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[svn-r11031] Purpose:

Browse Source 
New feature

Description:
    Initial checkin of B+ Tree code.

Platforms tested:
    FreeBSD 4.11 (sleipnir)
    h5committest

Misc. update:
This commit is contained in:
Quincey Koziol 2005-07-06 13:13:32 -05:00
parent 0023210504
commit 82a12612e3
18 changed files with 2182 additions and 45 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
src/H5AC.c
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@ -365,7 +365,9 @@ static const char * H5AC_entry_type_names[H5AC_NTYPES] =
"v2 B-tree internal nodes",
"v2 B-tree leaf nodes",
"block tracker nodes",
"segmented heaps"
"segmented heaps",
"B+ tree headers",
"B+ tree leaves"
};
herr_t

4
src/H5ACprivate.h
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@ -49,7 +49,9 @@
#define H5AC_BT2_LEAF_ID 7 /*v2 B-tree leaf node */
#define H5AC_BLTR_ID 8 /*block tracker */
#define H5AC_SHEAP_ID 9 /*segmented heap */
#define H5AC_NTYPES 10
#define H5AC_BPT_HDR_ID 10 /*B+ tree header */
#define H5AC_BPT_LEAF_ID 11 /*B+ tree leaf */
#define H5AC_NTYPES 12
/* H5AC_DUMP_STATS_ON_CLOSE should always be FALSE when
* H5C_COLLECT_CACHE_STATS is FALSE.

6
src/H5B2cache.c
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@ -284,7 +284,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5B_cache_hdr_dest
* Function: H5B2_cache_hdr_dest
*
* Purpose: Destroys a B-tree header in memory.
*
@ -556,7 +556,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5B_cache_leaf_dest
* Function: H5B2_cache_leaf_dest
*
* Purpose: Destroys a B-tree leaf node in memory.
*
@ -874,7 +874,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5B_cache_internal_dest
* Function: H5B2_cache_internal_dest
*
* Purpose: Destroys a B-tree internal node in memory.
*

469
src/H5BP.c Normal file
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@ -0,0 +1,469 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5BP.c
* Apr 14 2005
* Quincey Koziol <koziol@ncsa.uiuc.edu>
*
* Purpose: Implements a B+ tree, with several modifications from
* the "standard" methods.
*
* Please see the documentation in:
* doc/html/TechNotes/Btrees.html for a full description
* of how they work, etc.
*
*-------------------------------------------------------------------------
*/
#define H5BP_PACKAGE /*suppress error about including H5BPpkg */
/* Private headers */
#include "H5private.h" /* Generic Functions */
#include "H5BPpkg.h" /* B+ trees */
#include "H5Eprivate.h" /* Error handling */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
/* Local macros */
/* Uncomment this macro to enable extra sanity checking */
/* #define H5BP_DEBUG */
/* Local typedefs */
/* Local prototypes */
/* Helper functions */
/* Package variables */
/* Declare a free list to manage the H5BP_t struct */
H5FL_DEFINE(H5BP_t);
/* Declare a free list to manage the H5BP_branch_t struct */
H5FL_DEFINE(H5BP_branch_t);
/* Declare a free list to manage the H5BP_twig_t struct */
H5FL_DEFINE(H5BP_twig_t);
/* Declare a free list to manage the H5BP_leaf_t struct */
H5FL_DEFINE(H5BP_leaf_t);
/* Static variables */
/* Declare a free list to manage B-tree node pages to/from disk */
H5FL_BLK_DEFINE_STATIC(node_page);
/* Declare a free list to manage the H5BP_shared_t struct */
H5FL_DEFINE_STATIC(H5BP_shared_t);
/*-------------------------------------------------------------------------
* Function: H5BP_shared_init
*
* Purpose: Allocate & initialize shared B-tree info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 14 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5BP_shared_init (H5BP_t *bpt, const H5BP_class_t *type,
size_t node_size, unsigned split_percent, unsigned merge_percent)
{
H5BP_shared_t *shared = NULL; /* Shared B+ tree information */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5BP_shared_init)
/* Allocate space for the shared information */
if(NULL==(shared = H5FL_CALLOC(H5BP_shared_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B+ tree shared information")
/* Assign user's information */
shared->split_percent = split_percent;
shared->merge_percent = merge_percent;
shared->node_size = node_size;
/* Assign common type information */
shared->type = type;
/* Allocate "page" for node I/O */
if((shared->page=H5FL_BLK_MALLOC(node_page,shared->node_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
#ifdef H5_USING_PURIFY
HDmemset(shared->page,0,shared->node_size);
#endif /* H5_USING_PURIFY */
/* Make shared B-tree info reference counted */
if(NULL==(bpt->shared=H5RC_create(shared,H5BP_shared_free)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B+ tree info")
done:
if(ret_value<0)
if(shared)
H5BP_shared_free(shared);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5BP_shared_init() */
/*-------------------------------------------------------------------------
* Function: H5BP_shared_free
*
* Purpose: Free shared B+ tree info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 14 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5BP_shared_free (void *_shared)
{
H5BP_shared_t *shared = (H5BP_shared_t *)_shared;
herr_t ret_value=SUCCEED;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_shared_free)
/* Sanity check */
HDassert(shared);
/* Free the B-tree node buffer */
if(shared->page)
H5FL_BLK_FREE(node_page,shared->page);
/* Free the shared B-tree info itself */
H5FL_FREE(H5BP_shared_t,shared);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5BP_shared_free() */
/*-------------------------------------------------------------------------
* Function: H5BP_create
*
* Purpose: Creates a new empty B+ tree in the file.
*
* Return: Non-negative on success (with address of new B-tree
* filled in), negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5BP_create(H5F_t *f, hid_t dxpl_id, const H5BP_class_t *type,
size_t node_size, unsigned split_percent, unsigned merge_percent,
haddr_t *addr_p)
{
H5BP_t *bpt = NULL; /* The new B+ tree header information */
herr_t ret_value=SUCCEED;
FUNC_ENTER_NOAPI(H5BP_create, FAIL)
/*
* Check arguments.
*/
HDassert(f);
HDassert(type);
HDassert(node_size>0);
HDassert(merge_percent>0 && merge_percent<=100);
HDassert(split_percent>0 && split_percent<=100);
HDassert(merge_percent<(split_percent/2));
/*
* Allocate file and memory data structures.
*/
if (NULL==(bpt = H5FL_MALLOC(H5BP_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree header")
/* Assign internal information */
HDmemset(&bpt->cache_info,0,sizeof(H5AC_info_t));
bpt->cache_info.is_dirty = TRUE;
bpt->depth = 0;
bpt->root.addr = HADDR_UNDEF;
bpt->root.all_nrec = 0;
bpt->root.util = 0;
/* Initialize shared B-tree info */
if(H5BP_shared_init(bpt, type, node_size, split_percent, merge_percent)<0)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create shared B+ tree info")
/* Allocate space for the header on disk */
if (HADDR_UNDEF==(*addr_p=H5MF_alloc(f, H5FD_MEM_BTREE, dxpl_id, (hsize_t)H5BP_HEADER_SIZE(f))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "file allocation failed for B-tree header")
/* Cache the new B-tree node */
if (H5AC_set(f, dxpl_id, H5AC_BPT_HDR, *addr_p, bpt, H5AC__NO_FLAGS_SET) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "can't add B+ tree header to cache")
done:
if (ret_value<0) {
if (bpt)
(void)H5BP_cache_hdr_dest(f,bpt);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5BP_create() */
/*-------------------------------------------------------------------------
* Function: H5BP_create_leaf
*
* Purpose: Creates empty leaf node of a B+ tree and updates node pointer
* to point to it.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_create_leaf(H5F_t *f, hid_t dxpl_id, H5RC_t *bpt_shared, H5BP_node_ptr_t *node_ptr)
{
H5BP_leaf_t *leaf=NULL; /* Pointer to new leaf node created */
H5BP_shared_t *shared; /* Shared B+ tree information */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5BP_create_leaf, FAIL)
/* Check arguments. */
HDassert(f);
HDassert(bpt_shared);
HDassert(node_ptr);
/* Allocate memory for leaf information */
if (NULL==(leaf = H5FL_MALLOC(H5BP_leaf_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B+ tree leaf info")
/* Set metadata cache info */
HDmemset(&leaf->cache_info,0,sizeof(H5AC_info_t));
leaf->cache_info.is_dirty = TRUE;
/* Share common B+ tree information */
leaf->shared = bpt_shared;
H5RC_INC(leaf->shared);
/* Get the pointer to the shared B-tree info */
shared=H5RC_GET_OBJ(leaf->shared);
HDassert(shared);
/* Create record pool for leaf node */
if((leaf->rec_pool = H5MP_create(H5BP_LEAF_POOL_PAGE, H5MP_FLG_DEFAULT)) == NULL)
HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, NULL, "can't allocate memory pool")
/* Set number of records */
leaf->nrec=0;
leaf->flags=0;
/* Allocate space on disk for the leaf */
if (HADDR_UNDEF==(node_ptr->addr=H5MF_alloc(f, H5FD_MEM_BTREE, dxpl_id, (hsize_t)shared->node_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "file allocation failed for B+ tree leaf node")
/* Cache the new B+ tree node */
if (H5AC_set(f, dxpl_id, H5AC_BPT_LEAF, node_ptr->addr, leaf, H5AC__NO_FLAGS_SET) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "can't add B+ tree leaf to cache")
done:
if (ret_value<0) {
if (leaf)
(void)H5BP_cache_leaf_dest(f,leaf);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* H5BP_create_leaf() */
/*-------------------------------------------------------------------------
* Function: H5BP_insert_leaf
*
* Purpose: Adds a new record to a B+ tree leaf node.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 22 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_insert_leaf(H5F_t *f, hid_t dxpl_id, H5RC_t *bpt_shared,
H5BP_node_ptr_t *curr_node_ptr, void *udata)
{
H5BP_leaf_t *leaf; /* Pointer to leaf node */
H5BP_shared_t *shared; /* Pointer to B+ tree's shared information */
int cmp; /* Comparison value of records */
unsigned idx; /* Location of record which matches key */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT(H5BP_insert_leaf)
/* Check arguments. */
HDassert(f);
HDassert(bpt_shared);
HDassert(curr_node_ptr);
HDassert(H5F_addr_defined(curr_node_ptr->addr));
if( H5BP_NODE_OVERSIZE(curr_node_ptr->util)) {
HDfprintf(stderr,"%s: attempting to insert record into extent node\n",FUNC);
HGOTO_ERROR(H5E_BTREE, H5E_UNSUPPORTED, FAIL, "Can't handle extent node!")
}
/* Lock B+ tree node */
if (NULL == (leaf = H5AC_protect(f, dxpl_id, H5AC_BPT_LEAF, curr_node_ptr->addr, &(curr_node_ptr->util), bpt_shared, H5AC_WRITE)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to load B+ tree leaf node")
/* Get the pointer to the shared B+ tree info */
shared=H5RC_GET_OBJ(bpt_shared);
HDassert(shared);
#ifndef LATER
HDfprintf(stderr,"%s: finish record insertion code\n",FUNC);
HGOTO_ERROR(H5E_BTREE, H5E_UNSUPPORTED, FAIL, "Can't handle record insertion!")
#else /* LATER */
/* Check for inserting into empty leaf */
if(leaf->nrec==0)
idx=0;
else {
/* Find correct location to insert this record */
if((cmp = H5BP_locate_record(shared->type,leaf->nrec,shared->nat_off,leaf->leaf_native,udata,&idx)) == 0)
HGOTO_ERROR(H5E_BTREE, H5E_EXISTS, FAIL, "record is already in B+ tree")
if(cmp > 0)
idx++;
/* Make room for new record */
if(idx<leaf->nrec)
HDmemmove(H5BP_LEAF_NREC(leaf,shared,idx+1),H5BP_LEAF_NREC(leaf,shared,idx),shared->type->nrec_size*(leaf->nrec-idx));
} /* end else */
/* Make callback to store record in native form */
if((shared->type->store)(H5BP_LEAF_NREC(leaf,shared,idx),udata)<0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into leaf node")
#endif /* LATER */
/* Update record count for node pointer to current node */
curr_node_ptr->all_nrec++;
/* Update record count for current node */
leaf->nrec++;
done:
/* Release the B+ tree leaf node */
if (leaf && H5AC_unprotect(f, dxpl_id, H5AC_BPT_LEAF, curr_node_ptr->addr, leaf, H5AC__DIRTIED_FLAG) < 0)
HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release leaf B+ tree node")
FUNC_LEAVE_NOAPI(ret_value)
} /* H5BP_insert_leaf() */
/*-------------------------------------------------------------------------
* Function: H5BP_insert
*
* Purpose: Adds a new record to the B+ tree.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5BP_insert(H5F_t *f, hid_t dxpl_id, const H5BP_class_t *type, haddr_t addr,
void *udata)
{
H5BP_t *bpt=NULL; /* Pointer to the B+ tree header */
H5BP_shared_t *shared; /* Pointer to B+ tree's shared information */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5BP_insert, FAIL)
/* Check arguments. */
HDassert(f);
HDassert(type);
HDassert(H5F_addr_defined(addr));
/* Look up the B+ tree header */
if (NULL == (bpt = H5AC_protect(f, dxpl_id, H5AC_BPT_HDR, addr, type, NULL, H5AC_WRITE)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to load B+ tree header")
/* Get the pointer to the shared B+ tree info */
shared=H5RC_GET_OBJ(bpt->shared);
HDassert(shared);
/* Check if the root node is allocated yet */
if(!H5F_addr_defined(bpt->root.addr)) {
/* Create root node as leaf node in B+ tree */
if(H5BP_create_leaf(f, dxpl_id, bpt->shared, &(bpt->root))<0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "unable to create root node")
/* Mark B+ tree header as dirty, since we updated the address of the root node */
bpt->cache_info.is_dirty = TRUE;
} /* end if */
/* Check if we need to split the root node (equiv. to a 1->2 leaf node split) */
else if(H5BP_NODE_OVERSIZE(bpt->root.util) ||
(!H5BP_NODE_OVERSIZE(bpt->root.util) && bpt->root.util>=shared->split_percent)) {
/* Split root node */
#ifdef LATER
if(H5BP_split_root(f, dxpl_id, bpt, bpt->shared)<0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTSPLIT, FAIL, "unable to split root node")
#else /* LATER */
HDfprintf(stderr,"%s: attempting to split root node\n",FUNC);
HGOTO_ERROR(H5E_BTREE, H5E_UNSUPPORTED, FAIL, "Can't split root yet!")
#endif /* LATER */
} /* end if */
/* Attempt to insert record into B+ tree */
if(bpt->depth>0) {
#ifdef LATER
if(H5BP_insert_internal(f,dxpl_id,bpt->shared,bpt->depth,&(bpt->cache_info),&bpt->root,udata)<0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B+ tree internal node")
#else /* LATER */
HDfprintf(stderr,"%s: attempting to insert record with internal node\n",FUNC);
HGOTO_ERROR(H5E_BTREE, H5E_UNSUPPORTED, FAIL, "Can't insert records yet!")
#endif /* LATER */
} /* end if */
else {
if(H5BP_insert_leaf(f,dxpl_id,bpt->shared,&bpt->root,udata)<0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B+ tree leaf node")
} /* end else */
done:
/* Release the B+ tree header info */
if (bpt && H5AC_unprotect(f, dxpl_id, H5AC_BPT_HDR, addr, bpt, H5AC__DIRTIED_FLAG) < 0)
HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release B+ tree header info")
FUNC_LEAVE_NOAPI(ret_value)
} /* H5BP_insert() */

710
src/H5BPcache.c Normal file
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@ -0,0 +1,710 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5BPcache.c
* Apr 19 2005
* Quincey Koziol <koziol@ncsa.uiuc.edu>
*
* Purpose: Implement B+ tree metadata cache methods.
*
*-------------------------------------------------------------------------
*/
#define H5BP_PACKAGE /*suppress error about including H5BPpkg */
/* Private headers */
#include "H5private.h" /* Generic Functions */
#include "H5BPpkg.h" /* B+ trees */
#include "H5Eprivate.h" /* Error handling */
/* Local macros */
/* B+ tree format version #'s */
#define H5BP_HDR_VERSION 0 /* Header */
#define H5BP_LEAF_VERSION 0 /* Leaf nodes */
/* Local typedefs */
/* Local prototypes */
/* Metadata cache callbacks */
static H5BP_t *H5BP_cache_hdr_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void *_type, void *udata);
static herr_t H5BP_cache_hdr_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr, H5BP_t *b);
static herr_t H5BP_cache_hdr_clear(H5F_t *f, H5BP_t *b, hbool_t destroy);
static herr_t H5BP_cache_hdr_size(const H5F_t *f, const H5BP_t *bt, size_t *size_ptr);
static H5BP_leaf_t *H5BP_cache_leaf_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void *_nrec, void *_bpt_shared);
static herr_t H5BP_cache_leaf_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr, H5BP_leaf_t *l);
static herr_t H5BP_cache_leaf_clear(H5F_t *f, H5BP_leaf_t *l, hbool_t destroy);
static herr_t H5BP_cache_leaf_size(const H5F_t *f, const H5BP_leaf_t *l, size_t *size_ptr);
/* Package variables */
/* H5BP headers inherit cache-like properties from H5AC */
const H5AC_class_t H5AC_BPT_HDR[1] = {{
H5AC_BPT_HDR_ID,
(H5AC_load_func_t)H5BP_cache_hdr_load,
(H5AC_flush_func_t)H5BP_cache_hdr_flush,
(H5AC_dest_func_t)H5BP_cache_hdr_dest,
(H5AC_clear_func_t)H5BP_cache_hdr_clear,
(H5AC_size_func_t)H5BP_cache_hdr_size,
}};
/* H5BP leaves inherit cache-like properties from H5AC */
const H5AC_class_t H5AC_BPT_LEAF[1] = {{
H5AC_BPT_LEAF_ID,
(H5AC_load_func_t)H5BP_cache_leaf_load,
(H5AC_flush_func_t)H5BP_cache_leaf_flush,
(H5AC_dest_func_t)H5BP_cache_leaf_dest,
(H5AC_clear_func_t)H5BP_cache_leaf_clear,
(H5AC_size_func_t)H5BP_cache_leaf_size,
}};
/* Static variables */
/* Declare a free list to manage B+ tree header data to/from disk */
H5FL_BLK_DEFINE_STATIC(header_block);
/* Declare a free list to manage 'void *' array data */
typedef void *voidp;
H5FL_SEQ_DEFINE_STATIC(voidp);
/*-------------------------------------------------------------------------
* Function: H5BP_cache_hdr_load
*
* Purpose: Loads a B+ tree header from the disk.
*
* Return: Success: Pointer to a new B+ tree.
*
* Failure: NULL
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static H5BP_t *
H5BP_cache_hdr_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void *_type, void UNUSED *udata)
{
const H5BP_class_t *type = (const H5BP_class_t *) _type;
size_t node_size; /* Size info for B+ tree */
unsigned split_percent, merge_percent; /* Split & merge info for B+ tree */
H5BP_t *bpt = NULL;
size_t size;
uint8_t *buf = NULL;
uint8_t *p; /* Pointer into raw data buffer */
H5BP_t *ret_value;
FUNC_ENTER_NOAPI(H5BP_cache_hdr_load, NULL)
/* Check arguments */
HDassert(f);
HDassert(H5F_addr_defined(addr));
HDassert(type);
if (NULL==(bpt = H5FL_MALLOC(H5BP_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
HDmemset(&bpt->cache_info,0,sizeof(H5AC_info_t));
/* Compute the size of the B+ tree header on disk */
size = H5BP_HEADER_SIZE(f);
/* Allocate temporary buffer */
if ((buf=H5FL_BLK_MALLOC(header_block,size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Read header from disk */
if (H5F_block_read(f, H5FD_MEM_BTREE, addr, size, dxpl_id, buf)<0)
HGOTO_ERROR(H5E_BTREE, H5E_READERROR, NULL, "can't read B+ tree header")
p = buf;
/* magic number */
if (HDmemcmp(p, H5BP_HDR_MAGIC, H5BP_SIZEOF_MAGIC))
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, NULL, "wrong B+ tree header signature")
p += H5BP_SIZEOF_MAGIC;
/* version */
if (*p++ != H5BP_HDR_VERSION)
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, NULL, "wrong B+ tree header version")
/* B+ tree type */
if (*p++ != (uint8_t)type->id)
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, NULL, "incorrect B+ tree type")
/* node size (in bytes) */
UINT32DECODE(p, node_size);
/* depth of tree */
UINT16DECODE(p, bpt->depth);
/* split & merge %s */
UINT16DECODE(p, split_percent);
UINT16DECODE(p, merge_percent);
/* root node pointer */
H5F_addr_decode(f, (const uint8_t **)&p, &(bpt->root.addr));
H5F_DECODE_LENGTH(f, p, bpt->root.all_nrec);
bpt->root.util = *p++;
/* Initialize shared B+ tree info */
if(H5BP_shared_init(bpt, type, node_size, split_percent, merge_percent)<0)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "can't create shared B+ tree info")
/* Set return value */
ret_value = bpt;
done:
if(buf)
H5FL_BLK_FREE(header_block,buf);
if (!ret_value && bpt)
(void)H5BP_cache_hdr_dest(f,bpt);
FUNC_LEAVE_NOAPI(ret_value)
} /*lint !e818 Can't make udata a pointer to const */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_hdr_flush
*
* Purpose: Flushes a dirty B+ tree header to disk.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_cache_hdr_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr, H5BP_t *bpt)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5BP_cache_hdr_flush, FAIL)
/* check arguments */
HDassert(f);
HDassert(H5F_addr_defined(addr));
HDassert(bpt);
if (bpt->cache_info.is_dirty) {
H5BP_shared_t *shared; /* Shared B+ tree information */
uint8_t *buf = NULL;
uint8_t *p; /* Pointer into raw data buffer */
size_t size;
/* Get the pointer to the shared B+ tree info */
shared=H5RC_GET_OBJ(bpt->shared);
HDassert(shared);
/* Compute the size of the B+ tree header on disk */
size = H5BP_HEADER_SIZE(f);
/* Allocate temporary buffer */
if ((buf=H5FL_BLK_MALLOC(header_block,size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
p = buf;
/* magic number */
HDmemcpy(p, H5BP_HDR_MAGIC, H5BP_SIZEOF_MAGIC);
p += H5BP_SIZEOF_MAGIC;
/* version # */
*p++ = H5BP_HDR_VERSION;
/* B+ tree type */
*p++ = shared->type->id;
/* node size (in bytes) */
UINT32ENCODE(p, shared->node_size);
/* depth of tree */
UINT16ENCODE(p, bpt->depth);
/* split & merge %s */
UINT16ENCODE(p, shared->split_percent);
UINT16ENCODE(p, shared->merge_percent);
/* root node pointer */
H5F_addr_encode(f, &p, bpt->root.addr);
H5F_ENCODE_LENGTH(f, p, bpt->root.all_nrec);
*p++ = bpt->root.util;
/* Write the B+ tree header. */
if (H5F_block_write(f, H5FD_MEM_BTREE, addr, size, dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTFLUSH, FAIL, "unable to save B+ tree header to disk")
H5FL_BLK_FREE(header_block,buf);
bpt->cache_info.is_dirty = FALSE;
} /* end if */
if (destroy)
if (H5BP_cache_hdr_dest(f, bpt) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTFREE, FAIL, "unable to destroy B+ tree header")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5BP_cache_hdr_flush() */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_hdr_dest
*
* Purpose: Destroys a B+ tree header in memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
herr_t
H5BP_cache_hdr_dest(H5F_t UNUSED *f, H5BP_t *bpt)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_cache_hdr_dest)
/*
* Check arguments.
*/
HDassert(bpt);
/* Decrement reference count on shared B+ tree info */
if(bpt->shared)
H5RC_DEC(bpt->shared);
/* Free B+ tree header info */
H5FL_FREE(H5BP_t,bpt);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5BP_cache_hdr_dest() */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_hdr_clear
*
* Purpose: Mark a B+ tree header in memory as non-dirty.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_cache_hdr_clear(H5F_t *f, H5BP_t *bpt, hbool_t destroy)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT(H5BP_cache_hdr_clear)
/*
* Check arguments.
*/
HDassert(bpt);
/* Reset the dirty flag. */
bpt->cache_info.is_dirty = FALSE;
if (destroy)
if (H5BP_cache_hdr_dest(f, bpt) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTFREE, FAIL, "unable to destroy B+ tree header")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5BP_cache_hdr_clear() */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_hdr_size
*
* Purpose: Compute the size in bytes of a B+ tree header
* on disk, and return it in *size_ptr. On failure,
* the value of *size_ptr is undefined.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_cache_hdr_size(const H5F_t *f, const H5BP_t UNUSED *bpt, size_t *size_ptr)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_cache_hdr_size)
/* check arguments */
HDassert(f);
HDassert(size_ptr);
/* Set size value */
*size_ptr = H5BP_HEADER_SIZE(f);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5BP_cache_hdr_size() */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_leaf_load
*
* Purpose: Loads a B+ tree leaf from the disk.
*
* Return: Success: Pointer to a new B+ tree leaf node.
*
* Failure: NULL
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static H5BP_leaf_t *
H5BP_cache_leaf_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void *_nrec, void *_bpt_shared)
{
const unsigned char *nrec = (const unsigned char *)_nrec;
H5RC_t *bpt_shared=(H5RC_t *)_bpt_shared; /* Shared B+ tree information */
H5BP_shared_t *shared; /* Shared B+ tree information */
H5BP_leaf_t *leaf = NULL; /* Pointer to new leaf */
uint8_t *p; /* Pointer into raw data buffer */
size_t rec_size; /* Size of records */
unsigned u; /* Local index variable */
H5BP_leaf_t *ret_value;
FUNC_ENTER_NOAPI(H5BP_cache_leaf_load, NULL)
/* Check arguments */
HDassert(f);
HDassert(H5F_addr_defined(addr));
HDassert(bpt_shared);
if (NULL==(leaf = H5FL_MALLOC(H5BP_leaf_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
HDmemset(&leaf->cache_info,0,sizeof(H5AC_info_t));
/* Share common B+ tree information */
leaf->shared = bpt_shared;
H5RC_INC(leaf->shared);
/* Get the pointer to the shared B+ tree info */
shared=H5RC_GET_OBJ(leaf->shared);
HDassert(shared);
/* Check if we can use existing buffer for node */
/* Read header from disk */
if (H5F_block_read(f, H5FD_MEM_BTREE, addr, shared->node_size, dxpl_id, shared->page)<0)
HGOTO_ERROR(H5E_BTREE, H5E_READERROR, NULL, "can't read B+ tree leaf node")
p = shared->page;
/* magic number */
if (HDmemcmp(p, H5BP_LEAF_MAGIC, H5BP_SIZEOF_MAGIC))
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, NULL, "wrong B+ tree leaf node signature")
p += H5BP_SIZEOF_MAGIC;
/* version */
if (*p++ != H5BP_LEAF_VERSION)
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, NULL, "wrong B+ tree leaf node version")
/* B+ tree type */
if (*p++ != (uint8_t)shared->type->id)
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, NULL, "incorrect B+ tree type")
/* Set the number of records in the leaf */
leaf->nrec = *nrec;
/* Get the status flags for the leaf */
leaf->flags = *p++;
/* Create record pool for leaf node */
if((leaf->rec_pool = H5MP_create(H5BP_LEAF_POOL_PAGE, H5MP_FLG_DEFAULT)) == NULL)
HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, NULL, "can't allocate memory pool")
/* Retrieve variable-length record information, if present */
if(H5BP_LEAF_REC_VARLEN(leaf->flags)) {
/* Allocate space for the record pointers */
if((leaf->rec_ptr = H5FL_SEQ_MALLOC(voidp, leaf->nrec)) == NULL)
HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, NULL, "can't allocate record pointers for node")
/* Work through the records on disk and insert them into array for node */
for(u = 0; u < leaf->nrec; u++) {
size_t rec_len; /* Index of current record */
/* Determine the length of the record */
UINT16DECODE(p, rec_len);
/* Decode the record */
if((leaf->rec_ptr[u] = (shared->type->decode)(f, leaf->rec_pool, p, rec_len)) == NULL)
HGOTO_ERROR(H5E_BTREE, H5E_CANTDECODE, NULL, "can't decode B+ tree record")
p += rec_len;
} /* end for */
} /* end if */
else {
/* Retrieve the records' size */
UINT16DECODE(p, rec_size);
HDfprintf(stderr,"%s: attempting to decode fixed-size records from leaf node\n",FUNC);
HGOTO_ERROR(H5E_BTREE, H5E_UNSUPPORTED, NULL, "Can't decode records yet!")
} /* end else */
/* Set return value */
ret_value = leaf;
done:
if (!ret_value && leaf)
(void)H5BP_cache_leaf_dest(f,leaf);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5BP_cache_leaf_load() */ /*lint !e818 Can't make udata a pointer to const */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_leaf_flush
*
* Purpose: Flushes a dirty B+ tree leaf node to disk.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_cache_leaf_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr, H5BP_leaf_t *leaf)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5BP_cache_leaf_flush, FAIL)
/* check arguments */
HDassert(f);
HDassert(H5F_addr_defined(addr));
HDassert(leaf);
if (leaf->cache_info.is_dirty) {
H5BP_shared_t *shared; /* Shared B+ tree information */
uint8_t *p; /* Pointer into raw data buffer */
#ifdef LATER
uint8_t *native; /* Pointer to native keys */
unsigned u; /* Local index variable */
#endif /* LATER */
/* Get the pointer to the shared B+ tree info */
shared=H5RC_GET_OBJ(leaf->shared);
HDassert(shared);
p = shared->page;
/* magic number */
HDmemcpy(p, H5BP_LEAF_MAGIC, H5BP_SIZEOF_MAGIC);
p += H5BP_SIZEOF_MAGIC;
/* version # */
*p++ = H5BP_LEAF_VERSION;
/* B+ tree type */
*p++ = shared->type->id;
/* status flags */
*p++ = leaf->flags;
/* Serialize records */
if(H5BP_LEAF_REC_VARLEN(leaf->flags)) {
unsigned u; /* Local index */
/* Work through the records in memory and encode them to disk */
for(u = 0; u < leaf->nrec; u++) {
size_t rec_len; /* Index of current record */
uint8_t *tp; /* Temporary pointer into raw data buffer */
/* Save the location for the record length */
tp = p;
/* Skip over the location for the record length */
p += 2;
/* Encode the record */
if((shared->type->encode)(f, leaf->rec_ptr[u], p, &rec_len) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTENCODE, NULL, "can't encode B+ tree record")
assert(rec_len > 0);
p += rec_len;
/* Encode the record length */
UINT16ENCODE(tp, rec_len);
} /* end for */
} /* end if */
else {
HDfprintf(stderr,"%s: attempting to decode fixed-size records from leaf node\n",FUNC);
HGOTO_ERROR(H5E_BTREE, H5E_UNSUPPORTED, NULL, "Can't decode records yet!")
} /* end else */
#ifdef LATER
/* Serialize records for leaf node */
native=leaf->leaf_native;
for(u=0; u<leaf->nrec; u++) {
/* Encode record */
if((shared->type->encode)(f,p,native)<0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTENCODE, FAIL, "unable to encode B+ tree record")
/* Move to next record */
p += shared->rrec_size;
native += shared->type->nrec_size;
} /* end for */
#endif /* LATER */
/* Write the B+ tree leaf node */
if (H5F_block_write(f, H5FD_MEM_BTREE, addr, shared->node_size, dxpl_id, shared->page) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTFLUSH, FAIL, "unable to save B+ tree leaf node to disk")
leaf->cache_info.is_dirty = FALSE;
} /* end if */
if (destroy)
if (H5BP_cache_leaf_dest(f,leaf) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTFREE, FAIL, "unable to destroy B+ tree leaf node")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5BP_cache_leaf_flush() */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_leaf_dest
*
* Purpose: Destroys a B+ tree leaf node in memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
herr_t
H5BP_cache_leaf_dest(H5F_t UNUSED *f, H5BP_leaf_t *leaf)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_cache_leaf_dest)
/*
* Check arguments.
*/
HDassert(leaf);
/* Decrement reference count on shared B+ tree info */
if(leaf->shared)
H5RC_DEC(leaf->shared);
/* Release B+ tree leaf node record pointer array */
H5FL_SEQ_FREE(voidp, leaf->rec_ptr);
/* Release B+ tree leaf node record memory pool */
H5MP_close(leaf->rec_pool);
/* Free B+ tree leaf node info */
H5FL_FREE(H5BP_leaf_t, leaf);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5BP_cache_leaf_dest() */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_leaf_clear
*
* Purpose: Mark a B+ tree leaf node in memory as non-dirty.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_cache_leaf_clear(H5F_t *f, H5BP_leaf_t *leaf, hbool_t destroy)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT(H5BP_cache_leaf_clear)
/*
* Check arguments.
*/
HDassert(leaf);
/* Reset the dirty flag. */
leaf->cache_info.is_dirty = FALSE;
if (destroy)
if (H5BP_cache_leaf_dest(f, leaf) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTFREE, FAIL, "unable to destroy B+ tree leaf node")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5BP_cache_leaf_clear() */
/*-------------------------------------------------------------------------
* Function: H5BP_cache_leaf_size
*
* Purpose: Compute the size in bytes of a B+ tree leaf node
* on disk, and return it in *size_ptr. On failure,
* the value of *size_ptr is undefined.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_cache_leaf_size(const H5F_t UNUSED *f, const H5BP_leaf_t *leaf, size_t *size_ptr)
{
H5BP_shared_t *shared; /* Shared B+ tree information */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_cache_leaf_size)
/* check arguments */
HDassert(leaf);
HDassert(size_ptr);
/* Get the pointer to the shared B+ tree info */
shared=H5RC_GET_OBJ(leaf->shared);
HDassert(shared);
/* Set size value */
*size_ptr = shared->node_size;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5BP_cache_leaf_size() */

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5BPdbg.c
* Apr 19 2005
* Quincey Koziol <koziol@ncsa.uiuc.edu>
*
* Purpose: Dump debugging information about a B+ tree.
*
*-------------------------------------------------------------------------
*/
#define H5BP_PACKAGE /*suppress error about including H5BPpkg */
/* Private headers */
#include "H5private.h" /* Generic Functions */
#include "H5BPpkg.h" /* B+ trees */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
/*-------------------------------------------------------------------------
* Function: H5BP_hdr_debug
*
* Purpose: Prints debugging info about a B+ tree header.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@ncsa.uiuc.edu
* Apr 19 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5BP_hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, int fwidth,
const H5BP_class_t *type)
{
H5BP_t *bpt = NULL;
H5BP_shared_t *shared; /* Shared B+ tree information */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5BP_hdr_debug, FAIL)
/*
* Check arguments.
*/
assert(f);
assert(H5F_addr_defined(addr));
assert(stream);
assert(indent >= 0);
assert(fwidth >= 0);
/*
* Load the B+ tree header.
*/
if (NULL == (bpt = H5AC_protect(f, dxpl_id, H5AC_BPT_HDR, addr, type, NULL, H5AC_READ)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "unable to load B+ tree header")
/* Get the pointer to the shared B+ tree info */
shared=H5RC_GET_OBJ(bpt->shared);
assert(shared);
/*
* Print the values.
*/
HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
"Tree type ID:",
(shared->type->id == H5BP_TEST_ID ? "H5BP_TEST_ID" :
"Unknown!"));
HDfprintf(stream, "%*s%-*s %Zu\n", indent, "", fwidth,
"Size of node:",
shared->node_size);
HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
"Dirty flag:",
bpt->cache_info.is_dirty ? "True" : "False");
HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth,
"Depth:",
bpt->depth);
HDfprintf(stream, "%*s%-*s %Hu\n", indent, "", fwidth,
"Number of records in tree:",
bpt->root.all_nrec);
if(H5BP_NODE_OVERSIZE(bpt->root.util))
HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth,
"Root node size multiplier:",
(unsigned)(bpt->root.util & 0x7f));
else
HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth,
"Root node size utilization:",
(unsigned)bpt->root.util);
HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth,
"Address of root node:",
bpt->root.addr);
HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth,
"Split percent:",
shared->split_percent);
HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth,
"Merge percent:",
shared->merge_percent);
done:
if (bpt && H5AC_unprotect(f, dxpl_id, H5AC_BPT_HDR, addr, bpt, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B+ tree header")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5BP_hdr_debug() */

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Thursday, April 14, 2005
*
* Purpose: This file contains declarations which are visible only within
* the H5BP package. Source files outside the H5BP package should
* include H5BPprivate.h instead.
*/
#ifndef H5BP_PACKAGE
#error "Do not include this file outside the H5BP package!"
#endif
#ifndef _H5BPpkg_H
#define _H5BPpkg_H
/* Get package's private header */
#include "H5BPprivate.h"
/* Other private headers needed by this file */
#include "H5ACprivate.h" /* Metadata cache */
#include "H5FLprivate.h" /* Free Lists */
#include "H5RCprivate.h" /* Reference counted object functions */
/**************************/
/* Package Private Macros */
/**************************/
/* Size of signature information (on disk) */
#define H5BP_SIZEOF_MAGIC 4
/* B+ tree signatures */
#define H5BP_HDR_MAGIC "BPHD" /* Header */
#define H5BP_INT_MAGIC "BPBR" /* Branch node */
#define H5BP_TWIG_MAGIC "BPTW" /* Twig node */
#define H5BP_LEAF_MAGIC "BPLF" /* Leaf node */
#define H5BP_EXTENT_MAGIC "BPEX" /* Extent node */
/* Size of storage for number of separators per node (on disk) */
#define H5BP_SIZEOF_SEPS_PER_NODE 2
/* Size of storage for "node size multiplier" (on disk) */
#define H5BP_SIZEOF_NODE_MULT 1
/* Size of a "full" node pointer (on disk) */
#define H5BP_NODE_POINTER_SIZE(f) (H5F_SIZEOF_ADDR(f)+H5F_SIZEOF_SIZE(f)+H5BP_SIZEOF_NODE_MULT)
/* Size of the B+ tree header on disk */
#define H5BP_HEADER_SIZE(f) ( \
4 + /* Signature */ \
1 + /* Version */ \
1 + /* Tree type */ \
4 + /* Node size, in bytes */ \
2 + /* Depth of tree */ \
2 + /* Split % of full (as integer, ie. "98" means 98%) */ \
2 + /* Merge % of full (as integer, ie. "98" means 98%) */ \
H5BP_NODE_POINTER_SIZE(f)) /* Node pointer to root node in tree */
/* Determine whether a node is oversized */
/* The high bit is set in utilization field for oversized nodes */
#define H5BP_NODE_OVERSIZE(u) ((u) & 0x80)
/* Determine whether a leaf node has variable-length records */
/* The low bit is set in "flag" field for nodes w/variable-length records */
#define H5BP_LEAF_REC_VARLEN(u) ((u) & 0x01)
/* Size of memory pool pages for leaf nodes */
#define H5BP_LEAF_POOL_PAGE H5MP_PAGE_SIZE_DEFAULT
/****************************/
/* Package Private Typedefs */
/****************************/
/* A "node pointer" to another B+ tree node */
typedef struct {
haddr_t addr; /* Address of other node */
hsize_t all_nrec; /* Number of records in node pointed to and all it's children */
unsigned char util; /* Percent utilization/page node multiple */
} H5BP_node_ptr_t;
/* Each B+ tree has certain information that can be shared across all
* the instances of nodes in that B-tree.
*/
typedef struct H5BP_shared_t {
/* Shared internal data structures */
const H5BP_class_t *type; /* Type of tree */
uint8_t *page; /* Disk page */
/* Information set by user */
unsigned split_percent; /* Percent full at which to split the node, when inserting */
unsigned merge_percent; /* Percent full at which to merge the node, when deleting */
size_t node_size; /* Size of all nodes, in bytes */
} H5BP_shared_t;
/* The B+ tree information */
typedef struct H5BP_t {
/* Information for H5AC cache functions, _must_ be first field in structure */
H5AC_info_t cache_info;
/* Internal B+ tree information */
unsigned depth; /* B+ tree's overall depth */
H5BP_node_ptr_t root; /* Node pointer to root node in B+ tree */
H5RC_t *shared; /* Ref-counted shared info */
} H5BP_t;
/* B+ tree internal branch node information */
typedef struct H5BP_branch_t {
/* Information for H5AC cache functions, _must_ be first field in structure */
H5AC_info_t cache_info;
/* Internal B+ tree information */
H5RC_t *shared; /* Ref-counted shared info */
uint8_t *int_native; /* Pointer to native records */
H5BP_node_ptr_t *node_ptrs; /* Pointer to node pointers */
unsigned nrec; /* Number of records in node */
} H5BP_branch_t;
/* B+ tree internal twig node information */
typedef struct H5BP_twig_t {
/* Information for H5AC cache functions, _must_ be first field in structure */
H5AC_info_t cache_info;
/* Internal B+ tree information */
H5RC_t *shared; /* Ref-counted shared info */
uint8_t *int_native; /* Pointer to native records */
H5BP_node_ptr_t *node_ptrs; /* Pointer to node pointers */
unsigned nrec; /* Number of records in node */
} H5BP_twig_t;
/* B+ tree leaf node information */
typedef struct H5BP_leaf_t {
/* Information for H5AC cache functions, _must_ be first field in structure */
H5AC_info_t cache_info;
/* Internal B+ tree information */
H5RC_t *shared; /* Ref-counted shared info */
H5MP_pool_t *rec_pool; /* Pool containing records for node */
void **rec_ptr; /* Array of pointers to records in pool */
unsigned nrec; /* Number of records in node */
unsigned char flags; /* Status flags for leaf node */
} H5BP_leaf_t;
#ifdef H5BP_TESTING
/* Record for testing B+ trees */
typedef struct {
hsize_t count;
char *name;
} H5BP_test_rec_t;
#endif /* H5BP_TESTING */
/*****************************/
/* Package Private Variables */
/*****************************/
/* H5BP header inherits cache-like properties from H5AC */
H5_DLLVAR const H5AC_class_t H5AC_BPT_HDR[1];
/* H5BP branch node inherits cache-like properties from H5AC */
H5_DLLVAR const H5AC_class_t H5AC_BPT_BRANCH[1];
/* H5BP twig node inherits cache-like properties from H5AC */
H5_DLLVAR const H5AC_class_t H5AC_BPT_TWIG[1];
/* H5BP leaf node inherits cache-like properties from H5AC */
H5_DLLVAR const H5AC_class_t H5AC_BPT_LEAF[1];
/* Declare a free list to manage the H5BP_t struct */
H5FL_EXTERN(H5BP_t);
/* Declare a free list to manage the H5BP_branch_t struct */
H5FL_EXTERN(H5BP_branch_t);
/* Declare a free list to manage the H5BP_twig_t struct */
H5FL_EXTERN(H5BP_twig_t);
/* Declare a free list to manage the H5BP_leaf_t struct */
H5FL_EXTERN(H5BP_leaf_t);
/* Internal B+ tree testing class */
#ifdef H5BP_TESTING
H5_DLLVAR const H5BP_class_t H5BP_TEST[1];
#endif /* H5BP_TESTING */
/******************************/
/* Package Private Prototypes */
/******************************/
H5_DLL herr_t H5BP_shared_free (void *_shared);
H5_DLL herr_t H5BP_shared_init (H5BP_t *bpt, const H5BP_class_t *type,
size_t node_size, unsigned split_percent, unsigned merge_percent);
H5_DLL herr_t H5BP_cache_hdr_dest(H5F_t *f, H5BP_t *bpt);
H5_DLL herr_t H5BP_cache_leaf_dest(H5F_t UNUSED *f, H5BP_leaf_t *leaf);
H5_DLL herr_t H5BP_hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr,
FILE *stream, int indent, int fwidth, const H5BP_class_t *type);
#endif /* _H5BPpkg_H */

86
src/H5BPprivate.h Normal file
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@ -0,0 +1,86 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5BPprivate.h
* Apr 14 2005
* Quincey Koziol <koziol@ncsa.uiuc.edu>
*
* Purpose: Private header for library accessible B+ tree routines.
*
*-------------------------------------------------------------------------
*/
#ifndef _H5BPprivate_H
#define _H5BPprivate_H
/* Include package's public header */
#include "H5BPpublic.h"
/* Private headers needed by this file */
#include "H5Fprivate.h" /* File access */
#include "H5MPprivate.h" /* Memory Pools */
/**************************/
/* Library Private Macros */
/**************************/
/****************************/
/* Library Private Typedefs */
/****************************/
/* B+ tree IDs for various internal things. */
typedef enum H5BP_subid_t {
H5BP_TEST_ID = 0, /* B+ tree is for testing (do not use for actual data) */
H5BP_NUM_BTREE_ID /* Number of B-tree IDs (must be last) */
} H5BP_subid_t;
/*
* Each class of object that can be pointed to by a B+ tree has a
* variable of this type that contains class variables and methods.
*/
typedef struct H5BP_class_t {
H5BP_subid_t id; /*id as found in file*/
/* Copy native application record */
void * (*copy)(const void *record); /* Copy native record */
/* Compare key */
herr_t (*compare)(const void *key1, const void *key2); /* Compare two native keys */
/* Encode & decode record values */
/* (i.e. native application form <-> disk form) */
herr_t (*raw_len)(const H5F_t *f, const void *record, size_t *len); /* Determine length of raw (disk) form from native form */
herr_t (*encode)(const H5F_t *f, const uint8_t *native, uint8_t *raw, size_t *rec_len); /* Encode record from native form to disk storage form */
void * (*decode)(const H5F_t *f, H5MP_pool_t *pool, const uint8_t *raw, size_t rec_len); /* Decode record from disk storage form to native form */
/* Debug record values */
herr_t (*debug) (FILE *stream, const H5F_t *f, hid_t dxpl_id, /* Print a record for debugging */
int indent, int fwidth, const void *record, const void *udata);
} H5BP_class_t;
/***************************************/
/* Library-private Function Prototypes */
/***************************************/
H5_DLL herr_t H5BP_create(H5F_t *f, hid_t dxpl_id, const H5BP_class_t *type,
size_t node_size, unsigned split_percent, unsigned merge_percent,
haddr_t *addr_p);
H5_DLL herr_t H5BP_insert(H5F_t *f, hid_t dxpl_id, const H5BP_class_t *type,
haddr_t addr, void *udata);
#endif /* _H5BPprivate_H */

53
src/H5BPpublic.h Normal file
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@ -0,0 +1,53 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5BPpublic.h
* Apr 19 2005
* Quincey Koziol <koziol@ncsa.uiuc.edu>
*
* Purpose: Public declarations for the H5BP package.
*
*-------------------------------------------------------------------------
*/
#ifndef _H5BPpublic_H
#define _H5BPpublic_H
/* Public headers needed by this file */
#include "H5public.h"
/*****************/
/* Public Macros */
/*****************/
/*******************/
/* Public Typedefs */
/*******************/
/**********************************/
/* Public API Function Prototypes */
/**********************************/
#ifdef __cplusplus
extern "C" {
#endif
#ifdef __cplusplus
}
#endif
#endif /* _H5BPpublic_H */

237
src/H5BPtest.c Normal file
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@ -0,0 +1,237 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Thursday, April 19, 2005
*
* Purpose: B+ tree testing functions.
*/
#define H5BP_PACKAGE /*suppress error about including H5BPpkg */
#define H5BP_TESTING /*suppress warning about H5BP testing funcs*/
/* Private headers */
#include "H5private.h" /* Generic Functions */
#include "H5BPpkg.h" /* B+ trees */
#include "H5Eprivate.h" /* Error handling */
#include "H5MMprivate.h" /* Memory management */
/* Static Prototypes */
static void *H5BP_test_copy(const void *rec);
static herr_t H5BP_test_compare(const void *rec1, const void *rec2);
static herr_t H5BP_test_raw_len(const H5F_t *f, const void *record, size_t *len);
static herr_t H5BP_test_encode(const H5F_t *f, const uint8_t *native,
uint8_t *raw, size_t *rec_len);
static void *H5BP_test_decode(const H5F_t *f, H5MP_pool_t *pool,
const uint8_t *raw, size_t rec_len);
static herr_t H5BP_test_debug(FILE *stream, const H5F_t *f, hid_t dxpl_id,
int indent, int fwidth, const void *record, const void *_udata);
/* Package variables */
const H5BP_class_t H5BP_TEST[1]={{ /* B+ tree class information */
H5BP_TEST_ID, /* Type of B+ tree */
H5BP_test_copy, /* Record copy callback */
H5BP_test_compare, /* Record comparison callback */
H5BP_test_raw_len, /* Record 'raw len' callback */
H5BP_test_encode, /* Record encoding callback */
H5BP_test_decode, /* Record decoding callback */
H5BP_test_debug /* Record debugging callback */
}};
/*-------------------------------------------------------------------------
* Function: H5BP_test_copy
*
* Purpose: Copy native information record
*
* Return: Pointer to new record on success, NULL on failure
*
* Programmer: Quincey Koziol
* Monday, April 25, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5BP_test_copy(const void *rec)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_test_copy)
/* Copy record */
FUNC_LEAVE_NOAPI(HDstrdup(rec));
} /* H5BP_test_copy() */
/*-------------------------------------------------------------------------
* Function: H5BP_test_compare
*
* Purpose: Compare two native information records, according to some key
*
* Return: <0 if rec1 < rec2
* =0 if rec1 == rec2
* >0 if rec1 > rec2
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_test_compare(const void *rec1, const void *rec2)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_test_compare)
FUNC_LEAVE_NOAPI(HDstrcmp(*(const char **)rec1, *(const char **)rec2));
} /* H5BP_test_compare() */
/*-------------------------------------------------------------------------
* Function: H5BP_test_raw_len
*
* Purpose: Determine the length of the raw form of a record
*
* Return: <0 if rec1 < rec2
* =0 if rec1 == rec2
* >0 if rec1 > rec2
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_test_raw_len(const H5F_t UNUSED *f, const void *record, size_t *len)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_test_raw_len)
*len = HDstrlen((const char *)record);
FUNC_LEAVE_NOAPI(SUCCEED);
} /* H5BP_test_raw_len() */
/*-------------------------------------------------------------------------
* Function: H5BP_test_encode
*
* Purpose: Encode native information into raw form for storing on disk
*
* Return: Success: non-negative
*
* Failure: negative
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_test_encode(const H5F_t *f, const uint8_t *native, uint8_t *raw, size_t *rec_len)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_test_encode)
/* Sanity check */
HDassert(f);
HDassert(native);
HDassert(raw);
HDassert(rec_len);
/* Get the record length */
*rec_len = HDstrlen((const char *)native);
/* "Encode" the record */
HDmemcpy(raw, native, *rec_len);
FUNC_LEAVE_NOAPI(SUCCEED);
} /* H5BP_test_encode() */
/*-------------------------------------------------------------------------
* Function: H5BP_test_decode
*
* Purpose: Decode raw disk form of record into native form
*
* Return: Success: non-negative
*
* Failure: negative
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5BP_test_decode(const H5F_t *f, H5MP_pool_t *pool, const uint8_t *raw, size_t rec_len)
{
void *ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5BP_test_decode)
/* Sanity check */
HDassert(f);
HDassert(pool);
HDassert(raw);
HDassert(rec_len > 0);
/* Allocate space for the record */
if((ret_value = H5MP_malloc(pool, rec_len + 1)) == NULL)
HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, NULL, "Can't allocate space for record")
/* "Decode" the record */
HDmemcpy(ret_value, raw, rec_len);
*((unsigned char *)ret_value + rec_len) = '\0';
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5BP_test_decode() */
/*-------------------------------------------------------------------------
* Function: H5BP_test_debug
*
* Purpose: Debug native form of record
*
* Return: Success: non-negative
*
* Failure: negative
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5BP_test_debug(FILE *stream, const H5F_t UNUSED *f, hid_t UNUSED dxpl_id, int indent, int fwidth,
const void *record, const void UNUSED *_udata)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5BP_test_debug)
HDassert (record);
HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, "Record:",
*(const char *)record);
FUNC_LEAVE_NOAPI(SUCCEED);
} /* H5BP_test_debug() */

2
src/H5Cpkg.h
View File

@ -574,7 +574,7 @@
****************************************************************************/
#define H5C__H5C_T_MAGIC 0x005CAC0E
#define H5C__MAX_NUM_TYPE_IDS 10
#define H5C__MAX_NUM_TYPE_IDS 12
struct H5C_t
{

5
src/Makefile.am
View File

@ -42,7 +42,8 @@ DISTCLEAN=libhdf5.settings
# library sources
libhdf5_la_SOURCES= H5.c H5A.c H5AC.c H5B.c H5B2.c H5B2cache.c H5B2dbg.c \
H5B2test.c H5BT.c H5BTbtree2.c H5BTcache.c H5BTdbg.c H5BTtest.c H5C.c \
H5B2test.c H5BP.c H5BPcache.c H5BPdbg.c H5BPtest.c \
H5BT.c H5BTbtree2.c H5BTcache.c H5BTdbg.c H5BTtest.c H5C.c \
H5D.c \
H5Dcontig.c \
H5Dcompact.c \
@ -72,7 +73,7 @@ libhdf5_la_SOURCES= H5.c H5A.c H5AC.c H5B.c H5B2.c H5B2cache.c H5B2dbg.c \
# Public headers
include_HEADERS =H5public.h H5Apublic.h H5ACpublic.h H5Bpublic.h H5B2public.h \
H5BTpublic.h H5Cpublic.h H5Dpublic.h \
H5BPpublic.h H5BTpublic.h H5Cpublic.h H5Dpublic.h \
H5Epubgen.h H5Epublic.h H5Fpublic.h H5FDpublic.h H5FDcore.h H5FDfamily.h \
H5FDfphdf5.h H5FDlog.h H5FDmpi.h H5FDmpio.h H5FDmpiposix.h \
H5FDmulti.h H5FDsec2.h H5FDstdio.h H5FDstream.h H5FPpublic.h \

14
src/Makefile.in
View File

@ -83,8 +83,9 @@ libLTLIBRARIES_INSTALL = $(INSTALL)
LTLIBRARIES = $(lib_LTLIBRARIES)
libhdf5_la_LIBADD =
am_libhdf5_la_OBJECTS = H5.lo H5A.lo H5AC.lo H5B.lo H5B2.lo \
H5B2cache.lo H5B2dbg.lo H5B2test.lo H5BT.lo H5BTbtree2.lo \
H5BTcache.lo H5BTdbg.lo H5BTtest.lo H5C.lo H5D.lo H5Dcontig.lo \
H5B2cache.lo H5B2dbg.lo H5B2test.lo H5BP.lo H5BPcache.lo \
H5BPdbg.lo H5BPtest.lo H5BT.lo H5BTbtree2.lo H5BTcache.lo \
H5BTdbg.lo H5BTtest.lo H5C.lo H5D.lo H5Dcontig.lo \
H5Dcompact.lo H5Defl.lo H5Dio.lo H5Distore.lo H5Dmpio.lo \
H5Dselect.lo H5Dtest.lo H5E.lo H5F.lo H5Fdbg.lo H5Fmount.lo \
H5Fsuper.lo H5FD.lo H5FDcore.lo H5FDfamily.lo H5FDfphdf5.lo \
@ -362,7 +363,8 @@ DISTCLEAN = libhdf5.settings
# library sources
libhdf5_la_SOURCES = H5.c H5A.c H5AC.c H5B.c H5B2.c H5B2cache.c H5B2dbg.c \
H5B2test.c H5BT.c H5BTbtree2.c H5BTcache.c H5BTdbg.c H5BTtest.c H5C.c \
H5B2test.c H5BP.c H5BPcache.c H5BPdbg.c H5BPtest.c \
H5BT.c H5BTbtree2.c H5BTcache.c H5BTdbg.c H5BTtest.c H5C.c \
H5D.c \
H5Dcontig.c \
H5Dcompact.c \
@ -392,7 +394,7 @@ libhdf5_la_SOURCES = H5.c H5A.c H5AC.c H5B.c H5B2.c H5B2cache.c H5B2dbg.c \
# Public headers
include_HEADERS = H5public.h H5Apublic.h H5ACpublic.h H5Bpublic.h H5B2public.h \
H5BTpublic.h H5Cpublic.h H5Dpublic.h \
H5BPpublic.h H5BTpublic.h H5Cpublic.h H5Dpublic.h \
H5Epubgen.h H5Epublic.h H5Fpublic.h H5FDpublic.h H5FDcore.h H5FDfamily.h \
H5FDfphdf5.h H5FDlog.h H5FDmpi.h H5FDmpio.h H5FDmpiposix.h \
H5FDmulti.h H5FDsec2.h H5FDstdio.h H5FDstream.h H5FPpublic.h \
@ -529,6 +531,10 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5B2cache.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5B2dbg.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5B2test.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5BP.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5BPcache.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5BPdbg.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5BPtest.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5BT.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5BTbtree2.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5BTcache.Plo@am__quote@

5
test/Makefile.am
View File

@ -29,8 +29,7 @@ check_SCRIPTS = $(TEST_SCRIPT)
# These are our main targets. They should be listed in the order to be
# executed, generally most specific tests to least specific tests.
# JAMES debug: removed btree2 and cache tests since they take so long.
TEST_PROG=testhdf5 lheap ohdr stab gheap cache btree2 blocktrack sheap \
TEST_PROG=testhdf5 lheap ohdr stab gheap cache b+tree btree2 blocktrack sheap \
pool hyperslab istore bittests dt_arith \
dtypes dsets cmpd_dset extend external links unlink big mtime \
fillval mount flush1 flush2 enum \
@ -91,7 +90,7 @@ MOSTLYCLEANFILES+=cmpd_dset.h5 compact_dataset.h5 dataset.h5 extend.h5 istore.h5
family_file000[0-3][0-9].h5 multi_file-[rs].h5 core_file \
new_move_[ab].h5 ntypes.h5 dangle.h5 error_test.h5 err_compat.h5 \
dtransform.h5 test_filters.h5 get_file_name.h5 tstint[1-2].h5 \
unlink_chunked.h5 btree2.h5 blocktrack.h5 sheap.h5
unlink_chunked.h5 btree2.h5 blocktrack.h5 sheap.h5 b+tree.h5
# Sources for testhdf5 executable
testhdf5_SOURCES=testhdf5.c tarray.c tattr.c tconfig.c tfile.c tgenprop.c \

61
test/Makefile.in
View File

@ -29,7 +29,7 @@
#
# HDF5 Library Test Makefile(.in)
#
SOURCES = $(libh5test_la_SOURCES) big.c bittests.c blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c dtransform.c dtypes.c enum.c err_compat.c error_test.c extend.c external.c filename.c fillval.c flush1.c flush2.c getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c dtransform.c dtypes.c enum.c err_compat.c error_test.c extend.c external.c filename.c fillval.c flush1.c flush2.c getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
srcdir = @srcdir@
top_srcdir = @top_srcdir@
@ -71,17 +71,21 @@ libh5test_la_DEPENDENCIES = $(am__DEPENDENCIES_1)
am_libh5test_la_OBJECTS = h5test.lo testframe.lo
libh5test_la_OBJECTS = $(am_libh5test_la_OBJECTS)
am__EXEEXT_1 = testhdf5$(EXEEXT) lheap$(EXEEXT) ohdr$(EXEEXT) \
stab$(EXEEXT) gheap$(EXEEXT) cache$(EXEEXT) btree2$(EXEEXT) \
blocktrack$(EXEEXT) sheap$(EXEEXT) pool$(EXEEXT) \
hyperslab$(EXEEXT) istore$(EXEEXT) bittests$(EXEEXT) \
dt_arith$(EXEEXT) dtypes$(EXEEXT) dsets$(EXEEXT) \
cmpd_dset$(EXEEXT) extend$(EXEEXT) external$(EXEEXT) \
links$(EXEEXT) unlink$(EXEEXT) big$(EXEEXT) mtime$(EXEEXT) \
fillval$(EXEEXT) mount$(EXEEXT) flush1$(EXEEXT) \
stab$(EXEEXT) gheap$(EXEEXT) cache$(EXEEXT) b+tree$(EXEEXT) \
btree2$(EXEEXT) blocktrack$(EXEEXT) sheap$(EXEEXT) \
pool$(EXEEXT) hyperslab$(EXEEXT) istore$(EXEEXT) \
bittests$(EXEEXT) dt_arith$(EXEEXT) dtypes$(EXEEXT) \
dsets$(EXEEXT) cmpd_dset$(EXEEXT) extend$(EXEEXT) \
external$(EXEEXT) links$(EXEEXT) unlink$(EXEEXT) big$(EXEEXT) \
mtime$(EXEEXT) fillval$(EXEEXT) mount$(EXEEXT) flush1$(EXEEXT) \
flush2$(EXEEXT) enum$(EXEEXT) set_extent$(EXEEXT) \
ttsafe$(EXEEXT) stream_test$(EXEEXT) getname$(EXEEXT) \
vfd$(EXEEXT) ntypes$(EXEEXT) dangle$(EXEEXT) \
dtransform$(EXEEXT) filename$(EXEEXT) reserved$(EXEEXT)
b_tree_SOURCES = b+tree.c
b_tree_OBJECTS = b+tree.$(OBJEXT)
b_tree_LDADD = $(LDADD)
b_tree_DEPENDENCIES = libh5test.la $(am__DEPENDENCIES_1)
big_SOURCES = big.c
big_OBJECTS = big.$(OBJEXT)
big_LDADD = $(LDADD)
@ -266,22 +270,22 @@ LTCOMPILE = $(LIBTOOL) --tag=CC --mode=compile $(CC) $(DEFS) \
CCLD = $(CC)
LINK = $(LIBTOOL) --tag=CC --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(AM_LDFLAGS) $(LDFLAGS) -o $@
SOURCES = $(libh5test_la_SOURCES) big.c bittests.c blocktrack.c \
btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c \
dtransform.c dtypes.c enum.c err_compat.c error_test.c \
extend.c external.c filename.c fillval.c flush1.c flush2.c \
getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c \
mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c \
stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c \
$(ttsafe_SOURCES) unlink.c vfd.c
DIST_SOURCES = $(libh5test_la_SOURCES) big.c bittests.c blocktrack.c \
btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c \
dtransform.c dtypes.c enum.c err_compat.c error_test.c \
extend.c external.c filename.c fillval.c flush1.c flush2.c \
getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c \
mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c \
stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c \
$(ttsafe_SOURCES) unlink.c vfd.c
SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c \
dt_arith.c dtransform.c dtypes.c enum.c err_compat.c \
error_test.c extend.c external.c filename.c fillval.c flush1.c \
flush2.c getname.c gheap.c hyperslab.c istore.c lheap.c \
links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c \
set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) \
testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
DIST_SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c \
dt_arith.c dtransform.c dtypes.c enum.c err_compat.c \
error_test.c extend.c external.c filename.c fillval.c flush1.c \
flush2.c getname.c gheap.c hyperslab.c istore.c lheap.c \
links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c \
set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) \
testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@ -514,7 +518,7 @@ MOSTLYCLEANFILES = *.chkexe *.chksh cmpd_dset.h5 compact_dataset.h5 \
new_move_[ab].h5 ntypes.h5 dangle.h5 error_test.h5 \
err_compat.h5 dtransform.h5 test_filters.h5 get_file_name.h5 \
tstint[1-2].h5 unlink_chunked.h5 btree2.h5 blocktrack.h5 \
sheap.h5
sheap.h5 b+tree.h5
INCLUDES = -I$(top_srcdir)/src -I$(top_builddir)/src
# Test script for error_test and err_compat
@ -523,8 +527,7 @@ check_SCRIPTS = $(TEST_SCRIPT)
# These are our main targets. They should be listed in the order to be
# executed, generally most specific tests to least specific tests.
# JAMES debug: removed btree2 and cache tests since they take so long.
TEST_PROG = testhdf5 lheap ohdr stab gheap cache btree2 blocktrack sheap \
TEST_PROG = testhdf5 lheap ohdr stab gheap cache b+tree btree2 blocktrack sheap \
pool hyperslab istore bittests dt_arith \
dtypes dsets cmpd_dset extend external links unlink big mtime \
fillval mount flush1 flush2 enum \
@ -623,6 +626,9 @@ clean-checkPROGRAMS:
echo " rm -f $$p $$f"; \
rm -f $$p $$f ; \
done
b+tree$(EXEEXT): $(b_tree_OBJECTS) $(b_tree_DEPENDENCIES)
@rm -f b+tree$(EXEEXT)
$(LINK) $(b_tree_LDFLAGS) $(b_tree_OBJECTS) $(b_tree_LDADD) $(LIBS)
big$(EXEEXT): $(big_OBJECTS) $(big_DEPENDENCIES)
@rm -f big$(EXEEXT)
$(LINK) $(big_LDFLAGS) $(big_OBJECTS) $(big_LDADD) $(LIBS)
@ -753,6 +759,7 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/b+tree.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/big.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bittests.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/blocktrack.Po@am__quote@

209
test/b+tree.c Normal file
View File

@ -0,0 +1,209 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Tuesday, April 19, 2005
*/
#include "h5test.h"
/*
* This file needs to access private datatypes from the H5BP package.
* This file also needs to access the B+ tree testing code.
*/
#define H5BP_PACKAGE
#define H5BP_TESTING
#include "H5BPpkg.h"
/* Other private headers that this test requires */
#include "H5Iprivate.h"
const char *FILENAME[] = {
"b+tree",
NULL
};
#define NODE_SIZE 512
/*-------------------------------------------------------------------------
* Function: test_create
*
* Purpose: Basic tests for the B+ tree code
*
* Return: Success: 0
*
* Failure: 1
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
test_create(hid_t fapl)
{
hid_t file=-1;
char filename[1024];
H5F_t *f=NULL;
haddr_t bpt_addr; /* Address of B+ tree created */
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
/* Create the file to work on */
if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl))<0)
STACK_ERROR
/* Get a pointer to the internal file object */
if (NULL==(f=H5I_object(file)))
STACK_ERROR
/*
* Test B+ tree creation
*/
TESTING("B+ tree creation");
if (H5BP_create(f, H5P_DATASET_XFER_DEFAULT, H5BP_TEST, NODE_SIZE, 100, 40, &bpt_addr/*out*/)<0)
FAIL_STACK_ERROR
PASSED();
if (H5Fclose(file)<0)
STACK_ERROR
return 0;
error:
H5E_BEGIN_TRY {
H5Fclose(file);
} H5E_END_TRY;
return 1;
} /* test_create() */
/*-------------------------------------------------------------------------
* Function: test_insert_basic
*
* Purpose: Basic tests for the B+ tree code
*
* Return: Success: 0
*
* Failure: 1
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
test_insert_basic(hid_t fapl)
{
hid_t file=-1;
char filename[1024];
H5F_t *f=NULL;
char *record; /* Record to insert into tree */
haddr_t bpt_addr; /* Address of B+ tree created */
herr_t ret; /* Generic error return value */
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
/* Create the file to work on */
if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl))<0)
STACK_ERROR
/* Get a pointer to the internal file object */
if (NULL==(f=H5I_object(file)))
STACK_ERROR
/* Create B+ tree */
if (H5BP_create(f, H5P_DATASET_XFER_DEFAULT, H5BP_TEST, NODE_SIZE, 100, 40, &bpt_addr/*out*/)<0)
FAIL_STACK_ERROR
/*
* Test B+ tree creation
*/
TESTING("B+ tree single record insert");
record="Foo!";
if (H5BP_insert(f, H5P_DATASET_XFER_DEFAULT, H5BP_TEST, bpt_addr, &record)<0)
FAIL_STACK_ERROR
PASSED();
if (H5Fclose(file)<0)
STACK_ERROR
return 0;
error:
H5E_BEGIN_TRY {
H5Fclose(file);
} H5E_END_TRY;
return 1;
} /* test_insert_basic() */
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: Test the B+ tree code
*
* Return: Success:
*
* Failure:
*
* Programmer: Quincey Koziol
* Tuesday, April 19, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main(void)
{
hid_t fapl=-1;
int nerrors=0;
/* Reset library */
h5_reset();
fapl = h5_fileaccess();
/* Test B+ tree creation */
nerrors += test_create(fapl);
/* Test B+ tree record insertion */
/* Iteration, find & index routines tested in these routines as well */
#ifdef QAK
nerrors += test_insert_basic(fapl);
#endif /* QAK */
if (nerrors) goto error;
puts("All B+ tree tests passed.");
#ifndef QAK
h5_cleanup(FILENAME, fapl);
#else /* QAK */
HDfprintf(stderr,"Uncomment cleanup!\n");
#endif /* QAK */
return 0;
error:
puts("*** TESTS FAILED ***");
H5E_BEGIN_TRY {
H5Pclose(fapl);
} H5E_END_TRY;
return 1;
}

3
test/h5test.h
View File

@ -103,6 +103,9 @@ extern MPI_Info h5_io_info_g; /* MPI INFO object for IO */
#define H5_WARNING() {puts("*WARNING*");fflush(stdout);}
#define SKIPPED() {puts(" -SKIP-");fflush(stdout);}
#define TEST_ERROR {H5_FAILED(); AT(); goto error;}
#define STACK_ERROR {H5Eprint_stack(H5E_DEFAULT, stdout); goto error;}
#define FAIL_STACK_ERROR {H5_FAILED(); AT(); \
H5Eprint_stack(H5E_DEFAULT, stdout); goto error;}
#ifdef __cplusplus
extern "C" {

27
tools/misc/h5debug.c
View File

@ -28,12 +28,15 @@
#define H5O_PACKAGE /*suppress error about including H5Opkg */
#define H5B2_PACKAGE /*suppress error about including H5B2pkg */
#define H5B2_TESTING /*suppress warning about H5B2 testing funcs*/
#define H5BP_PACKAGE /*suppress error about including H5BPpkg */
#define H5BP_TESTING /*suppress warning about H5BP testing funcs*/
#define H5BT_PACKAGE /*suppress error about including H5BTpkg */
#define H5SH_PACKAGE /*suppress error about including H5SHpkg */
#include "H5private.h" /* Generic Functions */
#include "H5Bprivate.h"
#include "H5B2pkg.h" /* B-trees */
#include "H5BPpkg.h" /* B+ trees */
#include "H5BTpkg.h" /* Block tracker */
#include "H5Dprivate.h"
#include "H5Fpkg.h"
@ -189,7 +192,7 @@ main(int argc, char *argv[])
* subclass. The subclass identifier is two bytes after the
* B-tree signature.
*/
H5B2_subid_t subtype = (H5B_subid_t)sig[H5B2_SIZEOF_MAGIC+1];
H5B2_subid_t subtype = (H5B2_subid_t)sig[H5B2_SIZEOF_MAGIC+1];
switch (subtype) {
case H5B2_TEST_ID:
@ -211,7 +214,7 @@ main(int argc, char *argv[])
* subclass. The subclass identifier is two bytes after the
* B-tree signature.
*/
H5B2_subid_t subtype = (H5B_subid_t)sig[H5B2_SIZEOF_MAGIC+1];
H5B2_subid_t subtype = (H5B2_subid_t)sig[H5B2_SIZEOF_MAGIC+1];
switch (subtype) {
case H5B2_TEST_ID:
@ -233,7 +236,7 @@ main(int argc, char *argv[])
* subclass. The subclass identifier is two bytes after the
* B-tree signature.
*/
H5B2_subid_t subtype = (H5B_subid_t)sig[H5B2_SIZEOF_MAGIC+1];
H5B2_subid_t subtype = (H5B2_subid_t)sig[H5B2_SIZEOF_MAGIC+1];
switch (subtype) {
case H5B2_TEST_ID:
@ -261,6 +264,24 @@ main(int argc, char *argv[])
*/
status = H5SH_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL);
} else if (!HDmemcmp(sig, H5BP_HDR_MAGIC, H5BP_SIZEOF_MAGIC)) {
/*
* Debug a B+ tree. B+ trees are debugged through the B+ tree
* subclass. The subclass identifier is two bytes after the
* B+ tree signature.
*/
H5BP_subid_t subtype = (H5BP_subid_t)sig[H5BP_SIZEOF_MAGIC+1];
switch (subtype) {
case H5BP_TEST_ID:
status = H5BP_hdr_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL, H5BP_TEST);
break;
default:
fprintf(stderr, "Unknown B+ tree subtype %u\n", (unsigned)(subtype));
HDexit(4);
} /* end switch */
} else if (sig[0] == H5O_VERSION) {
/*
* This could be an object header. Since they don't have a signature