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-rw-r--r--src/H5Dbtree.c222
1 files changed, 158 insertions, 64 deletions
diff --git a/src/H5Dbtree.c b/src/H5Dbtree.c
index 4f6b988..2933e5e 100644
--- a/src/H5Dbtree.c
+++ b/src/H5Dbtree.c
@@ -49,11 +49,6 @@
/* Local Macros */
/****************/
-/*
- * Given a B-tree node return the dimensionality of the chunks pointed to by
- * that node.
- */
-#define H5D_BTREE_NDIMS(X) (((X)->sizeof_rkey-8)/8)
/******************/
/* Local Typedefs */
@@ -74,7 +69,7 @@
* The chunk's file address is part of the B-tree and not part of the key.
*/
typedef struct H5D_btree_key_t {
- hsize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
+ hsize_t scaled[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
uint32_t nbytes; /*size of stored data */
unsigned filter_mask; /*excluded filters */
} H5D_btree_key_t;
@@ -97,8 +92,9 @@ typedef struct H5D_btree_dbg_t {
/* Local Prototypes */
/********************/
+static herr_t H5D__btree_shared_free(void *_shared);
static herr_t H5D__btree_shared_create(const H5F_t *f, H5O_storage_chunk_t *store,
- unsigned ndims);
+ const H5O_layout_chunk_t *layout);
/* B-tree iterator callbacks */
static int H5D__btree_idx_iterate_cb(H5F_t *f, hid_t dxpl_id, const void *left_key,
@@ -203,6 +199,10 @@ H5B_class_t H5B_BTREE[1] = {{
/* Local Variables */
/*******************/
+/* Declare a free list to manage H5O_layout_chunk_t objects */
+H5FL_DEFINE_STATIC(H5O_layout_chunk_t);
+
+
/*-------------------------------------------------------------------------
* Function: H5D__btree_get_shared
@@ -287,7 +287,7 @@ H5D__btree_new_node(H5F_t *f, hid_t UNUSED dxpl_id, H5B_ins_t op,
H5_CHECKED_ASSIGN(lt_key->nbytes, uint32_t, udata->chunk_block.length, hsize_t);
lt_key->filter_mask = udata->filter_mask;
for(u = 0; u < udata->common.layout->ndims; u++)
- lt_key->offset[u] = udata->common.offset[u];
+ lt_key->scaled[u] = udata->common.scaled[u];
/*
* The right key might already be present. If not, then add a zero-width
@@ -297,9 +297,8 @@ H5D__btree_new_node(H5F_t *f, hid_t UNUSED dxpl_id, H5B_ins_t op,
rt_key->nbytes = 0;
rt_key->filter_mask = 0;
for(u = 0; u < udata->common.layout->ndims; u++) {
- HDassert(udata->common.offset[u] + udata->common.layout->dim[u] >
- udata->common.offset[u]);
- rt_key->offset[u] = udata->common.offset[u] + udata->common.layout->dim[u];
+ HDassert(udata->common.scaled[u] + 1 > udata->common.scaled[u]);
+ rt_key->scaled[u] = udata->common.scaled[u] + 1;
} /* end if */
} /* end if */
@@ -342,7 +341,7 @@ H5D__btree_cmp2(void *_lt_key, void *_udata, void *_rt_key)
HDassert(udata->layout->ndims > 0 && udata->layout->ndims <= H5O_LAYOUT_NDIMS);
/* Compare the offsets but ignore the other fields */
- ret_value = H5VM_vector_cmp_u(udata->layout->ndims, lt_key->offset, rt_key->offset);
+ ret_value = H5VM_vector_cmp_u(udata->layout->ndims, lt_key->scaled, rt_key->scaled);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__btree_cmp2() */
@@ -397,18 +396,18 @@ H5D__btree_cmp3(void *_lt_key, void *_udata, void *_rt_key)
/* indexed storage B-tree... */
/* (Dump the B-tree with h5debug to look at it) -QAK */
if(udata->layout->ndims == 2) {
- if(udata->offset[0] > rt_key->offset[0])
+ if(udata->scaled[0] > rt_key->scaled[0])
ret_value = 1;
- else if(udata->offset[0] == rt_key->offset[0] &&
- udata->offset[1] >= rt_key->offset[1])
+ else if(udata->scaled[0] == rt_key->scaled[0] &&
+ udata->scaled[1] >= rt_key->scaled[1])
ret_value = 1;
- else if(udata->offset[0] < lt_key->offset[0])
+ else if(udata->scaled[0] < lt_key->scaled[0])
ret_value = (-1);
} /* end if */
else {
- if(H5VM_vector_ge_u(udata->layout->ndims, udata->offset, rt_key->offset))
+ if(H5VM_vector_ge_u(udata->layout->ndims, udata->scaled, rt_key->scaled))
ret_value = 1;
- else if(H5VM_vector_lt_u(udata->layout->ndims, udata->offset, lt_key->offset))
+ else if(H5VM_vector_lt_u(udata->layout->ndims, udata->scaled, lt_key->scaled))
ret_value = (-1);
} /* end else */
@@ -460,7 +459,7 @@ H5D__btree_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void
/* Is this *really* the requested chunk? */
for(u = 0; u < udata->common.layout->ndims; u++)
- if(udata->common.offset[u] >= lt_key->offset[u] + udata->common.layout->dim[u])
+ if(udata->common.scaled[u] >= (lt_key->scaled[u] + 1))
HGOTO_DONE(FALSE)
/* Initialize return values */
@@ -475,6 +474,44 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_disjoint
+ *
+ * Purpose: Determines if two chunks are disjoint.
+ *
+ * Return: Success: FALSE if they are not disjoint.
+ * TRUE if they are disjoint.
+ *
+ * Programmer: Quincey Koziol
+ * Wednesday, May 6, 2015
+ *
+ * Note: Assumes that the chunk offsets are scaled coordinates
+ *
+ *-------------------------------------------------------------------------
+ */
+static hbool_t
+H5D__chunk_disjoint(unsigned n, const hsize_t *scaled1, const hsize_t *scaled2)
+{
+ unsigned u; /* Local index variable */
+ hbool_t ret_value = FALSE; /* Return value */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(n);
+ HDassert(scaled1);
+ HDassert(scaled2);
+
+ /* Loop over two chunks, detecting disjointness and getting out quickly */
+ for(u = 0; u < n; u++)
+ if((scaled1[u] + 1) <= scaled2[u] || (scaled2[u] + 1) <= scaled1[u])
+ HGOTO_DONE(TRUE)
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_disjoint() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D__btree_insert
*
* Purpose: This function is called when the B-tree insert engine finds
@@ -538,8 +575,7 @@ H5D__btree_insert(H5F_t *f, hid_t UNUSED dxpl_id, haddr_t addr, void *_lt_key,
HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error")
} else if(H5VM_vector_eq_u(udata->common.layout->ndims,
- udata->common.offset, lt_key->offset) &&
- lt_key->nbytes > 0) {
+ udata->common.scaled, lt_key->scaled) && lt_key->nbytes > 0) {
/*
* Already exists. If the new size is not the same as the old size
* then we should reallocate storage.
@@ -558,22 +594,18 @@ H5D__btree_insert(H5F_t *f, hid_t UNUSED dxpl_id, haddr_t addr, void *_lt_key,
ret_value = H5B_INS_NOOP;
}
- } else if (H5VM_hyper_disjointp(udata->common.layout->ndims,
- lt_key->offset, udata->common.layout->dim,
- udata->common.offset, udata->common.layout->dim)) {
- HDassert(H5VM_hyper_disjointp(udata->common.layout->ndims,
- rt_key->offset, udata->common.layout->dim,
- udata->common.offset, udata->common.layout->dim));
+ } else if (H5D__chunk_disjoint(udata->common.layout->ndims,
+ lt_key->scaled, udata->common.scaled)) {
+ HDassert(H5D__chunk_disjoint(udata->common.layout->ndims,
+ rt_key->scaled, udata->common.scaled));
/*
* Split this node, inserting the new new node to the right of the
* current node. The MD_KEY is where the split occurs.
*/
H5_CHECKED_ASSIGN(md_key->nbytes, uint32_t, udata->chunk_block.length, hsize_t);
md_key->filter_mask = udata->filter_mask;
- for(u = 0; u < udata->common.layout->ndims; u++) {
- HDassert(0 == udata->common.offset[u] % udata->common.layout->dim[u]);
- md_key->offset[u] = udata->common.offset[u];
- } /* end for */
+ for(u = 0; u < udata->common.layout->ndims; u++)
+ md_key->scaled[u] = udata->common.scaled[u];
HDassert(H5F_addr_defined(udata->chunk_block.offset));
*new_node_p = udata->chunk_block.offset;
@@ -643,9 +675,10 @@ done:
static herr_t
H5D__btree_decode_key(const H5B_shared_t *shared, const uint8_t *raw, void *_key)
{
- H5D_btree_key_t *key = (H5D_btree_key_t *) _key;
- size_t ndims;
- unsigned u;
+ const H5O_layout_chunk_t *layout; /* Chunk layout description */
+ H5D_btree_key_t *key = (H5D_btree_key_t *) _key; /* Pointer to decoded key */
+ hsize_t tmp_offset; /* Temporary coordinate offset, from file */
+ unsigned u; /* Local index variable */
FUNC_ENTER_STATIC_NOERR
@@ -653,14 +686,21 @@ H5D__btree_decode_key(const H5B_shared_t *shared, const uint8_t *raw, void *_key
HDassert(shared);
HDassert(raw);
HDassert(key);
- ndims = H5D_BTREE_NDIMS(shared);
- HDassert(ndims <= H5O_LAYOUT_NDIMS);
+ layout = (const H5O_layout_chunk_t *)shared->udata;
+ HDassert(layout);
+ HDassert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
/* decode */
UINT32DECODE(raw, key->nbytes);
UINT32DECODE(raw, key->filter_mask);
- for(u = 0; u < ndims; u++)
- UINT64DECODE(raw, key->offset[u]);
+ for(u = 0; u < layout->ndims; u++) {
+ /* Retrieve coordinate offset */
+ UINT64DECODE(raw, tmp_offset);
+ HDassert(0 == (tmp_offset % layout->dim[u]));
+
+ /* Convert to a scaled offset */
+ key->scaled[u] = tmp_offset / layout->dim[u];
+ } /* end for */
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5D__btree_decode_key() */
@@ -681,9 +721,10 @@ H5D__btree_decode_key(const H5B_shared_t *shared, const uint8_t *raw, void *_key
static herr_t
H5D__btree_encode_key(const H5B_shared_t *shared, uint8_t *raw, const void *_key)
{
+ const H5O_layout_chunk_t *layout; /* Chunk layout description */
const H5D_btree_key_t *key = (const H5D_btree_key_t *)_key;
- size_t ndims;
- unsigned u;
+ hsize_t tmp_offset; /* Temporary coordinate offset, from file */
+ unsigned u; /* Local index variable */
FUNC_ENTER_STATIC_NOERR
@@ -691,14 +732,18 @@ H5D__btree_encode_key(const H5B_shared_t *shared, uint8_t *raw, const void *_key
HDassert(shared);
HDassert(raw);
HDassert(key);
- ndims = H5D_BTREE_NDIMS(shared);
- HDassert(ndims <= H5O_LAYOUT_NDIMS);
+ layout = (const H5O_layout_chunk_t *)shared->udata;
+ HDassert(layout);
+ HDassert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
/* encode */
UINT32ENCODE(raw, key->nbytes);
UINT32ENCODE(raw, key->filter_mask);
- for(u = 0; u < ndims; u++)
- UINT64ENCODE(raw, key->offset[u]);
+ for(u = 0; u < layout->ndims; u++) {
+ /* Compute coordinate offset from scaled offset */
+ tmp_offset = key->scaled[u] * layout->dim[u];
+ UINT64ENCODE(raw, tmp_offset);
+ } /* end for */
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5D__btree_encode_key() */
@@ -733,7 +778,7 @@ H5D__btree_debug_key(FILE *stream, int indent, int fwidth, const void *_key,
HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth, "Filter mask:", key->filter_mask);
HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:");
for(u = 0; u < udata->ndims; u++)
- HDfprintf(stream, "%s%Hd", u?", ":"", key->offset[u]);
+ HDfprintf(stream, "%s%Hd", u?", ":"", (key->scaled[u] * udata->common.layout->dim[u]));
HDfputs("}\n", stream);
FUNC_LEAVE_NOAPI(SUCCEED)
@@ -741,6 +786,38 @@ H5D__btree_debug_key(FILE *stream, int indent, int fwidth, const void *_key,
/*-------------------------------------------------------------------------
+ * Function: H5D__btree_shared_free
+ *
+ * Purpose: Free "local" B-tree shared info
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, May 7, 2015
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__btree_shared_free(void *_shared)
+{
+ H5B_shared_t *shared = (H5B_shared_t *)_shared;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Free the chunk layout information */
+ shared->udata = H5FL_FREE(H5O_layout_chunk_t, shared->udata);
+
+ /* Chain up to the generic B-tree shared info free routine */
+ if(H5B_shared_free(shared) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't free shared B-tree info")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__btree_shared_free() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D__btree_shared_create
*
* Purpose: Create & initialize B-tree shared info
@@ -753,9 +830,11 @@ H5D__btree_debug_key(FILE *stream, int indent, int fwidth, const void *_key,
*-------------------------------------------------------------------------
*/
static herr_t
-H5D__btree_shared_create(const H5F_t *f, H5O_storage_chunk_t *store, unsigned ndims)
+H5D__btree_shared_create(const H5F_t *f, H5O_storage_chunk_t *store,
+ const H5O_layout_chunk_t *layout)
{
H5B_shared_t *shared; /* Shared B-tree node info */
+ H5O_layout_chunk_t *my_layout = NULL; /* Pointer to copy of layout info */
size_t sizeof_rkey; /* Size of raw (disk) key */
herr_t ret_value = SUCCEED; /* Return value */
@@ -764,20 +843,27 @@ H5D__btree_shared_create(const H5F_t *f, H5O_storage_chunk_t *store, unsigned nd
/* Set the raw key size */
sizeof_rkey = 4 + /*storage size */
4 + /*filter mask */
- ndims * 8; /*dimension indices */
+ layout->ndims * 8; /*dimension indices */
/* Allocate & initialize global info for the shared structure */
if(NULL == (shared = H5B_shared_new(f, H5B_BTREE, sizeof_rkey)))
- HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
+ HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
/* Set up the "local" information for this dataset's chunks */
- /* <none> */
+ if(NULL == (my_layout = H5FL_MALLOC(H5O_layout_chunk_t)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk layout")
+ HDmemcpy(my_layout, layout, sizeof(H5O_layout_chunk_t));
+ shared->udata = my_layout;
/* Make shared B-tree info reference counted */
- if(NULL == (store->u.btree.shared = H5UC_create(shared, H5B_shared_free)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
+ if(NULL == (store->u.btree.shared = H5UC_create(shared, H5D__btree_shared_free)))
+ HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
done:
+ if(ret_value < 0)
+ if(my_layout)
+ my_layout = H5FL_FREE(H5O_layout_chunk_t, my_layout);
+
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__btree_shared_create() */
@@ -813,7 +899,7 @@ H5D__btree_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t UNUSED *spac
idx_info->storage->u.btree.dset_ohdr_addr = dset_ohdr_addr;
/* Allocate the shared structure */
- if(H5D__btree_shared_create(idx_info->f, idx_info->storage, idx_info->layout->ndims) < 0)
+ if(H5D__btree_shared_create(idx_info->f, idx_info->storage, idx_info->layout) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
done:
@@ -1006,8 +1092,8 @@ H5D__btree_idx_iterate_cb(H5F_t UNUSED *f, hid_t UNUSED dxpl_id,
/* Sanity check for memcpy() */
HDcompile_assert(offsetof(H5D_chunk_rec_t, nbytes) == offsetof(H5D_btree_key_t, nbytes));
HDcompile_assert(sizeof(chunk_rec.nbytes) == sizeof(lt_key->nbytes));
- HDcompile_assert(offsetof(H5D_chunk_rec_t, offset) == offsetof(H5D_btree_key_t, offset));
- HDcompile_assert(sizeof(chunk_rec.offset) == sizeof(lt_key->offset));
+ HDcompile_assert(offsetof(H5D_chunk_rec_t, scaled) == offsetof(H5D_btree_key_t, scaled));
+ HDcompile_assert(sizeof(chunk_rec.scaled) == sizeof(lt_key->scaled));
HDcompile_assert(offsetof(H5D_chunk_rec_t, filter_mask) == offsetof(H5D_btree_key_t, filter_mask));
HDcompile_assert(sizeof(chunk_rec.filter_mask) == sizeof(lt_key->filter_mask));
@@ -1144,7 +1230,7 @@ H5D__btree_idx_delete(const H5D_chk_idx_info_t *idx_info)
tmp_storage = *idx_info->storage;
/* Set up the shared structure */
- if(H5D__btree_shared_create(idx_info->f, &tmp_storage, idx_info->layout->ndims) < 0)
+ if(H5D__btree_shared_create(idx_info->f, &tmp_storage, idx_info->layout) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
/* Set up B-tree user data */
@@ -1201,9 +1287,9 @@ H5D__btree_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src,
HDassert(!H5F_addr_defined(idx_info_dst->storage->idx_addr));
/* Create shared B-tree info for each file */
- if(H5D__btree_shared_create(idx_info_src->f, idx_info_src->storage, idx_info_src->layout->ndims) < 0)
+ if(H5D__btree_shared_create(idx_info_src->f, idx_info_src->storage, idx_info_src->layout) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for source shared B-tree info")
- if(H5D__btree_shared_create(idx_info_dst->f, idx_info_dst->storage, idx_info_dst->layout->ndims) < 0)
+ if(H5D__btree_shared_create(idx_info_dst->f, idx_info_dst->storage, idx_info_dst->layout) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for destination shared B-tree info")
/* Create the root of the B-tree that describes chunked storage in the dest. file */
@@ -1283,7 +1369,7 @@ H5D__btree_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size)
HDassert(index_size);
/* Initialize the shared info for the B-tree traversal */
- if(H5D__btree_shared_create(idx_info->f, idx_info->storage, idx_info->layout->ndims) < 0)
+ if(H5D__btree_shared_create(idx_info->f, idx_info->storage, idx_info->layout) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
shared_init = TRUE;
@@ -1415,11 +1501,13 @@ done:
*/
herr_t
H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent,
- int fwidth, unsigned ndims)
+ int fwidth, unsigned ndims, const uint32_t *dim)
{
H5D_btree_dbg_t udata; /* User data for B-tree callback */
H5O_storage_chunk_t storage; /* Storage information for B-tree callback */
+ H5O_layout_chunk_t layout; /* Layout information for B-tree callback */
hbool_t shared_init = FALSE; /* Whether B-tree shared info is initialized */
+ unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
@@ -1428,15 +1516,21 @@ H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent
HDmemset(&storage, 0, sizeof(storage));
storage.idx_type = H5D_CHUNK_IDX_BTREE;
+ /* Reset "fake" layout info */
+ HDmemset(&layout, 0, sizeof(layout));
+ layout.ndims = ndims;
+ for(u = 0; u < ndims; u++)
+ layout.dim[u] = dim[u];
+
/* Allocate the shared structure */
- if(H5D__btree_shared_create(f, &storage, ndims) < 0)
+ if(H5D__btree_shared_create(f, &storage, &layout) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
shared_init = TRUE;
/* Set up user data for callback */
- udata.common.layout = NULL;
+ udata.common.layout = &layout;
udata.common.storage = &storage;
- udata.common.offset = NULL;
+ udata.common.scaled = NULL;
udata.ndims = ndims;
/* Dump the records for the B-tree */
@@ -1446,10 +1540,10 @@ done:
if(shared_init) {
/* Free the raw B-tree node buffer */
if(NULL == storage.u.btree.shared)
- HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil")
+ HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted shared info nil")
else
if(H5UC_DEC(storage.u.btree.shared) < 0)
- HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page")
+ HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted shared info")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)