Jun 3 2008
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5B_iterate_size(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
- H5B_operator_t op, haddr_t addr, H5B_info_ud_t *bh_udata)
+static herr_t
+H5B_get_info_helper(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
+ const H5B_info_ud_t *info_udata)
{
- H5B_t *bt = NULL; /* Pointer to current B-tree node */
- H5B_shared_t *shared; /* Pointer to shared B-tree info */
- herr_t ret_value = SUCCEED; /* Return value */
+ H5B_t *bt = NULL; /* Pointer to current B-tree node */
+ H5B_shared_t *shared; /* Pointer to shared B-tree info */
+ unsigned level; /* Node level */
+ size_t sizeof_rnode; /* Size of raw (disk) node */
+ haddr_t next_addr; /* Address of next node to the right */
+ haddr_t left_child; /* Address of left-most child in node */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5B_iterate_size, FAIL)
+ FUNC_ENTER_NOAPI_NOINIT(H5B_get_info_helper)
/*
* Check arguments.
@@ -1857,61 +1974,123 @@ H5B_iterate_size(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
HDassert(f);
HDassert(type);
HDassert(H5F_addr_defined(addr));
- HDassert(bh_udata);
+ HDassert(info_udata);
+ HDassert(info_udata->bt_info);
+ HDassert(info_udata->udata);
/* Protect the initial/current node */
- if(NULL == (bt = (H5B_t *)H5AC_protect(f, dxpl_id, H5AC_BT, addr, type, bh_udata->udata, H5AC_READ)))
+ if(NULL == (bt = (H5B_t *)H5AC_protect(f, dxpl_id, H5AC_BT, addr, type, info_udata->udata, H5AC_READ)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "unable to load B-tree node")
- shared = H5RC_GET_OBJ(bt->rc_shared);
+
+ /* Get the shared B-tree information */
+ shared = (H5B_shared_t *)H5RC_GET_OBJ(bt->rc_shared);
HDassert(shared);
- /* Keep following the left-most child until we reach a leaf node. */
- if(bt->level > 0)
- if(H5B_iterate_size(f, dxpl_id, type, op, bt->child[0], bh_udata) < 0)
- HGOTO_ERROR(H5E_BTREE, H5E_CANTLIST, FAIL, "unable to list B-tree node")
+ /* Get the raw node size for iteration */
+ sizeof_rnode = shared->sizeof_rnode;
- /* Iterate through all nodes at this level of the tree */
- while(bt) {
- haddr_t next_addr; /* Address of next node to iterate over */
+ /* Cache information from this node */
+ left_child = bt->child[0];
+ next_addr = bt->right;
+ level = bt->level;
- /* for leaf node with callback, add in the space pointed to by each key */
- /* (currently only used for symbol table nodes) */
- if(bt->level == 0 && op) {
- haddr_t *child; /* Pointer to node's child addresses */
- uint8_t *key; /* Pointer to node's native keys */
- unsigned u; /* Local index variable */
+ /* Update B-tree info */
+ info_udata->bt_info->size += sizeof_rnode;
+ info_udata->bt_info->num_nodes++;
- for(u = 0, child = bt->child, key = bt->native; u < bt->nchildren; u++, child++, key += type->sizeof_nkey)
- if((*op)(f, dxpl_id, key, *child, key + type->sizeof_nkey, bh_udata->btree_size) < 0)
- HGOTO_ERROR(H5E_BTREE, H5E_CANTLIST, FAIL, "iterator function failed")
- } /* end if */
+ /* Release current node */
+ if(H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree node")
+ bt = NULL;
- /* count the size of this node */
- *(bh_udata->btree_size) += H5B_nodesize(f, shared, NULL);
+ /*
+ * Follow the right-sibling pointer from node to node until we've
+ * processed all nodes.
+ */
+ while(H5F_addr_defined(next_addr)) {
+ /* Protect the next node to the right */
+ addr = next_addr;
+ if(NULL == (bt = (H5B_t *)H5AC_protect(f, dxpl_id, H5AC_BT, addr, type, info_udata->udata, H5AC_READ)))
+ HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "B-tree node")
- /* Get the address of the next node to the right */
+ /* Cache information from this node */
next_addr = bt->right;
- /* Unprotect current node */
- if(H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
- HGOTO_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree node")
+ /* Update B-tree info */
+ info_udata->bt_info->size += sizeof_rnode;
+ info_udata->bt_info->num_nodes++;
- /* Protect bt's next node to the right, if there is one */
- if(H5F_addr_defined(next_addr)) {
- addr = next_addr;
- if(NULL == (bt = (H5B_t *)H5AC_protect(f, dxpl_id, H5AC_BT, addr, type, bh_udata->udata, H5AC_READ)))
- HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "B-tree node")
- } /* end if */
- else
- bt = NULL;
+ /* Unprotect node */
+ if(H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree node")
+ bt = NULL;
} /* end while */
+ /* Check for another "row" of B-tree nodes to iterate over */
+ if(level > 0) {
+ /* Keep following the left-most child until we reach a leaf node. */
+ if(H5B_get_info_helper(f, dxpl_id, type, left_child, info_udata) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_CANTLIST, FAIL, "unable to list B-tree node")
+ } /* end if */
+
done:
if(bt && H5AC_unprotect(f, dxpl_id, H5AC_BT, addr, bt, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree node")
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5B_iterate_size() */
+} /* end H5B_get_info_helper() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5B_get_info
+ *
+ * Purpose: Return the amount of storage used for the btree.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * June 19, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5B_get_info(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
+ H5B_info_t *bt_info, H5B_operator_t op, void *udata)
+{
+ H5B_info_ud_t info_udata; /* User-data for B-tree size iteration */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5B_get_info, FAIL)
+
+ /*
+ * Check arguments.
+ */
+ HDassert(f);
+ HDassert(type);
+ HDassert(bt_info);
+ HDassert(H5F_addr_defined(addr));
+ HDassert(udata);
+
+ /* Portably initialize B-tree info struct */
+ HDmemset(bt_info, 0, sizeof(*bt_info));
+
+ /* Set up internal user-data for the B-tree 'get info' helper routine */
+ info_udata.bt_info = bt_info;
+ info_udata.udata = udata;
+
+ /* Iterate over the B-tree nodes */
+ if(H5B_get_info_helper(f, dxpl_id, type, addr, &info_udata) < 0)
+ HGOTO_ERROR(H5E_BTREE, H5E_BADITER, FAIL, "B-tree iteration failed")
+
+ /* Iterate over the B-tree records, making any "leaf" callbacks */
+ /* (Only if operator defined) */
+ if(op)
+ if((ret_value = H5B_iterate_helper(f, dxpl_id, type, addr, op, udata)) < 0)
+ HERROR(H5E_BTREE, H5E_BADITER, "B-tree iteration failed");
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5B_get_info() */
/*-------------------------------------------------------------------------
diff --git a/src/H5Bcache.c b/src/H5Bcache.c
index 2748963..b129925 100644
--- a/src/H5Bcache.c
+++ b/src/H5Bcache.c
@@ -397,10 +397,8 @@ static herr_t
H5B_compute_size(const H5F_t *f, const H5B_t *bt, size_t *size_ptr)
{
H5B_shared_t *shared; /* Pointer to shared B-tree info */
- size_t size;
- herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI_NOINIT(H5B_compute_size)
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5B_compute_size)
/* check arguments */
HDassert(f);
@@ -411,13 +409,8 @@ H5B_compute_size(const H5F_t *f, const H5B_t *bt, size_t *size_ptr)
HDassert(shared->type);
HDassert(size_ptr);
- /* Check node's size */
- if ((size = H5B_nodesize(f, shared, NULL)) == 0)
- HGOTO_ERROR(H5E_RESOURCE, H5E_CANTGETSIZE, FAIL, "H5B_nodesize() failed")
-
/* Set size value */
- *size_ptr = size;
+ *size_ptr = shared->sizeof_rnode;
-done:
- FUNC_LEAVE_NOAPI(ret_value)
+ FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5B_compute_size() */
diff --git a/src/H5Bpkg.h b/src/H5Bpkg.h
index cd79cf7..7f1fd37 100644
--- a/src/H5Bpkg.h
+++ b/src/H5Bpkg.h
@@ -74,6 +74,7 @@ H5FL_EXTERN(H5B_t);
/******************************/
/* Package Private Prototypes */
/******************************/
-herr_t H5B_dest(H5F_t *f, H5B_t *b);
+H5_DLL herr_t H5B_dest(H5F_t *f, H5B_t *b);
#endif /*_H5Bpkg_H*/
+
diff --git a/src/H5Bprivate.h b/src/H5Bprivate.h
index 4dfea84..18a2c71 100644
--- a/src/H5Bprivate.h
+++ b/src/H5Bprivate.h
@@ -124,42 +124,40 @@ typedef struct H5B_class_t {
herr_t (*debug_key)(FILE*, H5F_t*, hid_t, int, int, const void*, const void*);
} H5B_class_t;
-/* "user data" for iterating over B-tree when collecting B-tree metadata size */
-typedef struct H5B_info_ud_t {
- void *udata; /* Node type's 'udata' for loading */
- hsize_t *btree_size; /* Accumulated size for B-tree metadata */
-} H5B_info_ud_t;
+/* Information about B-tree */
+typedef struct H5B_info_t {
+ hsize_t size; /* Size of B-tree nodes */
+ hsize_t num_nodes; /* Number of B-tree nodes */
+} H5B_info_t;
+
/*****************************/
/* Library-private Variables */
/*****************************/
-/* Declare a free list to manage the H5B_shared_t struct */
-H5FL_EXTERN(H5B_shared_t);
-
/***************************************/
/* Library-private Function Prototypes */
/***************************************/
-H5_DLL size_t H5B_nodesize(const H5F_t *f, const H5B_shared_t *shared,
- size_t *total_nkey_size);
-H5_DLL herr_t H5B_create(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, void *udata,
- haddr_t *addr_p/*out*/);
-H5_DLL herr_t H5B_find(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
- void *udata);
-H5_DLL herr_t H5B_insert(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
- void *udata);
-H5_DLL herr_t H5B_iterate(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, H5B_operator_t
- op, haddr_t addr, void *udata);
-H5_DLL herr_t H5B_iterate_size(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, H5B_operator_t
- op, haddr_t addr, H5B_info_ud_t *bh_udata);
-H5_DLL herr_t H5B_remove(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
- void *udata);
-H5_DLL herr_t H5B_delete(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr,
- void *udata);
+H5_DLL herr_t H5B_create(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
+ void *udata, haddr_t *addr_p/*out*/);
+H5_DLL herr_t H5B_find(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
+ haddr_t addr, void *udata);
+H5_DLL herr_t H5B_insert(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
+ haddr_t addr, void *udata);
+H5_DLL herr_t H5B_iterate(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
+ haddr_t addr, H5B_operator_t op, void *udata);
+H5_DLL herr_t H5B_get_info(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
+ haddr_t addr, H5B_info_t *bt_info, H5B_operator_t op, void *udata);
+H5_DLL herr_t H5B_remove(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
+ haddr_t addr, void *udata);
+H5_DLL herr_t H5B_delete(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type,
+ haddr_t addr, void *udata);
+H5_DLL H5B_shared_t *H5B_shared_new(const H5F_t *f, const H5B_class_t *type,
+ size_t sizeof_rkey);
+H5_DLL herr_t H5B_shared_free(void *_shared);
H5_DLL herr_t H5B_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream,
- int indent, int fwidth, const H5B_class_t *type,
- void *udata);
+ int indent, int fwidth, const H5B_class_t *type, void *udata);
#endif /* _H5Bprivate_H */
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index ba07725..711b91b 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -28,9 +28,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
-#ifdef H5_HAVE_PARALLEL
#include "H5MMprivate.h" /* Memory management */
-#endif /* H5_HAVE_PARALLEL */
#include "H5Vprivate.h" /* Vector and array functions */
@@ -39,24 +37,125 @@
/****************/
/* Default skip list height for storing list of chunks */
-#define H5D_DEFAULT_SKIPLIST_HEIGHT 8
+#define H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT 8
/* Macros for iterating over chunks to operate on */
#define H5D_CHUNK_GET_FIRST_NODE(map) (map->use_single ? (H5SL_node_t *)(1) : H5SL_first(map->sel_chunks))
#define H5D_CHUNK_GET_NODE_INFO(map, node) (map->use_single ? map->single_chunk_info : (H5D_chunk_info_t *)H5SL_item(node))
#define H5D_CHUNK_GET_NEXT_NODE(map, node) (map->use_single ? (H5SL_node_t *)NULL : H5SL_next(node))
+/*
+ * Feature: If this constant is defined then every cache preemption and load
+ * causes a character to be printed on the standard error stream:
+ *
+ * `.': Entry was preempted because it has been completely read or
+ * completely written but not partially read and not partially
+ * written. This is often a good reason for preemption because such
+ * a chunk will be unlikely to be referenced in the near future.
+ *
+ * `:': Entry was preempted because it hasn't been used recently.
+ *
+ * `#': Entry was preempted because another chunk collided with it. This
+ * is usually a relatively bad thing. If there are too many of
+ * these then the number of entries in the cache can be increased.
+ *
+ * c: Entry was preempted because the file is closing.
+ *
+ * w: A chunk read operation was eliminated because the library is
+ * about to write new values to the entire chunk. This is a good
+ * thing, especially on files where the chunk size is the same as
+ * the disk block size, chunks are aligned on disk block boundaries,
+ * and the operating system can also eliminate a read operation.
+ */
+
+/*#define H5D_CHUNK_DEBUG */
+
/******************/
/* Local Typedefs */
/******************/
+/* Callback info for iteration to prune chunks */
+typedef struct H5D_chunk_it_ud1_t {
+ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
+ const H5D_chk_idx_info_t *idx_info; /* Chunked index info */
+ const H5D_io_info_t *io_info; /* I/O info for dataset operation */
+ const hsize_t *dims; /* New dataset dimensions */
+ const hsize_t *down_chunks; /* "down" size of number of chunks in each dimension */
+ H5SL_t *outside; /* Skip list to hold chunks outside the new dimensions */
+ H5S_t *chunk_space; /* Dataspace for a chunk */
+ uint32_t elmts_per_chunk;/* Elements in chunk */
+ hsize_t *hyper_start; /* Starting location of hyperslab */
+ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
+ hbool_t fb_info_init; /* Whether the fill value buffer has been initialized */
+} H5D_chunk_it_ud1_t;
+
+/* Skip list node for storing chunks to remove during a "prune" iteration */
+typedef struct H5D_chunk_sl_ck_t {
+ hsize_t index; /* Index of chunk to remove (must be first) */
+ H5D_chunk_rec_t rec; /* Chunk record */
+} H5D_chunk_sl_ck_t;
+
+/* Skip list callback info when destroying list & removing chunks during "prune" */
+typedef struct H5D_chunk_sl_rm_t {
+ const H5D_chk_idx_info_t *idx_info; /* I/O info for dataset operation */
+ const H5O_layout_t *mesg; /* Layout message */
+} H5D_chunk_sl_rm_t;
+
+/* Callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */
+typedef struct H5D_chunk_id_ud2_t {
+ /* down */
+ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
+ const hsize_t *down_chunks; /* "down chunk" element counts for chunks */
+
+ /* up */
+ haddr_t *chunk_addr; /* Array of chunk addresses to fill in */
+} H5D_chunk_it_ud2_t;
+
+/* Callback info for iteration to copy data */
+typedef struct H5D_chunk_it_ud3_t {
+ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
+ H5F_t *file_src; /* Source file for copy */
+ H5D_chk_idx_info_t *idx_info_dst; /* Dest. chunk index info object */
+ void *buf; /* Buffer to hold chunk data for read/write */
+ void *bkg; /* Buffer for background information during type conversion */
+ size_t buf_size; /* Buffer size */
+ hbool_t do_convert; /* Whether to perform type conversions */
+
+ /* needed for converting variable-length data */
+ hid_t tid_src; /* Datatype ID for source datatype */
+ hid_t tid_dst; /* Datatype ID for destination datatype */
+ hid_t tid_mem; /* Datatype ID for memory datatype */
+ H5T_t *dt_src; /* Source datatype */
+ H5T_path_t *tpath_src_mem; /* Datatype conversion path from source file to memory */
+ H5T_path_t *tpath_mem_dst; /* Datatype conversion path from memory to dest. file */
+ void *reclaim_buf; /* Buffer for reclaiming data */
+ size_t reclaim_buf_size; /* Reclaim buffer size */
+ uint32_t nelmts; /* Number of elements in buffer */
+ H5S_t *buf_space; /* Dataspace describing buffer */
+
+ /* needed for compressed variable-length data */
+ H5O_pline_t *pline; /* Filter pipeline */
+
+ /* needed for copy object pointed by refs */
+ H5O_copy_t *cpy_info; /* Copy options */
+} H5D_chunk_it_ud3_t;
+
+/* Callback info for iteration to dump index */
+typedef struct H5D_chunk_it_ud4_t {
+ FILE *stream; /* Output stream */
+ hbool_t header_displayed; /* Node's header is displayed? */
+ unsigned ndims; /* Number of dimensions for chunk/dataset */
+} H5D_chunk_it_ud4_t;
+
/********************/
/* Local Prototypes */
/********************/
/* Chunked layout operation callbacks */
+static herr_t H5D_chunk_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset,
+ const H5P_genplist_t *dc_plist);
static herr_t H5D_chunk_io_init(const H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space,
const H5S_t *mem_space, H5D_chunk_map_t *fm);
@@ -74,6 +173,8 @@ static ssize_t H5D_null_readvv(const H5D_io_info_t *io_info,
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
/* Helper routines */
+static void *H5D_chunk_alloc(size_t size, const H5O_pline_t *pline);
+static void *H5D_chunk_xfree(void *chk, const H5O_pline_t *pline);
static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata);
static herr_t H5D_create_chunk_map_single(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
@@ -93,6 +194,7 @@ static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims,
/* Compact storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{
+ H5D_chunk_new,
H5D_chunk_io_init,
H5D_chunk_read,
H5D_chunk_write,
@@ -115,6 +217,7 @@ const H5D_layout_ops_t H5D_LOPS_NULL[1] = {{
NULL,
NULL,
NULL,
+ NULL,
#ifdef H5_HAVE_PARALLEL
NULL,
NULL,
@@ -124,9 +227,111 @@ const H5D_layout_ops_t H5D_LOPS_NULL[1] = {{
NULL
}};
+/* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */
+H5FL_SEQ_DEFINE_STATIC(H5D_rdcc_ent_ptr_t);
+
+/* Declare a free list to manage H5F_rdcc_ent_t objects */
+H5FL_DEFINE_STATIC(H5D_rdcc_ent_t);
+
/* Declare a free list to manage the H5D_chunk_info_t struct */
H5FL_DEFINE(H5D_chunk_info_t);
+/* Declare a free list to manage the chunk sequence information */
+H5FL_BLK_DEFINE_STATIC(chunk);
+
+/* Declare a free list to manage H5D_chunk_sl_ck_t objects */
+H5FL_DEFINE_STATIC(H5D_chunk_sl_ck_t);
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_new
+ *
+ * Purpose: Constructs new chunked layout information for dataset
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, May 22, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_chunk_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset,
+ const H5P_genplist_t *dc_plist)
+{
+ const H5T_t *type = dset->shared->type; /* Convenience pointer to dataset's datatype */
+ hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
+ uint64_t chunk_size; /* Size of chunk in bytes */
+ unsigned chunk_ndims = 0; /* Dimensionality of chunk */
+ int ndims; /* Rank of dataspace */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_new)
+
+ /* Sanity checks */
+ HDassert(f);
+ HDassert(dset);
+ HDassert(dc_plist);
+
+ /* Retrieve rank of chunks from property list */
+ if(H5P_get(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve chunk dimensions")
+
+ /* Set up layout information */
+ if((ndims = H5S_GET_EXTENT_NDIMS(dset->shared->space)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get rank")
+ dset->shared->layout.u.chunk.ndims = (unsigned)ndims + 1;
+ HDassert((unsigned)(dset->shared->layout.u.chunk.ndims) <= NELMTS(dset->shared->layout.u.chunk.dim));
+
+ /* Initialize to no address */
+ dset->shared->layout.u.chunk.addr = HADDR_UNDEF;
+
+ /*
+ * Chunked storage allows any type of data space extension, so we
+ * don't even bother checking.
+ */
+ if(chunk_ndims != (unsigned)ndims)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dimensionality of chunks doesn't match the data space")
+ if(dset->shared->dcpl_cache.efl.nused > 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "external storage not supported with chunked layout")
+
+ /*
+ * The chunk size of a dimension with a fixed size cannot exceed
+ * the maximum dimension size
+ */
+ if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, dset->shared->layout.u.chunk.dim) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve chunk size")
+ dset->shared->layout.u.chunk.dim[dset->shared->layout.u.chunk.ndims - 1] = H5T_get_size(type);
+
+ /* Sanity check dimensions */
+ if(H5S_get_simple_extent_dims(dset->shared->space, NULL, max_dim) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to query maximum dimensions")
+ for(u = 0; u < dset->shared->layout.u.chunk.ndims - 1; u++)
+ if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < dset->shared->layout.u.chunk.dim[u])
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be <= maximum dimension size for fixed-sized dimensions")
+
+ /* Compute the total size of a chunk */
+ /* (Use 64-bit value to ensure that we can detect >4GB chunks) */
+ for(u = 1, chunk_size = (uint64_t)dset->shared->layout.u.chunk.dim[0]; u < dset->shared->layout.u.chunk.ndims; u++)
+ chunk_size *= (uint64_t)dset->shared->layout.u.chunk.dim[u];
+
+ /* Check for chunk larger than can be represented in 32-bits */
+ /* (Chunk size is encoded in 32-bit value in v1 B-tree records) */
+ if(chunk_size > (uint64_t)0xffffffff)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be < 4GB")
+
+ /* Retain computed chunk size */
+ H5_ASSIGN_OVERFLOW(dset->shared->layout.u.chunk.size, chunk_size, uint64_t, uint32_t);
+
+ /* Initialize the chunk cache for the dataset */
+ if(H5D_chunk_init(f, dxpl_id, dset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_new() */
/*-------------------------------------------------------------------------
@@ -269,7 +474,7 @@ H5D_chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info
else {
/* Initialize skip list for chunk selections */
if(NULL == dataset->shared->cache.chunk.sel_chunks) {
- if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_DEFAULT_SKIPLIST_HEIGHT)))
+ if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections")
} /* end if */
fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks;
@@ -416,6 +621,7 @@ done:
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
if(file_space_normalized) {
+ /* (Casting away const OK -QAK) */
if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
} /* end if */
@@ -424,6 +630,71 @@ done:
} /* end H5D_chunk_io_init() */
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_alloc
+ *
+ * Purpose: Allocate space for a chunk in memory. This routine allocates
+ * memory space for non-filtered chunks from a block free list
+ * and uses malloc()/free() for filtered chunks.
+ *
+ * Return: Pointer to memory for chunk on success/NULL on failure
+ *
+ * Programmer: Quincey Koziol
+ * April 22, 2004
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D_chunk_alloc(size_t size, const H5O_pline_t *pline)
+{
+ void *ret_value = NULL; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_alloc)
+
+ HDassert(size);
+ HDassert(pline);
+
+ if(pline->nused > 0)
+ ret_value = H5MM_malloc(size);
+ else
+ ret_value = H5FL_BLK_MALLOC(chunk, size);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_chunk_alloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_xfree
+ *
+ * Purpose: Free space for a chunk in memory. This routine allocates
+ * memory space for non-filtered chunks from a block free list
+ * and uses malloc()/free() for filtered chunks.
+ *
+ * Return: NULL (never fails)
+ *
+ * Programmer: Quincey Koziol
+ * April 22, 2004
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D_chunk_xfree(void *chk, const H5O_pline_t *pline)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_xfree)
+
+ HDassert(pline);
+
+ if(chk) {
+ if(pline->nused > 0)
+ H5MM_xfree(chk);
+ else
+ (void)H5FL_BLK_FREE(chunk, chk);
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(NULL)
+} /* H5D_chunk_xfree() */
+
+
/*--------------------------------------------------------------------------
NAME
H5D_free_chunk_info
@@ -672,9 +943,9 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
new_chunk_info->coords[fm->f_ndims]=0;
/* Insert the new chunk into the skip list */
- if(H5SL_insert(fm->sel_chunks,new_chunk_info,&new_chunk_info->index) < 0) {
- H5D_free_chunk_info(new_chunk_info,NULL,NULL);
- HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list")
+ if(H5SL_insert(fm->sel_chunks, new_chunk_info, &new_chunk_info->index) < 0) {
+ H5D_free_chunk_info(new_chunk_info, NULL, NULL);
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert chunk into skip list")
} /* end if */
/* Get number of elements selected in chunk */
@@ -1100,26 +1371,29 @@ H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr)
*-------------------------------------------------------------------------
*/
static hbool_t
-H5D_chunk_in_cache(const H5D_io_info_t *io_info)
+H5D_chunk_in_cache(const H5D_t *dset, const hsize_t *chunk_offset,
+ hsize_t chunk_idx)
{
- H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);/*raw data chunk cache*/
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/
hbool_t found = FALSE; /*already in cache? */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_in_cache)
- HDassert(io_info);
+ /* Sanity checks */
+ HDassert(dset);
+ HDassert(chunk_offset);
/* Check if the chunk is in the cache (but hasn't been written to disk yet) */
if(rdcc->nslots > 0) {
- unsigned idx = H5D_CHUNK_HASH(io_info->dset->shared, io_info->store->chunk.index); /* Cache entry index */
+ unsigned idx = H5D_CHUNK_HASH(dset->shared, chunk_idx); /* Cache entry index */
H5D_rdcc_ent_t *ent = rdcc->slot[idx]; /* Cache entry */
/* Potential match... */
if(ent) {
size_t u; /* Local index variable */
- for(u = 0, found = TRUE; u < io_info->dset->shared->layout.u.chunk.ndims; u++) {
- if(io_info->store->chunk.offset[u] != ent->offset[u]) {
+ for(u = 0, found = TRUE; u < dset->shared->layout.u.chunk.ndims; u++) {
+ if(chunk_offset[u] != ent->offset[u]) {
found = FALSE;
break;
} /* end if */
@@ -1211,20 +1485,16 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
void *chunk; /* Pointer to locked chunk buffer */
haddr_t chunk_addr; /* Chunk address on disk */
- H5D_istore_ud1_t udata; /* B-tree pass-through */
+ H5D_chunk_ud_t udata; /* B-tree pass-through */
/* Get the actual chunk information from the skip list node */
chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
- /* Pass in chunk's coordinates in a union. */
- io_info->store->chunk.offset = chunk_info->coords;
- io_info->store->chunk.index = chunk_info->index;
-
/* Get the address of the chunk in the file */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
+ chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata);
/* Check for non-existant chunk & skip it if appropriate */
- if(!H5F_addr_defined(chunk_addr) && !H5D_chunk_in_cache(io_info)
+ if(!H5F_addr_defined(chunk_addr) && !H5D_chunk_in_cache(io_info->dset, chunk_info->coords, chunk_info->index)
&& skip_missing_chunks) {
/* No chunk cached */
chunk = NULL;
@@ -1235,14 +1505,15 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
else {
/* Load the chunk into cache and lock it. */
if(H5D_chunk_cacheable(io_info, chunk_addr)) {
- size_t tmp_src_accessed_bytes; /* Total accessed size in a chunk */
+ /* Pass in chunk's coordinates in a union. */
+ io_info->store->chunk.offset = chunk_info->coords;
+ io_info->store->chunk.index = chunk_info->index;
/* Compute # of bytes accessed in chunk */
- tmp_src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
- H5_ASSIGN_OVERFLOW(src_accessed_bytes, tmp_src_accessed_bytes, size_t, uint32_t);
+ src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
/* Lock the chunk into the cache */
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint)))
+ if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
@@ -1272,7 +1543,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed")
/* Release the cache lock on the chunk. */
- if(chunk && H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, src_accessed_bytes) < 0)
+ if(chunk && H5D_chunk_unlock(io_info, FALSE, idx_hint, chunk, src_accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
/* Advance to next chunk in list */
@@ -1342,25 +1613,23 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
void *chunk; /* Pointer to locked chunk buffer */
haddr_t chunk_addr; /* Chunk address on disk */
- H5D_istore_ud1_t udata; /* B-tree pass-through */
+ H5D_chunk_ud_t udata; /* B-tree pass-through */
/* Get the actual chunk information from the skip list node */
chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
- /* Pass in chunk's coordinates in a union. */
- io_info->store->chunk.offset = chunk_info->coords;
- io_info->store->chunk.index = chunk_info->index;
-
/* Load the chunk into cache. But if the whole chunk is written,
* simply allocate space instead of load the chunk. */
- chunk_addr = H5D_istore_get_addr(io_info, &udata);
+ chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata);
if(H5D_chunk_cacheable(io_info, chunk_addr)) {
hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */
- size_t tmp_dst_accessed_bytes; /* Total accessed size in a chunk */
+
+ /* Pass in chunk's coordinates in a union. */
+ io_info->store->chunk.offset = chunk_info->coords;
+ io_info->store->chunk.index = chunk_info->index;
/* Compute # of bytes accessed in chunk */
- tmp_dst_accessed_bytes = chunk_info->chunk_points * type_info->dst_type_size;
- H5_ASSIGN_OVERFLOW(dst_accessed_bytes, tmp_dst_accessed_bytes, size_t, uint32_t);
+ dst_accessed_bytes = chunk_info->chunk_points * type_info->dst_type_size;
/* Determine if we will access all the data in the chunk */
if(dst_accessed_bytes != ctg_store.contig.dset_size ||
@@ -1368,7 +1637,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
entire_chunk = FALSE;
/* Lock the chunk into the cache */
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, entire_chunk, &idx_hint)))
+ if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, entire_chunk, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
@@ -1397,7 +1666,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed")
/* Release the cache lock on the chunk. */
- if(chunk && H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, dst_accessed_bytes) < 0)
+ if(chunk && H5D_chunk_unlock(io_info, TRUE, idx_hint, chunk, dst_accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
/* Advance to next chunk in list */
@@ -1461,6 +1730,2712 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_init
+ *
+ * Purpose: Initialize the raw data chunk cache for a dataset. This is
+ * called when the dataset is initialized.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Monday, May 18, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Convenience pointer to dataset's chunk cache */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_init, FAIL)
+
+ /* Sanity check */
+ HDassert(f);
+ HDassert(dset);
+
+ if(H5F_RDCC_NBYTES(f) > 0 && H5F_RDCC_NELMTS(f) > 0) {
+ rdcc->nbytes = H5F_RDCC_NBYTES(f);
+ rdcc->nslots = H5F_RDCC_NELMTS(f);
+ rdcc->slot = H5FL_SEQ_CALLOC(H5D_rdcc_ent_ptr_t, rdcc->nslots);
+ if(NULL == rdcc->slot)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+
+ /* Reset any cached chunk info for this dataset */
+ H5D_chunk_cinfo_cache_reset(&(rdcc->last));
+ } /* end if */
+
+ /* Compose chunked index info struct */
+ idx_info.f = f;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Allocate any indexing structures */
+ if((dset->shared->layout.u.chunk.ops->init)(&idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_init() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_cinfo_cache_reset
+ *
+ * Purpose: Reset the cached chunk info
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * November 27, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_cinfo_cache_reset(H5D_chunk_cached_t *last)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_reset)
+
+ /* Sanity check */
+ HDassert(last);
+
+ /* Indicate that the cached info is not valid */
+ last->valid = FALSE;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_chunk_cinfo_cache_reset() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_cinfo_cache_update
+ *
+ * Purpose: Update the cached chunk info
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * November 27, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *udata)
+{
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_update)
+
+ /* Sanity check */
+ HDassert(last);
+ HDassert(udata);
+ HDassert(udata->common.mesg);
+ HDassert(udata->common.offset);
+
+ /* Stored the information to cache */
+ for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
+ last->offset[u] = udata->common.offset[u];
+ last->nbytes = udata->nbytes;
+ last->filter_mask = udata->filter_mask;
+ last->addr = udata->addr;
+
+ /* Indicate that the cached info is valid */
+ last->valid = TRUE;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_chunk_cinfo_cache_update() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_cinfo_cache_found
+ *
+ * Purpose: Look for chunk info in cache
+ *
+ * Return: TRUE/FALSE/FAIL
+ *
+ * Programmer: Quincey Koziol
+ * November 27, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static hbool_t
+H5D_chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *udata)
+{
+ hbool_t ret_value = FALSE; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_found)
+
+ /* Sanity check */
+ HDassert(last);
+ HDassert(udata);
+ HDassert(udata->common.mesg);
+ HDassert(udata->common.offset);
+
+ /* Check if the cached information is what is desired */
+ if(last->valid) {
+ unsigned u; /* Local index variable */
+
+ /* Check that the offset is the same */
+ for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
+ if(last->offset[u] != udata->common.offset[u])
+ HGOTO_DONE(FALSE)
+
+ /* Retrieve the information from the cache */
+ udata->nbytes = last->nbytes;
+ udata->filter_mask = last->filter_mask;
+ udata->addr = last->addr;
+
+ /* Indicate that the data was found */
+ HGOTO_DONE(TRUE)
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_chunk_cinfo_cache_found() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_create
+ *
+ * Purpose: Creates a new chunked storage index and initializes the
+ * layout information with information about the storage. The
+ * layout info should be immediately written to the object header.
+ *
+ * Return: Non-negative on success (with the layout information initialized
+ * and ready to write to an object header). Negative on failure.
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, May 22, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_create, FAIL)
+
+ /* Check args */
+ HDassert(dset);
+ HDassert(H5D_CHUNKED == dset->shared->layout.type);
+ HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
+#ifndef NDEBUG
+{
+ unsigned u; /* Local index variable */
+
+ for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
+ HDassert(dset->shared->layout.u.chunk.dim[u] > 0);
+}
+#endif
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Create the index for the chunks */
+ if((dset->shared->layout.u.chunk.ops->create)(&idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_create() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_get_addr
+ *
+ * Purpose: Get the file address of a chunk if file space has been
+ * assigned. Save the retrieved information in the udata
+ * supplied.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Albert Cheng
+ * June 27, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+haddr_t
+H5D_chunk_get_addr(const H5D_t *dset, hid_t dxpl_id, const hsize_t *chunk_offset,
+ H5D_chunk_ud_t *_udata)
+{
+ H5D_chunk_ud_t tmp_udata; /* Information about a chunk */
+ H5D_chunk_ud_t *udata; /* Pointer to information about a chunk */
+ haddr_t ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_get_addr)
+
+ HDassert(dset);
+ HDassert(dset->shared->layout.u.chunk.ndims > 0);
+ HDassert(chunk_offset);
+
+ /* Check for udata struct to return */
+ udata = (_udata != NULL ? _udata : &tmp_udata);
+
+ /* Initialize the information about the chunk we are looking for */
+ udata->common.mesg = &(dset->shared->layout);
+ udata->common.offset = chunk_offset;
+ udata->nbytes = 0;
+ udata->filter_mask = 0;
+ udata->addr = HADDR_UNDEF;
+
+ /* Check for cached information */
+ if(!H5D_chunk_cinfo_cache_found(&dset->shared->cache.chunk.last, udata)) {
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Go get the chunk information */
+ if(!H5F_addr_defined((dset->shared->layout.u.chunk.ops->get_addr)(&idx_info, udata))) {
+ /* Cache the fact that the chunk is not in the B-tree */
+ H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata);
+
+ HGOTO_DONE(HADDR_UNDEF)
+ } /* end if */
+
+ /* Cache the information retrieved */
+ HDassert(H5F_addr_defined(udata->addr));
+ H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata);
+ } /* end if */
+
+ /* Success! Set the return value */
+ ret_value = udata->addr;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_chunk_get_addr() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_flush_entry
+ *
+ * Purpose: Writes a chunk to disk. If RESET is non-zero then the
+ * entry is cleared -- it's slightly faster to flush a chunk if
+ * the RESET flag is turned on because it results in one fewer
+ * memory copy.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache,
+ H5D_rdcc_ent_t *ent, hbool_t reset)
+{
+ void *buf = NULL; /* Temporary buffer */
+ hbool_t point_of_no_return = FALSE;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_flush_entry)
+
+ HDassert(dset);
+ HDassert(dxpl_cache);
+ HDassert(ent);
+ HDassert(!ent->locked);
+
+ buf = ent->chunk;
+ if(ent->dirty) {
+ H5D_chunk_ud_t udata; /* pass through B-tree */
+ hbool_t must_insert = FALSE; /* Whether the chunk must go through the "insert" method */
+
+ /* Set up user data for index callbacks */
+ udata.common.mesg = &dset->shared->layout;
+ udata.common.offset = ent->offset;
+ udata.filter_mask = 0;
+ udata.nbytes = ent->chunk_size;
+ udata.addr = ent->chunk_addr;
+
+ /* Should the chunk be filtered before writing it to disk? */
+ if(dset->shared->dcpl_cache.pline.nused) {
+ size_t alloc = ent->alloc_size; /* Bytes allocated for BUF */
+ size_t nbytes; /* Chunk size (in bytes) */
+
+ if(!reset) {
+ /*
+ * Copy the chunk to a new buffer before running it through
+ * the pipeline because we'll want to save the original buffer
+ * for later.
+ */
+ H5_ASSIGN_OVERFLOW(alloc, ent->chunk_size, uint32_t, size_t);
+ if(NULL == (buf = H5MM_malloc(alloc)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline")
+ HDmemcpy(buf, ent->chunk, ent->chunk_size);
+ } /* end if */
+ else {
+ /*
+ * If we are reseting and something goes wrong after this
+ * point then it's too late to recover because we may have
+ * destroyed the original data by calling H5Z_pipeline().
+ * The only safe option is to continue with the reset
+ * even if we can't write the data to disk.
+ */
+ point_of_no_return = TRUE;
+ ent->chunk = NULL;
+ } /* end else */
+ H5_ASSIGN_OVERFLOW(nbytes, udata.nbytes, uint32_t, size_t);
+ if(H5Z_pipeline(&(dset->shared->dcpl_cache.pline), 0, &(udata.filter_mask), dxpl_cache->err_detect,
+ dxpl_cache->filter_cb, &nbytes, &alloc, &buf) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed")
+ H5_ASSIGN_OVERFLOW(udata.nbytes, nbytes, size_t, uint32_t);
+
+ /* Indicate that the chunk must go through 'insert' method */
+ must_insert = TRUE;
+ } /* end if */
+ else if(!H5F_addr_defined(udata.addr))
+ /* Indicate that the chunk must go through 'insert' method */
+ must_insert = TRUE;
+
+ /* Check if the chunk needs to be 'inserted' (could exist already and
+ * the 'insert' operation could resize it)
+ */
+ if(must_insert) {
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Create the chunk it if it doesn't exist, or reallocate the chunk
+ * if its size changed.
+ */
+ if((dset->shared->layout.u.chunk.ops->insert)(&idx_info, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk")
+
+ /* Update the chunk entry's address, in case it was allocated or relocated */
+ ent->chunk_addr = udata.addr;
+ } /* end if */
+
+ /* Write the data to the file */
+ HDassert(H5F_addr_defined(udata.addr));
+ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.nbytes, dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
+
+ /* Cache the chunk's info, in case it's accessed again shortly */
+ H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata);
+
+ /* Mark cache entry as clean */
+ ent->dirty = FALSE;
+
+ /* Increment # of flushed entries */
+ dset->shared->cache.chunk.stats.nflushes++;
+ } /* end if */
+
+ /* Reset, but do not free or removed from list */
+ if(reset) {
+ point_of_no_return = FALSE;
+ if(buf == ent->chunk)
+ buf = NULL;
+ if(ent->chunk != NULL)
+ ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
+ } /* end if */
+
+done:
+ /* Free the temp buffer only if it's different than the entry chunk */
+ if(buf != ent->chunk)
+ H5MM_xfree(buf);
+
+ /*
+ * If we reached the point of no return then we have no choice but to
+ * reset the entry. This can only happen if RESET is true but the
+ * output pipeline failed. Do not free the entry or remove it from the
+ * list.
+ */
+ if(ret_value < 0 && point_of_no_return) {
+ if(ent->chunk)
+ ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_flush_entry() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_cache_evict
+ *
+ * Purpose: Preempts the specified entry from the cache, flushing it to
+ * disk if necessary.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache,
+ H5D_rdcc_ent_t *ent, hbool_t flush)
+{
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_evict)
+
+ HDassert(dset);
+ HDassert(dxpl_cache);
+ HDassert(ent);
+ HDassert(!ent->locked);
+ HDassert(ent->idx < rdcc->nslots);
+
+ if(flush) {
+ /* Flush */
+ if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+ } /* end if */
+ else {
+ /* Don't flush, just free chunk */
+ if(ent->chunk != NULL)
+ ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
+ } /* end else */
+
+ /* Unlink from list */
+ if(ent->prev)
+ ent->prev->next = ent->next;
+ else
+ rdcc->head = ent->next;
+ if(ent->next)
+ ent->next->prev = ent->prev;
+ else
+ rdcc->tail = ent->prev;
+ ent->prev = ent->next = NULL;
+
+ /* Remove from cache */
+ rdcc->slot[ent->idx] = NULL;
+ ent->idx = UINT_MAX;
+ rdcc->nbytes -= ent->chunk_size;
+ --rdcc->nused;
+
+ /* Free */
+ H5FL_FREE(H5D_rdcc_ent_t, ent);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_cache_evict() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_cache_prune
+ *
+ * Purpose: Prune the cache by preempting some things until the cache has
+ * room for something which is SIZE bytes. Only unlocked
+ * entries are considered for preemption.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_chunk_cache_prune(const H5D_t *dset, hid_t dxpl_id,
+ const H5D_dxpl_cache_t *dxpl_cache, size_t size)
+{
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
+ size_t total = rdcc->nbytes;
+ const int nmeth = 2; /*number of methods */
+ int w[1]; /*weighting as an interval */
+ H5D_rdcc_ent_t *p[2], *cur; /*list pointers */
+ H5D_rdcc_ent_t *n[2]; /*list next pointers */
+ int nerrors = 0; /* Accumulated error count during preemptions */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_prune)
+
+ /*
+ * Preemption is accomplished by having multiple pointers (currently two)
+ * slide down the list beginning at the head. Pointer p(N+1) will start
+ * traversing the list when pointer pN reaches wN percent of the original
+ * list. In other words, preemption method N gets to consider entries in
+ * approximate least recently used order w0 percent before method N+1
+ * where 100% means tha method N will run to completion before method N+1
+ * begins. The pointers participating in the list traversal are each
+ * given a chance at preemption before any of the pointers are advanced.
+ */
+ w[0] = (int)(rdcc->nused * H5F_RDCC_W0(dset->oloc.file));
+ p[0] = rdcc->head;
+ p[1] = NULL;
+
+ while((p[0] || p[1]) && (rdcc->nbytes + size) > total) {
+ int i; /* Local index variable */
+
+ /* Introduce new pointers */
+ for(i = 0; i < nmeth - 1; i++)
+ if(0 == w[i])
+ p[i + 1] = rdcc->head;
+
+ /* Compute next value for each pointer */
+ for(i = 0; i < nmeth; i++)
+ n[i] = p[i] ? p[i]->next : NULL;
+
+ /* Give each method a chance */
+ for(i = 0; i < nmeth && (rdcc->nbytes + size) > total; i++) {
+ if(0 == i && p[0] && !p[0]->locked &&
+ ((0 == p[0]->rd_count && 0 == p[0]->wr_count) ||
+ (0 == p[0]->rd_count && p[0]->chunk_size == p[0]->wr_count) ||
+ (p[0]->chunk_size == p[0]->rd_count && 0 == p[0]->wr_count))) {
+ /*
+ * Method 0: Preempt entries that have been completely written
+ * and/or completely read but not entries that are partially
+ * written or partially read.
+ */
+ cur = p[0];
+ } else if(1 == i && p[1] && !p[1]->locked) {
+ /*
+ * Method 1: Preempt the entry without regard to
+ * considerations other than being locked. This is the last
+ * resort preemption.
+ */
+ cur = p[1];
+ } else {
+ /* Nothing to preempt at this point */
+ cur = NULL;
+ }
+
+ if(cur) {
+ int j; /* Local index variable */
+
+ for(j = 0; j < nmeth; j++) {
+ if(p[j] == cur)
+ p[j] = NULL;
+ if(n[j] == cur)
+ n[j] = cur->next;
+ } /* end for */
+ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, cur, TRUE) < 0)
+ nerrors++;
+ } /* end if */
+ } /* end for */
+
+ /* Advance pointers */
+ for(i = 0; i < nmeth; i++)
+ p[i] = n[i];
+ for(i = 0; i < nmeth - 1; i++)
+ w[i] -= 1;
+ } /* end while */
+
+ if(nerrors)
+ HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to preempt one or more raw data cache entry")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_cache_prune() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_lock
+ *
+ * Purpose: Return a pointer to a dataset chunk. The pointer points
+ * directly into the chunk cache and should not be freed
+ * by the caller but will be valid until it is unlocked. The
+ * input value IDX_HINT is used to speed up cache lookups and
+ * it's output value should be given to H5F_chunk_unlock().
+ * IDX_HINT is ignored if it is out of range, and if it points
+ * to the wrong entry then we fall back to the normal search
+ * method.
+ *
+ * If RELAX is non-zero and the chunk isn't in the cache then
+ * don't try to read it from the file, but just allocate an
+ * uninitialized buffer to hold the result. This is intended
+ * for output functions that are about to overwrite the entire
+ * chunk.
+ *
+ * Return: Success: Ptr to a file chunk.
+ *
+ * Failure: NULL
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+void *
+H5D_chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
+ hbool_t relax, unsigned *idx_hint/*in,out*/)
+{
+ H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
+ const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
+ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
+ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache*/
+ H5D_rdcc_ent_t *ent = NULL; /*cache entry */
+ unsigned idx = 0; /*hash index number */
+ hbool_t found = FALSE; /*already in cache? */
+ haddr_t chunk_addr = HADDR_UNDEF; /* Address of chunk on disk */
+ size_t chunk_size; /*size of a chunk */
+ void *chunk = NULL; /*the file chunk */
+ unsigned u; /*counters */
+ void *ret_value; /*return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_lock)
+
+ HDassert(io_info);
+ HDassert(dset);
+ HDassert(io_info->dxpl_cache);
+ HDassert(io_info->store);
+ HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER));
+
+ /* Get the chunk's size */
+ HDassert(layout->u.chunk.size > 0);
+ H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
+
+ /* Search for the chunk in the cache */
+ if(rdcc->nslots > 0) {
+ idx = H5D_CHUNK_HASH(dset->shared, io_info->store->chunk.index);
+ ent = rdcc->slot[idx];
+
+ if(ent)
+ for(u = 0, found = TRUE; u < layout->u.chunk.ndims; u++)
+ if(io_info->store->chunk.offset[u] != ent->offset[u]) {
+ found = FALSE;
+ break;
+ } /* end if */
+ } /* end if */
+
+ if(found) {
+ /*
+ * Already in the cache. Count a hit.
+ */
+ rdcc->stats.nhits++;
+ } /* end if */
+ else if(relax) {
+ /*
+ * Not in the cache, but we're about to overwrite the whole thing
+ * anyway, so just allocate a buffer for it but don't initialize that
+ * buffer with the file contents. Count this as a hit instead of a
+ * miss because we saved ourselves lots of work.
+ */
+ rdcc->stats.nhits++;
+
+ if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
+
+ /* In the case that some dataset functions look through this data,
+ * clear it to all 0s. */
+ HDmemset(chunk, 0, chunk_size);
+ } /* end if */
+ else {
+ H5D_chunk_ud_t tmp_udata; /*B-tree pass-through */
+
+ if(udata != NULL)
+ chunk_addr = udata->addr;
+ else {
+ /* Point at temporary storage for B-tree pass through */
+ udata = &tmp_udata;
+
+ /*
+ * Not in the cache. Read it from the file and count this as a miss
+ * if it's in the file or an init if it isn't.
+ */
+ chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, io_info->store->chunk.offset, udata);
+ } /* end else */
+
+ /* Check if the chunk exists on disk */
+ if(H5F_addr_defined(chunk_addr)) {
+ size_t chunk_alloc = 0; /*allocated chunk size */
+
+ /* Chunk size on disk isn't [likely] the same size as the final chunk
+ * size in memory, so allocate memory big enough. */
+ H5_ASSIGN_OVERFLOW(chunk_alloc, udata->nbytes, uint32_t, size_t);
+ if(NULL == (chunk = H5D_chunk_alloc(chunk_alloc, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
+ if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, chunk_addr, chunk_alloc, io_info->dxpl_id, chunk) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk")
+
+ if(pline->nused) {
+ if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &(udata->filter_mask), io_info->dxpl_cache->err_detect,
+ io_info->dxpl_cache->filter_cb, &chunk_alloc, &chunk_alloc, &chunk) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, NULL, "data pipeline read failed")
+ H5_ASSIGN_OVERFLOW(udata->nbytes, chunk_alloc, size_t, uint32_t);
+ } /* end if */
+
+ /* Increment # of cache misses */
+ rdcc->stats.nmisses++;
+ } /* end if */
+ else {
+ H5D_fill_value_t fill_status;
+
+#ifdef OLD_WAY
+ /* Clear the error stack from not finding the chunk on disk */
+ H5E_clear_stack(NULL);
+#endif /* OLD_WAY */
+
+ /* Chunk size on disk isn't [likely] the same size as the final chunk
+ * size in memory, so allocate memory big enough. */
+ if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
+
+ if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined")
+
+ if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
+ (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
+ /*
+ * The chunk doesn't exist in the file. Replicate the fill
+ * value throughout the chunk, if the fill value is defined.
+ */
+
+ /* Initialize the fill value buffer */
+ /* (use the compact dataset storage buffer as the fill value buffer) */
+ if(H5D_fill_init(&fb_info, chunk, FALSE,
+ NULL, NULL, NULL, NULL,
+ &dset->shared->dcpl_cache.fill, dset->shared->type,
+ dset->shared->type_id, (size_t)0, chunk_size, io_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize fill buffer info")
+ fb_info_init = TRUE;
+
+ /* Check for VL datatype & non-default fill value */
+ if(fb_info.has_vlen_fill_type)
+ /* Fill the buffer with VL datatype fill values */
+ if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, io_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, NULL, "can't refill fill value buffer")
+ } /* end if */
+ else
+ HDmemset(chunk, 0, chunk_size);
+
+ /* Increment # of creations */
+ rdcc->stats.ninits++;
+ } /* end else */
+ } /* end else */
+ HDassert(found || chunk_size > 0);
+
+ if(!found && rdcc->nslots > 0 && chunk_size <= rdcc->nbytes &&
+ (!ent || !ent->locked)) {
+ /*
+ * Add the chunk to the cache only if the slot is not already locked.
+ * Preempt enough things from the cache to make room.
+ */
+ if(ent) {
+ if(H5D_chunk_cache_evict(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, ent, TRUE) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk from cache")
+ } /* end if */
+ if(H5D_chunk_cache_prune(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, chunk_size) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk(s) from cache")
+
+ /* Create a new entry */
+ ent = H5FL_MALLOC(H5D_rdcc_ent_t);
+ ent->locked = 0;
+ ent->dirty = FALSE;
+ ent->chunk_addr = chunk_addr;
+ H5_ASSIGN_OVERFLOW(ent->chunk_size, chunk_size, size_t, uint32_t);
+ ent->alloc_size = chunk_size;
+ for(u = 0; u < layout->u.chunk.ndims; u++)
+ ent->offset[u] = io_info->store->chunk.offset[u];
+ H5_ASSIGN_OVERFLOW(ent->rd_count, chunk_size, size_t, uint32_t);
+ H5_ASSIGN_OVERFLOW(ent->wr_count, chunk_size, size_t, uint32_t);
+ ent->chunk = (uint8_t *)chunk;
+
+ /* Add it to the cache */
+ HDassert(NULL == rdcc->slot[idx]);
+ rdcc->slot[idx] = ent;
+ ent->idx = idx;
+ rdcc->nbytes += chunk_size;
+ rdcc->nused++;
+
+ /* Add it to the linked list */
+ ent->next = NULL;
+ if(rdcc->tail) {
+ rdcc->tail->next = ent;
+ ent->prev = rdcc->tail;
+ rdcc->tail = ent;
+ } /* end if */
+ else {
+ rdcc->head = rdcc->tail = ent;
+ ent->prev = NULL;
+ } /* end else */
+ found = TRUE;
+ } else if(!found) {
+ /*
+ * The chunk is larger than the entire cache so we don't cache it.
+ * This is the reason all those arguments have to be repeated for the
+ * unlock function.
+ */
+ ent = NULL;
+ idx = UINT_MAX;
+ } else {
+ /*
+ * The chunk is not at the beginning of the cache; move it backward
+ * by one slot. This is how we implement the LRU preemption
+ * algorithm.
+ */
+ HDassert(ent);
+ if(ent->next) {
+ if(ent->next->next)
+ ent->next->next->prev = ent;
+ else
+ rdcc->tail = ent;
+ ent->next->prev = ent->prev;
+ if(ent->prev)
+ ent->prev->next = ent->next;
+ else
+ rdcc->head = ent->next;
+ ent->prev = ent->next;
+ ent->next = ent->next->next;
+ ent->prev->next = ent;
+ } /* end if */
+ } /* end else */
+
+ /* Lock the chunk into the cache */
+ if(ent) {
+ HDassert(!ent->locked);
+ ent->locked = TRUE;
+ chunk = ent->chunk;
+ } /* end if */
+
+ if(idx_hint)
+ *idx_hint = idx;
+
+ /* Set return value */
+ ret_value = chunk;
+
+done:
+ /* Release the fill buffer info, if it's been initialized */
+ if(fb_info_init && H5D_fill_term(&fb_info) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "Can't release fill buffer info")
+
+ /* Release the chunk allocated, on error */
+ if(!ret_value)
+ if(chunk)
+ chunk = H5D_chunk_xfree(chunk, pline);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_lock() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_unlock
+ *
+ * Purpose: Unlocks a previously locked chunk. The LAYOUT, COMP, and
+ * OFFSET arguments should be the same as for H5D_chunk_lock().
+ * The DIRTY argument should be set to non-zero if the chunk has
+ * been modified since it was locked. The IDX_HINT argument is
+ * the returned index hint from the lock operation and BUF is
+ * the return value from the lock.
+ *
+ * The NACCESSED argument should be the number of bytes accessed
+ * for reading or writing (depending on the value of DIRTY).
+ * It's only purpose is to provide additional information to the
+ * preemption policy.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_unlock(const H5D_io_info_t *io_info, hbool_t dirty, unsigned idx_hint,
+ void *chunk, uint32_t naccessed)
+{
+ const H5O_layout_t *layout = &(io_info->dset->shared->layout); /* Dataset layout */
+ const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);
+ H5D_rdcc_ent_t *ent = NULL;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_unlock)
+
+ HDassert(io_info);
+
+ if(UINT_MAX == idx_hint) {
+ /*
+ * It's not in the cache, probably because it's too big. If it's
+ * dirty then flush it to disk. In any case, free the chunk.
+ * Note: we have to copy the layout and filter messages so we
+ * don't discard the `const' qualifier.
+ */
+ if(dirty) {
+ H5D_rdcc_ent_t x;
+
+ HDmemset(&x, 0, sizeof(x));
+ x.dirty = TRUE;
+ HDmemcpy(x.offset, io_info->store->chunk.offset, layout->u.chunk.ndims * sizeof(x.offset[0]));
+ HDassert(layout->u.chunk.size > 0);
+ x.chunk_addr = HADDR_UNDEF;
+ x.chunk_size = layout->u.chunk.size;
+ H5_ASSIGN_OVERFLOW(x.alloc_size, x.chunk_size, uint32_t, size_t);
+ x.chunk = (uint8_t *)chunk;
+
+ if(H5D_chunk_flush_entry(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, &x, TRUE) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+ } /* end if */
+ else {
+ if(chunk)
+ chunk = H5D_chunk_xfree(chunk, &(io_info->dset->shared->dcpl_cache.pline));
+ } /* end else */
+ } /* end if */
+ else {
+ /* Sanity check */
+ HDassert(idx_hint < rdcc->nslots);
+ HDassert(rdcc->slot[idx_hint]);
+ HDassert(rdcc->slot[idx_hint]->chunk == chunk);
+
+ /*
+ * It's in the cache so unlock it.
+ */
+ ent = rdcc->slot[idx_hint];
+ HDassert(ent->locked);
+ if(dirty) {
+ ent->dirty = TRUE;
+ ent->wr_count -= MIN(ent->wr_count, naccessed);
+ } /* end if */
+ else
+ ent->rd_count -= MIN(ent->rd_count, naccessed);
+ ent->locked = FALSE;
+ } /* end else */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_unlock() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_flush
+ *
+ * Purpose: Writes all dirty chunks to disk and optionally preempts them
+ * from the cache.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags)
+{
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
+ unsigned nerrors = 0;
+ H5D_rdcc_ent_t *ent, *next;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_flush, FAIL)
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Loop over all entries in the chunk cache */
+ for(ent = rdcc->head; ent; ent = next) {
+ next = ent->next;
+ if((flags & H5F_FLUSH_INVALIDATE)) {
+ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ nerrors++;
+ } else {
+ if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
+ nerrors++;
+ }
+ } /* end for */
+ if(nerrors)
+ HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_flush() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_allocated_cb
+ *
+ * Purpose: Simply counts the number of chunks for a dataset.
+ *
+ * Return: Success: Non-negative
+ * Failure: Negative
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static int
+H5D_chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ hsize_t *nbytes = (hsize_t *)_udata;
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_allocated_cb)
+
+ *(hsize_t *)nbytes += chunk_rec->nbytes;
+
+ FUNC_LEAVE_NOAPI(H5_ITER_CONT)
+} /* H5D_chunk_allocated_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_allocated
+ *
+ * Purpose: Return the number of bytes allocated in the file for storage
+ * of raw data in the chunked dataset
+ *
+ * Return: Success: Number of bytes stored in all chunks.
+ * Failure: 0
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, May 20, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
+ H5D_rdcc_ent_t *ent; /* Cache entry */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ hsize_t chunk_bytes = 0; /* Number of bytes allocated for chunks */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_allocated, FAIL)
+
+ HDassert(dset);
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Search for cached chunks that haven't been written out */
+ for(ent = rdcc->head; ent; ent = ent->next) {
+ /* Flush the chunk out to disk, to make certain the size is correct later */
+ if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+ } /* end for */
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Call the index-specific "get all the allocated chunks sizes" routine */
+ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_allocated_cb, &chunk_bytes) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
+
+ /* Set number of bytes for caller */
+ *nbytes = chunk_bytes;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_allocated() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_allocate
+ *
+ * Purpose: Allocate file space for all chunks that are not allocated yet.
+ * Return SUCCEED if all needed allocation succeed, otherwise
+ * FAIL.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Albert Cheng
+ * June 26, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ const H5D_chunk_ops_t *ops = dset->shared->layout.u.chunk.ops; /* Chunk operations */
+ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
+ size_t orig_chunk_size; /* Original size of chunk in bytes */
+ unsigned filter_mask = 0; /* Filter mask for chunks that have them */
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
+ const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
+ H5D_fill_value_t fill_status; /* The fill value status */
+ hbool_t should_fill = FALSE; /* Whether fill values should be written */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+#ifdef H5_HAVE_PARALLEL
+ MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */
+ int mpi_rank = (-1); /* This process's rank */
+ int mpi_code; /* MPI return code */
+ hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */
+ hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
+#endif /* H5_HAVE_PARALLEL */
+ hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
+ int space_ndims; /* Dataset's space rank */
+ hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
+ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
+ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
+ hid_t data_dxpl_id; /* DXPL ID to use for raw data I/O operations */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_allocate, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
+ HDassert(H5F_addr_defined(layout->u.chunk.addr));
+ HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
+
+ /* Retrieve the dataset dimensions */
+ if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info")
+ space_dim[space_ndims] = layout->u.chunk.dim[space_ndims];
+
+#ifdef H5_HAVE_PARALLEL
+ /* Retrieve MPI parameters */
+ if(IS_H5FD_MPI(dset->oloc.file)) {
+ /* Get the MPI communicator */
+ if(MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator")
+
+ /* Get the MPI rank */
+ if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file)) < 0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank")
+
+ /* Set the MPI-capable file driver flag */
+ using_mpi = TRUE;
+
+ /* Use the internal "independent" DXPL */
+ data_dxpl_id = H5AC_ind_dxpl_id;
+ } /* end if */
+ else {
+#endif /* H5_HAVE_PARALLEL */
+ /* Use the DXPL we were given */
+ data_dxpl_id = dxpl_id;
+#ifdef H5_HAVE_PARALLEL
+ } /* end else */
+#endif /* H5_HAVE_PARALLEL */
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D_get_dxpl_cache(data_dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Get original chunk size */
+ H5_ASSIGN_OVERFLOW(orig_chunk_size, layout->u.chunk.size, uint32_t, size_t);
+
+ /* Check the dataset's fill-value status */
+ if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
+
+ /* If we are filling the dataset on allocation or "if set" and
+ * the fill value _is_ set, _and_ we are not overwriting the new blocks,
+ * or if there are any pipeline filters defined,
+ * set the "should fill" flag
+ */
+ if((!full_overwrite && (fill->fill_time == H5D_FILL_TIME_ALLOC ||
+ (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)))
+ || pline->nused > 0)
+ should_fill = TRUE;
+
+ /* Check if fill values should be written to chunks */
+ if(should_fill) {
+ /* Initialize the fill value buffer */
+ /* (delay allocating fill buffer for VL datatypes until refilling) */
+ /* (casting away const OK - QAK) */
+ if(H5D_fill_init(&fb_info, NULL, (hbool_t)(pline->nused > 0),
+ (H5MM_allocate_t)H5D_chunk_alloc, (void *)pline,
+ (H5MM_free_t)H5D_chunk_xfree, (void *)pline,
+ &dset->shared->dcpl_cache.fill, dset->shared->type,
+ dset->shared->type_id, (size_t)0, orig_chunk_size, data_dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
+ fb_info_init = TRUE;
+
+ /* Check if there are filters which need to be applied to the chunk */
+ /* (only do this in advance when the chunk info can be re-used (i.e.
+ * it doesn't contain any non-default VL datatype fill values)
+ */
+ if(!fb_info.has_vlen_fill_type && pline->nused > 0) {
+ size_t buf_size = orig_chunk_size;
+
+ /* Push the chunk through the filters */
+ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
+ } /* end if */
+ } /* end if */
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Reset the chunk offset indices */
+ HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0])));
+
+ /* Loop over all chunks */
+ carry = FALSE;
+ while(!carry) {
+ haddr_t chunk_addr; /* Address of chunk */
+ int i; /* Local index variable */
+
+ /* Get the chunk's address */
+ chunk_addr = H5D_chunk_get_addr(dset, dxpl_id, chunk_offset, NULL);
+
+ /* Check if the chunk exists yet on disk */
+ if(!H5F_addr_defined(chunk_addr)) {
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
+ H5D_rdcc_ent_t *ent; /* Cache entry */
+ hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */
+ unsigned u; /* Local index variable */
+
+ /* Didn't find the chunk on disk */
+ chunk_exists = FALSE;
+
+ /* Look for chunk in cache */
+ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
+ /* Assume a match */
+ chunk_exists = TRUE;
+ for(u = 0; u < layout->u.chunk.ndims; u++)
+ if(ent->offset[u] != chunk_offset[u]) {
+ chunk_exists = FALSE; /* Reset if no match */
+ break;
+ } /* end if */
+ } /* end for */
+
+ /* Chunk wasn't in cache either, create it now */
+ if(!chunk_exists) {
+ H5D_chunk_ud_t udata; /* B-tree pass-through for creating chunk */
+ size_t chunk_size; /* Size of chunk in bytes, possibly filtered */
+
+ /* Check for VL datatype & non-default fill value */
+ if(fb_info_init && fb_info.has_vlen_fill_type) {
+ /* Sanity check */
+ HDassert(should_fill);
+
+ /* Fill the buffer with VL datatype fill values */
+ if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
+
+ /* Check if there are filters which need to be applied to the chunk */
+ if(pline->nused > 0) {
+ size_t buf_size = orig_chunk_size;
+ size_t nbytes = fb_info.fill_buf_size;
+
+ /* Push the chunk through the filters */
+ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &fb_info.fill_buf) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
+
+ /* Keep the number of bytes the chunk turned in to */
+ chunk_size = nbytes;
+ } /* end if */
+ else
+ H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
+ } /* end if */
+ else
+ chunk_size = orig_chunk_size;
+
+ /* Initialize the chunk information */
+ udata.common.mesg = layout;
+ udata.common.offset = chunk_offset;
+ H5_ASSIGN_OVERFLOW(udata.nbytes, chunk_size, size_t, uint32_t);
+ udata.filter_mask = filter_mask;
+ udata.addr = HADDR_UNDEF;
+
+ /* Allocate the chunk with all processes */
+ if((ops->insert)(&idx_info, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert record into chunk index")
+ HDassert(H5F_addr_defined(udata.addr));
+
+ /* Check if fill values should be written to chunks */
+ if(should_fill) {
+ /* Sanity check */
+ HDassert(fb_info_init);
+ HDassert(udata.nbytes == chunk_size);
+
+#ifdef H5_HAVE_PARALLEL
+ /* Check if this file is accessed with an MPI-capable file driver */
+ if(using_mpi) {
+ /* Write the chunks out from only one process */
+ /* !! Use the internal "independent" DXPL!! -QAK */
+ if(H5_PAR_META_WRITE == mpi_rank)
+ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
+
+ /* Indicate that blocks are being written */
+ blocks_written = TRUE;
+ } /* end if */
+ else {
+#endif /* H5_HAVE_PARALLEL */
+ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
+#ifdef H5_HAVE_PARALLEL
+ } /* end else */
+#endif /* H5_HAVE_PARALLEL */
+ } /* end if */
+
+ /* Release the fill buffer if we need to re-allocate it each time */
+ if(fb_info_init && fb_info.has_vlen_fill_type && pline->nused > 0)
+ H5D_fill_release(&fb_info);
+ } /* end if */
+ } /* end if */
+
+ /* Increment indices */
+ carry = TRUE;
+ for(i = (int)(space_ndims - 1); i >= 0; --i) {
+ chunk_offset[i] += layout->u.chunk.dim[i];
+ if(chunk_offset[i] >= space_dim[i])
+ chunk_offset[i] = 0;
+ else {
+ carry = FALSE;
+ break;
+ } /* end else */
+ } /* end for */
+ } /* end while */
+
+#ifdef H5_HAVE_PARALLEL
+ /* Only need to block at the barrier if we actually initialized a chunk */
+ /* using an MPI-capable file driver */
+ if(using_mpi && blocks_written) {
+ /* Wait at barrier to avoid race conditions where some processes are
+ * still writing out chunks and other processes race ahead to read
+ * them in, getting bogus data.
+ */
+ if(MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
+ } /* end if */
+#endif /* H5_HAVE_PARALLEL */
+
+ /* Reset any cached chunk info for this dataset */
+ H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last);
+
+done:
+ /* Release the fill buffer info, if it's been initialized */
+ if(fb_info_init && H5D_fill_term(&fb_info) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_allocate() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_prune_cb
+ *
+ * Purpose: Search for chunks that are no longer inside the pruned
+ * dataset's extent
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * March 26, 2002
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static int
+H5D_chunk_prune_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ H5D_chunk_it_ud1_t *udata = (H5D_chunk_it_ud1_t *)_udata; /* User data */
+ H5D_chunk_sl_ck_t *sl_node = NULL; /* Skip list node for chunk to remove */
+ unsigned rank; /* Current # of dimensions */
+ hbool_t should_delete = FALSE; /* Whether the chunk should be deleted */
+ hbool_t needs_fill = FALSE; /* Whether the chunk overlaps the new extent and needs fill valiues */
+ unsigned u; /* Local index variable */
+ int ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_cb)
+
+ /* Figure out what chunks are no longer in use for the specified extent and release them */
+ rank = udata->common.mesg->u.chunk.ndims - 1;
+ for(u = 0; u < rank; u++)
+ /* The chunk record points to a chunk of storage that contains the
+ * beginning of the logical address space represented by UDATA.
+ */
+ if(chunk_rec->offset[u] >= udata->dims[u]) {
+ /* Indicate that the chunk will be deleted */
+ should_delete = TRUE;
+
+ /* Break out of loop, we know the chunk is outside the current dimensions */
+ break;
+ } /* end if */
+ /* Check for chunk that overlaps new extent and will need fill values */
+ else if((chunk_rec->offset[u] + udata->common.mesg->u.chunk.dim[u]) > udata->dims[u])
+ /* Indicate that the chunk needs filling */
+ /* (but continue in loop, since it could be outside the extent in
+ * another dimension -QAK)
+ */
+ needs_fill = TRUE;
+
+ /* Check for chunk to delete */
+ if(should_delete) {
+ /* Allocate space for the shared structure */
+ if(NULL == (sl_node = H5FL_MALLOC(H5D_chunk_sl_ck_t)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for shared B-tree info")
+
+ /* Calculate the index of this chunk */
+ if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &sl_node->index) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index")
+
+ /* Store the key for the chunk */
+ sl_node->rec = *chunk_rec;
+
+ /* Insert the chunk description in the skip list */
+ if(H5SL_insert(udata->outside, sl_node, &sl_node->index) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTINSERT, H5_ITER_ERROR, "can't insert chunk into skip list")
+ } /* end if */
+ /* Check for chunk that overlaps the new dataset dimensions and needs filling */
+ else if(needs_fill) {
+ const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */
+ H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */
+ H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */
+ hssize_t sel_nelmts; /* Number of elements in selection */
+ hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */
+ void *chunk; /* The file chunk */
+ unsigned idx_hint; /* Which chunk we're dealing with */
+ H5D_chunk_ud_t chk_udata; /* User data for locking chunk */
+ uint32_t bytes_accessed; /* Bytes accessed in chunk */
+
+ /* Initialize the fill value buffer, if necessary */
+ if(!udata->fb_info_init) {
+ H5_CHECK_OVERFLOW(udata->elmts_per_chunk, uint32_t, size_t);
+ if(H5D_fill_init(&udata->fb_info, NULL, FALSE, NULL, NULL, NULL, NULL,
+ &dset->shared->dcpl_cache.fill,
+ dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk,
+ io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't initialize fill buffer info")
+ udata->fb_info_init = TRUE;
+ } /* end if */
+
+ /* Compute the # of elements to leave with existing value, in each dimension */
+ for(u = 0; u < rank; u++) {
+ count[u] = MIN(layout->u.chunk.dim[u], (udata->dims[u] - chunk_rec->offset[u]));
+ HDassert(count[u] > 0);
+ } /* end for */
+
+ /* Select all elements in chunk, to begin with */
+ if(H5S_select_all(udata->chunk_space, TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select space")
+
+ /* "Subtract out" the elements to keep */
+ if(H5S_select_hyperslab(udata->chunk_space, H5S_SELECT_NOTB, udata->hyper_start, NULL, count, NULL) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, H5_ITER_ERROR, "unable to select hyperslab")
+
+ /* Calculate the index of this chunk */
+ if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, udata->down_chunks, &io_info->store->chunk.index) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't get chunk index")
+
+ /* Lock the chunk into the cache, to get a pointer to the chunk buffer */
+ /* (Casting away const OK -QAK) */
+ io_info->store->chunk.offset = (hsize_t *)chunk_rec->offset;
+ chk_udata.common.mesg = layout;
+ chk_udata.common.offset = chunk_rec->offset;
+ chk_udata.nbytes = chunk_rec->nbytes;
+ chk_udata.filter_mask = chunk_rec->filter_mask;
+ chk_udata.addr = chunk_rec->chunk_addr;
+ if(NULL == (chunk = (void *)H5D_chunk_lock(udata->io_info, &chk_udata, FALSE, &idx_hint)))
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "unable to lock raw data chunk")
+
+
+ /* Fill the selection in the memory buffer */
+ /* Use the size of the elements in the chunk directly instead of */
+ /* relying on the fill.size, which might be set to 0 if there is */
+ /* no fill-value defined for the dataset -QAK */
+
+ /* Get the number of elements in the selection */
+ sel_nelmts = H5S_GET_SELECT_NPOINTS(udata->chunk_space);
+ HDassert(sel_nelmts >= 0);
+ H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, size_t);
+
+ /* Check for VL datatype & non-default fill value */
+ if(udata->fb_info.has_vlen_fill_type)
+ /* Re-fill the buffer to use for this I/O operation */
+ if(H5D_fill_refill_vl(&udata->fb_info, (size_t)sel_nelmts, io_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, H5_ITER_ERROR, "can't refill fill value buffer")
+
+ /* Create a selection iterator for scattering the elements to memory buffer */
+ if(H5S_select_iter_init(&chunk_iter, udata->chunk_space, layout->u.chunk.dim[rank]) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "unable to initialize chunk selection information")
+
+ /* Scatter the data into memory */
+ if(H5D_scatter_mem(udata->fb_info.fill_buf, udata->chunk_space, &chunk_iter, (size_t)sel_nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) {
+ H5S_SELECT_ITER_RELEASE(&chunk_iter);
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "scatter failed")
+ } /* end if */
+
+ /* Release the selection iterator */
+ if(H5S_SELECT_ITER_RELEASE(&chunk_iter) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "Can't release selection iterator")
+
+
+ /* The number of bytes accessed in the chunk */
+ /* (i.e. the bytes replaced with fill values) */
+ bytes_accessed = sel_nelmts * layout->u.chunk.dim[rank];
+
+ /* Release lock on chunk */
+ if(H5D_chunk_unlock(io_info, TRUE, idx_hint, chunk, bytes_accessed) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5_ITER_ERROR, "unable to unlock raw data chunk")
+ } /* end else-if */
+
+done:
+ if(ret_value != H5_ITER_CONT && sl_node)
+ H5FL_FREE(H5D_chunk_sl_ck_t, sl_node);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_prune_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_prune_sl_rm_cb
+ *
+ * Purpose: Destroy a skip list node for "pruning" chunks, also removes
+ * the chunk from the index.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol, koziol@hdfgroup.org
+ * May 3, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_chunk_prune_sl_rm_cb(void *item, void UNUSED *key, void *op_data)
+{
+ H5D_chunk_sl_ck_t *sl_node = (H5D_chunk_sl_ck_t *)item; /* Temporary pointer to chunk to remove */
+ H5D_chunk_sl_rm_t *rm_info = (H5D_chunk_sl_rm_t *)op_data; /* Information needed for removing chunk from B-tree */
+ H5D_chunk_common_ud_t idx_udata; /* User data for index removal routine */
+ herr_t ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_sl_rm_cb)
+
+ /* Sanity checks */
+ HDassert(sl_node);
+ HDassert(rm_info);
+
+ /* Initialize the user data for the index callback */
+ idx_udata.mesg = rm_info->mesg;
+ idx_udata.offset = sl_node->rec.offset;
+
+ /* Remove */
+ if((rm_info->idx_info->layout->u.chunk.ops->remove)(rm_info->idx_info, &idx_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, H5_ITER_ERROR, "unable to remove chunk entry from index")
+
+done:
+ H5FL_FREE(H5D_chunk_sl_ck_t, sl_node);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_chunk_prune_sl_rm_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_prune_by_extent
+ *
+ * Purpose: This function searches for chunks that are no longer necessary
+ * both in the raw data cache and in the chunk index.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * Algorithm: Robb Matzke
+ * March 27, 2002
+ *
+ * The algorithm is:
+ *
+ * For chunks that are no longer necessary:
+ *
+ * 1. Search in the raw data cache for each chunk
+ * 2. If found then preempt it from the cache
+ * 3. Search in the B-tree for each chunk
+ * 4. If found then remove it from the B-tree and deallocate file storage for the chunk
+ *
+ * This example shows a 2d dataset of 90x90 with a chunk size of 20x20.
+ *
+ *
+ * 0 20 40 60 80 90 100
+ * 0 +---------+---------+---------+---------+-----+...+
+ * |:::::X:::::::::::::: : : | :
+ * |:::::::X:::::::::::: : : | : Key
+ * |::::::::::X::::::::: : : | : --------
+ * |::::::::::::X::::::: : : | : +-+ Dataset
+ * 20+::::::::::::::::::::.........:.........:.....+...: | | Extent
+ * | :::::X::::: : : | : +-+
+ * | ::::::::::: : : | :
+ * | ::::::::::: : : | : ... Chunk
+ * | :::::::X::: : : | : : : Boundary
+ * 40+.........:::::::::::.........:.........:.....+...: :.:
+ * | : : : : | :
+ * | : : : : | : ... Allocated
+ * | : : : : | : ::: & Filled
+ * | : : : : | : ::: Chunk
+ * 60+.........:.........:.........:.........:.....+...:
+ * | : :::::::X::: : | : X Element
+ * | : ::::::::::: : | : Written
+ * | : ::::::::::: : | :
+ * | : ::::::::::: : | :
+ * 80+.........:.........:::::::::::.........:.....+...: O Fill Val
+ * | : : ::::::::::: | : Explicitly
+ * | : : ::::::X:::: | : Written
+ * 90+---------+---------+---------+---------+-----+ :
+ * : : : ::::::::::: :
+ * 100:.........:.........:.........:::::::::::.........:
+ *
+ *
+ * We have 25 total chunks for this dataset, 5 of which have space
+ * allocated in the file because they were written to one or more
+ * elements. These five chunks (and only these five) also have entries in
+ * the storage B-tree for this dataset.
+ *
+ * Now lets say we want to shrink the dataset down to 70x70:
+ *
+ *
+ * 0 20 40 60 70 80 90 100
+ * 0 +---------+---------+---------+----+----+-----+...+
+ * |:::::X:::::::::::::: : | : | :
+ * |:::::::X:::::::::::: : | : | : Key
+ * |::::::::::X::::::::: : | : | : --------
+ * |::::::::::::X::::::: : | : | : +-+ Dataset
+ * 20+::::::::::::::::::::.........:....+....:.....|...: | | Extent
+ * | :::::X::::: : | : | : +-+
+ * | ::::::::::: : | : | :
+ * | ::::::::::: : | : | : ... Chunk
+ * | :::::::X::: : | : | : : : Boundary
+ * 40+.........:::::::::::.........:....+....:.....|...: :.:
+ * | : : : | : | :
+ * | : : : | : | : ... Allocated
+ * | : : : | : | : ::: & Filled
+ * | : : : | : | : ::: Chunk
+ * 60+.........:.........:.........:....+....:.....|...:
+ * | : :::::::X::: | : | : X Element
+ * | : ::::::::::: | : | : Written
+ * +---------+---------+---------+----+ : | :
+ * | : ::::::::::: : | :
+ * 80+.........:.........:::::::::X:.........:.....|...: O Fill Val
+ * | : : ::::::::::: | : Explicitly
+ * | : : ::::::X:::: | : Written
+ * 90+---------+---------+---------+---------+-----+ :
+ * : : : ::::::::::: :
+ * 100:.........:.........:.........:::::::::::.........:
+ *
+ *
+ * That means that the nine chunks along the bottom and right side should
+ * no longer exist. Of those nine chunks, (0,80), (20,80), (40,80),
+ * (60,80), (80,80), (80,60), (80,40), (80,20), and (80,0), one is actually allocated
+ * that needs to be released.
+ * To release the chunks, we traverse the B-tree to obtain a list of unused
+ * allocated chunks, and then call H5B_remove() for each chunk.
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ H5D_io_info_t chk_io_info; /* Chunked I/O info object */
+ H5D_storage_t chk_store; /* Chunk storage information */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
+ H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Cache entries */
+ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dataspace dimensions */
+ H5D_chunk_it_ud1_t udata; /* Chunk index iterator user data */
+ hbool_t udata_init = FALSE; /* Whether the chunk index iterator user data has been initialized */
+ H5D_chunk_sl_rm_t rm_info; /* User data for skip list destroy callback */
+ H5S_t *chunk_space = NULL; /* Dataspace for a chunk */
+ hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */
+ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Current number of chunks in each dimension */
+ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
+ hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */
+ uint32_t elmts_per_chunk; /* Elements in chunk */
+ unsigned rank; /* Current # of dimensions */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_prune_by_extent, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
+ HDassert(H5F_addr_defined(layout->u.chunk.addr));
+ HDassert(dxpl_cache);
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Go get the rank & dimensions (including the element size) */
+ rank = layout->u.chunk.ndims - 1;
+ if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
+ curr_dims[rank] = layout->u.chunk.dim[rank];
+
+ /*-------------------------------------------------------------------------
+ * Figure out what chunks are no longer in use for the specified extent
+ * and release them from the linked list raw data cache
+ *-------------------------------------------------------------------------
+ */
+ for(ent = rdcc->head; ent; ent = next) {
+ /* Get pointer to next extry in cache, in case this one is evicted */
+ next = ent->next;
+
+ /* Check for chunk offset outside of new dimensions */
+ for(u = 0; u < rank; u++)
+ if((hsize_t)ent->offset[u] > curr_dims[u]) {
+ /* Evict the entry from the cache, but do not flush it to disk */
+ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+
+ /* Break out of loop, chunk is evicted */
+ break;
+ } /* end if */
+ } /* end for */
+
+ /* Round up to the next integer # of chunks, to accomodate partial chunks */
+ /* (also compute the number of elements per chunk) */
+ /* (also copy the chunk dimensions into 'hsize_t' array for creating dataspace) */
+ elmts_per_chunk = 1;
+ for(u = 0; u < rank; u++) {
+ chunks[u] = ((old_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u];
+ elmts_per_chunk *= layout->u.chunk.dim[u];
+ chunk_dims[u] = layout->u.chunk.dim[u];
+ } /* end for */
+
+ /* Get the "down" sizes for each dimension */
+ if(H5V_array_down(rank, chunks, down_chunks) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
+
+ /* Create a data space for a chunk & set the extent */
+ if(NULL == (chunk_space = H5S_create_simple(rank, chunk_dims, NULL)))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
+
+ /* Reset hyperslab start array */
+ /* (hyperslabs will always start from origin) */
+ HDmemset(hyper_start, 0, sizeof(hyper_start));
+
+ /* Set up chunked I/O info object, for operations on chunks (in callback) */
+ /* (Casting away const OK -QAK) */
+ H5D_BUILD_IO_INFO_RD(&chk_io_info, dset, dxpl_cache, dxpl_id, &chk_store, NULL);
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Initialize the user data for the iteration */
+ HDmemset(&udata, 0, sizeof udata);
+ udata.common.mesg = layout;
+ udata.io_info = &chk_io_info;
+ udata.idx_info = &idx_info;
+ udata.dims = curr_dims;
+ udata.down_chunks = down_chunks;
+ udata.elmts_per_chunk = elmts_per_chunk;
+ udata.chunk_space = chunk_space;
+ udata.hyper_start = hyper_start;
+ udata_init = TRUE;
+
+ /* Initialize the skip list that will hold the chunks outside the dimensions */
+ if(NULL == (udata.outside = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_CHUNK_DEFAULT_SKIPLIST_HEIGHT)))
+ HGOTO_ERROR(H5E_IO, H5E_CANTCREATE, FAIL, "can't create skip list for chunks outside new dimensions")
+
+ /* Iterate over the chunks */
+ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_prune_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve prune chunks from index")
+
+ /* Set up user data for skip list callback */
+ rm_info.idx_info = &idx_info;
+ rm_info.mesg = layout;
+
+ /* Destroy the skip list, deleting the chunks in the callback */
+ H5SL_destroy(udata.outside, H5D_chunk_prune_sl_rm_cb, &rm_info);
+
+ /* Reset any cached chunk info for this dataset */
+ H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last);
+
+done:
+ /* Release resources */
+ if(chunk_space && H5S_close(chunk_space) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
+ if(udata_init) {
+ if(udata.fb_info_init && H5D_fill_term(&udata.fb_info) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_prune_by_extent() */
+
+#ifdef H5_HAVE_PARALLEL
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_addrmap_cb
+ *
+ * Purpose: Callback when obtaining the chunk addresses for all existing chunks
+ *
+ * Return: Success: Non-negative
+ * Failure: Negative
+ *
+ * Programmer: Kent Yang
+ * Tuesday, November 15, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D_chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ H5D_chunk_it_ud2_t *udata = (H5D_chunk_it_ud2_t *)_udata; /* User data for callback */
+ unsigned rank = udata->common.mesg->u.chunk.ndims - 1; /* # of dimensions of dataset */
+ hsize_t chunk_index;
+ int ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_addrmap_cb)
+
+ /* Compute the index for this chunk */
+ if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index")
+
+ /* Set it in the userdata to return */
+ udata->chunk_addr[chunk_index] = chunk_rec->chunk_addr;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_chunk_addrmap_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_addrmap
+ *
+ * Purpose: Obtain the chunk addresses for all existing chunks
+ *
+ * Return: Success: Non-negative on succeed.
+ * Failure: negative value
+ *
+ * Programmer: Kent Yang
+ * November 15, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],
+ const hsize_t down_chunks[])
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ H5D_t *dset = io_info->dset; /* Local pointer to dataset info */
+ H5D_chunk_it_ud2_t udata; /* User data for iteration callback */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_addrmap, FAIL)
+
+ HDassert(dset);
+ HDassert(chunk_addr);
+ HDassert(down_chunks);
+
+ /* Set up user data for B-tree callback */
+ HDmemset(&udata, 0, sizeof(udata));
+ udata.common.mesg = &dset->shared->layout;
+ udata.down_chunks = down_chunks;
+ udata.chunk_addr = chunk_addr;
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = io_info->dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Iterate over chunks to build mapping of chunk addresses */
+ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_addrmap_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to iterate over chunk index to build address map")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_addrmap() */
+#endif /* H5_HAVE_PARALLEL */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_delete
+ *
+ * Purpose: Delete raw data storage for entire dataset (i.e. all chunks)
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, March 20, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_delete, FAIL)
+
+ /* Compose chunked index info struct */
+ idx_info.f = f;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = layout;
+
+ /* Check if the index has been created in the file */
+ if(H5F_addr_defined(layout->u.chunk.addr)) {
+ /* Delete the chunked storage information in the file */
+ if((layout->u.chunk.ops->delete)(&idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk index")
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_delete() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_update_cache
+ *
+ * Purpose: Update any cached chunks index values after the dataspace
+ * size has changed
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, May 29, 2004
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id)
+{
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
+ H5D_rdcc_ent_t *ent, *next; /*cache entry */
+ H5D_rdcc_ent_t *old_ent; /* Old cache entry */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ unsigned rank; /*current # of dimensions */
+ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */
+ hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */
+ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
+ unsigned u; /*counters */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_update_cache, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == dset->shared->layout.type);
+ HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
+
+ /* Get the rank */
+ rank = dset->shared->layout.u.chunk.ndims-1;
+ HDassert(rank > 0);
+
+ /* 1-D dataset's chunks can't have their index change */
+ if(rank == 1)
+ HGOTO_DONE(SUCCEED)
+
+ /* Go get the dimensions */
+ if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
+
+ /* Round up to the next integer # of chunks, to accomodate partial chunks */
+ for(u = 0; u < rank; u++)
+ chunks[u] = ((curr_dims[u] + dset->shared->layout.u.chunk.dim[u]) - 1) / dset->shared->layout.u.chunk.dim[u];
+
+ /* Get the "down" sizes for each dimension */
+ if(H5V_array_down(rank, chunks, down_chunks) < 0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Recompute the index for each cached chunk that is in a dataset */
+ for(ent = rdcc->head; ent; ent = next) {
+ hsize_t idx; /* Chunk index */
+ unsigned old_idx; /* Previous index number */
+
+ /* Get the pointer to the next cache entry */
+ next = ent->next;
+
+ /* Calculate the index of this chunk */
+ if(H5V_chunk_index(rank, ent->offset, dset->shared->layout.u.chunk.dim, down_chunks, &idx) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
+
+ /* Compute the index for the chunk entry */
+ old_idx = ent->idx; /* Save for later */
+ ent->idx = H5D_CHUNK_HASH(dset->shared, idx);
+
+ if(old_idx != ent->idx) {
+ /* Check if there is already a chunk at this chunk's new location */
+ old_ent = rdcc->slot[ent->idx];
+ if(old_ent != NULL) {
+ HDassert(old_ent->locked == 0);
+
+ /* Check if we are removing the entry we would walk to next */
+ if(old_ent == next)
+ next = old_ent->next;
+
+ /* Remove the old entry from the cache */
+ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, old_ent, TRUE) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
+ } /* end if */
+
+ /* Insert this chunk into correct location in hash table */
+ rdcc->slot[ent->idx] = ent;
+
+ /* Null out previous location */
+ rdcc->slot[old_idx] = NULL;
+ } /* end if */
+ } /* end for */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_update_cache() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_copy_cb
+ *
+ * Purpose: Copy chunked raw data from source file and insert to the
+ * index in the destination file
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Peter Cao
+ * August 20, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D_chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ H5D_chunk_it_ud3_t *udata = (H5D_chunk_it_ud3_t *)_udata; /* User data for callback */
+ H5D_chunk_ud_t udata_dst; /* User data about new destination chunk */
+ hbool_t is_vlen = FALSE; /* Whether datatype is variable-length */
+ hbool_t fix_ref = FALSE; /* Whether to fix up references in the dest. file */
+
+ /* General information about chunk copy */
+ void *bkg = udata->bkg; /* Background buffer for datatype conversion */
+ void *buf = udata->buf; /* Chunk buffer for I/O & datatype conversions */
+ size_t buf_size = udata->buf_size; /* Size of chunk buffer */
+ H5O_pline_t *pline = udata->pline; /* I/O pipeline for applying filters */
+
+ /* needed for commpressed variable length data */
+ hbool_t has_filters = FALSE; /* Whether chunk has filters */
+ size_t nbytes; /* Size of chunk in file (in bytes) */
+ H5Z_cb_t cb_struct; /* Filter failure callback struct */
+
+ int ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_copy_cb)
+
+ /* Get 'size_t' local value for number of bytes in chunk */
+ H5_ASSIGN_OVERFLOW(nbytes, chunk_rec->nbytes, uint32_t, size_t);
+
+ /* Check parameter for type conversion */
+ if(udata->do_convert) {
+ if(H5T_detect_class(udata->dt_src, H5T_VLEN) > 0)
+ is_vlen = TRUE;
+ else if((H5T_get_class(udata->dt_src, FALSE) == H5T_REFERENCE) && (udata->file_src != udata->idx_info_dst->f))
+ fix_ref = TRUE;
+ else
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements")
+ } /* end if */
+
+ /* Check for filtered chunks */
+ if(pline && pline->nused) {
+ has_filters = TRUE;
+ cb_struct.func = NULL; /* no callback function when failed */
+ } /* end if */
+
+ /* Resize the buf if it is too small to hold the data */
+ if(nbytes > buf_size) {
+ void *new_buf; /* New buffer for data */
+
+ /* Re-allocate memory for copying the chunk */
+ if(NULL == (new_buf = H5MM_realloc(udata->buf, nbytes)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
+ udata->buf = new_buf;
+ if(udata->bkg) {
+ if(NULL == (new_buf = H5MM_realloc(udata->bkg, nbytes)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
+ udata->bkg = new_buf;
+ if(!udata->cpy_info->expand_ref)
+ HDmemset((uint8_t *)udata->bkg + buf_size, 0, (size_t)(nbytes - buf_size));
+
+ bkg = udata->bkg;
+ } /* end if */
+
+ buf = udata->buf;
+ udata->buf_size = buf_size = nbytes;
+ } /* end if */
+
+ /* read chunk data from the source file */
+ if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
+
+ /* Need to uncompress variable-length & reference data elements */
+ if(has_filters && (is_vlen || fix_ref)) {
+ unsigned filter_mask = chunk_rec->filter_mask;
+
+ if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "data pipeline read failed")
+ } /* end if */
+
+ /* Perform datatype conversion, if necessary */
+ if(is_vlen) {
+ H5T_path_t *tpath_src_mem = udata->tpath_src_mem;
+ H5T_path_t *tpath_mem_dst = udata->tpath_mem_dst;
+ H5S_t *buf_space = udata->buf_space;
+ hid_t tid_src = udata->tid_src;
+ hid_t tid_dst = udata->tid_dst;
+ hid_t tid_mem = udata->tid_mem;
+ void *reclaim_buf = udata->reclaim_buf;
+ size_t reclaim_buf_size = udata->reclaim_buf_size;
+
+ /* Convert from source file to memory */
+ H5_CHECK_OVERFLOW(udata->nelmts, uint32_t, size_t);
+ if(H5T_convert(tpath_src_mem, tid_src, tid_mem, (size_t)udata->nelmts, (size_t)0, (size_t)0, buf, NULL, udata->idx_info_dst->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
+
+ /* Copy into another buffer, to reclaim memory later */
+ HDmemcpy(reclaim_buf, buf, reclaim_buf_size);
+
+ /* Set background buffer to all zeros */
+ HDmemset(bkg, 0, buf_size);
+
+ /* Convert from memory to destination file */
+ if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, udata->nelmts, (size_t)0, (size_t)0, buf, bkg, udata->idx_info_dst->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
+
+ /* Reclaim space from variable length data */
+ if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADITER, H5_ITER_ERROR, "unable to reclaim variable-length data")
+ } /* end if */
+ else if(fix_ref) {
+ /* Check for expanding references */
+ /* (background buffer has already been zeroed out, if not expanding) */
+ if(udata->cpy_info->expand_ref) {
+ size_t ref_count;
+
+ /* Determine # of reference elements to copy */
+ ref_count = nbytes / H5T_get_size(udata->dt_src);
+
+ /* Copy the reference elements */
+ if(H5O_copy_expand_ref(udata->file_src, buf, udata->idx_info_dst->dxpl_id, udata->idx_info_dst->f, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute")
+ } /* end if */
+
+ /* After fix ref, copy the new reference elements to the buffer to write out */
+ HDmemcpy(buf, bkg, buf_size);
+ } /* end if */
+
+ /* Set up destination chunk callback information for insertion */
+ udata_dst.common.mesg = udata->idx_info_dst->layout;
+ udata_dst.common.offset = chunk_rec->offset;
+ udata_dst.nbytes = chunk_rec->nbytes;
+ udata_dst.filter_mask = chunk_rec->filter_mask;
+ udata_dst.addr = HADDR_UNDEF;
+
+ /* Need to compress variable-length & reference data elements before writing to file */
+ if(has_filters && (is_vlen || fix_ref) ) {
+ if(H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed")
+ H5_ASSIGN_OVERFLOW(udata_dst.nbytes, nbytes, size_t, uint32_t);
+ udata->buf = buf;
+ udata->buf_size = buf_size;
+ } /* end if */
+
+ /* Insert chunk into the destination index */
+ if((udata->idx_info_dst->layout->u.chunk.ops->insert)(udata->idx_info_dst, &udata_dst) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk into index")
+
+ /* Write chunk data to destination file */
+ HDassert(H5F_addr_defined(udata_dst.addr));
+ if(H5F_block_write(udata->idx_info_dst->f, H5FD_MEM_DRAW, udata_dst.addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_copy_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_copy
+ *
+ * Purpose: Copy chunked storage from SRC file to DST file.
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Peter Cao
+ * August 20, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst,
+ H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info,
+ H5O_pline_t *pline, hid_t dxpl_id)
+{
+ H5D_chunk_it_ud3_t udata; /* User data for iteration callback */
+ H5D_chk_idx_info_t idx_info_dst; /* Dest. chunked index info */
+ H5D_chk_idx_info_t idx_info_src; /* Source chunked index info */
+ H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */
+ hid_t tid_src = -1; /* Datatype ID for source datatype */
+ hid_t tid_dst = -1; /* Datatype ID for destination datatype */
+ hid_t tid_mem = -1; /* Datatype ID for memory datatype */
+ size_t buf_size; /* Size of copy buffer */
+ size_t reclaim_buf_size; /* Size of reclaim buffer */
+ void *buf = NULL; /* Buffer for copying data */
+ void *bkg = NULL; /* Buffer for background during type conversion */
+ void *reclaim_buf = NULL; /* Buffer for reclaiming data */
+ H5S_t *buf_space = NULL; /* Dataspace describing buffer */
+ hid_t sid_buf = -1; /* ID for buffer dataspace */
+ uint32_t nelmts = 0; /* Number of elements in buffer */
+ hbool_t do_convert = FALSE; /* Indicate that type conversions should be performed */
+ hbool_t copy_setup_done = FALSE; /* Indicate that 'copy setup' is done */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_copy, FAIL)
+
+ /* Check args */
+ HDassert(f_src);
+ HDassert(f_dst);
+ HDassert(layout_src && H5D_CHUNKED == layout_src->type);
+ HDassert(layout_dst && H5D_CHUNKED == layout_dst->type);
+ HDassert(dt_src);
+
+ /* Compose source & dest chunked index info structs */
+ idx_info_src.f = f_src;
+ idx_info_src.dxpl_id = dxpl_id;
+ idx_info_src.layout = layout_src;
+
+ idx_info_dst.f = f_dst;
+ idx_info_dst.dxpl_id = dxpl_id;
+ idx_info_dst.layout = layout_dst;
+
+ /* Call the index-specific "copy setup" routine */
+ if((layout_src->u.chunk.ops->copy_setup)(&idx_info_src, &idx_info_dst) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up index-specific chunk copying information")
+ HDassert(H5F_addr_defined(layout_dst->u.chunk.addr));
+ copy_setup_done = TRUE;
+
+ /* Create datatype ID for src datatype */
+ if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
+
+ /* If there's a VLEN source datatype, set up type conversion information */
+ if(H5T_detect_class(dt_src, H5T_VLEN) > 0) {
+ H5T_t *dt_dst; /* Destination datatype */
+ H5T_t *dt_mem; /* Memory datatype */
+ size_t mem_dt_size; /* Memory datatype size */
+ size_t tmp_dt_size; /* Temp. datatype size */
+ size_t max_dt_size; /* Max atatype size */
+ hsize_t buf_dim; /* Dimension for buffer */
+ unsigned u;
+
+ /* create a memory copy of the variable-length datatype */
+ if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
+ if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
+
+ /* create variable-length datatype at the destinaton file */
+ if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
+ if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
+ if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
+
+ /* Set up the conversion functions */
+ if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
+ if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
+
+ /* Determine largest datatype size */
+ if(0 == (max_dt_size = H5T_get_size(dt_src)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+ if(0 == (mem_dt_size = H5T_get_size(dt_mem)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+ max_dt_size = MAX(max_dt_size, mem_dt_size);
+ if(0 == (tmp_dt_size = H5T_get_size(dt_dst)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+ max_dt_size = MAX(max_dt_size, tmp_dt_size);
+
+ /* Compute the number of elements per chunk */
+ nelmts = 1;
+ for(u = 0; u < (layout_src->u.chunk.ndims - 1); u++)
+ nelmts *= layout_src->u.chunk.dim[u];
+
+ /* Create the space and set the initial extent */
+ buf_dim = nelmts;
+ if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
+
+ /* Atomize */
+ if((sid_buf = H5I_register(H5I_DATASPACE, buf_space)) < 0) {
+ H5S_close(buf_space);
+ HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
+ } /* end if */
+
+ /* Set initial buffer sizes */
+ buf_size = nelmts * max_dt_size;
+ reclaim_buf_size = nelmts * mem_dt_size;
+
+ /* Allocate memory for reclaim buf */
+ if(NULL == (reclaim_buf = H5MM_malloc(reclaim_buf_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
+
+ /* Indicate that type conversion should be performed */
+ do_convert = TRUE;
+ } /* end if */
+ else {
+ if(H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) {
+ /* Indicate that type conversion should be performed */
+ do_convert = TRUE;
+ } /* end if */
+
+ H5_ASSIGN_OVERFLOW(buf_size, layout_src->u.chunk.size, uint32_t, size_t);
+ reclaim_buf_size = 0;
+ } /* end else */
+
+ /* Set up conversion buffer, if appropriate */
+ if(do_convert) {
+ /* Allocate background memory for converting the chunk */
+ if(NULL == (bkg = H5MM_malloc(buf_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
+
+ /* Check for reference datatype and no expanding references & clear background buffer */
+ if(!cpy_info->expand_ref &&
+ ((H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) && (f_src != f_dst)))
+ /* Reset value to zero */
+ HDmemset(bkg, 0, buf_size);
+ } /* end if */
+
+ /* Allocate memory for copying the chunk */
+ if(NULL == (buf = H5MM_malloc(buf_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
+
+ /* Initialize the callback structure for the source */
+ HDmemset(&udata, 0, sizeof udata);
+ udata.common.mesg = layout_src;
+ udata.file_src = f_src;
+ udata.idx_info_dst = &idx_info_dst;
+ udata.buf = buf;
+ udata.bkg = bkg;
+ udata.buf_size = buf_size;
+ udata.tid_src = tid_src;
+ udata.tid_mem = tid_mem;
+ udata.tid_dst = tid_dst;
+ udata.dt_src = dt_src;
+ udata.do_convert = do_convert;
+ udata.tpath_src_mem = tpath_src_mem;
+ udata.tpath_mem_dst = tpath_mem_dst;
+ udata.reclaim_buf = reclaim_buf;
+ udata.reclaim_buf_size = reclaim_buf_size;
+ udata.buf_space = buf_space;
+ udata.nelmts = nelmts;
+ udata.pline = pline;
+ udata.cpy_info = cpy_info;
+
+ /* Iterate over chunks to copy data */
+ if((layout_src->u.chunk.ops->iterate)(&idx_info_src, H5D_chunk_copy_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to copy data")
+
+ /* I/O buffers may have been re-allocated */
+ buf = udata.buf;
+ bkg = udata.bkg;
+
+done:
+ if(sid_buf > 0)
+ if(H5I_dec_ref(sid_buf) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID")
+ if(tid_src > 0)
+ if(H5I_dec_ref(tid_src) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+ if(tid_dst > 0)
+ if(H5I_dec_ref(tid_dst) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+ if(tid_mem > 0)
+ if(H5I_dec_ref(tid_mem) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+ if(buf)
+ H5MM_xfree(buf);
+ if(bkg)
+ H5MM_xfree(bkg);
+ if(reclaim_buf)
+ H5MM_xfree(reclaim_buf);
+
+ /* Clean up any index information */
+ if(copy_setup_done)
+ if((layout_src->u.chunk.ops->copy_shutdown)(layout_src, layout_dst) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to shut down index copying info")
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_copy() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_bh_size
+ *
+ * Purpose: Retrieve the amount of index storage for chunked dataset
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * June 8, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout,
+ hsize_t *index_size)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_bh_info, FAIL)
+
+ /* Check args */
+ HDassert(f);
+ HDassert(layout);
+ HDassert(index_size);
+
+ /* Compose chunked index info struct */
+ idx_info.f = f;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = layout;
+
+ /* Get size of index structure */
+ if((layout->u.chunk.ops->size)(&idx_info, index_size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve chunk index info")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_bh_info() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_istore_iter_dump
+ *
+ * Purpose: If the UDATA.STREAM member is non-null then debugging
+ * information is written to that stream.
+ *
+ * Return: Success: Non-negative
+ *
+ * Failure: Negative
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static int
+H5D_chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ H5D_chunk_it_ud4_t *udata = (H5D_chunk_it_ud4_t *)_udata; /* User data from caller */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_dump_index_cb)
+
+ if(udata->stream) {
+ unsigned u; /* Local index variable */
+
+ /* Print header if not already displayed */
+ if(!udata->header_displayed) {
+ HDfprintf(udata->stream, " Flags Bytes Address Logical Offset\n");
+ HDfprintf(udata->stream, " ========== ======== ========== ==============================\n");
+
+ /* Set flag that the headers has been printed */
+ udata->header_displayed = TRUE;
+ } /* end if */
+
+ /* Print information about this chunk */
+ HDfprintf(udata->stream, " 0x%08x %8Zu %10a [", chunk_rec->filter_mask, chunk_rec->nbytes, chunk_rec->chunk_addr);
+ for(u = 0; u < udata->ndims; u++)
+ HDfprintf(udata->stream, "%s%Hd", (u ? ", " : ""), chunk_rec->offset[u]);
+ HDfputs("]\n", udata->stream);
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(H5_ITER_CONT)
+} /* H5D_chunk_dump_index_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_dump_index
+ *
+ * Purpose: Prints information about the storage index to the specified
+ * stream.
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 28, 1999
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream)
+{
+ H5D_chunk_it_ud4_t udata; /* User data for callback */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_dump_index, FAIL)
+
+ /* Sanity check */
+ HDassert(dset);
+
+ /* Only display info if stream is defined */
+ if(stream) {
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+
+ /* Display address of index */
+ HDfprintf(stream, " Address: %a\n", dset->shared->layout.u.chunk.addr);
+
+ /* Set up user data for callback */
+ udata.stream = stream;
+ udata.header_displayed = FALSE;
+ udata.ndims = dset->shared->layout.u.chunk.ndims;
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Iterate over index and dump chunk info */
+ if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_dump_index_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to dump chunk info")
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_dump_index() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_dest
+ *
+ * Purpose: Destroy the entire chunk cache by flushing dirty entries,
+ * preempting all entries, and freeing the cache itself.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Dataset's chunk cache */
+ H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Pointer to current & next cache entries */
+ int nerrors = 0; /* Accumulated count of errors */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_dest, FAIL)
+
+ HDassert(f);
+ HDassert(dset);
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Flush all the cached chunks */
+ for(ent = rdcc->head; ent; ent = next) {
+ next = ent->next;
+ if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ nerrors++;
+ } /* end for */
+ if(nerrors)
+ HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
+
+ /* Release cache structures */
+ if(rdcc->slot)
+ H5FL_SEQ_FREE(H5D_rdcc_ent_ptr_t, rdcc->slot);
+ HDmemset(rdcc, 0, sizeof(H5D_rdcc_t));
+
+ /* Compose chunked index info struct */
+ idx_info.f = f;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.layout = &dset->shared->layout;
+
+ /* Free any index structures */
+ if((dset->shared->layout.u.chunk.ops->dest)(&idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_dest() */
+
+#ifdef H5D_CHUNK_DEBUG
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_stats
+ *
+ * Purpose: Print raw data cache statistics to the debug stream. If
+ * HEADERS is non-zero then print table column headers,
+ * otherwise assume that the H5AC layer has already printed them.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, May 21, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_chunk_stats(const H5D_t *dset, hbool_t headers)
+{
+ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
+ double miss_rate;
+ char ascii[32];
+ herr_t ret_value=SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_chunk_stats, FAIL)
+
+ if (!H5DEBUG(AC))
+ HGOTO_DONE(SUCCEED)
+
+ if (headers) {
+ fprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n");
+ fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n",
+ "Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes");
+ fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n",
+ "-----", "----", "------", "--------", "-----", "-------");
+ }
+
+#ifdef H5AC_DEBUG
+ if (H5DEBUG(AC)) headers = TRUE;
+#endif
+
+ if (headers) {
+ if (rdcc->nhits>0 || rdcc->nmisses>0) {
+ miss_rate = 100.0 * rdcc->nmisses /
+ (rdcc->nhits + rdcc->nmisses);
+ } else {
+ miss_rate = 0.0;
+ }
+ if (miss_rate > 100) {
+ sprintf(ascii, "%7d%%", (int) (miss_rate + 0.5));
+ } else {
+ sprintf(ascii, "%7.2f%%", miss_rate);
+ }
+
+ fprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n",
+ "raw data chunks", rdcc->nhits, rdcc->nmisses, ascii,
+ rdcc->ninits, (long)(rdcc->nflushes)-(long)(rdcc->ninits));
+ }
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_chunk_stats() */
+#endif /* H5D_CHUNK_DEBUG */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D_null_readvv
*
* Purpose: Performs "no-op" I/O operation, advancing through two I/O
diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c
index c3abab6..0458e74 100644
--- a/src/H5Dcompact.c
+++ b/src/H5Dcompact.c
@@ -57,6 +57,8 @@
/********************/
/* Layout operation callbacks */
+static herr_t H5D_compact_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset,
+ const H5P_genplist_t *dc_plist);
static herr_t H5D_compact_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *cm);
@@ -74,6 +76,7 @@ static ssize_t H5D_compact_writevv(const H5D_io_info_t *io_info,
/* Compact storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_COMPACT[1] = {{
+ H5D_compact_new,
H5D_compact_io_init,
H5D_contig_read,
H5D_contig_write,
@@ -149,6 +152,53 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5D_compact_new
+ *
+ * Purpose: Constructs new compact layout information for dataset
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, May 22, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static herr_t
+H5D_compact_new(H5F_t *f, hid_t UNUSED dxpl_id, H5D_t *dset,
+ const H5P_genplist_t UNUSED *dc_plist)
+{
+ hssize_t tmp_size; /* Temporary holder for raw data size */
+ hsize_t comp_data_size; /* Size of compact data */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_compact_new)
+
+ /* Sanity checks */
+ HDassert(f);
+ HDassert(dset);
+ HDassert(dc_plist);
+
+ /*
+ * Compact dataset is stored in dataset object header message of
+ * layout.
+ */
+ tmp_size = H5S_GET_EXTENT_NPOINTS(dset->shared->space) * H5T_get_size(dset->shared->type);
+ H5_ASSIGN_OVERFLOW(dset->shared->layout.u.compact.size, tmp_size, hssize_t, size_t);
+
+ /* Verify data size is smaller than maximum header message size
+ * (64KB) minus other layout message fields.
+ */
+ comp_data_size = H5O_MESG_MAX_SIZE - H5O_layout_meta_size(f, &(dset->shared->layout));
+ if(dset->shared->layout.u.compact.size > comp_data_size)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "compact dataset size is bigger than header message maximum size")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_compact_new() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D_compact_io_init
*
* Purpose: Performs initialization before any sort of I/O on the raw data
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c
index 1a3fda5..14ad520 100644
--- a/src/H5Dcontig.c
+++ b/src/H5Dcontig.c
@@ -61,6 +61,8 @@
/********************/
/* Layout operation callbacks */
+static herr_t H5D_contig_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset,
+ const H5P_genplist_t *dc_plist);
static herr_t H5D_contig_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *cm);
@@ -76,6 +78,7 @@ static herr_t H5D_contig_write_one(H5D_io_info_t *io_info, hsize_t offset,
/* Contiguous storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_CONTIG[1] = {{
+ H5D_contig_new,
H5D_contig_io_init,
H5D_contig_read,
H5D_contig_write,
@@ -102,7 +105,7 @@ H5FL_BLK_EXTERN(type_conv);
/*-------------------------------------------------------------------------
- * Function: H5D_contig_create
+ * Function: H5D_contig_alloc
*
* Purpose: Allocate file space for a contiguously stored dataset
*
@@ -114,11 +117,11 @@ H5FL_BLK_EXTERN(type_conv);
*-------------------------------------------------------------------------
*/
herr_t
-H5D_contig_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */ )
+H5D_contig_alloc(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */ )
{
herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5D_contig_create, FAIL)
+ FUNC_ENTER_NOAPI(H5D_contig_alloc, FAIL)
/* check args */
HDassert(f);
@@ -130,7 +133,7 @@ H5D_contig_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */ )
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_contig_create */
+} /* end H5D_contig_alloc */
/*-------------------------------------------------------------------------
@@ -355,6 +358,63 @@ H5D_contig_get_addr(const H5D_t *dset)
/*-------------------------------------------------------------------------
+ * Function: H5D_contig_new
+ *
+ * Purpose: Constructs new contiguous layout information for dataset
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, May 22, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static herr_t
+H5D_contig_new(H5F_t *f, hid_t UNUSED dxpl_id, H5D_t *dset,
+ const H5P_genplist_t UNUSED *dc_plist)
+{
+ const H5T_t *type = dset->shared->type; /* Convenience pointer to dataset's datatype */
+ hssize_t tmp_size; /* Temporary holder for raw data size */
+ hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */
+ hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
+ int ndims; /* Rank of dataspace */
+ int i; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_contig_new)
+
+ /* Sanity checks */
+ HDassert(f);
+ HDassert(dset);
+
+ /*
+ * The maximum size of the dataset cannot exceed the storage size.
+ * Also, only the slowest varying dimension of a simple data space
+ * can be extendible (currently only for external data storage).
+ */
+ dset->shared->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */
+
+ /* Check for invalid dataset dimensions */
+ if((ndims = H5S_get_simple_extent_dims(dset->shared->space, dim, max_dim)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage")
+ for(i = 0; i < ndims; i++)
+ if(max_dim[i] > dim[i])
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "extendible contiguous non-external dataset")
+
+ /* Compute the total size of dataset */
+ tmp_size = H5S_GET_EXTENT_NPOINTS(dset->shared->space) * H5T_get_size(type);
+ H5_ASSIGN_OVERFLOW(dset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t);
+
+ /* Get the sieve buffer size for this dataset */
+ dset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(f);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_contig_new() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D_contig_io_init
*
* Purpose: Performs initialization before any sort of I/O on the raw data
@@ -1137,7 +1197,7 @@ H5D_contig_copy(H5F_t *f_src, const H5O_layout_t *layout_src, H5F_t *f_dst,
HDassert(dt_src);
/* Allocate space for destination raw data */
- if(H5D_contig_create(f_dst, dxpl_id, layout_dst) < 0)
+ if(H5D_contig_alloc(f_dst, dxpl_id, layout_dst) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to allocate contiguous storage")
/* Set up number of bytes to copy, and initial buffer size */
diff --git a/src/H5Ddbg.c b/src/H5Ddbg.c
index 4ca5b21..714c2e3 100644
--- a/src/H5Ddbg.c
+++ b/src/H5Ddbg.c
@@ -113,7 +113,7 @@ H5Ddebug(hid_t dset_id)
/* Print B-tree information */
if(H5D_CHUNKED == dset->shared->layout.type)
- (void)H5D_istore_dump_btree(dset->oloc.file, H5AC_dxpl_id, stdout, dset->shared->layout.u.chunk.ndims, dset->shared->layout.u.chunk.addr);
+ (void)H5D_chunk_dump_index(dset, H5AC_dxpl_id, stdout);
else if(H5D_CONTIGUOUS == dset->shared->layout.type)
HDfprintf(stdout, " %-10s %a\n", "Address:", dset->shared->layout.u.contig.addr);
diff --git a/src/H5Ddeprec.c b/src/H5Ddeprec.c
index fd1d2e8..a07c86f 100644
--- a/src/H5Ddeprec.c
+++ b/src/H5Ddeprec.c
@@ -346,13 +346,13 @@ H5D_extend(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id)
if(changed) {
/* Update the index values for the cached chunks for this dataset */
if(H5D_CHUNKED == dataset->shared->layout.type)
- if(H5D_istore_update_cache(dataset, dxpl_id) < 0)
+ if(H5D_chunk_update_cache(dataset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices")
/* Allocate space for the new parts of the dataset, if appropriate */
fill = &dataset->shared->dcpl_cache.fill;
if(fill->alloc_time == H5D_ALLOC_TIME_EARLY)
- if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_EXTEND, FALSE) < 0)
+ if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_EXTEND, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value")
/* Mark the dataspace as dirty, for later writing to the file */
diff --git a/src/H5Defl.c b/src/H5Defl.c
index 7dac29b..15bcd60 100644
--- a/src/H5Defl.c
+++ b/src/H5Defl.c
@@ -49,6 +49,8 @@
/********************/
/* Layout operation callbacks */
+static herr_t H5D_efl_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset,
+ const H5P_genplist_t *dc_plist);
static herr_t H5D_efl_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *cm);
@@ -72,6 +74,7 @@ static herr_t H5D_efl_write(const H5O_efl_t *efl, haddr_t addr, size_t size,
/* External File List (EFL) storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_EFL[1] = {{
+ H5D_efl_new,
H5D_efl_io_init,
H5D_contig_read,
H5D_contig_write,
@@ -92,6 +95,77 @@ const H5D_layout_ops_t H5D_LOPS_EFL[1] = {{
/*-------------------------------------------------------------------------
+ * Function: H5D_efl_new
+ *
+ * Purpose: Constructs new EFL layout information for dataset
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, May 22, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_efl_new(H5F_t *f, hid_t UNUSED dxpl_id, H5D_t *dset,
+ const H5P_genplist_t *dc_plist)
+{
+ const H5T_t *type = dset->shared->type; /* Convenience pointer to dataset's datatype */
+ hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */
+ hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
+ hssize_t tmp_size; /* Temporary holder for raw data size */
+ hsize_t max_points; /* Maximum elements */
+ hsize_t max_storage; /* Maximum storage size */
+ int ndims; /* Rank of dataspace */
+ int i; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_efl_new)
+
+ /* Sanity checks */
+ HDassert(f);
+ HDassert(dset);
+ HDassert(dc_plist);
+
+ /*
+ * The maximum size of the dataset cannot exceed the storage size.
+ * Also, only the slowest varying dimension of a simple data space
+ * can be extendible (currently only for external data storage).
+ */
+ dset->shared->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */
+
+ /* Check for invalid dataset dimensions */
+ if((ndims = H5S_get_simple_extent_dims(dset->shared->space, dim, max_dim)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage")
+ for(i = 1; i < ndims; i++)
+ if(max_dim[i] > dim[i])
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "only the first dimension can be extendible")
+
+ /* Check for storage overflows */
+ max_points = H5S_get_npoints_max(dset->shared->space);
+ max_storage = H5O_efl_total_size(&dset->shared->dcpl_cache.efl);
+ if(H5S_UNLIMITED == max_points) {
+ if(H5O_EFL_UNLIMITED != max_storage)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unlimited data space but finite storage")
+ } /* end if */
+ else if(max_points * H5T_get_size(type) < max_points)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data space * type size overflowed")
+ else if(max_points * H5T_get_size(type) > max_storage)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data space size exceeds external storage size")
+
+ /* Compute the total size of dataset */
+ tmp_size = H5S_GET_EXTENT_NPOINTS(dset->shared->space) * H5T_get_size(type);
+ H5_ASSIGN_OVERFLOW(dset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t);
+
+ /* Get the sieve buffer size for this dataset */
+ dset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(f);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_efl_new() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D_efl_io_init
*
* Purpose: Performs initialization before any sort of I/O on the raw data
diff --git a/src/H5Dint.c b/src/H5Dint.c
index f8577cc..162a14f 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -710,17 +710,21 @@ H5D_set_io_ops(H5D_t *dataset)
switch(dataset->shared->layout.type) {
case H5D_CONTIGUOUS:
if(dataset->shared->dcpl_cache.efl.nused > 0)
- dataset->shared->layout_ops = H5D_LOPS_EFL;
+ dataset->shared->layout.ops = H5D_LOPS_EFL;
else
- dataset->shared->layout_ops = H5D_LOPS_CONTIG;
+ dataset->shared->layout.ops = H5D_LOPS_CONTIG;
break;
case H5D_CHUNKED:
- dataset->shared->layout_ops = H5D_LOPS_CHUNK;
+ dataset->shared->layout.ops = H5D_LOPS_CHUNK;
+
+ /* Set the chunk operations */
+ /* (Only "istore" indexing type currently supported */
+ dataset->shared->layout.u.chunk.ops = H5D_COPS_ISTORE;
break;
case H5D_COMPACT:
- dataset->shared->layout_ops = H5D_LOPS_COMPACT;
+ dataset->shared->layout.ops = H5D_LOPS_COMPACT;
break;
default:
@@ -831,6 +835,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset)
/* Create an object header for the dataset */
if(H5O_create(file, dxpl_id, ohdr_size, dset->shared->dcpl_id, oloc/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header")
+ HDassert(file == dset->oloc.file);
/* Get a pointer to the object header itself */
if((oh = H5O_protect(oloc, dxpl_id)) == NULL)
@@ -877,7 +882,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset)
* allocation until later.
*/
if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY)
- if(H5D_alloc_storage(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE) < 0)
+ if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
/* Update external storage message, if it's used */
@@ -1000,13 +1005,10 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
{
const H5T_t *type; /* Datatype for dataset */
H5D_t *new_dset = NULL;
- int i, ndims;
- unsigned chunk_ndims = 0; /* Dimensionality of chunk */
H5P_genplist_t *dc_plist = NULL; /* New Property list */
hbool_t has_vl_type = FALSE; /* Flag to indicate a VL-type for dataset */
- hbool_t chunk_init = FALSE; /* Flag to indicate that chunk information was initialized */
+ hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */
H5G_loc_t dset_loc; /* Dataset location */
- unsigned u; /* Local index variable */
H5D_t *ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_create, NULL)
@@ -1101,10 +1103,6 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
if(IS_H5FD_MPI(file) && pline->nused > 0)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet")
- /* Chunked datasets are non-default, so retrieve their info here */
- if(H5P_get(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk dimensions")
-
/* Get the dataset's external file list information */
if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->shared->dcpl_cache.efl) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list")
@@ -1125,140 +1123,17 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
if(IS_H5FD_MPI(file))
new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY;
- switch(new_dset->shared->layout.type) {
- case H5D_CONTIGUOUS:
- {
- hssize_t tmp_size; /* Temporary holder for raw data size */
- hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */
- hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
-
- /*
- * The maximum size of the dataset cannot exceed the storage size.
- * Also, only the slowest varying dimension of a simple data space
- * can be extendible (currently only for external data storage).
- */
- new_dset->shared->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */
-
- if((ndims = H5S_get_simple_extent_dims(new_dset->shared->space, dim, max_dim)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage")
- for(i = 1; i < ndims; i++)
- if(max_dim[i] > dim[i])
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible")
- if(new_dset->shared->dcpl_cache.efl.nused > 0) {
- hsize_t max_points = H5S_get_npoints_max(new_dset->shared->space);
- hsize_t max_storage = H5O_efl_total_size(&new_dset->shared->dcpl_cache.efl);
-
- if(H5S_UNLIMITED == max_points) {
- if(H5O_EFL_UNLIMITED != max_storage)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage")
- } else if(max_points * H5T_get_size(type) < max_points) {
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed")
- } else if(max_points * H5T_get_size(type) > max_storage) {
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size")
- }
- } /* end if */
- else {
- if(ndims > 0 && max_dim[0] > dim[0])
- HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset")
- } /* end else */
-
- /* Compute the total size of a chunk */
- tmp_size = H5S_GET_EXTENT_NPOINTS(new_dset->shared->space) * H5T_get_size(new_dset->shared->type);
- H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t);
-
- /* Get the sieve buffer size for this dataset */
- new_dset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(file);
- } /* end case */
- break;
-
- case H5D_CHUNKED:
- {
- hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
- uint64_t chunk_size; /* Size of chunk in bytes */
-
- /* Set up layout information */
- if((ndims = H5S_GET_EXTENT_NDIMS(new_dset->shared->space)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank")
- new_dset->shared->layout.u.chunk.ndims = (unsigned)ndims + 1;
- HDassert((unsigned)(new_dset->shared->layout.u.chunk.ndims) <= NELMTS(new_dset->shared->layout.u.chunk.dim));
-
- /* Initialize to no address */
- new_dset->shared->layout.u.chunk.addr = HADDR_UNDEF;
-
- /*
- * Chunked storage allows any type of data space extension, so we
- * don't even bother checking.
- */
- if(chunk_ndims != (unsigned)ndims)
- HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space")
- if(new_dset->shared->dcpl_cache.efl.nused > 0)
- HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout")
-
- /*
- * The chunk size of a dimension with a fixed size cannot exceed
- * the maximum dimension size
- */
- if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, new_dset->shared->layout.u.chunk.dim) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size")
- new_dset->shared->layout.u.chunk.dim[new_dset->shared->layout.u.chunk.ndims-1] = H5T_get_size(new_dset->shared->type);
-
- if(H5S_get_simple_extent_dims(new_dset->shared->space, NULL, max_dim) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions")
- for(u = 0; u < new_dset->shared->layout.u.chunk.ndims - 1; u++)
- if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < new_dset->shared->layout.u.chunk.dim[u])
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions")
-
- /* Compute the total size of a chunk */
- /* (Use 64-bit value to ensure that we can detect >4GB chunks) */
- for(u = 1, chunk_size = (uint64_t)new_dset->shared->layout.u.chunk.dim[0]; u < new_dset->shared->layout.u.chunk.ndims; u++)
- chunk_size *= (uint64_t)new_dset->shared->layout.u.chunk.dim[u];
-
- /* Check for chunk larger than can be represented in 32-bits */
- /* (Chunk size is encoded in 32-bit value in v1 B-tree records) */
- if(chunk_size > (uint64_t)0xffffffff)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be < 4GB")
-
- /* Retain computed chunk size */
- H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.chunk.size, chunk_size, uint64_t, uint32_t);
-
- /* Initialize the chunk cache for the dataset */
- if(H5D_istore_init(file, new_dset) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize chunk cache")
-
- /* Indicate that the chunk information was initialized */
- chunk_init = TRUE;
- } /* end case */
- break;
-
- case H5D_COMPACT:
- {
- hssize_t tmp_size; /* Temporary holder for raw data size */
- hsize_t comp_data_size;
-
- /*
- * Compact dataset is stored in dataset object header message of
- * layout.
- */
- tmp_size = H5S_GET_EXTENT_NPOINTS(space) * H5T_get_size(new_dset->shared->type);
- H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.compact.size, tmp_size, hssize_t, size_t);
-
- /* Verify data size is smaller than maximum header message size
- * (64KB) minus other layout message fields.
- */
- comp_data_size = H5O_MESG_MAX_SIZE - H5O_layout_meta_size(file, &(new_dset->shared->layout));
- if(new_dset->shared->layout.u.compact.size > comp_data_size)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size")
- } /* end case */
- break;
-
- default:
- HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet")
- } /* end switch */ /*lint !e788 All appropriate cases are covered */
-
/* Set the dataset's I/O operations */
if(H5D_set_io_ops(new_dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize I/O operations")
+ /* Create the layout information for the new dataset */
+ if((new_dset->shared->layout.ops->new)(file, dxpl_id, new_dset, dc_plist) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize layout information")
+
+ /* Indicate that the layout information was initialized */
+ layout_init = TRUE;
+
/* Update the dataset's object header info. */
if(H5D_update_oh_info(file, dxpl_id, new_dset) != SUCCEED)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache")
@@ -1277,8 +1152,8 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
done:
if(!ret_value && new_dset && new_dset->shared) {
if(new_dset->shared) {
- if(new_dset->shared->layout.type == H5D_CHUNKED && chunk_init) {
- if(H5D_istore_dest(new_dset,H5AC_dxpl_id) < 0)
+ if(new_dset->shared->layout.type == H5D_CHUNKED && layout_init) {
+ if(H5D_chunk_dest(file, dxpl_id, new_dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy chunk cache")
} /* end if */
if(new_dset->shared->space) {
@@ -1482,6 +1357,30 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message")
if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout.type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout")
+
+ /* Get the external file list message, which might not exist. Space is
+ * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */
+ if((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
+ || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) {
+ if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
+ if(msg_exists) {
+ /* Retrieve the EFL message */
+ if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
+
+ /* Set the EFL info in the property list */
+ if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list")
+
+ /* Set the dataset's I/O operations */
+ dataset->shared->layout.ops = H5D_LOPS_EFL;
+ } /* end if */
+ } /* end if */
+
+ /* Sanity check that the layout operations are set up */
+ HDassert(dataset->shared->layout.ops);
+
switch(dataset->shared->layout.type) {
case H5D_CONTIGUOUS:
/* Compute the size of the contiguous storage for versions of the
@@ -1516,7 +1415,7 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk size")
/* Initialize the chunk cache for the dataset */
- if(H5D_istore_init(dataset->oloc.file, dataset) < 0)
+ if(H5D_chunk_init(dataset->oloc.file, dxpl_id, dataset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache")
}
break;
@@ -1584,27 +1483,6 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set allocation time state")
} /* end if */
- /* Get the external file list message, which might not exist. Space is
- * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */
- if((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
- || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) {
- if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
- if(msg_exists) {
- /* Retrieve the EFL message */
- if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
-
- /* Set the EFL info in the property list */
- if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list")
- } /* end if */
- } /* end if */
-
- /* Set the dataset's I/O operations */
- if(H5D_set_io_ops(dataset) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize I/O operations")
-
/*
* Make sure all storage is properly initialized.
* This is important only for parallel I/O where the space must
@@ -1614,7 +1492,7 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id)
&& ((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
&& IS_H5FD_MPI(dataset->oloc.file)) {
- if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_OPEN, FALSE) < 0)
+ if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_OPEN, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage")
} /* end if */
@@ -1671,9 +1549,9 @@ H5D_close(H5D_t *dataset)
HDassert(dataset->shared->fo_count >0);
/* Dump debugging info */
-#ifdef H5D_ISTORE_DEBUG
- H5D_istore_stats(dataset, FALSE);
-#endif /* H5F_ISTORE_DEBUG */
+#ifdef H5D_CHUNK_DEBUG
+ H5D_chunk_stats(dataset, FALSE);
+#endif /* H5D_CHUNK_DEBUG */
dataset->shared->fo_count--;
if(dataset->shared->fo_count == 0) {
@@ -1714,7 +1592,7 @@ H5D_close(H5D_t *dataset)
} /* end if */
/* Flush and destroy chunks in the cache */
- if(H5D_istore_dest(dataset, H5AC_dxpl_id) < 0)
+ if(H5D_chunk_dest(dataset->oloc.file, H5AC_dxpl_id, dataset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
break;
@@ -1899,10 +1777,11 @@ H5D_get_file(const H5D_t *dset)
*-------------------------------------------------------------------------
*/
herr_t
-H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc,
+H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_alloc,
hbool_t full_overwrite)
{
- struct H5O_layout_t *layout; /* The dataset's layout information */
+ H5F_t *f = dset->oloc.file; /* The dataset's file pointer */
+ H5O_layout_t *layout; /* The dataset's layout information */
hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */
hbool_t addr_set = FALSE; /* Flag to indicate that the dataset's storage address was set */
herr_t ret_value = SUCCEED; /* Return value */
@@ -1910,8 +1789,8 @@ H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc
FUNC_ENTER_NOAPI_NOINIT(H5D_alloc_storage)
/* check args */
- HDassert(f);
HDassert(dset);
+ HDassert(f);
/* If the data is stored in external files, don't set an address for the layout
* We assume that external storage is already
@@ -1925,7 +1804,7 @@ H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc
case H5D_CONTIGUOUS:
if(!H5F_addr_defined(layout->u.contig.addr)) {
/* Reserve space in the file for the entire array */
- if(H5D_contig_create(f, dxpl_id, layout/*out*/) < 0)
+ if(H5D_contig_alloc(f, dxpl_id, layout/*out*/) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage")
/* Indicate that we set the storage addr */
@@ -1939,7 +1818,7 @@ H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc
case H5D_CHUNKED:
if(!H5F_addr_defined(layout->u.chunk.addr)) {
/* Create the root of the B-tree that describes chunked storage */
- if(H5D_istore_create(f, dxpl_id, layout/*out*/) < 0)
+ if(H5D_chunk_create(dset /*in,out*/, dxpl_id) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
/* Indicate that we set the storage addr */
@@ -2079,7 +1958,7 @@ H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id)
* Allocate file space
* for all chunks now and initialize each chunk with the fill value.
*/
- if(H5D_istore_allocate(dset, dxpl_id, full_overwrite) < 0)
+ if(H5D_chunk_allocate(dset, dxpl_id, full_overwrite) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset")
break;
@@ -2122,7 +2001,8 @@ H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id)
if(dset->shared->layout.u.chunk.addr == HADDR_UNDEF)
ret_value = 0;
else
- ret_value = H5D_istore_allocated(dset, dxpl_id);
+ if(H5D_chunk_allocated(dset, dxpl_id, &ret_value) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't retrieve chunked dataset allocated size")
break;
case H5D_CONTIGUOUS:
@@ -2428,7 +2308,7 @@ done:
* Function: H5D_set_extent
*
* Purpose: Based on H5D_extend, allows change to a lower dimension,
- * calls H5S_set_extent and H5D_istore_prune_by_extent instead
+ * calls H5S_set_extent and H5D_chunk_prune_by_extent instead
*
* Return: Non-negative on success, negative on failure
*
@@ -2491,12 +2371,12 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id)
*/
/* Update the index values for the cached chunks for this dataset */
if(H5D_CHUNKED == dset->shared->layout.type)
- if(H5D_istore_update_cache(dset, dxpl_id) < 0)
+ if(H5D_chunk_update_cache(dset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices")
/* Allocate space for the new parts of the dataset, if appropriate */
if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY)
- if(H5D_alloc_storage(dset->oloc.file, dxpl_id, dset, H5D_ALLOC_EXTEND, FALSE) < 0)
+ if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_EXTEND, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage")
@@ -2506,24 +2386,9 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id)
*-------------------------------------------------------------------------
*/
if(shrink && H5D_CHUNKED == dset->shared->layout.type) {
- H5D_io_info_t io_info; /* Dataset I/O info */
- H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
-
- /* Fill the DXPL cache values for later use */
- if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
-
- /* Construct dataset I/O info */
- H5D_BUILD_IO_INFO_RD(&io_info, dset, dxpl_cache, dxpl_id, NULL, NULL);
-
/* Remove excess chunks */
- if(H5D_istore_prune_by_extent(&io_info, curr_dims) < 0)
+ if(H5D_chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ")
-
- /* Reset the elements outsize the new dimensions, but in existing chunks */
- if(H5D_istore_initialize_by_extent(&io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ")
} /* end if */
/* Mark the dataspace as dirty, for later writing to the file */
@@ -2611,7 +2476,7 @@ H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags)
case H5D_CHUNKED:
/* Flush the raw data cache */
- if(H5D_istore_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0)
+ if(H5D_chunk_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache")
break;
diff --git a/src/H5Dio.c b/src/H5Dio.c
index b43ec04..92d88f4 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -392,7 +392,7 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
|| dataset->shared->layout.type == H5D_COMPACT);
/* Call storage method's I/O initialization routine */
- if(io_info.layout_ops.init && (*io_info.layout_ops.init)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
+ if(io_info.layout_ops.io_init && (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info")
io_op_init = TRUE;
@@ -408,7 +408,7 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
done:
/* Shut down the I/O op information */
- if(io_op_init && io_info.layout_ops.term && (*io_info.layout_ops.term)(&fm) < 0)
+ if(io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(&fm) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info")
#ifdef H5_HAVE_PARALLEL
/* Shut down io_info struct */
@@ -553,7 +553,7 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
full_overwrite = (hsize_t)file_nelmts == nelmts ? TRUE : FALSE;
/* Allocate storage */
- if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_WRITE, full_overwrite) < 0)
+ if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_WRITE, full_overwrite) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
} /* end if */
@@ -567,7 +567,7 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
#endif /*H5_HAVE_PARALLEL*/
/* Call storage method's I/O initialization routine */
- if(io_info.layout_ops.init && (*io_info.layout_ops.init)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
+ if(io_info.layout_ops.io_init && (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, &fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info")
io_op_init = TRUE;
@@ -598,7 +598,7 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
done:
/* Shut down the I/O op information */
- if(io_op_init && io_info.layout_ops.term && (*io_info.layout_ops.term)(&fm) < 0)
+ if(io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(&fm) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info")
#ifdef H5_HAVE_PARALLEL
/* Shut down io_info struct */
@@ -646,11 +646,11 @@ H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
io_info->store = store;
/* Set I/O operations to initial values */
- io_info->layout_ops = *dset->shared->layout_ops;
+ io_info->layout_ops = *dset->shared->layout.ops;
/* Set the "high-level" I/O operations for the dataset */
- io_info->io_ops.multi_read = dset->shared->layout_ops->ser_read;
- io_info->io_ops.multi_write = dset->shared->layout_ops->ser_write;
+ io_info->io_ops.multi_read = dset->shared->layout.ops->ser_read;
+ io_info->io_ops.multi_write = dset->shared->layout.ops->ser_write;
/* Set the I/O operations for reading/writing single blocks on disk */
if(type_info->is_xform_noop && type_info->is_conv_noop) {
@@ -887,8 +887,8 @@ H5D_ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset,
/* Check if we can use the optimized parallel I/O routines */
if(opt == TRUE) {
/* Override the I/O op pointers to the MPI-specific routines */
- io_info->io_ops.multi_read = dset->shared->layout_ops->par_read;
- io_info->io_ops.multi_write = dset->shared->layout_ops->par_write;
+ io_info->io_ops.multi_read = dset->shared->layout.ops->par_read;
+ io_info->io_ops.multi_write = dset->shared->layout.ops->par_write;
io_info->io_ops.single_read = H5D_mpio_select_read;
io_info->io_ops.single_write = H5D_mpio_select_write;
} /* end if */
diff --git a/src/H5Distore.c b/src/H5Distore.c
index aed5add..b6005db 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -73,44 +73,36 @@
/****************/
/*
- * 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 */
-
-/*
* Given a B-tree node return the dimensionality of the chunks pointed to by
* that node.
*/
#define H5D_ISTORE_NDIMS(X) (((X)->sizeof_rkey-8)/8)
-#define H5D_ISTORE_DEFAULT_SKIPLIST_HEIGHT 8
-
/******************/
/* Local Typedefs */
/******************/
/*
+ * B-tree key. A key contains the minimum logical N-dimensional coordinates 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 */
+ hsize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
+ unsigned filter_mask; /*excluded filters */
+} H5D_istore_key_t;
+
+/*
* Data exchange structure for indexed storage nodes. This structure is
* passed through the B-link tree layer to the methods for the objects
* to which the B-link tree points for operations which require no
@@ -118,99 +110,25 @@
*
* (Just an alias for the "common" info).
*/
-typedef H5D_istore_bt_ud_common_t H5D_istore_ud0_t;
-
-/* B-tree callback info for iteration to total allocated space */
-typedef struct H5D_istore_it_ud1_t {
- H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */
- hsize_t total_storage; /*output from iterator */
-} H5D_istore_it_ud1_t;
-
-/* B-tree callback info for iteration to dump node's info */
-typedef struct H5D_istore_it_ud2_t {
- H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */
- FILE *stream; /*debug output stream */
- hbool_t header_displayed; /* Node's header is displayed? */
-} H5D_istore_it_ud2_t;
-
-/* B-tree callback info for iteration to prune chunks */
-typedef struct H5D_istore_it_ud3_t {
- H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */
- const hsize_t *dims; /* New dataset dimensions */
- const hsize_t *down_chunks; /* "down" size of number of chunks in each dimension */
- H5SL_t *outside; /* Skip list to hold chunks outside the new dimensions */
-} H5D_istore_it_ud3_t;
-
-/* B-tree callback info for iteration to copy data */
-typedef struct H5D_istore_it_ud4_t {
- H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */
- H5F_t *file_src; /* Source file for copy */
- haddr_t addr_dst; /* Address of dest. B-tree */
- void *buf; /* Buffer to hold chunk data for read/write */
- void *bkg; /* Buffer for background information during type conversion */
- size_t buf_size; /* Buffer size */
- hbool_t do_convert; /* Whether to perform type conversions */
-
- /* needed for converting variable-length data */
- hid_t tid_src; /* Datatype ID for source datatype */
- hid_t tid_dst; /* Datatype ID for destination datatype */
- hid_t tid_mem; /* Datatype ID for memory datatype */
- H5T_t *dt_src; /* Source datatype */
- H5T_path_t *tpath_src_mem; /* Datatype conversion path from source file to memory */
- H5T_path_t *tpath_mem_dst; /* Datatype conversion path from memory to dest. file */
- void *reclaim_buf; /* Buffer for reclaiming data */
- size_t reclaim_buf_size; /* Reclaim buffer size */
- uint32_t nelmts; /* Number of elements in buffer */
- H5S_t *buf_space; /* Dataspace describing buffer */
-
- /* needed for compressed variable-length data */
- H5O_pline_t *pline; /* Filter pipeline */
-
- /* needed for copy object pointed by refs */
- H5F_t *file_dst; /* Destination file for copy */
- H5O_copy_t *cpy_info; /* Copy options */
-} H5D_istore_it_ud4_t;
-
-/* B-tree callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */
-typedef struct H5D_istore_it_ud5_t {
- H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */
- const hsize_t *down_chunks;
- haddr_t *chunk_addr;
-} H5D_istore_it_ud5_t;
-
-/* Skip list node for storing chunks to remove during an iteration */
-typedef struct H5D_istore_sl_ck_t {
- hsize_t index; /* Index of chunk to remove (must be first) */
- H5D_istore_key_t key; /* Chunk key */
-} H5D_istore_sl_ck_t;
-
-/* Skip list callback info when destroying list & removing chunks */
-typedef struct H5D_istore_sl_rm_t {
- H5F_t *f; /* Pointer to file for B-tree */
- hid_t dxpl_id; /* DXPL to use */
- const H5O_layout_t *mesg; /* Layout message */
-} H5D_istore_sl_rm_t;
+typedef H5D_chunk_common_ud_t H5D_istore_ud0_t;
+
+/* B-tree callback info for iteration over chunks */
+typedef struct H5D_istore_it_ud_t {
+ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
+ H5D_chunk_cb_func_t cb; /* Chunk callback routine */
+ void *udata; /* User data for chunk callback routine */
+} H5D_istore_it_ud_t;
+
/********************/
/* Local Prototypes */
/********************/
-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_create (const H5F_t *f, H5O_layout_t *layout);
-static herr_t H5D_istore_shared_free (void *page);
+static herr_t H5D_istore_shared_create(const H5F_t *f, H5O_layout_t *layout);
/* B-tree iterator callbacks */
-static int H5D_istore_iter_chunkmap(H5F_t *f, hid_t dxpl_id, const void *left_key, haddr_t addr,
- const void *right_key, void *_udata);
-static int H5D_istore_iter_allocated(H5F_t *f, hid_t dxpl_id, const void *left_key, haddr_t addr,
- const void *right_key, void *_udata);
-static int H5D_istore_iter_dump(H5F_t *f, hid_t dxpl_id, const void *left_key, haddr_t addr,
- const void *right_key, void *_udata);
-static int H5D_istore_prune_check(H5F_t *f, hid_t dxpl_id, const void *_lt_key, haddr_t addr,
- const void *_rt_key, void *_udata);
-static int H5D_istore_iter_copy(H5F_t *f, hid_t dxpl_id, const void *_lt_key, haddr_t addr,
- const void *_rt_key, void *_udata);
+static int H5D_istore_idx_iterate_cb(H5F_t *f, hid_t dxpl_id, const void *left_key,
+ haddr_t addr, const void *right_key, void *_udata);
/* B-tree callbacks */
static H5RC_t *H5D_istore_get_shared(const H5F_t *f, const void *_udata);
@@ -239,6 +157,51 @@ 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);
+/* Chunked layout indexing callbacks */
+static herr_t H5D_istore_idx_init(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D_istore_idx_create(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D_istore_idx_insert(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+static haddr_t H5D_istore_idx_get_addr(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+static int H5D_istore_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata);
+static herr_t H5D_istore_idx_remove(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_common_ud_t *udata);
+static herr_t H5D_istore_idx_delete(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D_istore_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src,
+ const H5D_chk_idx_info_t *idx_info_dst);
+static herr_t H5D_istore_idx_copy_shutdown(H5O_layout_t *layout_src,
+ H5O_layout_t *layout_dst);
+static herr_t H5D_istore_idx_size(const H5D_chk_idx_info_t *idx_info,
+ hsize_t *size);
+static herr_t H5D_istore_idx_dest(const H5D_chk_idx_info_t *idx_info);
+
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/* v1 B-tree indexed chunk I/O ops */
+const H5D_chunk_ops_t H5D_COPS_ISTORE[1] = {{
+ H5D_istore_idx_init,
+ H5D_istore_idx_create,
+ H5D_istore_idx_insert,
+ H5D_istore_idx_get_addr,
+ H5D_istore_idx_iterate,
+ H5D_istore_idx_remove,
+ H5D_istore_idx_delete,
+ H5D_istore_idx_copy_setup,
+ H5D_istore_idx_copy_shutdown,
+ H5D_istore_idx_size,
+ H5D_istore_idx_dest
+}};
+
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
/* inherits B-tree like properties from H5B */
H5B_class_t H5B_ISTORE[1] = {{
H5B_ISTORE_ID, /*id */
@@ -257,36 +220,11 @@ H5B_class_t H5B_ISTORE[1] = {{
H5D_istore_debug_key, /*debug */
}};
-/*********************/
-/* Package Variables */
-/*********************/
-
-/*****************************/
-/* Library Private Variables */
-/*****************************/
/*******************/
/* Local Variables */
/*******************/
-/* 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);
-
-/* Declare a free list to manage H5D_istore_sl_ck_t objects */
-H5FL_DEFINE_STATIC(H5D_istore_sl_ck_t);
-
/*-------------------------------------------------------------------------
* Function: H5D_istore_get_shared
@@ -580,7 +518,7 @@ H5D_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op,
{
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;
+ H5D_chunk_ud_t *udata = (H5D_chunk_ud_t *) _udata;
unsigned u;
herr_t ret_value = SUCCEED; /* Return value */
@@ -658,7 +596,7 @@ static herr_t
H5D_istore_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void *_lt_key,
void *_udata)
{
- H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata;
+ H5D_chunk_ud_t *udata = (H5D_chunk_ud_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 */
@@ -726,7 +664,7 @@ H5D_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key,
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;
+ H5D_chunk_ud_t *udata = (H5D_chunk_ud_t *) _udata;
int cmp;
unsigned u;
H5B_ins_t ret_value;
@@ -825,738 +763,43 @@ done:
/*-------------------------------------------------------------------------
- * 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
- *
- *-------------------------------------------------------------------------
- */
-/* ARGSUSED */
-static int
-H5D_istore_iter_allocated (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_lt_key, haddr_t UNUSED addr,
- const void UNUSED *_rt_key, void *_udata)
-{
- H5D_istore_it_ud1_t *udata = (H5D_istore_it_ud1_t *)_udata;
- const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key;
-
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_iter_allocated)
-
- udata->total_storage += lt_key->nbytes;
-
- FUNC_LEAVE_NOAPI(H5_ITER_CONT)
-} /* H5D_istore_iter_allocated() */
-
-/*-------------------------------------------------------------------------
- * Function: H5D_istore_iter_chunkmap
- *
- * Purpose: obtain chunk address and the corresponding index
- *
- * Return: Success: Non-negative
- *
- * Failure: Negative
- *
- * Programmer: Kent Yang
- * Tuesday, November 15, 2005
- *
- *-------------------------------------------------------------------------
- */
-/* ARGSUSED */
-static int
-H5D_istore_iter_chunkmap (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_lt_key, haddr_t addr,
- const void UNUSED *_rt_key, void *_udata)
-{
- H5D_istore_it_ud5_t *udata = (H5D_istore_it_ud5_t *)_udata;
- const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key;
- unsigned rank = udata->common.mesg->u.chunk.ndims - 1;
- hsize_t chunk_index;
- int ret_value = H5_ITER_CONT; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_iter_chunkmap)
-
- if(H5V_chunk_index(rank, lt_key->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
-
- udata->chunk_addr[chunk_index] = addr;
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_istore_iter_chunkmap() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_istore_iter_dump
- *
- * Purpose: If the UDATA.STREAM member is non-null then debugging
- * information is written to that stream.
- *
- * Return: Success: Non-negative
- *
- * Failure: Negative
- *
- * Programmer: Robb Matzke
- * Wednesday, April 21, 1999
- *
- *-------------------------------------------------------------------------
- */
-/* ARGSUSED */
-static int
-H5D_istore_iter_dump (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_lt_key, haddr_t UNUSED addr,
- const void UNUSED *_rt_key, void *_udata)
-{
- H5D_istore_it_ud2_t *udata = (H5D_istore_it_ud2_t *)_udata;
- const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key;
- unsigned u;
-
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_iter_dump)
-
- if(udata->stream) {
- if(!udata->header_displayed) {
- HDfprintf(udata->stream, " Flags Bytes Address Logical Offset\n");
- HDfprintf(udata->stream, " ========== ======== ========== ==============================\n");
-
- /* Set flag that the headers has been printed */
- udata->header_displayed = TRUE;
- } /* end if */
- HDfprintf(udata->stream, " 0x%08x %8Zu %10a [", lt_key->filter_mask, lt_key->nbytes, addr);
- for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
- HDfprintf(udata->stream, "%s%Hd", (u ? ", " : ""), lt_key->offset[u]);
- HDfputs("]\n", udata->stream);
- } /* end if */
-
- FUNC_LEAVE_NOAPI(H5_ITER_CONT)
-} /* H5D_istore_iter_dump() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_istore_iter_copy
- *
- * Purpose: copy chunked raw data from source file and insert to the
- * B-tree node in the destination file
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Peter Cao
- * August 20, 2005
- *
- *-------------------------------------------------------------------------
- */
-static int
-H5D_istore_iter_copy(H5F_t *f_src, hid_t dxpl_id, const void *_lt_key,
- haddr_t addr_src, const void UNUSED *_rt_key, void *_udata)
-{
- H5D_istore_it_ud4_t *udata = (H5D_istore_it_ud4_t *)_udata;
- const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key;
- H5D_istore_ud1_t udata_dst; /* User data about new destination chunk */
- hbool_t is_vlen = FALSE;
- hbool_t fix_ref = FALSE;
-
- /* General information about chunk copy */
- void *bkg = udata->bkg;
- void *buf = udata->buf;
- size_t buf_size = udata->buf_size;
- H5O_pline_t *pline = udata->pline;
-
- /* needed for commpressed variable length data */
- hbool_t is_compressed = FALSE;
- H5Z_EDC_t edc_read = H5Z_NO_EDC;
- size_t nbytes; /* Size of chunk (in bytes) */
- H5Z_cb_t cb_struct;
-
- int ret_value = H5_ITER_CONT; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_iter_copy)
-
- /* Get 'size_t' local value for number of bytes in chunk */
- H5_ASSIGN_OVERFLOW(nbytes, lt_key->nbytes, uint32_t, size_t);
-
- /* Check parameter for type conversion */
- if(udata->do_convert) {
- if(H5T_detect_class(udata->dt_src, H5T_VLEN) > 0)
- is_vlen = TRUE;
- else if((H5T_get_class(udata->dt_src, FALSE) == H5T_REFERENCE) && (udata->file_src != udata->file_dst))
- fix_ref = TRUE;
- else
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements")
- } /* end if */
-
- /* Check for filtered chunks */
- if(pline && pline->nused) {
- is_compressed = TRUE;
- cb_struct.func = NULL; /* no callback function when failed */
- } /* end if */
-
- /* Resize the buf if it is too small to hold the data */
- if(nbytes > buf_size) {
- void *new_buf; /* New buffer for data */
-
- /* Re-allocate memory for copying the chunk */
- if(NULL == (new_buf = H5MM_realloc(udata->buf, nbytes)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
- udata->buf = new_buf;
- if(udata->bkg) {
- if(NULL == (new_buf = H5MM_realloc(udata->bkg, nbytes)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
- udata->bkg = new_buf;
- if(!udata->cpy_info->expand_ref)
- HDmemset((uint8_t *)udata->bkg + buf_size, 0, (size_t)(nbytes - buf_size));
-
- bkg = udata->bkg;
- } /* end if */
-
- buf = udata->buf;
- udata->buf_size = buf_size = nbytes;
- } /* end if */
-
- /* read chunk data from the source file */
- if(H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, nbytes, dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
-
- /* Need to uncompress variable-length & reference data elements */
- if(is_compressed && (is_vlen || fix_ref)) {
- unsigned filter_mask = lt_key->filter_mask;
-
- if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, edc_read, cb_struct, &nbytes, &buf_size, &buf) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "data pipeline read failed")
- } /* end if */
-
- /* Perform datatype conversion, if necessary */
- if(is_vlen) {
- H5T_path_t *tpath_src_mem = udata->tpath_src_mem;
- H5T_path_t *tpath_mem_dst = udata->tpath_mem_dst;
- H5S_t *buf_space = udata->buf_space;
- hid_t tid_src = udata->tid_src;
- hid_t tid_dst = udata->tid_dst;
- hid_t tid_mem = udata->tid_mem;
- void *reclaim_buf = udata->reclaim_buf;
- size_t reclaim_buf_size = udata->reclaim_buf_size;
-
- /* Convert from source file to memory */
- H5_CHECK_OVERFLOW(udata->nelmts, uint32_t, size_t);
- if(H5T_convert(tpath_src_mem, tid_src, tid_mem, (size_t)udata->nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
-
- /* Copy into another buffer, to reclaim memory later */
- HDmemcpy(reclaim_buf, buf, reclaim_buf_size);
-
- /* Set background buffer to all zeros */
- HDmemset(bkg, 0, buf_size);
-
- /* Convert from memory to destination file */
- if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, udata->nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
-
- /* Reclaim space from variable length data */
- if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_BADITER, H5_ITER_ERROR, "unable to reclaim variable-length data")
- } /* end if */
- else if(fix_ref) {
- /* Check for expanding references */
- /* (background buffer has already been zeroed out, if not expanding) */
- if(udata->cpy_info->expand_ref) {
- size_t ref_count;
-
- /* Determine # of reference elements to copy */
- ref_count = nbytes / H5T_get_size(udata->dt_src);
-
- /* Copy the reference elements */
- if(H5O_copy_expand_ref(f_src, buf, dxpl_id, udata->file_dst, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute")
- } /* end if */
-
- /* After fix ref, copy the new reference elements to the buffer to write out */
- HDmemcpy(buf, bkg, buf_size);
- } /* end if */
-
- /* Set up destination chunk callback information for insertion */
- udata_dst.common.mesg = udata->common.mesg; /* Share this pointer for a short while */
- udata_dst.common.offset = lt_key->offset;
- udata_dst.nbytes = lt_key->nbytes;
- udata_dst.filter_mask = lt_key->filter_mask;
- udata_dst.addr = HADDR_UNDEF;
-
- /* Need to compress variable-length & reference data elements before writing to file */
- if(is_compressed && (is_vlen || fix_ref) ) {
- if(H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), edc_read,
- cb_struct, &nbytes, &buf_size, &buf) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed")
- H5_ASSIGN_OVERFLOW(udata_dst.nbytes, nbytes, size_t, uint32_t);
- udata->buf = buf;
- udata->buf_size = buf_size;
- } /* end if */
-
- /* Insert chunk into the destination Btree */
- if(H5B_insert(udata->file_dst, dxpl_id, H5B_ISTORE, udata->addr_dst, &udata_dst) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5_ITER_ERROR, "unable to allocate chunk")
-
- /* Write chunk data to destination file */
- HDassert(H5F_addr_defined(udata_dst.addr));
- if(H5F_block_write(udata->file_dst, H5FD_MEM_DRAW, udata_dst.addr, nbytes, dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file")
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_iter_copy() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_istore_cinfo_cache_reset
- *
- * Purpose: Reset the cached chunk info
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Quincey Koziol
- * November 27, 2007
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_istore_cinfo_cache_reset(H5D_chunk_cached_t *last)
-{
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_cinfo_cache_reset)
-
- /* Sanity check */
- HDassert(last);
-
- /* Indicate that the cached info is not valid */
- last->valid = FALSE;
-
- FUNC_LEAVE_NOAPI(SUCCEED)
-} /* H5D_istore_cinfo_cache_reset() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_istore_cinfo_cache_update
- *
- * Purpose: Update the cached chunk info
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Quincey Koziol
- * November 27, 2007
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_istore_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_istore_ud1_t *udata)
-{
- unsigned u; /* Local index variable */
-
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_cinfo_cache_update)
-
- /* Sanity check */
- HDassert(last);
- HDassert(udata);
- HDassert(udata->common.mesg);
- HDassert(udata->common.offset);
-
- /* Stored the information to cache */
- for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
- last->offset[u] = udata->common.offset[u];
- last->nbytes = udata->nbytes;
- last->filter_mask = udata->filter_mask;
- last->addr = udata->addr;
-
- /* Indicate that the cached info is valid */
- last->valid = TRUE;
-
- FUNC_LEAVE_NOAPI(SUCCEED)
-} /* H5D_istore_cinfo_cache_update() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_istore_cinfo_cache_found
- *
- * Purpose: Look for chunk info in cache
- *
- * Return: TRUE/FALSE/FAIL
- *
- * Programmer: Quincey Koziol
- * November 27, 2007
- *
- *-------------------------------------------------------------------------
- */
-static hbool_t
-H5D_istore_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_istore_ud1_t *udata)
-{
- hbool_t ret_value = FALSE; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_cinfo_cache_found)
-
- /* Sanity check */
- HDassert(last);
- HDassert(udata);
- HDassert(udata->common.mesg);
- HDassert(udata->common.offset);
-
- /* Check if the cached information is what is desired */
- if(last->valid) {
- unsigned u; /* Local index variable */
-
- /* Check that the offset is the same */
- for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
- if(last->offset[u] != udata->common.offset[u])
- HGOTO_DONE(FALSE)
-
- /* Retrieve the information from the cache */
- udata->nbytes = last->nbytes;
- udata->filter_mask = last->filter_mask;
- udata->addr = last->addr;
-
- /* Indicate that the data was found */
- HGOTO_DONE(TRUE)
- } /* end if */
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_istore_cinfo_cache_found() */
-
-
-/*-------------------------------------------------------------------------
- * 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
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5D_istore_init(const H5F_t *f, const H5D_t *dset)
-{
- H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_istore_init, FAIL)
-
- if(H5F_RDCC_NBYTES(f) > 0 && H5F_RDCC_NELMTS(f) > 0) {
- rdcc->nbytes = H5F_RDCC_NBYTES(f);
- rdcc->nslots = H5F_RDCC_NELMTS(f);
- rdcc->slot = H5FL_SEQ_CALLOC (H5D_rdcc_ent_ptr_t,rdcc->nslots);
- if(NULL==rdcc->slot)
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
-
- /* Reset any cached chunk info for this dataset */
- H5D_istore_cinfo_cache_reset(&(rdcc->last));
- } /* end if */
-
- /* Allocate the shared structure */
- if(H5D_istore_shared_create(f, &dset->shared->layout) < 0)
- HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create 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
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_istore_flush_entry(const H5D_io_info_t *io_info, H5D_rdcc_ent_t *ent, hbool_t reset)
-{
- void *buf = NULL; /*temporary buffer */
- hbool_t point_of_no_return = FALSE;
- herr_t ret_value = SUCCEED; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_flush_entry)
-
- assert(io_info);
- assert(io_info->dset);
- assert(ent);
- assert(!ent->locked);
-
- buf = ent->chunk;
- if(ent->dirty) {
- H5D_istore_ud1_t udata; /*pass through B-tree */
-
- /* Set up user data for B-tree callbacks */
- udata.common.mesg = &io_info->dset->shared->layout;
- udata.common.offset = ent->offset;
- udata.filter_mask = 0;
- udata.nbytes = ent->chunk_size;
- udata.addr = HADDR_UNDEF;
-
- /* Should the chunk be filtered before writing it to disk? */
- if(io_info->dset->shared->dcpl_cache.pline.nused) {
- size_t alloc = ent->alloc_size; /* Bytes allocated for BUF */
- size_t nbytes; /* Chunk size (in bytes) */
-
- if(!reset) {
- /*
- * Copy the chunk to a new buffer before running it through
- * the pipeline because we'll want to save the original buffer
- * for later.
- */
- H5_ASSIGN_OVERFLOW(alloc, ent->chunk_size, uint32_t, size_t);
- if(NULL == (buf = H5MM_malloc(alloc)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline")
- HDmemcpy(buf, ent->chunk, alloc);
- } /* end if */
- else {
- /*
- * If we are reseting and something goes wrong after this
- * point then it's too late to recover because we may have
- * destroyed the original data by calling H5Z_pipeline().
- * The only safe option is to continue with the reset
- * even if we can't write the data to disk.
- */
- point_of_no_return = TRUE;
- ent->chunk = NULL;
- } /* end else */
- H5_ASSIGN_OVERFLOW(nbytes, udata.nbytes, uint32_t, size_t);
- if(H5Z_pipeline(&(io_info->dset->shared->dcpl_cache.pline), 0, &(udata.filter_mask), io_info->dxpl_cache->err_detect,
- io_info->dxpl_cache->filter_cb, &nbytes, &alloc, &buf) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed")
- H5_ASSIGN_OVERFLOW(udata.nbytes, nbytes, size_t, uint32_t);
- } /* end if */
-
- /*
- * 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(io_info->dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, io_info->dset->shared->layout.u.chunk.addr, &udata)<0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk")
- H5_CHECK_OVERFLOW(udata.nbytes, uint32_t, size_t);
- if(H5F_block_write(io_info->dset->oloc.file, H5FD_MEM_DRAW, udata.addr, (size_t)udata.nbytes, io_info->dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
-
- /* Cache the chunk's info, in case it's accessed again shortly */
- H5D_istore_cinfo_cache_update(&io_info->dset->shared->cache.chunk.last, &udata);
-
- /* Mark cache entry as clean */
- ent->dirty = FALSE;
-#ifdef H5D_ISTORE_DEBUG
- io_info->dset->shared->cache.chunk.nflushes++;
-#endif /* H5D_ISTORE_DEBUG */
- } /* end if */
-
- /* Reset, but do not free or removed from list */
- if(reset) {
- point_of_no_return = FALSE;
- if(buf == ent->chunk)
- buf = NULL;
- if(ent->chunk != NULL)
- ent->chunk = (uint8_t *)H5D_istore_chunk_xfree(ent->chunk, &(io_info->dset->shared->dcpl_cache.pline));
- } /* end if */
-
-done:
- /* Free the temp buffer only if it's different than the entry chunk */
- if(buf != ent->chunk)
- H5MM_xfree(buf);
-
- /*
- * If we reached the point of no return then we have no choice but to
- * reset the entry. This can only happen if RESET is true but the
- * output pipeline failed. Do not free the entry or remove it from the
- * list.
- */
- if(ret_value < 0 && point_of_no_return) {
- if(ent->chunk)
- ent->chunk = (uint8_t *)H5D_istore_chunk_xfree(ent->chunk, &(io_info->dset->shared->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
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D_istore_preempt(const H5D_io_info_t *io_info, H5D_rdcc_ent_t * ent, hbool_t flush)
-{
- H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);
- herr_t ret_value=SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_preempt)
-
- assert(io_info);
- assert(ent);
- assert(!ent->locked);
- assert(ent->idx < rdcc->nslots);
-
- if(flush) {
- /* Flush */
- if(H5D_istore_flush_entry(io_info, ent, TRUE) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
- } /* end if */
- else {
- /* Don't flush, just free chunk */
- if(ent->chunk != NULL)
- ent->chunk = (uint8_t *)H5D_istore_chunk_xfree(ent->chunk, &(io_info->dset->shared->dcpl_cache.pline));
- } /* end else */
-
- /* Unlink from list */
- if(ent->prev)
- ent->prev->next = ent->next;
- else
- rdcc->head = ent->next;
- if(ent->next)
- ent->next->prev = ent->prev;
- else
- rdcc->tail = ent->prev;
- ent->prev = ent->next = NULL;
-
- /* Remove from cache */
- rdcc->slot[ent->idx] = NULL;
- ent->idx = UINT_MAX;
- rdcc->nbytes -= ent->chunk_size;
- --rdcc->nused;
-
- /* Free */
- H5FL_FREE(H5D_rdcc_ent_t, ent);
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_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
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5D_istore_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags)
-{
- H5D_io_info_t io_info; /* Temporary I/O info object */
- H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
- H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
- unsigned nerrors = 0;
- H5D_rdcc_ent_t *ent, *next;
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_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")
-
- /* Construct dataset I/O info */
- H5D_BUILD_IO_INFO_WRT(&io_info, dset, dxpl_cache, dxpl_id, NULL, NULL);
-
- /* Loop over all entries in the chunk cache */
- for(ent = rdcc->head; ent; ent = next) {
- next = ent->next;
- if((flags & H5F_FLUSH_INVALIDATE)) {
- if(H5D_istore_preempt(&io_info, ent, TRUE) < 0)
- nerrors++;
- } else {
- if(H5D_istore_flush_entry(&io_info, 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
+ * Function: H5D_istore_remove
*
- * Purpose: Destroy the entire chunk cache by flushing dirty entries,
- * preempting all entries, and freeing the cache itself.
+ * Purpose: Removes chunks that are no longer necessary in the B-tree.
*
* Return: Non-negative on success/Negative on failure
*
- * Programmer: Robb Matzke
- * Thursday, May 21, 1998
+ * Programmer: Robb Matzke
+ * Pedro Vicente, pvn@ncsa.uiuc.edu
+ * March 28, 2002
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5D_istore_dest(H5D_t *dset, hid_t dxpl_id)
+/* ARGSUSED */
+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_io_info_t io_info; /* Temporary I/O info object */
- H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
- H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
- 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)
-
- HDassert(dset);
-
- /* Fill the DXPL cache values for later use */
- if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
-
- /* Construct dataset I/O info */
- H5D_BUILD_IO_INFO_WRT(&io_info, dset, dxpl_cache, dxpl_id, NULL, NULL);
+ H5D_istore_key_t *lt_key = (H5D_istore_key_t *)_lt_key;
+ H5B_ins_t ret_value=H5B_INS_REMOVE; /* Return value */
- /* 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(&io_info, ent, TRUE) < 0)
- nerrors++;
- } /* end for */
- if(nerrors)
- HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_remove)
- if(rdcc->slot)
- H5FL_SEQ_FREE(H5D_rdcc_ent_ptr_t, rdcc->slot);
- HDmemset(rdcc, 0, sizeof(H5D_rdcc_t));
+ /* Remove raw data chunk from file */
+ H5_CHECK_OVERFLOW(lt_key->nbytes, uint32_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")
- /* Free the raw B-tree node buffer */
- if(dset->shared->layout.u.chunk.btree_shared == NULL)
- HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
- if(H5RC_DEC(dset->shared->layout.u.chunk.btree_shared) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
+ /* Mark keys as unchanged */
+ *lt_key_changed = FALSE;
+ *rt_key_changed = FALSE;
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_dest() */
+} /* end H5D_istore_remove() */
/*-------------------------------------------------------------------------
@@ -1572,41 +815,28 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_istore_shared_create (const H5F_t *f, H5O_layout_t *layout)
+H5D_istore_shared_create(const H5F_t *f, H5O_layout_t *layout)
{
H5B_shared_t *shared; /* Shared B-tree node info */
- size_t u; /* Local index variable */
- herr_t ret_value=SUCCEED; /* Return value */
+ size_t sizeof_rkey; /* Size of raw (disk) key */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_shared_create)
- /* 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 = 4 + /*storage size */
- 4 + /*filter mask */
- layout->u.chunk.ndims*8; /*dimension indices */
- 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")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(shared->page, 0, shared->sizeof_rnode);
-#endif /* H5_CLEAR_MEMORY */
- 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[0].sizeof_nkey;
+ /* Set the raw key size */
+ sizeof_rkey = 4 + /*storage size */
+ 4 + /*filter mask */
+ layout->u.chunk.ndims * 8; /*dimension indices */
+
+ /* Allocate & initialize global info for the shared structure */
+ if(NULL == (shared = H5B_shared_new(f, H5B_ISTORE, sizeof_rkey)))
+ HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
+
+ /* Set up the "local" information for this dataset's chunks */
+ /* <none> */
/* Make shared B-tree info reference counted */
- if(NULL==(layout->u.chunk.btree_shared=H5RC_create(shared,H5D_istore_shared_free)))
+ if(NULL == (layout->u.chunk.btree_shared = H5RC_create(shared, H5B_shared_free)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
done:
@@ -1615,538 +845,49 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5D_istore_shared_free
+ * Function: H5D_istore_idx_init
*
- * Purpose: Free B-tree shared info
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Quincey Koziol
- * Thursday, July 8, 2004
- *
- *-------------------------------------------------------------------------
- */
-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 */
- (void)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.
+ * Purpose: Initialize the indexing information for a dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
- * Thursday, May 21, 1998
+ * Monday, May 18, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_istore_prune (const H5D_io_info_t *io_info, size_t size)
-{
- int i, j, nerrors=0;
- const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);
- size_t total = rdcc->nbytes;
- const int nmeth=2; /*number of methods */
- int w[1]; /*weighting as an interval */
- H5D_rdcc_ent_t *p[2], *cur; /*list pointers */
- H5D_rdcc_ent_t *n[2]; /*list next pointers */
- 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(io_info->dset->oloc.file));
- 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(io_info, 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
- *
- *-------------------------------------------------------------------------
- */
-void *
-H5D_istore_lock(const H5D_io_info_t *io_info, H5D_istore_ud1_t *udata,
- hbool_t relax, unsigned *idx_hint/*in,out*/)
-{
- H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
- const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
- const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
- const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
- H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
- hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
- H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache*/
- H5D_rdcc_ent_t *ent = NULL; /*cache entry */
- unsigned idx = 0; /*hash index number */
- hbool_t found = FALSE; /*already in cache? */
- size_t chunk_size; /*size of a chunk */
- void *chunk = NULL; /*the file chunk */
- unsigned u; /*counters */
- void *ret_value; /*return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_lock)
-
- HDassert(io_info);
- HDassert(dset);
- HDassert(io_info->dxpl_cache);
- HDassert(io_info->store);
- HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER));
-
- /* Get the chunk's size */
- HDassert(layout->u.chunk.size > 0);
- H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
-
- /* Search for the chunk in the cache */
- if(rdcc->nslots > 0) {
- idx = H5D_CHUNK_HASH(dset->shared, io_info->store->chunk.index);
- ent = rdcc->slot[idx];
-
- if(ent)
- for(u = 0, found = TRUE; u < layout->u.chunk.ndims; u++)
- if(io_info->store->chunk.offset[u] != ent->offset[u]) {
- found = FALSE;
- break;
- } /* end if */
- } /* end if */
-
- if(found) {
- /*
- * Already in the cache. Count a hit.
- */
-#ifdef H5D_ISTORE_DEBUG
- rdcc->nhits++;
-#endif /* H5D_ISTORE_DEBUG */
- } /* end if */
- else if(relax) {
- /*
- * Not in the cache, but we're about to overwrite the whole thing
- * anyway, so just allocate a buffer for it but don't initialize that
- * buffer with the file contents. Count this as a hit instead of a
- * miss because we saved ourselves lots of work.
- */
-#ifdef H5D_ISTORE_DEBUG
- HDputc('w', stderr);
- HDfflush(stderr);
- rdcc->nhits++;
-#endif
- if(NULL == (chunk = H5D_istore_chunk_alloc(chunk_size, pline)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
-
- /* In the case that some dataset functions look through this data,
- * clear it to all 0s. */
- HDmemset(chunk, 0, chunk_size);
- } /* end if */
- else {
- H5D_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(io_info, udata);
- } /* end else */
-
- /* Check if the chunk exists on disk */
- if(H5F_addr_defined(chunk_addr)) {
- size_t chunk_alloc; /* Allocated chunk size */
-
- /* Chunk size on disk isn't [likely] the same size as the final chunk
- * size in memory, so allocate memory big enough. */
- H5_ASSIGN_OVERFLOW(chunk_alloc, udata->nbytes, uint32_t, size_t);
- if(NULL == (chunk = H5D_istore_chunk_alloc(chunk_alloc, pline)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
- if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, chunk_addr, chunk_alloc, io_info->dxpl_id, chunk) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk")
-
- if(pline->nused) {
- if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &(udata->filter_mask), io_info->dxpl_cache->err_detect,
- io_info->dxpl_cache->filter_cb, &chunk_alloc, &chunk_alloc, &chunk) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, NULL, "data pipeline read failed")
- H5_ASSIGN_OVERFLOW(udata->nbytes, chunk_alloc, size_t, uint32_t);
- } /* end if */
-#ifdef H5D_ISTORE_DEBUG
- rdcc->nmisses++;
-#endif /* H5D_ISTORE_DEBUG */
- } else {
- H5D_fill_value_t fill_status;
-
-#ifdef OLD_WAY
- /* Clear the error stack from not finding the chunk on disk */
- H5E_clear_stack(NULL);
-#endif /* OLD_WAY */
-
- /* Chunk size on disk isn't [likely] the same size as the final chunk
- * size in memory, so allocate memory big enough. */
- if(NULL == (chunk = H5D_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->fill_time == H5D_FILL_TIME_ALLOC ||
- (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
- /*
- * The chunk doesn't exist in the file. Replicate the fill
- * value throughout the chunk, if the fill value is defined.
- */
-
- /* Initialize the fill value buffer */
- /* (use the compact dataset storage buffer as the fill value buffer) */
- if(H5D_fill_init(&fb_info, chunk, FALSE,
- NULL, NULL, NULL, NULL,
- &dset->shared->dcpl_cache.fill, dset->shared->type,
- dset->shared->type_id, (size_t)0, chunk_size, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize fill buffer info")
- fb_info_init = TRUE;
-
- /* Check for VL datatype & non-default fill value */
- if(fb_info.has_vlen_fill_type)
- /* Fill the buffer with VL datatype fill values */
- if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, NULL, "can't refill fill value buffer")
- } /* end if */
- else
- HDmemset(chunk, 0, chunk_size);
-#ifdef H5D_ISTORE_DEBUG
- rdcc->ninits++;
-#endif /* H5D_ISTORE_DEBUG */
- } /* end else */
- } /* end else */
- HDassert(found || chunk_size > 0);
-
- if(!found && rdcc->nslots > 0 && chunk_size <= rdcc->nbytes &&
- (!ent || !ent->locked)) {
- /*
- * Add the chunk to the cache only if the slot is not already locked.
- * Preempt enough things from the cache to make room.
- */
- if(ent) {
-#ifdef H5D_ISTORE_DEBUG
- HDputc('#', stderr);
- HDfflush(stderr);
-#endif
- if(H5D_istore_preempt(io_info, ent, TRUE) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk from cache")
- } /* end if */
- if(H5D_istore_prune(io_info, 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;
- H5_ASSIGN_OVERFLOW(ent->chunk_size, chunk_size, size_t, uint32_t);
- ent->alloc_size = chunk_size;
- for(u = 0; u < layout->u.chunk.ndims; u++)
- ent->offset[u] = io_info->store->chunk.offset[u];
- H5_ASSIGN_OVERFLOW(ent->rd_count, chunk_size, size_t, uint32_t);
- H5_ASSIGN_OVERFLOW(ent->wr_count, chunk_size, size_t, uint32_t);
- ent->chunk = (uint8_t *)chunk;
-
- /* Add it to the cache */
- HDassert(NULL == rdcc->slot[idx]);
- rdcc->slot[idx] = ent;
- ent->idx = idx;
- rdcc->nbytes += chunk_size;
- rdcc->nused++;
-
- /* Add it to the linked list */
- ent->next = NULL;
- if(rdcc->tail) {
- rdcc->tail->next = ent;
- ent->prev = rdcc->tail;
- rdcc->tail = ent;
- } /* end if */
- else {
- rdcc->head = rdcc->tail = ent;
- ent->prev = NULL;
- } /* end else */
- found = TRUE;
- } else if(!found) {
- /*
- * The chunk is larger than the entire cache so we don't cache it.
- * This is the reason all those arguments have to be repeated for the
- * unlock function.
- */
- ent = NULL;
- idx = UINT_MAX;
- } else {
- /*
- * The chunk is not at the beginning of the cache; move it backward
- * by one slot. This is how we implement the LRU preemption
- * algorithm.
- */
- HDassert(ent);
- if(ent->next) {
- if(ent->next->next)
- ent->next->next->prev = ent;
- else
- rdcc->tail = ent;
- ent->next->prev = ent->prev;
- if(ent->prev)
- ent->prev->next = ent->next;
- else
- rdcc->head = ent->next;
- ent->prev = ent->next;
- ent->next = ent->next->next;
- ent->prev->next = ent;
- } /* end if */
- } /* end else */
-
- /* Lock the chunk into the cache */
- if(ent) {
- HDassert(!ent->locked);
- ent->locked = TRUE;
- chunk = ent->chunk;
- } /* end if */
-
- if(idx_hint)
- *idx_hint = idx;
-
- /* Set return value */
- ret_value = chunk;
-
-done:
- /* Release the fill buffer info, if it's been initialized */
- if(fb_info_init && H5D_fill_term(&fb_info) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "Can't release fill buffer info")
-
- /* Release the chunk allocated, on error */
- if(!ret_value)
- if(chunk)
- chunk = H5D_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
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5D_istore_unlock(const H5D_io_info_t *io_info,
- hbool_t dirty, unsigned idx_hint, void *chunk, uint32_t naccessed)
+H5D_istore_idx_init(const H5D_chk_idx_info_t *idx_info)
{
- const H5O_layout_t *layout=&(io_info->dset->shared->layout); /* Dataset layout */
- const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);
- H5D_rdcc_ent_t *ent = NULL;
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_unlock)
+ herr_t ret_value = SUCCEED; /* Return value */
- assert(io_info);
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_init)
- if(UINT_MAX == idx_hint) {
- /*
- * It's not in the cache, probably because it's too big. If it's
- * dirty then flush it to disk. In any case, free the chunk.
- * Note: we have to copy the layout and filter messages so we
- * don't discard the `const' qualifier.
- */
- if (dirty) {
- H5D_rdcc_ent_t x;
-
- HDmemset(&x, 0, sizeof(x));
- x.dirty = TRUE;
- HDassert(sizeof(x.offset[0]) == sizeof(io_info->store->chunk.offset[0]));
- HDmemcpy(x.offset, io_info->store->chunk.offset, layout->u.chunk.ndims * sizeof(x.offset[0]));
- HDassert(layout->u.chunk.size > 0);
- x.chunk_size = layout->u.chunk.size;
- H5_ASSIGN_OVERFLOW(x.alloc_size, x.chunk_size, uint32_t, size_t);
- x.chunk = (uint8_t *)chunk;
-
- if(H5D_istore_flush_entry(io_info, &x, TRUE) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
- } /* end if */
- else {
- if(chunk)
- chunk = H5D_istore_chunk_xfree(chunk, &(io_info->dset->shared->dcpl_cache.pline));
- } /* end else */
- } /* end if */
- else {
- /* Sanity check */
- HDassert(idx_hint < rdcc->nslots);
- HDassert(rdcc->slot[idx_hint]);
- HDassert(rdcc->slot[idx_hint]->chunk == chunk);
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
- /*
- * It's in the cache so unlock it.
- */
- ent = rdcc->slot[idx_hint];
- HDassert(ent->locked);
- if(dirty) {
- ent->dirty = TRUE;
- ent->wr_count -= MIN(ent->wr_count, naccessed);
- } /* end if */
- else
- ent->rd_count -= MIN(ent->rd_count, naccessed);
- ent->locked = FALSE;
- } /* end else */
+ /* Allocate the shared structure */
+ if(H5D_istore_shared_create(idx_info->f, idx_info->layout) < 0)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_unlock() */
+} /* end H5D_istore_idx_init() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_create
+ * Function: H5D_istore_idx_create
*
* Purpose: Creates a new indexed-storage B-tree and initializes the
- * istore struct with information about the storage. The
+ * layout struct with information about the storage. The
* struct should be immediately written to the object header.
*
- * This function must be called before passing ISTORE to any of
+ * This function must be called before passing LAYOUT to any of
* the other indexed storage functions!
*
- * Return: Non-negative on success (with the ISTORE argument initialized
+ * Return: Non-negative on success (with the LAYOUT argument initialized
* and ready to write to an object header). Negative on failure.
*
* Programmer: Robb Matzke
@@ -2154,138 +895,70 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5D_istore_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */)
+static herr_t
+H5D_istore_idx_create(const H5D_chk_idx_info_t *idx_info)
{
- H5D_istore_ud0_t udata;
-#ifndef NDEBUG
- unsigned u;
-#endif
- herr_t ret_value = SUCCEED; /* Return value */
+ H5D_istore_ud0_t udata; /* User data for B-tree callback */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5D_istore_create, FAIL)
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_create)
/* Check args */
- HDassert(f);
- HDassert(layout && H5D_CHUNKED == layout->type);
- HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
-#ifndef NDEBUG
- for(u = 0; u < layout->u.chunk.ndims; u++)
- HDassert(layout->u.chunk.dim[u] > 0);
-#endif
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
/* Initialize "user" data for B-tree callbacks, etc. */
- udata.mesg = layout;
+ udata.mesg = idx_info->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")
+ /* Create the v1 B-tree for the chunk index */
+ if(H5B_create(idx_info->f, idx_info->dxpl_id, H5B_ISTORE, &udata, &(idx_info->layout->u.chunk.addr)/*out*/) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create B-tree")
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_create() */
+} /* end H5D_istore_idx_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).
+ * Function: H5D_istore_idx_insert
*
- * Return: Success: Number of bytes stored in all chunks.
+ * Purpose: Create the chunk it if it doesn't exist, or reallocate the
+ * chunk if its size changed.
*
- * Failure: 0
+ * Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
- * Wednesday, April 21, 1999
- *
- *-------------------------------------------------------------------------
- */
-hsize_t
-H5D_istore_allocated(H5D_t *dset, hid_t dxpl_id)
-{
- H5D_io_info_t io_info; /* Temporary I/O info object */
- const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
- H5D_rdcc_ent_t *ent; /*cache entry */
- H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */
- H5D_istore_it_ud1_t udata;
- hsize_t ret_value; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_istore_allocated, 0)
-
- HDassert(dset);
-
- /* Fill the DXPL cache values for later use */
- if(H5D_get_dxpl_cache(dxpl_id,&dxpl_cache) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't fill dxpl cache")
-
- /* Construct dataset I/O info */
- H5D_BUILD_IO_INFO_WRT(&io_info, dset, dxpl_cache, dxpl_id, NULL, NULL);
-
- /* 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(&io_info, ent, FALSE) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, 0, "cannot flush indexed storage buffer")
- } /* end for */
-
- HDmemset(&udata, 0, sizeof udata);
- udata.common.mesg = &dset->shared->layout;
- if(H5B_iterate(dset->oloc.file, dxpl_id, H5B_ISTORE, H5D_istore_iter_allocated, dset->shared->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_chunkmap
- *
- * Purpose: obtain the chunk address and corresponding chunk index
- *
- * Return: Success: Non-negative on succeed.
- *
- * Failure: negative value
- *
- * Programmer: Kent Yang
- * November 15, 2005
+ * Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5D_istore_chunkmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],
- const hsize_t down_chunks[])
+static herr_t
+H5D_istore_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
{
- H5D_t *dset = io_info->dset; /* Local pointer to dataset info */
- H5D_istore_it_ud5_t udata;
- herr_t ret_value = SUCCEED; /* Return value */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5D_istore_chunkmap, FAIL)
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_insert)
- HDassert(dset);
-
- /* Set up user data for B-tree callback */
- HDmemset(&udata, 0, sizeof(udata));
- udata.common.mesg = &dset->shared->layout;
- udata.down_chunks = down_chunks;
- udata.chunk_addr = chunk_addr;
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
+ HDassert(udata);
- /* Build mapping of chunk addresses and indices */
- if(H5B_iterate(dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, H5D_istore_iter_chunkmap, dset->shared->layout.u.chunk.addr, &udata) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to iterate over chunk B-tree")
+ /*
+ * Create the chunk it if it doesn't exist, or reallocate the chunk if
+ * its size changed.
+ */
+ if(H5B_insert(idx_info->f, idx_info->dxpl_id, H5B_ISTORE, idx_info->layout->u.chunk.addr, udata) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk")
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_chunkmap() */
+} /* H5D_istore_idx_insert() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_get_addr
+ * Function: H5D_istore_idx_get_addr
*
* Purpose: Get the file address of a chunk if file space has been
* assigned. Save the retrieved information in the udata
@@ -2298,985 +971,169 @@ done:
*
*-------------------------------------------------------------------------
*/
-haddr_t
-H5D_istore_get_addr(const H5D_io_info_t *io_info, H5D_istore_ud1_t *_udata)
+static haddr_t
+H5D_istore_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
{
- H5D_istore_ud1_t tmp_udata; /* Information about a chunk */
- H5D_istore_ud1_t *udata; /* Pointer to information about a chunk */
haddr_t ret_value; /* Return value */
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_get_addr)
-
- HDassert(io_info);
- HDassert(io_info->dset);
- HDassert(io_info->dset->shared->layout.u.chunk.ndims > 0);
- HDassert(io_info->store->chunk.offset);
-
- /* Check for udata struct to return */
- udata = (_udata != NULL ? _udata : &tmp_udata);
-
- /* Initialize the information about the chunk we are looking for */
- udata->common.mesg = &(io_info->dset->shared->layout);
- udata->common.offset = io_info->store->chunk.offset;
- udata->nbytes = 0;
- udata->filter_mask = 0;
- udata->addr = HADDR_UNDEF;
-
- /* Check for cached information */
- if(!H5D_istore_cinfo_cache_found(&io_info->dset->shared->cache.chunk.last, udata)) {
- /* Go get the chunk information */
- if(H5B_find(io_info->dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, io_info->dset->shared->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
- */
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_idx_get_addr)
+
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->layout->u.chunk.ndims > 0);
+ HDassert(udata);
+
+ /* Go get the chunk information */
+ if(H5B_find(idx_info->f, idx_info->dxpl_id, H5B_ISTORE, idx_info->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_stack(NULL);
+ H5E_clear_stack(NULL);
- HGOTO_ERROR(H5E_BTREE, H5E_NOTFOUND, HADDR_UNDEF, "Can't locate chunk info")
+ HGOTO_ERROR(H5E_BTREE, H5E_NOTFOUND, HADDR_UNDEF, "Can't locate chunk info")
#else /* OLD_WAY */
- /* Cache the fact that the chunk is not in the B-tree */
- H5D_istore_cinfo_cache_update(&io_info->dset->shared->cache.chunk.last, udata);
-
- HGOTO_DONE(HADDR_UNDEF)
+ HGOTO_DONE(HADDR_UNDEF)
#endif /* OLD_WAY */
- } /* end if */
-
- /* Cache the information retrieved */
- HDassert(H5F_addr_defined(udata->addr));
- H5D_istore_cinfo_cache_update(&io_info->dset->shared->cache.chunk.last, udata);
- } /* end else */
+ } /* 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
- *
- *-------------------------------------------------------------------------
- */
-static void *
-H5D_istore_chunk_alloc(size_t size, const H5O_pline_t *pline)
-{
- void *ret_value = NULL; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_chunk_alloc)
-
- HDassert(size);
- HDassert(pline);
-
- if(pline->nused > 0)
- ret_value = H5MM_malloc(size);
- else
- ret_value = H5FL_BLK_MALLOC(chunk, size);
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_istore_chunk_alloc() */
+} /* H5D_istore_idx_get_addr() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_chunk_xfree
+ * Function: H5D_istore_idx_iterate_cb
*
- * 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.
+ * Purpose: Translate the B-tree specific chunk record into a generic
+ * form and make the callback to the generic chunk callback
+ * routine.
*
- * Return: NULL (never fails)
+ * Return: Success: Non-negative
+ * Failure: Negative
*
* Programmer: Quincey Koziol
- * April 22, 2004
- *
- *-------------------------------------------------------------------------
- */
-static void *
-H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline)
-{
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_chunk_xfree)
-
- HDassert(pline);
-
- if(chk) {
- if(pline->nused > 0)
- H5MM_xfree(chk);
- else
- (void)H5FL_BLK_FREE(chunk, chk);
- } /* end if */
-
- FUNC_LEAVE_NOAPI(NULL)
-} /* H5D_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 cached 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.
- *
- * Programmer: Albert Cheng
- * June 26, 1998
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
-{
- H5D_io_info_t io_info; /* Dataset I/O info */
- H5D_storage_t store; /* Dataset storage information */
- hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
- size_t orig_chunk_size; /* Original size of chunk in bytes */
- unsigned filter_mask = 0; /* Filter mask for chunks that have them */
- const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
- const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
- const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
- H5D_fill_value_t fill_status; /* The fill value status */
- hbool_t should_fill = FALSE; /* Whether fill values should be written */
- H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
-#ifdef H5_HAVE_PARALLEL
- MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */
- int mpi_rank = (-1); /* This process's rank */
- int mpi_code; /* MPI return code */
- hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */
- hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
-#endif /* H5_HAVE_PARALLEL */
- hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
- int space_ndims; /* Dataset's space rank */
- hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
- H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
- hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
- hid_t data_dxpl_id; /* DXPL ID to use for raw data I/O operations */
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_istore_allocate, FAIL)
-
- /* Check args */
- HDassert(dset && H5D_CHUNKED == layout->type);
- HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
- HDassert(H5F_addr_defined(layout->u.chunk.addr));
- HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
-
- /* Retrieve the dataset dimensions */
- if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info")
- space_dim[space_ndims] = layout->u.chunk.dim[space_ndims];
-
-#ifdef H5_HAVE_PARALLEL
- /* Retrieve MPI parameters */
- if(IS_H5FD_MPI(dset->oloc.file)) {
- /* Get the MPI communicator */
- if(MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file)))
- HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator")
-
- /* Get the MPI rank */
- if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file)) < 0)
- HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank")
-
- /* Set the MPI-capable file driver flag */
- using_mpi = TRUE;
-
- /* Use the internal "independent" DXPL */
- data_dxpl_id = H5AC_ind_dxpl_id;
- } /* end if */
- else {
-#endif /* H5_HAVE_PARALLEL */
- /* Use the DXPL we were given */
- data_dxpl_id = dxpl_id;
-#ifdef H5_HAVE_PARALLEL
- } /* end else */
-#endif /* H5_HAVE_PARALLEL */
-
- /* Fill the DXPL cache values for later use */
- if(H5D_get_dxpl_cache(data_dxpl_id, &dxpl_cache) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
-
- /* Get original chunk size */
- H5_ASSIGN_OVERFLOW(orig_chunk_size, layout->u.chunk.size, uint32_t, size_t);
-
- /* Check the dataset's fill-value status */
- if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
-
- /* If we are filling the dataset on allocation or "if set" and
- * the fill value _is_ set, _and_ we are not overwriting the new blocks,
- * or if there are any pipeline filters defined,
- * set the "should fill" flag
- */
- if((!full_overwrite && (fill->fill_time == H5D_FILL_TIME_ALLOC ||
- (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)))
- || pline->nused > 0)
- should_fill = TRUE;
-
- /* Check if fill values should be written to chunks */
- if(should_fill) {
- /* Initialize the fill value buffer */
- /* (delay allocating fill buffer for VL datatypes until refilling) */
- /* (casting away const OK - QAK) */
- if(H5D_fill_init(&fb_info, NULL, (hbool_t)(pline->nused > 0),
- (H5MM_allocate_t)H5D_istore_chunk_alloc, (void *)pline,
- (H5MM_free_t)H5D_istore_chunk_xfree, (void *)pline,
- &dset->shared->dcpl_cache.fill, dset->shared->type,
- dset->shared->type_id, (size_t)0, orig_chunk_size, data_dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
- fb_info_init = TRUE;
-
- /* Check if there are filters which need to be applied to the chunk */
- /* (only do this in advance when the chunk info can be re-used (i.e.
- * it doesn't contain any non-default VL datatype fill values)
- */
- if(!fb_info.has_vlen_fill_type && pline->nused > 0) {
- size_t buf_size = orig_chunk_size;
-
- /* Push the chunk through the filters */
- if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
- } /* end if */
- } /* end if */
-
- /* Set up dataset I/O info */
- store.chunk.offset = chunk_offset;
- H5D_BUILD_IO_INFO_WRT(&io_info, dset, dxpl_cache, data_dxpl_id, &store, NULL);
-
- /* Reset the chunk offset indices */
- HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0])));
-
- /* Loop over all chunks */
- carry = FALSE;
- while(!carry) {
- int i; /* Local index variable */
-
- /* Check if the chunk exists yet on disk */
- if(!H5F_addr_defined(H5D_istore_get_addr(&io_info, NULL))) {
- const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
- H5D_rdcc_ent_t *ent; /* Cache entry */
- hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */
- unsigned u; /* Local index variable */
-
- /* Didn't find the chunk on disk */
- chunk_exists = FALSE;
-
- /* Look for chunk in cache */
- for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
- /* Assume a match */
- chunk_exists = TRUE;
- for(u = 0; u < layout->u.chunk.ndims; u++)
- if(ent->offset[u] != chunk_offset[u]) {
- chunk_exists = FALSE; /* Reset if no match */
- break;
- } /* end if */
- } /* end for */
-
- /* Chunk wasn't in cache either, create it now */
- if(!chunk_exists) {
- H5D_istore_ud1_t udata; /* B-tree pass-through for creating chunk */
- size_t chunk_size; /* Size of chunk in bytes, possibly filtered */
-
- /* Check for VL datatype & non-default fill value */
- if(fb_info_init && fb_info.has_vlen_fill_type) {
- /* Sanity check */
- HDassert(should_fill);
-
- /* Fill the buffer with VL datatype fill values */
- if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
-
- /* Check if there are filters which need to be applied to the chunk */
- if(pline->nused > 0) {
- size_t buf_size = orig_chunk_size;
- size_t nbytes = fb_info.fill_buf_size;
-
- /* Push the chunk through the filters */
- if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &fb_info.fill_buf) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
-
- /* Keep the number of bytes the chunk turned in to */
- chunk_size = nbytes;
- } /* end if */
- else
- H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
- } /* end if */
- else
- chunk_size = orig_chunk_size;
-
- /* Initialize the chunk information */
- udata.common.mesg = layout;
- udata.common.offset = chunk_offset;
- H5_ASSIGN_OVERFLOW(udata.nbytes, chunk_size, size_t, uint32_t);
- udata.filter_mask = filter_mask;
- udata.addr = HADDR_UNDEF;
-
- /* Allocate the chunk with all processes */
- if(H5B_insert(dset->oloc.file, dxpl_id, H5B_ISTORE, 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 chunks */
- if(should_fill) {
- /* Sanity check */
- HDassert(fb_info_init);
-
-#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) {
- HDassert(udata.nbytes == chunk_size);
- if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
- } /* end if */
-
- /* Indicate that blocks are being written */
- blocks_written = TRUE;
- } /* end if */
- else {
-#endif /* H5_HAVE_PARALLEL */
- HDassert(udata.nbytes == chunk_size);
- if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
-#ifdef H5_HAVE_PARALLEL
- } /* end else */
-#endif /* H5_HAVE_PARALLEL */
- } /* end if */
-
- /* Release the fill buffer if we need to re-allocate it each time */
- if(fb_info_init && fb_info.has_vlen_fill_type && pline->nused > 0)
- H5D_fill_release(&fb_info);
- } /* end if */
- } /* end if */
-
- /* Increment indices */
- carry = TRUE;
- for(i = (int)(space_ndims - 1); i >= 0; --i) {
- chunk_offset[i] += layout->u.chunk.dim[i];
- if(chunk_offset[i] >= space_dim[i])
- chunk_offset[i] = 0;
- else {
- carry = FALSE;
- break;
- } /* end else */
- } /* end for */
- } /* end while */
-
-#ifdef H5_HAVE_PARALLEL
- /* Only need to block at the barrier if we actually initialized a chunk */
- /* using an MPI-capable file driver */
- if(using_mpi && blocks_written) {
- /* Wait at barrier to avoid race conditions where some processes are
- * still writing out chunks and other processes race ahead to read
- * them in, getting bogus data.
- */
- if(MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm)))
- HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
- } /* end if */
-#endif /* H5_HAVE_PARALLEL */
-
- /* Reset any cached chunk info for this dataset */
- H5D_istore_cinfo_cache_reset(&dset->shared->cache.chunk.last);
-
-done:
- /* Release the fill buffer info, if it's been initialized */
- if(fb_info_init && H5D_fill_term(&fb_info) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_allocate() */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5D_istore_prune_check
- *
- * Purpose: Search for chunks that are no longer necessary in the B-tree.
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- * March 26, 2002
+ * Tuesday, May 20, 2008
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static int
-H5D_istore_prune_check(H5F_t UNUSED *f, hid_t UNUSED dxpl_id,
- const void *_lt_key, haddr_t UNUSED addr, const void UNUSED *_rt_key,
+H5D_istore_idx_iterate_cb(H5F_t UNUSED *f, hid_t UNUSED dxpl_id,
+ const void *_lt_key, haddr_t addr, const void UNUSED *_rt_key,
void *_udata)
{
- H5D_istore_it_ud3_t *udata = (H5D_istore_it_ud3_t *)_udata;
- const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key;
- unsigned rank; /*current # of dimensions */
- unsigned u;
- int ret_value = H5_ITER_CONT; /* Return value */
-
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_prune_check)
-
- /* Figure out what chunks are no longer in use for the specified extent and release them */
- rank = udata->common.mesg->u.chunk.ndims - 1;
- for(u = 0; u < rank; u++)
- /* The 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.
- */
- if((hsize_t)lt_key->offset[u] > udata->dims[u]) {
- H5D_istore_sl_ck_t *sl_node; /* Skip list node for chunk to remove */
-
- /* Allocate space for the shared structure */
- if(NULL == (sl_node = H5FL_MALLOC(H5D_istore_sl_ck_t)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for shared B-tree info")
+ H5D_istore_it_ud_t *udata = (H5D_istore_it_ud_t *)_udata; /* User data */
+ const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key; /* B-tree key for chunk */
+ H5D_chunk_rec_t chunk_rec; /* Generic chunk record for callback */
+ int ret_value; /* Return value */
- /* Calculate the index of this chunk */
- if(H5V_chunk_index(rank, lt_key->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &sl_node->index) < 0) {
- H5FL_FREE(H5D_istore_sl_ck_t, sl_node);
- HGOTO_ERROR(H5E_IO, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index")
- } /* end if */
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_iterate_cb)
- /* Store the key for the chunk */
- sl_node->key = *lt_key;
+ /* Sanity check for memcpy() */
+ HDassert(offsetof(H5D_chunk_rec_t, nbytes) == offsetof(H5D_istore_key_t, nbytes));
+ HDassert(offsetof(H5D_chunk_rec_t, offset) == offsetof(H5D_istore_key_t, offset));
+ HDassert(offsetof(H5D_chunk_rec_t, filter_mask) == offsetof(H5D_istore_key_t, filter_mask));
- /* Insert the chunk description in the skip list */
- if(H5SL_insert(udata->outside, sl_node, &sl_node->index) < 0) {
- H5FL_FREE(H5D_istore_sl_ck_t, sl_node);
- HGOTO_ERROR(H5E_IO, H5E_CANTINSERT, H5_ITER_ERROR, "can't insert chunk into skip list")
- } /* end if */
+ /* Compose generic chunk record for callback */
+ HDmemcpy(&chunk_rec, lt_key, sizeof(*lt_key));
+ chunk_rec.chunk_addr = addr;
- /* Break out of loop, we know the chunk is outside the current dimensions */
- break;
- } /* end if */
+ /* Make "generic chunk" callback */
+ if((ret_value = (udata->cb)(&chunk_rec, udata->udata)) < 0)
+ HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback");
-done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_prune_check() */
+} /* H5D_istore_idx_iterate_cb() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_prune_remove
+ * Function: H5D_istore_idx_iterate
*
- * Purpose: Destroy a skip list node for "pruning" chunks, also removes
- * the chunk from the B-tree.
+ * Purpose: Iterate over the chunks in the B-tree index, making a callback
+ * for each one.
*
* Return: Non-negative on success/Negative on failure
*
- * Programmer: Quincey Koziol, koziol@hdfgroup.org
- * May 3, 2007
+ * Programmer: Quincey Koziol
+ * Tuesday, May 20, 2008
*
*-------------------------------------------------------------------------
*/
-static herr_t
-H5D_istore_prune_remove(void *item, void UNUSED *key, void *op_data)
+static int
+H5D_istore_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata)
{
- H5D_istore_sl_ck_t *sl_node = (H5D_istore_sl_ck_t *)item; /* Temporary pointer to chunk to remove */
- H5D_istore_sl_rm_t *rm_info = (H5D_istore_sl_rm_t *)op_data; /* Information needed for removing chunk from B-tree */
- H5D_istore_ud0_t bt_udata; /* User data for B-tree removal routine */
- herr_t ret_value = H5_ITER_CONT; /* Return value */
+ H5D_istore_it_ud_t udata; /* User data for B-tree iterator callback */
+ int ret_value; /* Return value */
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_prune_remove)
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_iterate)
- /* Sanity checks */
- HDassert(sl_node);
- HDassert(rm_info);
-
- /* Initialize the user data for the B-tree callback */
- bt_udata.mesg = rm_info->mesg;
- bt_udata.offset = sl_node->key.offset;
-
- /* Remove */
- if(H5B_remove(rm_info->f, rm_info->dxpl_id, H5B_ISTORE, rm_info->mesg->u.chunk.addr, &bt_udata) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTINIT, H5_ITER_ERROR, "unable to remove entry")
-
- /* Free the chunk checking node */
- H5FL_FREE(H5D_istore_sl_ck_t, sl_node);
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_istore_prune_remove() */
-
-
-/*-------------------------------------------------------------------------
- * 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: Non-negative on success/Negative on failure
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- * Algorithm: Robb Matzke
- * March 27, 2002
- *
- * The algorithm is:
- *
- * For chunks that are no longer necessary:
- *
- * 1. Search in the raw data cache for each chunk
- * 2. If found then preempt it from the cache
- * 3. Search in the B-tree for each chunk
- * 4. If found then remove it from the B-tree and deallocate file storage for the chunk
- *
- * This example shows a 2d dataset of 90x90 with a chunk size of 20x20.
- *
- *
- * 0 20 40 60 80 90 100
- * 0 +---------+---------+---------+---------+-----+...+
- * |:::::X:::::::::::::: : : | :
- * |:::::::X:::::::::::: : : | : Key
- * |::::::::::X::::::::: : : | : --------
- * |::::::::::::X::::::: : : | : +-+ Dataset
- * 20+::::::::::::::::::::.........:.........:.....+...: | | Extent
- * | :::::X::::: : : | : +-+
- * | ::::::::::: : : | :
- * | ::::::::::: : : | : ... Chunk
- * | :::::::X::: : : | : : : Boundary
- * 40+.........:::::::::::.........:.........:.....+...: :.:
- * | : : : : | :
- * | : : : : | : ... Allocated
- * | : : : : | : ::: & Filled
- * | : : : : | : ::: Chunk
- * 60+.........:.........:.........:.........:.....+...:
- * | : :::::::X::: : | : X Element
- * | : ::::::::::: : | : Written
- * | : ::::::::::: : | :
- * | : ::::::::::: : | :
- * 80+.........:.........:::::::::::.........:.....+...: O Fill Val
- * | : : ::::::::::: | : Explicitly
- * | : : ::::::X:::: | : Written
- * 90+---------+---------+---------+---------+-----+ :
- * : : : ::::::::::: :
- * 100:.........:.........:.........:::::::::::.........:
- *
- *
- * We have 25 total chunks for this dataset, 5 of which have space
- * allocated in the file because they were written to one or more
- * elements. These five chunks (and only these five) also have entries in
- * the storage B-tree for this dataset.
- *
- * Now lets say we want to shrink the dataset down to 70x70:
- *
- *
- * 0 20 40 60 70 80 90 100
- * 0 +---------+---------+---------+----+----+-----+...+
- * |:::::X:::::::::::::: : | : | :
- * |:::::::X:::::::::::: : | : | : Key
- * |::::::::::X::::::::: : | : | : --------
- * |::::::::::::X::::::: : | : | : +-+ Dataset
- * 20+::::::::::::::::::::.........:....+....:.....|...: | | Extent
- * | :::::X::::: : | : | : +-+
- * | ::::::::::: : | : | :
- * | ::::::::::: : | : | : ... Chunk
- * | :::::::X::: : | : | : : : Boundary
- * 40+.........:::::::::::.........:....+....:.....|...: :.:
- * | : : : | : | :
- * | : : : | : | : ... Allocated
- * | : : : | : | : ::: & Filled
- * | : : : | : | : ::: Chunk
- * 60+.........:.........:.........:....+....:.....|...:
- * | : :::::::X::: | : | : X Element
- * | : ::::::::::: | : | : Written
- * +---------+---------+---------+----+ : | :
- * | : ::::::::::: : | :
- * 80+.........:.........:::::::::X:.........:.....|...: O Fill Val
- * | : : ::::::::::: | : Explicitly
- * | : : ::::::X:::: | : Written
- * 90+---------+---------+---------+---------+-----+ :
- * : : : ::::::::::: :
- * 100:.........:.........:.........:::::::::::.........:
- *
- *
- * That means that the nine chunks along the bottom and right side should
- * no longer exist. Of those nine chunks, (0,80), (20,80), (40,80),
- * (60,80), (80,80), (80,60), (80,40), (80,20), and (80,0), one is actually allocated
- * that needs to be released.
- * To release the chunks, we traverse the B-tree to obtain a list of unused
- * allocated chunks, and then call H5B_remove() for each chunk.
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5D_istore_prune_by_extent(const H5D_io_info_t *io_info, const hsize_t *old_dims)
-{
- H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
- const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
- H5D_rdcc_ent_t *ent = NULL, *next = NULL; /*cache entry */
- H5D_istore_it_ud3_t udata; /*B-tree pass-through */
- H5D_istore_sl_rm_t rm_info; /* User data for skip list destroy callback */
- hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */
- hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */
- hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
- unsigned rank; /* Current # of dimensions */
- unsigned u; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_istore_prune_by_extent, FAIL)
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
+ HDassert(chunk_cb);
+ HDassert(chunk_udata);
- /* Check args */
- HDassert(io_info);
- HDassert(dset && H5D_CHUNKED == dset->shared->layout.type);
- HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
- HDassert(H5F_addr_defined(dset->shared->layout.u.chunk.addr));
-
- /* Go get the rank & dimensions */
- rank = dset->shared->layout.u.chunk.ndims - 1;
- if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
-
- /*-------------------------------------------------------------------------
- * Figure out what chunks are no longer in use for the specified extent
- * and release them from the linked list raw data cache
- *-------------------------------------------------------------------------
- */
- for(ent = rdcc->head; ent; ent = next) {
- /* Get pointer to next extry in cache, in case this one is evicted */
- next = ent->next;
-
- /* Check for chunk offset outside of new dimensions */
- for(u = 0; u < rank; u++)
- if((hsize_t)ent->offset[u] > curr_dims[u]) {
-#ifdef H5D_ISTORE_DEBUG
- HDfputs("cache:remove:[", stderr);
- for(u = 0; u < rank; 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(io_info, ent, FALSE) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to preempt chunk")
-
- /* Break out of loop, chunk is evicted */
- break;
- } /* end if */
- } /* end for */
-
- /* Round up to the next integer # of chunks, to accomodate partial chunks */
- for(u = 0; u < rank; u++)
- chunks[u] = ((old_dims[u] + dset->shared->layout.u.chunk.dim[u]) - 1) / dset->shared->layout.u.chunk.dim[u];
-
- /* Get the "down" sizes for each dimension */
- if(H5V_array_down(rank, chunks, down_chunks) < 0)
- HGOTO_ERROR(H5E_IO, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
-
- /* Initialize the user data for the iteration */
+ /* Initialize userdata */
HDmemset(&udata, 0, sizeof udata);
- udata.common.mesg = &dset->shared->layout;
- udata.dims = curr_dims;
- udata.down_chunks = down_chunks;
-
- /* Initialize the skip list that will hold the chunks outside the dimensions */
- if(NULL == (udata.outside = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_ISTORE_DEFAULT_SKIPLIST_HEIGHT)))
- HGOTO_ERROR(H5E_IO, H5E_CANTCREATE, FAIL, "can't create skip list for chunks outside new dimensions")
-
- /* Iterate over chunks in dataset, creating a list of chunks which are
- * now completely outside the dataset's dimensions.
- *
- * Note: It would be more efficient to create a new B-tree routine that
- * performed a "remove if" operation on the B-tree and remove all
- * the chunks that were outside the dataset's dimensions through
- * that routine. However, that's a fair amount of work and it's
- * unlikely that shrinking a dataset is a performance critical
- * operation. - QAK
- */
- if(H5B_iterate(dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, H5D_istore_prune_check, dset->shared->layout.u.chunk.addr, &udata) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to iterate over B-tree")
-
- /* Set up user data for skip list callback */
- rm_info.f = dset->oloc.file;
- rm_info.dxpl_id = io_info->dxpl_id;
- rm_info.mesg = &dset->shared->layout;
+ udata.common.mesg = idx_info->layout;
+ udata.cb = chunk_cb;
+ udata.udata = chunk_udata;
- /* Destroy the skip list, deleting the chunks in the callback */
- H5SL_destroy(udata.outside, H5D_istore_prune_remove, &rm_info);
+ /* Iterate over existing chunks */
+ if((ret_value = H5B_iterate(idx_info->f, idx_info->dxpl_id, H5B_ISTORE, idx_info->layout->u.chunk.addr, H5D_istore_idx_iterate_cb, &udata)) < 0)
+ HERROR(H5E_DATASET, H5E_BADITER, "unable to iterate over chunk B-tree");
- /* Reset any cached chunk info for this dataset */
- H5D_istore_cinfo_cache_reset(&dset->shared->cache.chunk.last);
-
-done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_prune_by_extent() */
+} /* end H5D_istore_idx_iterate() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_remove
+ * Function: H5D_istore_idx_remove
*
- * Purpose: Removes chunks that are no longer necessary in the B-tree.
+ * Purpose: Remove chunk from v1 B-tree index.
*
* Return: Non-negative on success/Negative on failure
*
- * Programmer: Robb Matzke
- * Pedro Vicente, pvn@ncsa.uiuc.edu
- * March 28, 2002
+ * Programmer: Quincey Koziol
+ * Thursday, May 22, 2008
*
*-------------------------------------------------------------------------
*/
-/* ARGSUSED */
-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 */ )
+static herr_t
+H5D_istore_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata)
{
- H5D_istore_key_t *lt_key = (H5D_istore_key_t *)_lt_key;
- H5B_ins_t ret_value = H5B_INS_REMOVE; /* Return value */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI_NOINIT(H5D_istore_remove)
-
- /* Remove raw data chunk from file */
- H5_CHECK_OVERFLOW(lt_key->nbytes, uint32_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")
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_remove)
- /* Mark keys as unchanged */
- *lt_key_changed = FALSE;
- *rt_key_changed = FALSE;
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* 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: Non-negative on success/Negative on failure
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- * 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.
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
-{
- H5S_t *space_chunk = NULL; /* Dataspace for a chunk */
- H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
- const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */
- H5D_storage_t store; /* Dataset storage information */
- H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
- hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
- hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* Current dataspace dimensions */
- hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Current chunk dimensions */
- hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Logical location of the chunks */
- hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */
- hsize_t nchunks[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 */
- uint32_t elmts_per_chunk; /* Elements in a chunk */
- int srank; /* # of chunk dimensions (signed) */
- unsigned rank; /* # of chunk dimensions */
- hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
- unsigned u; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_istore_initialize_by_extent, FAIL)
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
+ HDassert(udata);
- /* Check args */
- HDassert(io_info);
- HDassert(io_info->dset && H5D_CHUNKED == layout->type);
- HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
- HDassert(H5F_addr_defined(layout->u.chunk.addr));
-
- /* Go get the rank & dimensions */
- if((srank = H5S_get_simple_extent_dims(dset->shared->space, dset_dims, NULL)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
- H5_ASSIGN_OVERFLOW(rank, srank, int, unsigned);
-
- /* Set size of lowest chunk dimension (the dataset element size) */
- dset_dims[rank] = layout->u.chunk.dim[rank];
-
- /* Compute the number of chunks in dataset & the # of elements in a chunk */
- /* (round up to the next integer # of chunks, to accomodate partial chunks) */
- for(u = 0, elmts_per_chunk = 1; u < rank; u++) {
- nchunks[u] = ((dset_dims[u] - 1) / layout->u.chunk.dim[u]) + 1;
- elmts_per_chunk *= layout->u.chunk.dim[u];
- } /* end for */
-
- /* Get the "down" sizes for each dimension */
- if(H5V_array_down(rank, nchunks, 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] = 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")
-
- /* Point to local dataset storage info */
- HDassert(io_info->store == NULL); /* Make certain we aren't blowing anything away */
- io_info->store = &store;
-
- /* Reset hyperslab start array */
- HDmemset(hyper_start, 0, sizeof(hyper_start));
-
- /* Initialize current chunk offset to the origin (0, 0, 0, ...) */
- HDmemset(chunk_offset, 0, sizeof(chunk_offset));
-
- /* Loop over all chunks */
- carry = FALSE;
- while(!carry) {
- hbool_t found; /* Initialize this entry */
- int i; /* Local index variable */
-
- /*
- * Figure out what chunks have to be initialized. These are the chunks where the dataspace
- * extent boundary is within the chunk
- */
- found = FALSE;
- for(u = 0; u < rank; u++)
- if((chunk_offset[u] + layout->u.chunk.dim[u]) > dset_dims[u]) {
- found = TRUE;
- break;
- } /* end if */
-
- if(found) {
- H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */
- hssize_t nelmts; /* Number of data elements */
- hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */
- uint8_t *chunk; /* The file chunk */
- unsigned idx_hint; /* Which chunk we're dealing with */
- hsize_t bytes_accessed; /* Bytes accessed in chunk */
-
- /* Initialize the fill value buffer, if necessary */
- if(!fb_info_init) {
- H5_CHECK_OVERFLOW(elmts_per_chunk, uint32_t, size_t);
- if(H5D_fill_init(&fb_info, NULL, FALSE, NULL, NULL, NULL, NULL,
- &dset->shared->dcpl_cache.fill,
- dset->shared->type, dset->shared->type_id, (size_t)elmts_per_chunk,
- io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
- fb_info_init = TRUE;
- } /* end if */
-
- /* Compute the # of elements to leave with existing value, in each dimension */
- for(u = 0; u < rank; u++)
- count[u] = MIN(layout->u.chunk.dim[u], (dset_dims[u] - chunk_offset[u]));
-
-#ifdef H5D_ISTORE_DEBUG
- HDfputs("cache:initialize:offset:[", stdout);
- for(u = 0; u < rank; u++)
- HDfprintf(stdout, "%s%Hd", u ? ", " : "", chunk_offset[u]);
- HDfputs("]", stdout);
- HDfputs(":count:[", stdout);
- for(u = 0; u < rank; u++)
- HDfprintf(stdout, "%s%Hd", u ? ", " : "", count[u]);
- HDfputs("]\n", stdout);
-#endif
-
- /* Select all elements in chunk, to begin with */
- if(H5S_select_all(space_chunk, TRUE) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select space")
-
- /* "Subtract out" the elements to keep */
- if(H5S_select_hyperslab(space_chunk, H5S_SELECT_NOTB, hyper_start, NULL, count, NULL) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select hyperslab")
-
- /* Calculate the index of this chunk */
- if(H5V_chunk_index(rank, chunk_offset, layout->u.chunk.dim, down_chunks, &store.chunk.index) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
-
- /* Lock the chunk into the cache, to get a pointer to the chunk buffer */
- store.chunk.offset = chunk_offset;
- if(NULL == (chunk = (uint8_t *)H5D_istore_lock(io_info, NULL, FALSE, &idx_hint)))
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk")
-
-
- /* Fill the selection in the memory buffer */
- /* Use the size of the elements in the chunk directly instead of */
- /* relying on the fill.size, which might be set to 0 if there is */
- /* no fill-value defined for the dataset -QAK */
-
- /* Get the number of elements in the selection */
- nelmts = H5S_GET_SELECT_NPOINTS(space_chunk);
- HDassert(nelmts >= 0);
- H5_CHECK_OVERFLOW(nelmts, hssize_t, size_t);
-
- /* Check for VL datatype & non-default fill value */
- if(fb_info.has_vlen_fill_type)
- /* Re-fill the buffer to use for this I/O operation */
- if(H5D_fill_refill_vl(&fb_info, (size_t)nelmts, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
-
- /* Create a selection iterator for scattering the elements to memory buffer */
- H5_CHECK_OVERFLOW(layout->u.chunk.dim[rank], uint32_t, size_t);
- if(H5S_select_iter_init(&chunk_iter, space_chunk, (size_t)layout->u.chunk.dim[rank]) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunk selection information")
-
- /* Scatter the data into memory */
- if(H5D_scatter_mem(fb_info.fill_buf, space_chunk, &chunk_iter, (size_t)nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) {
- H5S_SELECT_ITER_RELEASE(&chunk_iter);
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
- } /* end if */
-
- /* Release the selection iterator */
- if(H5S_SELECT_ITER_RELEASE(&chunk_iter) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
-
-
- /* The number of bytes accessed in the chunk */
- /* (i.e. the bytes replaced with fill values) */
- bytes_accessed = nelmts * layout->u.chunk.dim[rank];
-
- /* Release lock on chunk */
- H5_CHECK_OVERFLOW(bytes_accessed, hsize_t, uint32_t);
- if(H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, (uint32_t)bytes_accessed) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk")
- } /* end if */
-
- /* Increment indices */
- carry = TRUE;
- for(i = (int)(rank - 1); i >= 0; --i) {
- chunk_offset[i] += layout->u.chunk.dim[i];
- if(chunk_offset[i] >= dset_dims[i])
- chunk_offset[i] = 0;
- else {
- carry = FALSE;
- break;
- } /* end else */
- } /* end for */
- } /* end while */
+ /* Remove the chunk from the v1 B-tree index and release the space for the
+ * chunk (in the B-tree callback).
+ */
+ if(H5B_remove(idx_info->f, idx_info->dxpl_id, H5B_ISTORE, idx_info->layout->u.chunk.addr, udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to remove chunk entry")
done:
- /* Release resources */
- if(space_chunk && H5S_close(space_chunk) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
- if(fb_info_init && H5D_fill_term(&fb_info) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
-
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_initialize_by_extent() */
+} /* H5D_istore_idx_remove() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_delete
+ * Function: H5D_istore_idx_delete
*
- * Purpose: Delete raw data storage for entire dataset (i.e. all chunks)
+ * Purpose: Delete v1 B-tree index and raw data storage for entire dataset
+ * (i.e. all chunks)
*
* Return: Success: Non-negative
* Failure: negative
@@ -3286,365 +1143,123 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5D_istore_delete(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout)
+static herr_t
+H5D_istore_idx_delete(const H5D_chk_idx_info_t *idx_info)
{
- herr_t ret_value=SUCCEED; /* Return value */
+ H5O_layout_t tmp_layout; /* Local copy of layout info */
+ H5D_istore_ud0_t udata; /* User data for B-tree iterator call */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5D_istore_delete, FAIL)
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_delete)
- /* Check if the B-tree has been created in the file */
- if(H5F_addr_defined(layout->u.chunk.addr)) {
- H5O_layout_t tmp_layout=*layout;/* Local copy of layout info */
- H5D_istore_ud0_t udata; /* User data for B-tree iterator call */
+ /* Sanity checks */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
+ HDassert(H5F_addr_defined(idx_info->layout->u.chunk.addr));
- /* Set up user data for B-tree deletion */
- HDmemset(&udata, 0, sizeof udata);
- udata.mesg = &tmp_layout;
+ /* Set up user data for B-tree deletion */
+ HDmemset(&udata, 0, sizeof udata);
+ tmp_layout = *idx_info->layout;
+ udata.mesg = &tmp_layout;
- /* Allocate the shared structure */
- if(H5D_istore_shared_create(f, &tmp_layout)<0)
- HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
+ /* Set up the shared structure */
+ if(H5D_istore_shared_create(idx_info->f, &tmp_layout) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
- /* Delete entire B-tree */
- if(H5B_delete(f, dxpl_id, H5B_ISTORE, tmp_layout.u.chunk.addr, &udata)<0)
- HGOTO_ERROR(H5E_IO, H5E_CANTDELETE, 0, "unable to delete chunk B-tree")
+ /* Delete entire B-tree */
+ if(H5B_delete(idx_info->f, idx_info->dxpl_id, H5B_ISTORE, tmp_layout.u.chunk.addr, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk B-tree")
- /* Free the raw B-tree node buffer */
- if(tmp_layout.u.chunk.btree_shared==NULL)
- HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
- if(H5RC_DEC(tmp_layout.u.chunk.btree_shared)<0)
- HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
- } /* end if */
+ /* Free the raw B-tree node buffer */
+ if(NULL == tmp_layout.u.chunk.btree_shared)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "ref-counted page nil")
+ if(H5RC_DEC(tmp_layout.u.chunk.btree_shared) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_delete() */
+} /* end H5D_istore_idx_delete() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_update_cache
+ * Function: H5D_istore_idx_copy_setup
*
- * Purpose: Update any cached chunks index values after the dataspace
- * size has changed
+ * Purpose: Set up any necessary information for copying chunks
*
- * Return: Success: Non-negative
- * Failure: negative
+ * Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
- * Saturday, May 29, 2004
+ * Thursday, May 29, 2008
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5D_istore_update_cache(H5D_t *dset, hid_t dxpl_id)
+static herr_t
+H5D_istore_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src,
+ const H5D_chk_idx_info_t *idx_info_dst)
{
- H5D_io_info_t io_info; /* Temporary I/O info object */
- H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
- H5D_rdcc_ent_t *ent, *next; /*cache entry */
- H5D_rdcc_ent_t *old_ent; /* Old cache entry */
- H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
- H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
- unsigned rank; /*current # of dimensions */
- hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */
- hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */
- hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
- unsigned u; /*counters */
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_istore_update_cache, FAIL)
-
- /* Check args */
- HDassert(dset && H5D_CHUNKED == dset->shared->layout.type);
- HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
-
- /* Get the rank */
- rank = dset->shared->layout.u.chunk.ndims-1;
- HDassert(rank > 0);
+ herr_t ret_value = SUCCEED; /* Return value */
- /* 1-D dataset's chunks can't have their index change */
- if(rank == 1)
- HGOTO_DONE(SUCCEED)
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_copy_setup)
- /* Go get the dimensions */
- if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
+ HDassert(idx_info_src);
+ HDassert(idx_info_src->f);
+ HDassert(idx_info_src->layout);
+ HDassert(idx_info_dst);
+ HDassert(idx_info_dst->f);
+ HDassert(idx_info_dst->layout);
+ HDassert(!H5F_addr_defined(idx_info_dst->layout->u.chunk.addr));
- /* Round up to the next integer # of chunks, to accomodate partial chunks */
- for(u = 0; u < rank; u++)
- chunks[u] = ((curr_dims[u] + dset->shared->layout.u.chunk.dim[u]) - 1) / dset->shared->layout.u.chunk.dim[u];
-
- /* Get the "down" sizes for each dimension */
- if(H5V_array_down(rank, chunks, down_chunks) < 0)
- HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
-
- /* Fill the DXPL cache values for later use */
- if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
-
- /* Construct dataset I/O info */
- H5D_BUILD_IO_INFO_WRT(&io_info, dset, dxpl_cache, dxpl_id, NULL, NULL);
-
- /* Recompute the index for each cached chunk that is in a dataset */
- for(ent = rdcc->head; ent; ent = next) {
- hsize_t idx; /* Chunk index */
- unsigned old_idx; /* Previous index number */
-
- /* Get the pointer to the next cache entry */
- next = ent->next;
-
- /* Calculate the index of this chunk */
- if(H5V_chunk_index(rank, ent->offset, dset->shared->layout.u.chunk.dim, down_chunks, &idx) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
-
- /* Compute the index for the chunk entry */
- old_idx = ent->idx; /* Save for later */
- ent->idx = H5D_CHUNK_HASH(dset->shared, idx);
-
- if(old_idx != ent->idx) {
- /* Check if there is already a chunk at this chunk's new location */
- old_ent = rdcc->slot[ent->idx];
- if(old_ent != NULL) {
- HDassert(old_ent->locked == 0);
-
- /* Check if we are removing the entry we would walk to next */
- if(old_ent == next)
- next = old_ent->next;
-
- /* Remove the old entry from the cache */
- if(H5D_istore_preempt(&io_info, old_ent, TRUE) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
- } /* end if */
+ /* Create shared B-tree info for each file */
+ if(H5D_istore_shared_create(idx_info_src->f, idx_info_src->layout) < 0)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for source shared B-tree info")
+ if(H5D_istore_shared_create(idx_info_dst->f, idx_info_dst->layout) < 0)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for destination shared B-tree info")
- /* 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 */
+ /* Create the root of the B-tree that describes chunked storage in the dest. file */
+ if(H5D_istore_idx_create(idx_info_dst) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5F_istore_update_cache() */
+} /* end H5D_istore_idx_copy_setup() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_copy
+ * Function: H5D_istore_idx_copy_shutdown
*
- * Purpose: copy an indexed storage B-tree from SRC file to DST file.
+ * Purpose: Shutdown any information from copying chunks
*
- * Return: Non-negative on success (with the ISTORE argument initialized
- * and ready to write to an object header). Negative on failure.
+ * Return: Non-negative on success/Negative on failure
*
- * Programmer: Peter Cao
- * August 20, 2005
+ * Programmer: Quincey Koziol
+ * Thursday, May 29, 2008
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5D_istore_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst,
- H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, H5O_pline_t *pline, hid_t dxpl_id)
+static herr_t
+H5D_istore_idx_copy_shutdown(H5O_layout_t *layout_src, H5O_layout_t *layout_dst)
{
- H5D_istore_it_ud4_t udata;
- H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */
- hid_t tid_src = -1; /* Datatype ID for source datatype */
- hid_t tid_dst = -1; /* Datatype ID for destination datatype */
- hid_t tid_mem = -1; /* Datatype ID for memory datatype */
- size_t buf_size; /* Size of copy buffer */
- size_t reclaim_buf_size; /* Size of reclaim buffer */
- void *buf = NULL; /* Buffer for copying data */
- void *bkg = NULL; /* Buffer for background during type conversion */
- void *reclaim_buf = NULL; /* Buffer for reclaiming data */
- H5S_t *buf_space = NULL; /* Dataspace describing buffer */
- hid_t sid_buf = -1; /* ID for buffer dataspace */
- uint32_t nelmts = 0; /* Number of elements in buffer */
- hbool_t do_convert = FALSE; /* Indicate that type conversions should be performed */
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_istore_copy, FAIL)
-
- /* Check args */
- HDassert(f_src);
- HDassert(f_dst);
- HDassert(layout_src && H5D_CHUNKED == layout_src->type);
- HDassert(layout_dst && H5D_CHUNKED == layout_dst->type);
- HDassert(dt_src);
-
- /* Create datatype ID for src datatype */
- if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
-
- /* Create shared B-tree info for each file */
- if(H5D_istore_shared_create(f_src, layout_src) < 0)
- HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
- if(H5D_istore_shared_create(f_dst, layout_dst) < 0)
- HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
-
- /* Check if we need to create the B-tree in the dest. file */
- if(layout_dst->u.chunk.addr == HADDR_UNDEF) {
- /* Create the root of the B-tree that describes chunked storage */
- if(H5D_istore_create(f_dst, dxpl_id, layout_dst) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
- } /* end if */
-
- /* If there's a VLEN source datatype, set up type conversion information */
- if(H5T_detect_class(dt_src, H5T_VLEN) > 0) {
- H5T_t *dt_dst; /* Destination datatype */
- H5T_t *dt_mem; /* Memory datatype */
- size_t mem_dt_size; /* Memory datatype size */
- size_t tmp_dt_size; /* Temp. datatype size */
- size_t max_dt_size; /* Max atatype size */
- hsize_t buf_dim; /* Dimension for buffer */
- unsigned u;
-
- /* create a memory copy of the variable-length datatype */
- if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
- if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
-
- /* create variable-length datatype at the destinaton file */
- if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
- if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
- if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
-
- /* Set up the conversion functions */
- if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
- if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
-
- /* Determine largest datatype size */
- if(0 == (max_dt_size = H5T_get_size(dt_src)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
- if(0 == (mem_dt_size = H5T_get_size(dt_mem)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
- max_dt_size = MAX(max_dt_size, mem_dt_size);
- if(0 == (tmp_dt_size = H5T_get_size(dt_dst)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
- max_dt_size = MAX(max_dt_size, tmp_dt_size);
-
- /* Compute the number of elements per chunk */
- nelmts = 1;
- for(u = 0; u < (layout_src->u.chunk.ndims - 1); u++)
- nelmts *= layout_src->u.chunk.dim[u];
-
- /* Create the space and set the initial extent */
- buf_dim = nelmts;
- if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
-
- /* Atomize */
- if((sid_buf = H5I_register(H5I_DATASPACE, buf_space)) < 0) {
- H5S_close(buf_space);
- HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
- } /* end if */
-
- /* Set initial buffer sizes */
- buf_size = nelmts * max_dt_size;
- reclaim_buf_size = nelmts * mem_dt_size;
-
- /* Allocate memory for reclaim buf */
- if(NULL == (reclaim_buf = H5MM_malloc(reclaim_buf_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
-
- /* Indicate that type conversion should be performed */
- do_convert = TRUE;
- } /* end if */
- else {
- if(H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) {
- /* Indicate that type conversion should be performed */
- do_convert = TRUE;
- } /* end if */
-
- H5_ASSIGN_OVERFLOW(buf_size, layout_src->u.chunk.size, uint32_t, size_t);
- reclaim_buf_size = 0;
- } /* end else */
-
- /* Set up conversion buffer, if appropriate */
- if(do_convert) {
- /* Allocate background memory for converting the chunk */
- if(NULL == (bkg = H5MM_malloc(buf_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
-
- /* Check for reference datatype and no expanding references & clear background buffer */
- if(!cpy_info->expand_ref &&
- ((H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) && (f_src != f_dst)))
- /* Reset value to zero */
- HDmemset(bkg, 0, buf_size);
- } /* end if */
+ herr_t ret_value = SUCCEED; /* Return value */
- /* Allocate memory for copying the chunk */
- if(NULL == (buf = H5MM_malloc(buf_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_copy_shutdown)
- /* Initialize the callback structure for the source */
- HDmemset(&udata, 0, sizeof udata);
- udata.common.mesg = layout_src;
- udata.file_src = f_src;
- udata.addr_dst = layout_dst->u.chunk.addr;
- udata.buf = buf;
- udata.bkg = bkg;
- udata.buf_size = buf_size;
- udata.tid_src = tid_src;
- udata.tid_mem = tid_mem;
- udata.tid_dst = tid_dst;
- udata.dt_src = dt_src;
- udata.do_convert = do_convert;
- udata.tpath_src_mem = tpath_src_mem;
- udata.tpath_mem_dst = tpath_mem_dst;
- udata.reclaim_buf = reclaim_buf;
- udata.reclaim_buf_size = reclaim_buf_size;
- udata.buf_space = buf_space;
- udata.nelmts = nelmts;
- udata.pline = pline;
- udata.file_dst = f_dst;
- udata.cpy_info = cpy_info;
-
- /* copy the chunked data by iteration */
- if(H5B_iterate(f_src, dxpl_id, H5B_ISTORE, H5D_istore_iter_copy, layout_src->u.chunk.addr, &udata) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to iterate over chunk B-tree")
-
- /* I/O buffers may have been re-allocated */
- buf = udata.buf;
- bkg = udata.bkg;
-
-done:
- if(sid_buf > 0)
- if(H5I_dec_ref(sid_buf) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID")
- if(tid_src > 0)
- if(H5I_dec_ref(tid_src) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
- if(tid_dst > 0)
- if(H5I_dec_ref(tid_dst) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
- if(tid_mem > 0)
- if(H5I_dec_ref(tid_mem) < 0)
- HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
- if(buf)
- H5MM_xfree(buf);
- if(bkg)
- H5MM_xfree(bkg);
- if(reclaim_buf)
- H5MM_xfree(reclaim_buf);
+ HDassert(layout_src);
+ HDassert(layout_dst);
+ /* Decrement refcount on shared B-tree info */
if(H5RC_DEC(layout_src->u.chunk.btree_shared) < 0)
- HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
-
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to decrement ref-counted page")
if(H5RC_DEC(layout_dst->u.chunk.btree_shared) < 0)
- HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to decrement ref-counted page")
+done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_copy() */
+} /* end H5D_istore_idx_copy_shutdown() */
/*-------------------------------------------------------------------------
- * Function: H5D_istore_bh_size
+ * Function: H5D_istore_idx_size
*
* Purpose: Retrieve the amount of B-tree storage for chunked dataset
*
@@ -3657,88 +1272,53 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5D_istore_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout, hsize_t *btree_size)
+H5D_istore_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size)
{
- H5D_istore_it_ud1_t udata; /* User-data for loading istore nodes */
- H5B_info_ud_t bh_udata; /* User-data for B-tree size iteration */
- herr_t ret_value = SUCCEED;
+ H5D_istore_ud0_t udata; /* User-data for loading istore nodes */
+ H5B_info_t bt_info; /* B-tree info */
+ hbool_t shared_init = FALSE; /* Whether shared B-tree info is initialized */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5D_istore_bh_info, FAIL)
+ FUNC_ENTER_NOAPI(H5D_istore_idx_size, FAIL)
/* Check args */
- HDassert(f);
- HDassert(layout);
- HDassert(btree_size);
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
+ HDassert(index_size);
/* Initialize the shared info for the B-tree traversal */
- if(H5D_istore_shared_create(f, layout) < 0)
+ if(H5D_istore_shared_create(idx_info->f, idx_info->layout) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
+ shared_init = TRUE;
/* Initialize istore node user-data */
HDmemset(&udata, 0, sizeof udata);
- udata.common.mesg = layout;
+ udata.mesg = idx_info->layout;
- /* Iterate over B-tree, accumulating metadata size */
- bh_udata.udata = &udata;
- bh_udata.btree_size = btree_size;
- if(H5B_iterate_size(f, dxpl_id, H5B_ISTORE, NULL, layout->u.chunk.addr, &bh_udata) < 0)
+ /* Get metadata information for B-tree */
+ if(H5B_get_info(idx_info->f, idx_info->dxpl_id, H5B_ISTORE, idx_info->layout->u.chunk.addr, &bt_info, NULL, &udata) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "unable to iterate over chunk B-tree")
-done:
- if(layout->u.chunk.btree_shared == NULL)
- HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
- if(H5RC_DEC(layout->u.chunk.btree_shared) < 0)
- HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
-
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_bh_info() */
-
-
-/*-------------------------------------------------------------------------
- * 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
- *
- *-------------------------------------------------------------------------
- */
-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_it_ud2_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.common.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")
+ /* Set the size of the B-tree */
+ *index_size = bt_info.size;
done:
+ if(shared_init) {
+ if(idx_info->layout->u.chunk.btree_shared == NULL)
+ HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
+ if(H5RC_DEC(idx_info->layout->u.chunk.btree_shared) < 0)
+ HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
+ } /* end if */
+
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_istore_dump_btree() */
+} /* end H5D_istore_idx_size() */
-#ifdef H5D_ISTORE_DEBUG
/*-------------------------------------------------------------------------
- * Function: H5D_istore_stats
+ * Function: H5D_istore_idx_dest
*
- * 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.
+ * Purpose: Release indexing information in memory.
*
* Return: Non-negative on success/Negative on failure
*
@@ -3747,53 +1327,26 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5D_istore_stats (H5D_t *dset, hbool_t headers)
+static herr_t
+H5D_istore_idx_dest(const H5D_chk_idx_info_t *idx_info)
{
- H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
- double miss_rate;
- char ascii[32];
- herr_t ret_value=SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5D_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",
- "-----", "----", "------", "--------", "-----", "-------");
- }
+ herr_t ret_value = SUCCEED; /* Return value */
-#ifdef H5AC_DEBUG
- if (H5DEBUG(AC)) headers = TRUE;
-#endif
+ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_idx_dest)
- 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);
- }
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->layout);
- 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));
- }
+ /* Free the raw B-tree node buffer */
+ if(idx_info->layout->u.chunk.btree_shared == NULL)
+ HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
+ if(H5RC_DEC(idx_info->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_stats() */
-#endif /* H5D_ISTORE_DEBUG */
+} /* end H5D_istore_idx_dest() */
/*-------------------------------------------------------------------------
@@ -3812,17 +1365,20 @@ herr_t
H5D_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent,
int fwidth, unsigned ndims)
{
- H5O_layout_t layout;
H5D_istore_ud0_t udata; /* B-tree user data */
+ H5O_layout_t layout; /* Layout information for B-tree callback */
+ hbool_t shared_init = FALSE; /* Whether B-tree shared info is initialized */
herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5D_istore_debug,FAIL)
+ FUNC_ENTER_NOAPI(H5D_istore_debug, FAIL)
+ /* Set up "fake" layout info */
layout.u.chunk.ndims = ndims;
/* Allocate the shared structure */
- if(H5D_istore_shared_create(f, &layout)<0)
+ if(H5D_istore_shared_create(f, &layout) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
+ shared_init = TRUE;
/* Set up B-tree user data */
HDmemset(&udata, 0, sizeof udata);
@@ -3830,13 +1386,15 @@ H5D_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int inden
(void)H5B_debug(f, dxpl_id, addr, stream, indent, fwidth, H5B_ISTORE, &udata);
- /* Free the raw B-tree node buffer */
- if(layout.u.chunk.btree_shared==NULL)
- HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
- if(H5RC_DEC(layout.u.chunk.btree_shared)<0)
- HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
-
done:
+ if(shared_init) {
+ /* Free the raw B-tree node buffer */
+ if(layout.u.chunk.btree_shared == NULL)
+ HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
+ if(H5RC_DEC(layout.u.chunk.btree_shared) < 0)
+ HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
+ } /* end if */
+
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_istore_debug() */
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index dd0c602..a87c9d3 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -822,7 +822,6 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type
* equivalent of compressed contiguous datasets - QAK]
*/
if(total_chunks == 1) {
- H5D_storage_t chk_store; /* Temporary storage info for chunk address lookup */
hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */
H5SL_node_t *chunk_node; /* Pointer to chunk node for selection */
H5S_t *fspace; /* Dataspace describing chunk & selection in it */
@@ -833,10 +832,7 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type
HDmemset(coords, 0, sizeof(coords));
/* Look up address of chunk */
- io_info->store = &chk_store;
- chk_store.chunk.offset = coords;
- chk_store.chunk.index = 0;
- if(HADDR_UNDEF == (ctg_store.contig.dset_addr = H5D_istore_get_addr(io_info, NULL)))
+ if(HADDR_UNDEF == (ctg_store.contig.dset_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, coords, NULL)))
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list")
/* Check for this process having selection in this chunk */
@@ -968,7 +964,7 @@ if(H5DEBUG(D))
total_chunk_addr_array = H5MM_malloc(sizeof(haddr_t) * total_chunks);
/* Retrieve chunk address map */
- if(H5D_istore_chunkmap(io_info, total_chunk_addr_array, fm->down_chunks) < 0)
+ if(H5D_chunk_addrmap(io_info, total_chunk_addr_array, fm->down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address")
/* Get chunk with lowest address */
@@ -1181,7 +1177,7 @@ if(H5DEBUG(D))
/* Check if this process has somethign to do with this chunk */
if(chunk_info) {
H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
- H5D_istore_ud1_t udata; /* B-tree pass-through */
+ H5D_chunk_ud_t udata; /* B-tree pass-through */
void *chunk; /* Pointer to the data chunk in cache */
uint32_t accessed_bytes; /* Total accessed size in a chunk */
unsigned idx_hint = 0; /* Cache index hint */
@@ -1197,17 +1193,15 @@ if(H5DEBUG(D))
/* Load the chunk into cache. But if the whole chunk is written,
* simply allocate space instead of load the chunk.
*/
- if(HADDR_UNDEF == (caddr = H5D_istore_get_addr(io_info, &udata)))
+ if(HADDR_UNDEF == (caddr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata)))
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list")
/* Load the chunk into cache and lock it. */
if(H5D_chunk_cacheable(io_info, caddr)) {
hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */
- size_t tmp_accessed_bytes; /* Total accessed size in a chunk */
/* Compute # of bytes accessed in chunk */
- tmp_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
- H5_ASSIGN_OVERFLOW(accessed_bytes, tmp_accessed_bytes, size_t, uint32_t);
+ accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
/* Determine if we will access all the data in the chunk */
if(((io_info->op_type == H5D_IO_OP_WRITE) && (accessed_bytes != ctg_store.contig.dset_size))
@@ -1215,7 +1209,7 @@ if(H5DEBUG(D))
entire_chunk = FALSE;
/* Lock the chunk into the cache */
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, entire_chunk, &idx_hint)))
+ if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, entire_chunk, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
@@ -1247,7 +1241,7 @@ if(H5DEBUG(D))
} /* end else */
/* Release the cache lock on the chunk. */
- if(chunk && H5D_istore_unlock(io_info, (io_info->op_type == H5D_IO_OP_WRITE), idx_hint, chunk, accessed_bytes) < 0)
+ if(chunk && H5D_chunk_unlock(io_info, (io_info->op_type == H5D_IO_OP_WRITE), idx_hint, chunk, accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
} /* end if */
#else /* !defined(H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS) || !defined(H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS) */
@@ -1377,7 +1371,7 @@ if(H5DEBUG(D)) {
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
haddr_t chunk_addr; /* Address of chunk in file */
- H5D_istore_ud1_t udata; /* B-tree pass-through */
+ H5D_chunk_ud_t udata; /* B-tree pass-through */
hbool_t make_ind, make_coll; /* Flags to indicate that the MPI mode should change */
/* Get the actual chunk information from the skip list node */
@@ -1414,7 +1408,7 @@ if(H5DEBUG(D)) {
#endif /* H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS */
/* Retrieve the chunk's address */
- if(HADDR_UNDEF == (chunk_addr = H5D_istore_get_addr(io_info, &udata)))
+ if(HADDR_UNDEF == (chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata)))
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list")
/* Independent I/O */
@@ -1431,11 +1425,9 @@ if(H5DEBUG(D)) {
/* Load the chunk into cache and lock it. */
if(H5D_chunk_cacheable(io_info, chunk_addr)) {
hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */
- size_t tmp_accessed_bytes; /* Total accessed size in a chunk */
/* Compute # of bytes accessed in chunk */
- tmp_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
- H5_ASSIGN_OVERFLOW(accessed_bytes, tmp_accessed_bytes, size_t, uint32_t);
+ accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
/* Determine if we will access all the data in the chunk */
if(((io_info->op_type == H5D_IO_OP_WRITE) && (accessed_bytes != ctg_store.contig.dset_size))
@@ -1443,7 +1435,7 @@ if(H5DEBUG(D)) {
entire_chunk = FALSE;
/* Lock the chunk into the cache */
- if(NULL == (chunk = H5D_istore_lock(io_info, &udata, entire_chunk, &idx_hint)))
+ if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, entire_chunk, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
@@ -1476,7 +1468,7 @@ if(H5DEBUG(D)) {
/* Release the cache lock on the chunk. */
if(chunk)
- if(H5D_istore_unlock(io_info, (io_info->op_type == H5D_IO_OP_WRITE), idx_hint, chunk, accessed_bytes) < 0)
+ if(H5D_chunk_unlock(io_info, (io_info->op_type == H5D_IO_OP_WRITE), idx_hint, chunk, accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
} /* end if */
else { /*collective I/O */
@@ -1657,7 +1649,6 @@ H5D_sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm,
H5D_chunk_info_t *chunk_info; /* Current chunking info. of this node. */
haddr_t chunk_addr; /* Current chunking address of this node */
haddr_t *total_chunk_addr_array = NULL; /* The array of chunk address for the total number of chunk */
- H5D_storage_t store; /*union of EFL and chunk pointer in file space */
hbool_t do_sort = FALSE; /* Whether the addresses need to be sorted */
int bsearch_coll_chunk_threshold;
int many_chunk_opt = H5D_OBTAIN_ONE_CHUNK_ADDR_IND;
@@ -1706,7 +1697,7 @@ if(H5DEBUG(D))
if((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0)
HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank")
if(mpi_rank == 0) {
- if(H5D_istore_chunkmap(io_info, total_chunk_addr_array, fm->down_chunks) < 0)
+ if(H5D_chunk_addrmap(io_info, total_chunk_addr_array, fm->down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address")
} /* end if */
@@ -1715,9 +1706,6 @@ if(H5DEBUG(D))
HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code)
} /* end if */
- /* Set dataset storage for I/O info */
- io_info->store = &store;
-
/* Start at first node in chunk skip list */
i = 0;
if(NULL == (chunk_node = H5SL_first(fm->sel_chunks)))
@@ -1729,9 +1717,7 @@ if(H5DEBUG(D))
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list")
if(many_chunk_opt == H5D_OBTAIN_ONE_CHUNK_ADDR_IND) {
- store.chunk.offset = chunk_info->coords;
- store.chunk.index = chunk_info->index;
- if(HADDR_UNDEF == (chunk_addr = H5D_istore_get_addr(io_info, NULL)))
+ if(HADDR_UNDEF == (chunk_addr = H5D_chunk_get_addr(io_info->dset, io_info->dxpl_id, chunk_info->coords, NULL)))
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list")
} /* end if */
else
@@ -1846,7 +1832,7 @@ H5D_obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm,
#if defined(H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS) && defined(H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS)
chunk_opt_mode = (H5FD_mpio_chunk_opt_t)H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_HARD_NAME);
if((chunk_opt_mode == H5FD_MPIO_CHUNK_MULTI_IO) || (percent_nproc_per_chunk == 0)) {
- if(H5D_istore_chunkmap(io_info, chunk_addr, fm->down_chunks) < 0)
+ if(H5D_chunk_addrmap(io_info, chunk_addr, fm->down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address");
for(ic = 0; ic < total_chunks; ic++)
assign_io_mode[ic] = H5D_CHUNK_IO_MODE_COL;
@@ -1903,7 +1889,7 @@ H5D_obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm,
#endif
/* calculating the chunk address */
- if(H5D_istore_chunkmap(io_info, chunk_addr, fm->down_chunks) < 0) {
+ if(H5D_chunk_addrmap(io_info, chunk_addr, fm->down_chunks) < 0) {
HDfree(nproc_per_chunk);
#if !defined(H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS) || !defined(H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS)
HDfree(ind_this_chunk);
diff --git a/src/H5Doh.c b/src/H5Doh.c
index 37f011b..e99f9ee 100644
--- a/src/H5Doh.c
+++ b/src/H5Doh.c
@@ -361,7 +361,7 @@ H5O_dset_bh_info(H5F_t *f, hid_t dxpl_id, H5O_t *oh, H5_ih_info_t *bh_info)
/* Check for chunked dataset storage */
if((layout.type == H5D_CHUNKED) && H5F_addr_defined(layout.u.chunk.addr))
- if(H5D_istore_bh_info(f, dxpl_id, &layout, &(bh_info->index_size)) < 0)
+ if(H5D_chunk_bh_info(f, dxpl_id, &layout, &(bh_info->index_size)) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "can't determine chunked dataset btree info")
done:
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 1b20ad8..33f628d 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -100,7 +100,9 @@ struct H5D_io_info_t;
struct H5D_chunk_map_t;
/* Function pointers for I/O on particular types of dataset layouts */
-typedef herr_t (*H5D_layout_init_func_t)(const struct H5D_io_info_t *io_info,
+typedef herr_t (*H5D_layout_new_func_t)(H5F_t *f, hid_t dxpl_id,
+ H5D_t *dset, const H5P_genplist_t *dc_plist);
+typedef herr_t (*H5D_layout_io_init_func_t)(const struct H5D_io_info_t *io_info,
const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
struct H5D_chunk_map_t *cm);
@@ -116,11 +118,12 @@ typedef ssize_t (*H5D_layout_readvv_func_t)(const struct H5D_io_info_t *io_info,
typedef ssize_t (*H5D_layout_writevv_func_t)(const struct H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
-typedef herr_t (*H5D_layout_term_func_t)(const struct H5D_chunk_map_t *cm);
+typedef herr_t (*H5D_layout_io_term_func_t)(const struct H5D_chunk_map_t *cm);
/* Typedef for grouping layout I/O routines */
typedef struct H5D_layout_ops_t {
- H5D_layout_init_func_t init; /* I/O initialization routine */
+ H5D_layout_new_func_t new; /* Layout constructor for new datasets */
+ H5D_layout_io_init_func_t io_init; /* I/O initialization routine */
H5D_layout_read_func_t ser_read; /* High-level I/O routine for reading data in serial */
H5D_layout_write_func_t ser_write; /* High-level I/O routine for writing data in serial */
#ifdef H5_HAVE_PARALLEL
@@ -129,7 +132,7 @@ typedef struct H5D_layout_ops_t {
#endif /* H5_HAVE_PARALLEL */
H5D_layout_readvv_func_t readvv; /* Low-level I/O routine for reading data */
H5D_layout_writevv_func_t writevv; /* Low-level I/O routine for writing data */
- H5D_layout_term_func_t term; /* I/O shutdown routine */
+ H5D_layout_io_term_func_t io_term; /* I/O shutdown routine */
} H5D_layout_ops_t;
/* Function pointers for either multiple or single block I/O access */
@@ -201,6 +204,96 @@ typedef struct H5D_io_info_t {
} u;
} H5D_io_info_t;
+
+/******************/
+/* Chunk typedefs */
+/******************/
+
+/* Typedef for chunked dataset index operation info */
+typedef struct H5D_chk_idx_info_t {
+ H5F_t *f; /* File pointer for operation */
+ hid_t dxpl_id; /* DXPL ID for operation */
+ H5O_layout_t *layout; /* Layout info for chunks */
+} H5D_chk_idx_info_t;
+
+/*
+ * "Generic" chunk record. Each chunk is keyed by the minimum logical
+ * N-dimensional coordinates and the datatype size of the chunk.
+ * 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).
+ *
+ * The chunk's file address, filter mask and size on disk are not key values.
+ */
+typedef struct H5D_chunk_rec_t {
+ uint32_t nbytes; /* Size of stored data */
+ hsize_t offset[H5O_LAYOUT_NDIMS]; /* Logical offset to start*/
+ unsigned filter_mask; /* Excluded filters */
+ haddr_t chunk_addr; /* Address of chunk in file */
+} H5D_chunk_rec_t;
+
+/*
+ * Common data exchange structure for indexed storage nodes. This structure is
+ * passed through the indexing layer to the methods for the objects
+ * to which the index points.
+ */
+typedef struct H5D_chunk_common_ud_t {
+ /* downward */
+ const H5O_layout_t *mesg; /*layout message */
+ const hsize_t *offset; /*logical offset of chunk*/
+} H5D_chunk_common_ud_t;
+
+/* B-tree callback info for various operations */
+typedef struct H5D_chunk_ud_t {
+ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
+
+ /* Upward */
+ uint32_t nbytes; /*size of stored data */
+ unsigned filter_mask; /*excluded filters */
+ haddr_t addr; /*file address of chunk */
+} H5D_chunk_ud_t;
+
+/* Typedef for "generic" chunk callbacks */
+typedef int (*H5D_chunk_cb_func_t)(const H5D_chunk_rec_t *chunk_rec,
+ void *udata);
+
+/* Typedefs for chunk operations */
+typedef herr_t (*H5D_chunk_init_func_t)(const H5D_chk_idx_info_t *idx_info);
+typedef herr_t (*H5D_chunk_create_func_t)(const H5D_chk_idx_info_t *idx_info);
+typedef herr_t (*H5D_chunk_insert_func_t)(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+typedef haddr_t (*H5D_chunk_get_addr_func_t)(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+typedef int (*H5D_chunk_iterate_func_t)(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata);
+typedef herr_t (*H5D_chunk_remove_func_t)(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_common_ud_t *udata);
+typedef herr_t (*H5D_chunk_delete_func_t)(const H5D_chk_idx_info_t *idx_info);
+typedef herr_t (*H5D_chunk_copy_setup_func_t)(const H5D_chk_idx_info_t *idx_info_src,
+ const H5D_chk_idx_info_t *idx_info_dst);
+typedef herr_t (*H5D_chunk_copy_shutdown_func_t)(H5O_layout_t *layout_src,
+ H5O_layout_t *layout_dst);
+typedef herr_t (*H5D_chunk_size_func_t)(const H5D_chk_idx_info_t *idx_info,
+ hsize_t *idx_size);
+typedef herr_t (*H5D_chunk_dest_func_t)(const H5D_chk_idx_info_t *idx_info);
+
+/* Typedef for grouping chunk I/O routines */
+typedef struct H5D_chunk_ops_t {
+ H5D_chunk_init_func_t init; /* Routine to initialize indexing information in memory */
+ H5D_chunk_create_func_t create; /* Routine to create chunk index */
+ H5D_chunk_insert_func_t insert; /* Routine to insert a chunk into an index */
+ H5D_chunk_get_addr_func_t get_addr; /* Routine to retrieve address of chunk in file */
+ H5D_chunk_iterate_func_t iterate; /* Routine to iterate over chunks */
+ H5D_chunk_remove_func_t remove; /* Routine to remove a chunk from an index */
+ H5D_chunk_delete_func_t delete; /* Routine to delete index & all chunks from file*/
+ H5D_chunk_copy_setup_func_t copy_setup; /* Routine to perform any necessary setup for copying chunks */
+ H5D_chunk_copy_shutdown_func_t copy_shutdown; /* Routine to perform any necessary shutdown for copying chunks */
+ H5D_chunk_size_func_t size; /* Routine to get size of indexing information */
+ H5D_chunk_dest_func_t dest; /* Routine to destroy indexing information in memory */
+} H5D_chunk_ops_t;
+
/* Structure holding information about a chunk's selection for mapping */
typedef struct H5D_chunk_info_t {
hsize_t index; /* "Index" of chunk in dataset */
@@ -212,6 +305,40 @@ typedef struct H5D_chunk_info_t {
unsigned mspace_shared; /* Indicate that the memory space for a chunk is shared and shouldn't be freed */
} H5D_chunk_info_t;
+/* Main structure holding the mapping between file chunks and memory */
+typedef struct H5D_chunk_map_t {
+ H5O_layout_t *layout; /* Dataset layout information*/
+ hsize_t nelmts; /* Number of elements selected in file & memory dataspaces */
+
+ const H5S_t *file_space; /* Pointer to the file dataspace */
+ unsigned f_ndims; /* Number of dimensions for file dataspace */
+ hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */
+
+ const H5S_t *mem_space; /* Pointer to the memory dataspace */
+ H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */
+ H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
+ unsigned m_ndims; /* Number of dimensions for memory dataspace */
+ H5S_sel_type msel_type; /* Selection type in memory */
+
+ H5SL_t *sel_chunks; /* Skip list containing information for each chunk selected */
+
+ H5S_t *single_space; /* Dataspace for single chunk */
+ H5D_chunk_info_t *single_chunk_info; /* Pointer to single chunk's info */
+ hbool_t use_single; /* Whether I/O is on a single element */
+
+ hsize_t last_index; /* Index of last chunk operated on */
+ H5D_chunk_info_t *last_chunk_info; /* Pointer to last chunk's info */
+
+ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */
+ hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */
+ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */
+
+#ifdef H5_HAVE_PARALLEL
+ hsize_t total_chunks; /* Number of chunks covered by dataspace */
+ H5D_chunk_info_t **select_chunk; /* Store the information about whether this chunk is selected or not */
+#endif /* H5_HAVE_PARALLEL */
+} H5D_chunk_map_t;
+
/* Cached information about a particular chunk */
typedef struct H5D_chunk_cached_t{
hbool_t valid; /*whether cache info is valid*/
@@ -223,12 +350,12 @@ typedef struct H5D_chunk_cached_t{
/* The raw data chunk cache */
typedef struct H5D_rdcc_t {
-#ifdef H5D_ISTORE_DEBUG
- unsigned ninits; /* Number of chunk creations */
- unsigned nhits; /* Number of cache hits */
- unsigned nmisses;/* Number of cache misses */
- unsigned nflushes;/* Number of cache flushes */
-#endif /* H5D_ISTORE_DEBUG */
+ struct {
+ unsigned ninits; /* Number of chunk creations */
+ unsigned nhits; /* Number of cache hits */
+ unsigned nmisses;/* Number of cache misses */
+ unsigned nflushes;/* Number of cache flushes */
+ } stats;
size_t nbytes; /* Current cached raw data in bytes */
size_t nslots; /* Number of chunk slots allocated */
struct H5D_rdcc_ent_t *head; /* Head of doubly linked list */
@@ -266,7 +393,6 @@ typedef struct H5D_shared_t {
hid_t dcpl_id; /* dataset creation property id */
H5D_dcpl_cache_t dcpl_cache; /* Cached DCPL values */
H5O_layout_t layout; /* data layout */
- const H5D_layout_ops_t *layout_ops; /* Pointer to data layout I/O operations */
hbool_t checked_filters;/* TRUE if dataset passes can_apply check */
/* Buffered/cached information for types of raw data storage*/
@@ -295,40 +421,6 @@ typedef enum {
} H5D_time_alloc_t;
-/* Main structure holding the mapping between file chunks and memory */
-typedef struct H5D_chunk_map_t {
- H5O_layout_t *layout; /* Dataset layout information*/
- hsize_t nelmts; /* Number of elements selected in file & memory dataspaces */
-
- const H5S_t *file_space; /* Pointer to the file dataspace */
- unsigned f_ndims; /* Number of dimensions for file dataspace */
- hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */
-
- const H5S_t *mem_space; /* Pointer to the memory dataspace */
- H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */
- H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
- unsigned m_ndims; /* Number of dimensions for memory dataspace */
- H5S_sel_type msel_type; /* Selection type in memory */
-
- H5SL_t *sel_chunks; /* Skip list containing information for each chunk selected */
-
- H5S_t *single_space; /* Dataspace for single chunk */
- H5D_chunk_info_t *single_chunk_info; /* Pointer to single chunk's info */
- hbool_t use_single; /* Whether I/O is on a single element */
-
- hsize_t last_index; /* Index of last chunk operated on */
- H5D_chunk_info_t *last_chunk_info; /* Pointer to last chunk's info */
-
- hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */
- hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */
- hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */
-
-#ifdef H5_HAVE_PARALLEL
- hsize_t total_chunks; /* Number of chunks covered by dataspace */
- H5D_chunk_info_t **select_chunk; /* Store the information about whether this chunk is selected or not */
-#endif /* H5_HAVE_PARALLEL */
-} H5D_chunk_map_t;
-
/* Typedef for dataset creation operation */
typedef struct {
hid_t type_id; /* Datatype for dataset */
@@ -361,51 +453,6 @@ typedef struct {
hbool_t has_vlen_fill_type; /* Whether the datatype for the fill value has a variable-length component */
} H5D_fill_buf_info_t;
-/*************************/
-/* For chunk lock */
-/*************************/
-/*
- * 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 {
- uint32_t nbytes; /*size of stored data */
- hsize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
- unsigned filter_mask; /*excluded filters */
-} H5D_istore_key_t;
-
-
-/*
- * Common data exchange structure for indexed storage nodes. This structure is
- * passed through the B-link tree layer to the methods for the objects
- * to which the B-link tree points.
- */
-typedef struct H5D_istore_bt_ud_common_t {
- /* downward */
- const H5O_layout_t *mesg; /*layout message */
- const hsize_t *offset; /*logical offset of chunk*/
-} H5D_istore_bt_ud_common_t;
-
-/* B-tree callback info for various operations */
-typedef struct H5D_istore_ud1_t {
- H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */
-
- /* Upward */
- uint32_t nbytes; /*size of stored data */
- unsigned filter_mask; /*excluded filters */
- haddr_t addr; /*file address of chunk */
-} H5D_istore_ud1_t;
-
/* Internal data structure for computing variable-length dataset's total size */
typedef struct {
hid_t dataset_id; /* ID of the dataset we are working on */
@@ -424,6 +471,7 @@ typedef struct H5D_rdcc_ent_t {
hsize_t offset[H5O_LAYOUT_NDIMS]; /*chunk name */
uint32_t rd_count; /*bytes remaining to be read */
uint32_t wr_count; /*bytes remaining to be written */
+ haddr_t chunk_addr; /*address of chunk in file */
uint32_t chunk_size; /*size of a chunk */
size_t alloc_size; /*amount allocated for the chunk */
uint8_t *chunk; /*the unfiltered chunk data */
@@ -439,12 +487,15 @@ typedef H5D_rdcc_ent_t *H5D_rdcc_ent_ptr_t; /* For free lists */
/*****************************/
extern H5D_dxpl_cache_t H5D_def_dxpl_cache;
-/* Storage layout classes */
+/* Storage layout class I/O operations */
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_CONTIG[1];
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_EFL[1];
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_COMPACT[1];
H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_CHUNK[1];
+/* Chunked layout operations */
+H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_ISTORE[1];
+
/******************************/
/* Package Private Prototypes */
@@ -457,7 +508,7 @@ H5_DLL H5D_t *H5D_create_named(const H5G_loc_t *loc, const char *name,
hid_t dapl_id, hid_t dxpl_id);
H5_DLL herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation,
hid_t dxpl_id);
-H5_DLL herr_t H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset, H5D_time_alloc_t time_alloc,
+H5_DLL herr_t H5D_alloc_storage(H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc,
hbool_t full_overwrite);
H5_DLL hsize_t H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id);
H5_DLL haddr_t H5D_get_offset(const H5D_t *dset);
@@ -490,7 +541,7 @@ H5_DLL herr_t H5D_scatgath_write(const H5D_io_info_t *io_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space);
/* Functions that operate on contiguous storage */
-H5_DLL herr_t H5D_contig_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout);
+H5_DLL herr_t H5D_contig_alloc(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout);
H5_DLL herr_t H5D_contig_fill(H5D_t *dset, hid_t dxpl_id);
H5_DLL haddr_t H5D_contig_get_addr(const H5D_t *dset);
H5_DLL herr_t H5D_contig_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
@@ -510,45 +561,41 @@ H5_DLL herr_t H5D_contig_copy(H5F_t *f_src, const H5O_layout_t *layout_src, H5F_
/* Functions that operate on chunked dataset storage */
H5_DLL hbool_t H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr);
+H5_DLL herr_t H5D_chunk_cinfo_cache_reset(H5D_chunk_cached_t *last);
+H5_DLL herr_t H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id);
+H5_DLL herr_t H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset);
+H5_DLL haddr_t H5D_chunk_get_addr(const H5D_t *dset, hid_t dxpl_id,
+ const hsize_t *chunk_offset, H5D_chunk_ud_t *udata);
+H5_DLL void *H5D_chunk_lock(const H5D_io_info_t *io_info,
+ H5D_chunk_ud_t *udata, hbool_t relax, unsigned *idx_hint/*in,out*/);
+H5_DLL herr_t H5D_chunk_unlock(const H5D_io_info_t *io_info,
+ hbool_t dirty, unsigned idx_hint, void *chunk, uint32_t naccessed);
+H5_DLL herr_t H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags);
+H5_DLL herr_t H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes);
+H5_DLL herr_t H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite);
+H5_DLL herr_t H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id,
+ const hsize_t *old_dims);
+#ifdef H5_HAVE_PARALLEL
+H5_DLL herr_t H5D_chunk_addrmap(const H5D_io_info_t *io_info,
+ haddr_t chunk_addr[], const hsize_t down_chunks[]);
+#endif /* H5_HAVE_PARALLEL */
+H5_DLL herr_t H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id);
+H5_DLL herr_t H5D_chunk_copy(H5F_t *f_src, H5O_layout_t *layout_src,
+ H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *src_dtype,
+ H5O_copy_t *cpy_info, H5O_pline_t *pline, hid_t dxpl_id);
+H5_DLL herr_t H5D_chunk_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout,
+ hsize_t *btree_size);
+H5_DLL herr_t H5D_chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream);
+H5_DLL herr_t H5D_chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset);
+#ifdef H5D_CHUNK_DEBUG
+H5_DLL herr_t H5D_chunk_stats(const H5D_t *dset, hbool_t headers);
+#endif /* H5D_CHUNK_DEBUG */
/* Functions that operate on compact dataset storage */
H5_DLL herr_t H5D_compact_fill(H5D_t *dset, hid_t dxpl_id);
H5_DLL herr_t H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src,
H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *src_dtype, H5O_copy_t *cpy_info, hid_t dxpl_id);
-/* Functions that operate on indexed storage */
-/* forward reference for collective-chunk IO use */
-struct H5D_istore_ud1_t; /*define in H5Distore.c*/
-H5_DLL herr_t H5D_istore_init (const H5F_t *f, const H5D_t *dset);
-H5_DLL herr_t H5D_istore_flush (H5D_t *dset, hid_t dxpl_id, unsigned flags);
-H5_DLL herr_t H5D_istore_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout);
-H5_DLL herr_t H5D_istore_dest (H5D_t *dset, hid_t dxpl_id);
-H5_DLL herr_t H5D_istore_allocate (H5D_t *dset, hid_t dxpl_id,
- hbool_t full_overwrite);
-H5_DLL hsize_t H5D_istore_allocated(H5D_t *dset, hid_t dxpl_id);
-H5_DLL herr_t H5D_istore_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout,
- hsize_t *btree_size);
-H5_DLL herr_t H5D_istore_prune_by_extent(const H5D_io_info_t *io_info,
- const hsize_t *old_dims);
-H5_DLL herr_t H5D_istore_initialize_by_extent(H5D_io_info_t *io_info);
-H5_DLL herr_t H5D_istore_update_cache(H5D_t *dset, hid_t dxpl_id);
-H5_DLL herr_t H5D_istore_dump_btree(H5F_t *f, hid_t dxpl_id, FILE *stream, unsigned ndims,
- haddr_t addr);
-H5_DLL herr_t H5D_istore_chunkmap(const H5D_io_info_t *io_info,
- haddr_t chunk_addr[], const hsize_t down_chunks[]);
-#ifdef H5D_ISTORE_DEBUG
-H5_DLL herr_t H5D_istore_stats (H5D_t *dset, hbool_t headers);
-#endif /* H5D_ISTORE_DEBUG */
-H5_DLL haddr_t H5D_istore_get_addr(const H5D_io_info_t *io_info,
- struct H5D_istore_ud1_t *_udata);
-H5_DLL herr_t H5D_istore_copy(H5F_t *f_src, H5O_layout_t *layout_src,
- H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *src_dtype,
- H5O_copy_t *cpy_info, H5O_pline_t *pline, hid_t dxpl_id);
-H5_DLL void * H5D_istore_lock(const H5D_io_info_t *io_info, H5D_istore_ud1_t *udata,
- hbool_t relax, unsigned *idx_hint/*in,out*/);
-H5_DLL herr_t H5D_istore_unlock(const H5D_io_info_t *io_info,
- hbool_t dirty, unsigned idx_hint, void *chunk, uint32_t naccessed);
-
/* Functions that perform fill value operations on datasets */
H5_DLL herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf,
const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id);
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index 8cf134f..f1180a3 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -154,9 +154,10 @@ H5_DLL herr_t H5D_vlen_reclaim(hid_t type_id, H5S_t *space, hid_t plist_id,
H5_DLL herr_t H5D_contig_delete(H5F_t *f, hid_t dxpl_id,
const H5O_layout_t *layout);
+/* Functions that operate on chunked storage */
+H5_DLL herr_t H5D_chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout);
+
/* Functions that operate on indexed storage */
-H5_DLL herr_t H5D_istore_delete(H5F_t *f, hid_t dxpl_id,
- const H5O_layout_t *layout);
H5_DLL herr_t H5D_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream,
int indent, int fwidth, unsigned ndims);
diff --git a/src/H5Gname.c b/src/H5Gname.c
index f5db1d0..1efb91e 100644
--- a/src/H5Gname.c
+++ b/src/H5Gname.c
@@ -67,9 +67,6 @@ typedef struct H5G_gnba_iter_t {
/* Declare extern the PQ free list for the wrapped strings */
H5FL_BLK_EXTERN(str_buf);
-/* Declare the free list to manage haddr_t's */
-H5FL_DEFINE_STATIC(haddr_t);
-
/* PRIVATE PROTOTYPES */
static htri_t H5G_common_path(const H5RS_str_t *fullpath_r, const H5RS_str_t *prefix_r);
static H5RS_str_t *H5G_build_fullpath(const char *prefix, const char *name);
diff --git a/src/H5Gnode.c b/src/H5Gnode.c
index 92d5717..f494f99 100644
--- a/src/H5Gnode.c
+++ b/src/H5Gnode.c
@@ -74,7 +74,6 @@ typedef struct H5G_node_t {
/* PRIVATE PROTOTYPES */
static herr_t H5G_node_serialize(H5F_t *f, H5G_node_t *sym, size_t size, uint8_t *buf);
static size_t H5G_node_size_real(const H5F_t *f);
-static herr_t H5G_node_shared_free(void *shared);
/* Metadata cache callbacks */
static H5G_node_t *H5G_node_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void *_udata1,
@@ -146,12 +145,6 @@ H5FL_DEFINE_STATIC(H5G_node_t);
/* Declare a free list to manage sequences of H5G_entry_t's */
H5FL_SEQ_DEFINE_STATIC(H5G_entry_t);
-/* 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(grp_page);
-
/*-------------------------------------------------------------------------
* Function: H5G_node_get_shared
@@ -1590,39 +1583,26 @@ herr_t
H5G_node_init(H5F_t *f)
{
H5B_shared_t *shared; /* Shared B-tree node info */
- size_t u; /* Local index variable */
+ size_t sizeof_rkey; /* Size of raw (disk) key */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5G_node_init, FAIL);
/* Check arguments. */
- assert(f);
+ HDassert(f);
- /* 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_SNODE;
- shared->two_k=2*H5F_KVALUE(f,H5B_SNODE);
- shared->sizeof_rkey = H5F_SIZEOF_SIZE(f); /*the name offset */
- 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(grp_page,shared->sizeof_rnode)))
- HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(shared->page, 0, shared->sizeof_rnode);
-#endif /* H5_CLEAR_MEMORY */
- if(NULL==(shared->nkey=H5FL_SEQ_MALLOC(size_t,(size_t)(2*H5F_KVALUE(f,H5B_SNODE)+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_SNODE)+1); u++)
- shared->nkey[u]=u*H5B_SNODE->sizeof_nkey;
+ /* Set the raw key size */
+ sizeof_rkey = H5F_SIZEOF_SIZE(f); /*name offset */
+
+ /* Allocate & initialize global info for the shared structure */
+ if(NULL == (shared = H5B_shared_new(f, H5B_SNODE, sizeof_rkey)))
+ HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
+
+ /* Set up the "local" information for this file's groups */
+ /* <none> */
/* Make shared B-tree info reference counted */
- if(NULL==(f->shared->grp_btree_shared=H5RC_create(shared,H5G_node_shared_free)))
+ if(NULL == (f->shared->grp_btree_shared = H5RC_create(shared, H5B_shared_free)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
done:
@@ -1662,40 +1642,6 @@ H5G_node_close(const H5F_t *f)
/*-------------------------------------------------------------------------
- * Function: H5G_node_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
-H5G_node_shared_free (void *_shared)
-{
- H5B_shared_t *shared = (H5B_shared_t *)_shared;
-
- FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5G_node_shared_free)
-
- /* Free the raw B-tree node buffer */
- H5FL_BLK_FREE(grp_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 H5G_node_shared_free() */
-
-
-/*-------------------------------------------------------------------------
* Function: H5G_node_copy
*
* Purpose: This function gets called during a group iterate operation
diff --git a/src/H5Gstab.c b/src/H5Gstab.c
index 61af068..a5280b5 100644
--- a/src/H5Gstab.c
+++ b/src/H5Gstab.c
@@ -518,7 +518,7 @@ H5G_stab_iterate(const H5O_loc_t *oloc, hid_t dxpl_id, H5_iter_order_t order,
udata.op_data = op_data;
/* Iterate over the group members */
- if((ret_value = H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, H5G_node_iterate, stab.btree_addr, &udata)) < 0)
+ if((ret_value = H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_iterate, &udata)) < 0)
HERROR(H5E_SYM, H5E_CANTNEXT, "iteration operator failed");
/* Check for too high of a starting index (ex post facto :-) */
@@ -535,8 +535,7 @@ H5G_stab_iterate(const H5O_loc_t *oloc, hid_t dxpl_id, H5_iter_order_t order,
udata.ltable = &ltable;
/* Iterate over the group members */
- if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, H5G_node_build_table,
- stab.btree_addr, &udata) < 0)
+ if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_build_table, &udata) < 0)
HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, FAIL, "unable to build link table")
/* Check for skipping out of bounds */
@@ -595,7 +594,7 @@ H5G_stab_count(H5O_loc_t *oloc, hsize_t *num_objs, hid_t dxpl_id)
HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, FAIL, "unable to determine local heap address")
/* Iterate over the group members */
- if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, H5G_node_sumup, stab.btree_addr, num_objs) < 0)
+ if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_sumup, num_objs) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, FAIL, "iteration operator failed")
done:
@@ -616,10 +615,12 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5G_stab_bh_size(H5F_t *f, hid_t dxpl_id, const H5O_stab_t *stab, H5_ih_info_t *bh_info)
+H5G_stab_bh_size(H5F_t *f, hid_t dxpl_id, const H5O_stab_t *stab,
+ H5_ih_info_t *bh_info)
{
- H5B_info_ud_t bh_udata; /* User-data for B-tree callbacks */
- herr_t ret_value = SUCCEED;
+ hsize_t snode_size; /* Symbol table node size */
+ H5B_info_t bt_info; /* B-tree node info */
+ herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5G_stab_bh_size, FAIL)
@@ -628,14 +629,16 @@ H5G_stab_bh_size(H5F_t *f, hid_t dxpl_id, const H5O_stab_t *stab, H5_ih_info_t *
HDassert(stab);
HDassert(bh_info);
- /* Set up user data for B-tree callback */
- bh_udata.udata = NULL;
- bh_udata.btree_size = &(bh_info->index_size);
+ /* Set up user data for B-tree iteration */
+ snode_size = 0;
/* Get the B-tree & symbol table node size info */
- if(H5B_iterate_size(f, dxpl_id, H5B_SNODE, H5G_node_iterate_size, stab->btree_addr, &bh_udata) < 0)
+ if(H5B_get_info(f, dxpl_id, H5B_SNODE, stab->btree_addr, &bt_info, H5G_node_iterate_size, &snode_size) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "iteration operator failed")
+ /* Add symbol table & B-tree node sizes to index info */
+ bh_info->index_size += snode_size + bt_info.size;
+
/* Get the size of the local heap for the group */
if(H5HL_heapsize(f, dxpl_id, stab->heap_addr, &(bh_info->heap_size)) < 0)
HGOTO_ERROR(H5E_HEAP, H5E_CANTINIT, FAIL, "iteration operator failed")
@@ -723,7 +726,7 @@ H5G_stab_get_name_by_idx(H5O_loc_t *oloc, H5_iter_order_t order, hsize_t n,
hsize_t nlinks = 0; /* Number of links in group */
/* Iterate over the symbol table nodes, to count the links */
- if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, H5G_node_sumup, stab.btree_addr, &nlinks) < 0)
+ if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_sumup, &nlinks) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, FAIL, "iteration operator failed")
/* Map decreasing iteration order index to increasing iteration order index */
@@ -739,7 +742,7 @@ H5G_stab_get_name_by_idx(H5O_loc_t *oloc, H5_iter_order_t order, hsize_t n,
udata.name = NULL;
/* Iterate over the group members */
- if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, H5G_node_by_idx, stab.btree_addr, &udata) < 0)
+ if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_by_idx, &udata) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "iteration operator failed")
/* If we don't know the name now, we almost certainly went out of bounds */
@@ -947,7 +950,7 @@ H5G_stab_lookup_by_idx(H5O_loc_t *grp_oloc, H5_iter_order_t order, hsize_t n,
hsize_t nlinks = 0; /* Number of links in group */
/* Iterate over the symbol table nodes, to count the links */
- if(H5B_iterate(grp_oloc->file, dxpl_id, H5B_SNODE, H5G_node_sumup, stab.btree_addr, &nlinks) < 0)
+ if(H5B_iterate(grp_oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_sumup, &nlinks) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, FAIL, "iteration operator failed")
/* Map decreasing iteration order index to increasing iteration order index */
@@ -964,7 +967,7 @@ H5G_stab_lookup_by_idx(H5O_loc_t *grp_oloc, H5_iter_order_t order, hsize_t n,
udata.found = FALSE;
/* Iterate over the group members */
- if(H5B_iterate(grp_oloc->file, dxpl_id, H5B_SNODE, H5G_node_by_idx, stab.btree_addr, &udata) < 0)
+ if(H5B_iterate(grp_oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_by_idx, &udata) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "iteration operator failed")
/* If we didn't find the link, we almost certainly went out of bounds */
@@ -1076,7 +1079,7 @@ H5G_stab_get_type_by_idx(H5O_loc_t *oloc, hsize_t idx, hid_t dxpl_id)
udata.type = H5G_UNKNOWN;
/* Iterate over the group members */
- if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, H5G_node_by_idx, stab.btree_addr, &udata) < 0)
+ if(H5B_iterate(oloc->file, dxpl_id, H5B_SNODE, stab.btree_addr, H5G_node_by_idx, &udata) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5G_UNKNOWN, "iteration operator failed")
/* If we don't know the type now, we almost certainly went out of bounds */
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index e750d48..1f371f3 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -136,11 +136,30 @@ H5O_layout_decode(H5F_t *f, hid_t UNUSED dxpl_id, unsigned UNUSED mesg_flags,
p += 5;
/* Address */
- if(mesg->type == H5D_CONTIGUOUS)
+ if(mesg->type == H5D_CONTIGUOUS) {
H5F_addr_decode(f, &p, &(mesg->u.contig.addr));
- else if(mesg->type == H5D_CHUNKED)
+
+ /* Set the layout operations */
+ mesg->ops = H5D_LOPS_CONTIG;
+ } /* end if */
+ else if(mesg->type == H5D_CHUNKED) {
H5F_addr_decode(f, &p, &(mesg->u.chunk.addr));
+ /* Set the layout operations */
+ mesg->ops = H5D_LOPS_CHUNK;
+
+ /* Set the chunk operations */
+ /* (Only "istore" indexing type currently supported */
+ mesg->u.chunk.ops = H5D_COPS_ISTORE;
+ } /* end if */
+ else {
+ /* Sanity check */
+ HDassert(mesg->type == H5D_COMPACT);
+
+ /* Set the layout operations */
+ mesg->ops = H5D_LOPS_COMPACT;
+ } /* end else */
+
/* Read the size */
if(mesg->type != H5D_CHUNKED) {
/* Don't compute size of contiguous storage here, due to possible
@@ -185,11 +204,17 @@ H5O_layout_decode(H5F_t *f, hid_t UNUSED dxpl_id, unsigned UNUSED mesg_flags,
HDmemcpy(mesg->u.compact.buf, p, mesg->u.compact.size);
p += mesg->u.compact.size;
} /* end if */
+
+ /* Set the layout operations */
+ mesg->ops = H5D_LOPS_COMPACT;
break;
case H5D_CONTIGUOUS:
H5F_addr_decode(f, &p, &(mesg->u.contig.addr));
H5F_DECODE_LENGTH(f, p, mesg->u.contig.size);
+
+ /* Set the layout operations */
+ mesg->ops = H5D_LOPS_CONTIG;
break;
case H5D_CHUNKED:
@@ -208,6 +233,13 @@ H5O_layout_decode(H5F_t *f, hid_t UNUSED dxpl_id, unsigned UNUSED mesg_flags,
/* Compute chunk size */
for(u = 1, mesg->u.chunk.size = mesg->u.chunk.dim[0]; u < mesg->u.chunk.ndims; u++)
mesg->u.chunk.size *= mesg->u.chunk.dim[u];
+
+ /* Set the layout operations */
+ mesg->ops = H5D_LOPS_CHUNK;
+
+ /* Set the chunk operations */
+ /* (Only "istore" indexing type currently supported */
+ mesg->u.chunk.ops = H5D_COPS_ISTORE;
break;
default:
@@ -576,8 +608,8 @@ H5O_layout_delete(H5F_t *f, hid_t dxpl_id, H5O_t UNUSED *open_oh, void *_mesg)
break;
case H5D_CHUNKED: /* Chunked blocks on disk */
- /* Free the file space for the raw data */
- if(H5D_istore_delete(f, dxpl_id, mesg) < 0)
+ /* Free the file space for the index & chunk raw data */
+ if(H5D_chunk_delete(f, dxpl_id, mesg) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free raw data")
break;
@@ -670,7 +702,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
layout_dst->u.chunk.addr = HADDR_UNDEF;
/* create chunked layout */
- if(H5D_istore_copy(file_src, layout_src, file_dst, layout_dst, udata->src_dtype, cpy_info, udata->src_pline, dxpl_id) < 0)
+ if(H5D_chunk_copy(file_src, layout_src, file_dst, layout_dst, udata->src_dtype, cpy_info, udata->src_pline, dxpl_id) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to copy chunked storage")
/* Freed by copy routine */
diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h
index 3c5204f..36ff226 100644
--- a/src/H5Oprivate.h
+++ b/src/H5Oprivate.h
@@ -326,6 +326,10 @@ typedef struct H5O_efl_t {
*/
#define H5O_LAYOUT_NDIMS (H5S_MAX_RANK+1)
+/* Forward declaration of structs used below */
+struct H5D_layout_ops_t; /* Defined in H5Dpkg.h */
+struct H5D_chunk_ops_t; /* Defined in H5Dpkg.h */
+
typedef struct H5O_layout_contig_t {
haddr_t addr; /* File address of data */
hsize_t size; /* Size of data in bytes */
@@ -337,6 +341,7 @@ typedef struct H5O_layout_chunk_t {
uint32_t dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in elements */
uint32_t size; /* Size of chunk in bytes */
H5RC_t *btree_shared; /* Ref-counted info for B-tree nodes */
+ const struct H5D_chunk_ops_t *ops; /* Pointer to chunked layout operations */
} H5O_layout_chunk_t;
typedef struct H5O_layout_compact_t {
@@ -348,6 +353,7 @@ typedef struct H5O_layout_compact_t {
typedef struct H5O_layout_t {
H5D_layout_t type; /* Type of layout */
unsigned version; /* Version of message */
+ const struct H5D_layout_ops_t *ops; /* Pointer to data layout I/O operations */
union {
H5O_layout_contig_t contig; /* Information for contiguous layout */
H5O_layout_chunk_t chunk; /* Information for chunked layout */
diff --git a/src/H5Ostab.c b/src/H5Ostab.c
index 978b9c5..231f2ce 100644
--- a/src/H5Ostab.c
+++ b/src/H5Ostab.c
@@ -386,7 +386,7 @@ H5O_stab_post_copy_file(const H5O_loc_t *src_oloc, const void *mesg_src, H5O_loc
udata.cpy_info = cpy_info;
/* Iterate over objects in group, copying them */
- if((H5B_iterate(src_oloc->file, dxpl_id, H5B_SNODE, H5G_node_copy, stab_src->btree_addr, &udata)) < 0)
+ if((H5B_iterate(src_oloc->file, dxpl_id, H5B_SNODE, stab_src->btree_addr, H5G_node_copy, &udata)) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, FAIL, "iteration operator failed")
done:
diff --git a/src/H5Pint.c b/src/H5Pint.c
index 46eb293..233e187 100644
--- a/src/H5Pint.c
+++ b/src/H5Pint.c
@@ -3556,7 +3556,7 @@ done:
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
-H5P_get(H5P_genplist_t *plist, const char *name, void *value)
+H5P_get(const H5P_genplist_t *plist, const char *name, void *value)
{
H5P_genclass_t *tclass; /* Temporary class pointer */
H5P_genprop_t *prop; /* Temporary property pointer */
diff --git a/src/H5Pprivate.h b/src/H5Pprivate.h
index a96df21..adb57c1 100644
--- a/src/H5Pprivate.h
+++ b/src/H5Pprivate.h
@@ -59,7 +59,7 @@ H5_DLL herr_t H5P_init(void);
H5_DLL herr_t H5P_close(void *_plist);
H5_DLL hid_t H5P_create_id(H5P_genclass_t *pclass);
H5_DLL hid_t H5P_copy_plist(H5P_genplist_t *old_plist);
-H5_DLL herr_t H5P_get(H5P_genplist_t *plist, const char *name, void *value);
+H5_DLL herr_t H5P_get(const H5P_genplist_t *plist, const char *name, void *value);
H5_DLL herr_t H5P_set(H5P_genplist_t *plist, const char *name, const void *value);
H5_DLL herr_t H5P_insert(H5P_genplist_t *plist, const char *name, size_t size,
void *value, H5P_prp_set_func_t prp_set, H5P_prp_get_func_t prp_get,
diff --git a/src/H5S.c b/src/H5S.c
index 4996f1f..dd16498 100644
--- a/src/H5S.c
+++ b/src/H5S.c
@@ -43,7 +43,6 @@ static herr_t H5S_set_extent_simple (H5S_t *space, unsigned rank,
static htri_t H5S_is_simple(const H5S_t *sdim);
static herr_t H5S_encode(H5S_t *obj, unsigned char *buf, size_t *nalloc);
static H5S_t *H5S_decode(const unsigned char *buf);
-static htri_t H5S_extent_equal(const H5S_t *ds1, const H5S_t *ds2);
#ifdef H5_HAVE_PARALLEL
/* Global vars whose value can be set from environment variable also */
@@ -1933,7 +1932,7 @@ done:
DESCRIPTION
Compare two dataspaces if their extents are identical.
--------------------------------------------------------------------------*/
-static htri_t
+htri_t
H5S_extent_equal(const H5S_t *ds1, const H5S_t *ds2)
{
unsigned u; /* Local index variable */
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index 8744872..e78fb51 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -196,7 +196,9 @@ H5_DLL herr_t H5S_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE *stream
H5_DLL int H5S_extend(H5S_t *space, const hsize_t *size);
#endif /* H5_NO_DEPRECATED_SYMBOLS */
+/* Operations on dataspace extents */
H5_DLL hsize_t H5S_extent_nelem(const H5S_extent_t *ext);
+H5_DLL htri_t H5S_extent_equal(const H5S_t *ds1, const H5S_t *ds2);
/* Operations on selections */
H5_DLL herr_t H5S_select_deserialize(H5S_t *space, const uint8_t *buf);
generated by cgit v0.12 at 2024-11-01 23:51:55 (GMT)