diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5AC.c | 21 | ||||
| -rw-r--r-- | src/H5ACprivate.h | 13 | ||||
| -rw-r--r-- | src/H5B.c | 37 | ||||
| -rw-r--r-- | src/H5D.c | 2 | ||||
| -rw-r--r-- | src/H5F.c | 1 | ||||
| -rw-r--r-- | src/H5G.c | 124 | ||||
| -rw-r--r-- | src/H5Gnode.c | 14 | ||||
| -rw-r--r-- | src/H5Gprivate.h | 20 | ||||
| -rw-r--r-- | src/H5H.c | 48 | ||||
| -rw-r--r-- | src/H5Hprivate.h | 1 | ||||
| -rw-r--r-- | src/H5Ocont.c | 2 | ||||
| -rw-r--r-- | src/H5Onull.c | 2 | ||||
| -rw-r--r-- | src/H5Oprivate.h | 6 | ||||
| -rw-r--r-- | src/H5Ostab.c | 26 | ||||
| -rw-r--r-- | src/debug.c | 8 | ||||
| -rw-r--r-- | src/hdf5.h | 1 | ||||
| -rw-r--r-- | src/hdf5pabl.h | 2 | ||||
| -rw-r--r-- | src/hdf5plat.h | 4 |
18 files changed, 217 insertions, 115 deletions
@@ -28,7 +28,6 @@ #include "H5MMprivate.h" #define PABLO_MASK H5AC_mask -#define HASH(addr) ((unsigned)(addr) % H5AC_NSLOTS) static int interface_initialize_g = FALSE; /*initialized?*/ @@ -99,7 +98,7 @@ H5AC_dest (hdf5_file_t *f) /*------------------------------------------------------------------------- - * Function: H5AC_find + * Function: H5AC_find_f * * Purpose: Given an object type and the address at which that object * is located in the file, return a pointer to the object. @@ -127,10 +126,10 @@ H5AC_dest (hdf5_file_t *f) *------------------------------------------------------------------------- */ void * -H5AC_find (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, - const void *udata) +H5AC_find_f (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, + const void *udata) { - unsigned idx = HASH(addr); + unsigned idx = H5AC_HASH(addr); herr_t status; void *thing = NULL; herr_t (*flush)(hdf5_file_t*,hbool_t,haddr_t,void*)=NULL; @@ -159,6 +158,10 @@ H5AC_find (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, HRETURN_ERROR (H5E_CACHE, H5E_BADTYPE, NULL); } +#ifdef DO_NOT_CACHE + H5AC_flush (f, NULL, 0, TRUE); +#endif + /* * Load a new thing. If it can't be loaded, then return an error * without preempting anything. @@ -220,7 +223,7 @@ herr_t H5AC_flush (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, hbool_t destroy) { - uintn i = HASH(addr); + uintn i = H5AC_HASH(addr); herr_t status; herr_t (*flush)(hdf5_file_t*,hbool_t,haddr_t,void*)=NULL; @@ -287,7 +290,7 @@ herr_t H5AC_set (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, void *thing) { herr_t status; - uintn idx = HASH (addr); + uintn idx = H5AC_HASH (addr); herr_t (*flush)(hdf5_file_t*,hbool_t,haddr_t,void*)=NULL; FUNC_ENTER (H5AC_set, NULL, FAIL); @@ -337,8 +340,8 @@ herr_t H5AC_rename (hdf5_file_t *f, const H5AC_class_t *type, haddr_t old_addr, haddr_t new_addr) { - uintn old_idx = HASH (old_addr); - uintn new_idx = HASH (new_addr); + uintn old_idx = H5AC_HASH (old_addr); + uintn new_idx = H5AC_HASH (new_addr); herr_t (*flush)(hdf5_file_t*, hbool_t, haddr_t, void*); herr_t status; diff --git a/src/H5ACprivate.h b/src/H5ACprivate.h index d5c8cad..7bee4b6 100644 --- a/src/H5ACprivate.h +++ b/src/H5ACprivate.h @@ -47,7 +47,8 @@ typedef struct H5AC_class_t { * cache entry by hashing the object's file address. Each file has its * own cache, an array of slots. */ -#define H5AC_NSLOTS 1033 /*prime number tend to work best */ +#define H5AC_NSLOTS 10330 /*prime number tend to work best */ +#define H5AC_HASH(ADDR) ((unsigned)(ADDR) % H5AC_NSLOTS) typedef struct H5AC_cache_t { const H5AC_class_t *type; /*type of object stored here */ @@ -59,8 +60,8 @@ typedef struct H5AC_cache_t { * Library prototypes. */ herr_t H5AC_dest (hdf5_file_t *f); -void *H5AC_find (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, - const void *udata); +void *H5AC_find_f (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, + const void *udata); herr_t H5AC_flush (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, hbool_t destroy); herr_t H5AC_new (hdf5_file_t *f); @@ -69,4 +70,10 @@ herr_t H5AC_rename (hdf5_file_t *f, const H5AC_class_t *type, herr_t H5AC_set (hdf5_file_t *f, const H5AC_class_t *type, haddr_t addr, void *thing); +#define H5AC_find(F,TYPE,ADDR,UDATA) \ + (((F)->cache[H5AC_HASH(ADDR)].type==(TYPE) && \ + (F)->cache[H5AC_HASH(ADDR)].addr==(ADDR)) ? \ + (F)->cache[H5AC_HASH(ADDR)].thing : \ + H5AC_find_f (F, TYPE, ADDR, UDATA)) + #endif /* !_H5ACprivate_H */ @@ -583,6 +583,7 @@ H5B_split (hdf5_file_t *f, const H5B_class_t *type, haddr_t addr, intn anchor) if (NULL==(old=H5AC_find (f, H5AC_BT, addr, type))) { HRETURN_ERROR (H5E_BTREE, H5E_CANTLOAD, FAIL); } + assert (old->nchildren == 2*type->k); bt = H5MM_xmalloc (sizeof(H5B_t)); recsize = old->sizeof_rkey + H5F_SIZEOF_OFFSET(f); @@ -591,11 +592,12 @@ H5B_split (hdf5_file_t *f, const H5B_class_t *type, haddr_t addr, intn anchor) */ size = H5B_nodesize (f, type, &total_nkey_size, old->sizeof_rkey); bt->dirty = 1; + bt->sizeof_rkey = old->sizeof_rkey; bt->ndirty = BOUND (0, old->ndirty-delta, type->k); bt->type = type; bt->level = old->level; bt->nchildren = type->k; - bt->page = H5MM_xmalloc (size); + bt->page = H5MM_xcalloc (size, 1); /*use calloc() to keep file clean*/ bt->native = H5MM_xmalloc (total_nkey_size); bt->child = H5MM_xmalloc (2*type->k * sizeof(haddr_t)); bt->key = H5MM_xmalloc ((2*type->k+1) * sizeof(H5B_key_t)); @@ -615,7 +617,7 @@ H5B_split (hdf5_file_t *f, const H5B_class_t *type, haddr_t addr, intn anchor) /* key */ if (i<=type->k) { bt->key[i].dirty = old->key[delta+i].dirty; - bt->key[i].rkey = bt->native + offset; + bt->key[i].rkey = bt->page + offset; if (old->key[delta+i].nkey) { bt->key[i].nkey = bt->native + i*type->sizeof_nkey; } else { @@ -957,6 +959,11 @@ H5B_insert_child (hdf5_file_t *f, const H5B_class_t *type, haddr_t addr, for (i=bt->nchildren; i>=idx; --i) { bt->key[i+1].dirty = bt->key[i].dirty; + if (bt->key[i].nkey) { + bt->key[i+1].nkey = bt->native + (i+1) * type->sizeof_nkey; + } else { + bt->key[i+1].nkey = NULL; + } } bt->key[idx].dirty = 1; bt->key[idx].nkey = bt->native + idx * type->sizeof_nkey; @@ -978,10 +985,14 @@ H5B_insert_child (hdf5_file_t *f, const H5B_class_t *type, haddr_t addr, for (i=bt->nchildren; i>idx; --i) { bt->key[i+1].dirty = bt->key[i].dirty; + if (bt->key[i].nkey) { + bt->key[i+1].nkey = bt->native + (i+1) * type->sizeof_nkey; + } else { + bt->key[i+1].nkey = NULL; + } } bt->key[idx+1].dirty = 1; - bt->key[idx+1].nkey = bt->native + - (idx+1) * type->sizeof_nkey; + bt->key[idx+1].nkey = bt->native + (idx+1) * type->sizeof_nkey; memcpy (bt->key[idx+1].nkey, md_key, type->sizeof_nkey); } @@ -1411,6 +1422,7 @@ H5B_debug (hdf5_file_t *f, haddr_t addr, FILE *stream, intn indent, intn fwidth, const H5B_class_t *type) { H5B_t *bt = NULL; + int i; FUNC_ENTER (H5B_debug, NULL, FAIL); @@ -1455,9 +1467,20 @@ H5B_debug (hdf5_file_t *f, haddr_t addr, FILE *stream, intn indent, fprintf (stream, "%*s%-*s %lu\n", indent, "", fwidth, "Address of right sibling:", (unsigned long)(bt->right)); - fprintf (stream, "%*s%-*s %d\n", indent, "", fwidth, - "Number of children:", - (int)(bt->nchildren)); + fprintf (stream, "%*s%-*s %d (%d)\n", indent, "", fwidth, + "Number of children (max):", + (int)(bt->nchildren), + (int)(2*type->k)); + + /* + * Print the child addresses + */ + for (i=0; i<bt->nchildren; i++) { + fprintf (stream, "%*sChild %d...\n", indent, "", i); + fprintf (stream, "%*s%-*s %lu\n", indent+3, "", MAX(0,fwidth-3), + "Address:", + (unsigned long)(bt->child[i])); + } FUNC_LEAVE (SUCCEED); } @@ -196,7 +196,7 @@ herr_t H5Dwrite(hatom_t oid, hatom_t did, VOIDP buf) uintn towrite; /* number of bytes to write out */ herr_t ret_value = SUCCEED; - FUNC_ENTER(H5Dset_info, H5D_init_interface, FAIL); + FUNC_ENTER(H5Dwrite, H5D_init_interface, FAIL); /* Clear errors and check args and all the boring stuff. */ H5ECLEAR; @@ -369,6 +369,7 @@ H5F_dest (hdf5_file_t *f) H5AC_dest (f); f->dir = H5MM_xfree (f->dir); f->filename = H5MM_xfree (f->filename); + f->root_sym = H5MM_xfree (f->root_sym); H5MM_xfree (f); } return NULL; @@ -8,7 +8,17 @@ * Jul 18 1997 * Robb Matzke <matzke@llnl.gov> * - * Purpose: + * Purpose: Symbol table functions. The functions that + * begin with `H5G_stab_' don't understand the + * directory hierarchy; they operate on a single + * symbol table at a time. + * + * The functions that begin with `H5G_node_' operate + * on the leaf nodes of a symbol table B-tree. They + * should be defined in the H5Gnode.c file. + * + * The remaining functions know about the directory + * hierarchy. * * Modifications: * @@ -37,10 +47,9 @@ /* Is the interface initialized? */ static intn interface_initialize_g = FALSE; - /*------------------------------------------------------------------------- - * Function: H5G_new + * Function: H5G_stab_new * * Purpose: Creates a new empty symbol table (object header, name heap, * and B-tree). The caller can specify an initial size for the @@ -54,7 +63,10 @@ static intn interface_initialize_g = FALSE; * item in the heap is the empty string, and must appear at * heap offset zero. * - * Return: Success: Address of new symbol table. + * Return: Success: Address of new symbol table header. If + * the caller supplies a symbol table entry + * SELF then it will be initialized to point to + * this symbol table. * * Failure: FAIL * @@ -67,13 +79,13 @@ static intn interface_initialize_g = FALSE; *------------------------------------------------------------------------- */ haddr_t -H5G_new (hdf5_file_t *f, size_t init) +H5G_stab_new (hdf5_file_t *f, H5G_entry_t *self, size_t init) { off_t name; /*offset of "" name */ haddr_t addr; /*object header address */ H5O_stab_t stab; /*symbol table message */ - FUNC_ENTER (H5G_new, NULL, FAIL); + FUNC_ENTER (H5G_stab_new, NULL, FAIL); /* * Check arguments. @@ -102,11 +114,18 @@ H5G_new (hdf5_file_t *f, size_t init) /* The B-tree is created on demand later */ stab.btree = 0; - /* Create symbol table object header */ - if ((addr = H5O_new (f, 0, 4+2*H5F_SIZEOF_OFFSET(f)))<0) { + /* Create symbol table object header with a single link */ + if ((addr = H5O_new (f, 1, 4+2*H5F_SIZEOF_OFFSET(f)))<0) { HRETURN_ERROR (H5E_SYM, H5E_CANTINIT, FAIL); } - if (H5O_modify(f, addr, NULL, NULL, H5O_STAB, H5O_NEW_MESG, &stab)<0) { + if (self) { + self->name_off = 0; + self->header = addr; + self->type = H5G_NOTHING_CACHED; + } + + /* insert the symbol table message */ + if (H5O_modify(f, addr, self, NULL, H5O_STAB, H5O_NEW_MESG, &stab)<0) { HRETURN_ERROR (H5E_SYM, H5E_CANTINIT, FAIL); } @@ -115,11 +134,11 @@ H5G_new (hdf5_file_t *f, size_t init) /*------------------------------------------------------------------------- - * Function: H5G_find + * Function: H5G_stab_find * - * Purpose: Finds a symbol named NAME in the symbol table whose address - * is ADDR and returns a copy of the symbol table entry through - * the ENTRY argument. + * Purpose: Finds a symbol named NAME in the symbol table whose + * description is stored in SELF in file F and returns a + * copy of the symbol table entry through the ENT argument. * * Return: Success: Address corresponding to the name. * @@ -134,21 +153,22 @@ H5G_new (hdf5_file_t *f, size_t init) *------------------------------------------------------------------------- */ haddr_t -H5G_find (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) +H5G_stab_find (hdf5_file_t *f, H5G_entry_t *self, const char *name, + H5G_entry_t *ent) { H5G_node_ud1_t udata; /*data to pass through B-tree */ H5O_stab_t stab; /*symbol table message */ - FUNC_ENTER (H5G_find, NULL, FAIL); + FUNC_ENTER (H5G_stab_find, NULL, FAIL); /* Check arguments */ assert (f); - assert (addr>=0); + assert (self && self->header>=0); assert (name && *name); - assert (entry); + assert (ent); /* set up the udata */ - if (NULL==H5O_read (f, addr, NULL, H5O_STAB, 0, &stab)) { + if (NULL==H5O_read (f, self->header, self, H5O_STAB, 0, &stab)) { HRETURN_ERROR (H5E_SYM, H5E_BADMESG, FAIL); } if (stab.btree<=0 || stab.heap<=0) { @@ -164,17 +184,17 @@ H5G_find (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) } /* return the result */ - if (entry) *entry = udata.entry; + if (ent) *ent = udata.entry; FUNC_LEAVE (udata.entry.header); } /*------------------------------------------------------------------------- - * Function: H5G_modify + * Function: H5G_stab_modify * * Purpose: Modifies the entry for an existing symbol. The name of the - * symbol is NAME in the symbol table whose address is ADDR in - * file F. ENTRY is the new symbol table entry to use for the + * symbol is NAME in the symbol table described by SELF in + * file F. ENT is the new symbol table entry to use for the * symbol. * * Return: Success: SUCCEED @@ -190,21 +210,22 @@ H5G_find (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) *------------------------------------------------------------------------- */ herr_t -H5G_modify (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) +H5G_stab_modify (hdf5_file_t *f, H5G_entry_t *self, const char *name, + H5G_entry_t *ent) { H5G_node_ud1_t udata; /*data to pass through B-tree */ H5O_stab_t stab; /*symbol table message */ - FUNC_ENTER (H5G_modify, NULL, FAIL); + FUNC_ENTER (H5G_stab_modify, NULL, FAIL); /* check arguments */ assert (f); - assert (addr>=0); + assert (self && self->header>=0); assert (name && *name); - assert (entry); + assert (ent); /* set up the udata */ - if (NULL==H5O_read (f, addr, NULL, H5O_STAB, 0, &stab)) { + if (NULL==H5O_read (f, self->header, self, H5O_STAB, 0, &stab)) { HRETURN_ERROR (H5E_SYM, H5E_BADMESG, FAIL); } if (stab.btree<=0 || stab.heap<=0) { @@ -213,7 +234,7 @@ H5G_modify (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) udata.operation = H5G_OPER_MODIFY; udata.name = name; udata.heap = stab.heap; - udata.entry = *entry; + udata.entry = *ent; /* search and modify the B-tree */ if (H5B_find (f, H5B_SNODE, stab.btree, &udata)<0) { @@ -225,11 +246,11 @@ H5G_modify (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) /*------------------------------------------------------------------------- - * Function: H5G_insert + * Function: H5G_stab_insert * - * Purpose: Insert a new symbol into the table whose address is ADDR in + * Purpose: Insert a new symbol into the table described by SELF in * file F. The name of the new symbol is NAME and its symbol - * table entry is ENTRY. + * table entry is ENT. * * Return: Success: SUCCEED * @@ -244,22 +265,23 @@ H5G_modify (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) *------------------------------------------------------------------------- */ herr_t -H5G_insert (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) +H5G_stab_insert (hdf5_file_t *f, H5G_entry_t *self, const char *name, + H5G_entry_t *ent) { H5O_stab_t stab; /*symbol table message */ H5G_node_ud1_t udata; /*data to pass through B-tree */ off_t offset; /*offset of name within heap */ - FUNC_ENTER (H5G_insert, NULL, FAIL); + FUNC_ENTER (H5G_stab_insert, NULL, FAIL); /* check arguments */ assert (f); - assert (addr>=0); + assert (self && self->header>=0); assert (name && *name); - assert (entry); + assert (ent); /* make sure we have a B-tree and a heap */ - if (NULL==H5O_read (f, addr, NULL, H5O_STAB, 0, &stab)) { + if (NULL==H5O_read (f, self->header, self, H5O_STAB, 0, &stab)) { HRETURN_ERROR (H5E_SYM, H5E_BADMESG, FAIL); } if (stab.btree<=0 || stab.heap<=0) { @@ -277,7 +299,7 @@ H5G_insert (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) HRETURN_ERROR (H5E_INTERNAL, H5E_CANTINIT, FAIL); } } - if (H5O_modify (f, addr, NULL, NULL, H5O_STAB, 0, &stab)<0) { + if (H5O_modify (f, self->header, self, NULL, H5O_STAB, 0, &stab)<0) { HRETURN_ERROR (H5E_SYM, H5E_CANTINIT, FAIL); } } @@ -285,7 +307,7 @@ H5G_insert (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) /* initialize data to pass through B-tree */ udata.name = name; udata.heap = stab.heap; - udata.entry = *entry; + udata.entry = *ent; if (H5B_insert (f, H5B_SNODE, stab.btree, &udata)<0) { HRETURN_ERROR (H5E_SYM, H5E_CANTINSERT, FAIL); } @@ -295,7 +317,7 @@ H5G_insert (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) /*------------------------------------------------------------------------- - * Function: H5G_list + * Function: H5G_stab_list * * Purpose: Returns a list of all the symbols in a symbol table. * The caller allocates an array of pointers which this @@ -322,16 +344,21 @@ H5G_insert (hdf5_file_t *f, haddr_t addr, const char *name, H5G_entry_t *entry) *------------------------------------------------------------------------- */ intn -H5G_list (hdf5_file_t *f, haddr_t addr, int maxentries, - char *names[], H5G_entry_t entries[]) +H5G_stab_list (hdf5_file_t *f, H5G_entry_t *self, intn maxentries, + char *names[], H5G_entry_t entries[]) { H5G_node_list_t udata; H5O_stab_t stab; intn i; - FUNC_ENTER (H5G_list, NULL, FAIL); + FUNC_ENTER (H5G_stab_list, NULL, FAIL); + + /* check args */ + assert (f); + assert (self && self->header>=0); + assert (maxentries>=0); - if (NULL==H5O_read (f, addr, NULL, H5O_STAB, 0, &stab)) { + if (NULL==H5O_read (f, self->header, self, H5O_STAB, 0, &stab)) { HRETURN_ERROR (H5E_SYM, H5E_BADMESG, FAIL); } if (stab.btree<=0 || stab.heap<=0) HRETURN (0); /*empty directory*/ @@ -520,12 +547,16 @@ H5G_encode_vec (hdf5_file_t *f, uint8 **pp, H5G_entry_t *ent, intn n) * * Modifications: * + * Robb Matzke, 8 Aug 1997 + * Writes zeros for the bytes that aren't used so the file doesn't + * contain junk. + * *------------------------------------------------------------------------- */ herr_t H5G_encode (hdf5_file_t *f, uint8 **pp, H5G_entry_t *ent) { - uint8 *p_ret = *pp; + uint8 *p_ret = *pp + H5G_SIZEOF_ENTRY(f); FUNC_ENTER (H5G_encode, NULL, FAIL); @@ -562,7 +593,10 @@ H5G_encode (hdf5_file_t *f, uint8 **pp, H5G_entry_t *ent) abort(); } - *pp = p_ret + H5G_SIZEOF_ENTRY(f); + /* fill with zero */ + while (*pp<p_ret) *(*pp)++ = 0; + + *pp = p_ret; FUNC_LEAVE (SUCCEED); } diff --git a/src/H5Gnode.c b/src/H5Gnode.c index 9e66188..11950f2 100644 --- a/src/H5Gnode.c +++ b/src/H5Gnode.c @@ -237,8 +237,6 @@ H5G_node_new (hdf5_file_t *f, void *_lt_key, void *_udata, void *_rt_key) * Check arguments. */ assert (f); - assert (lt_key); - assert (rt_key); sym = H5MM_xcalloc (1, sizeof(H5G_node_t)); size = H5G_node_size (f); @@ -320,9 +318,9 @@ H5G_node_flush (hdf5_file_t *f, hbool_t destroy, haddr_t addr, H5G_node_t *sym) /* entries */ H5G_encode_vec (f, &p, sym->entry, sym->nsyms); - + memset (p, 0, size - (p-buf)); - status = H5F_block_write (f, addr, p-buf, buf); + status = H5F_block_write (f, addr, size, buf); buf = H5MM_xfree (buf); if (status<0) HRETURN_ERROR (H5E_SYM, H5E_WRITEERROR, FAIL); } @@ -855,12 +853,13 @@ H5G_node_list (hdf5_file_t *f, haddr_t addr, void *_udata) */ herr_t H5G_node_debug (hdf5_file_t *f, haddr_t addr, FILE *stream, intn indent, - intn fwidth) + intn fwidth, haddr_t heap) { int i, j; char buf[64]; H5G_node_t *sn = NULL; herr_t status; + const char *s; FUNC_ENTER (H5G_node_debug, NULL, FAIL); @@ -897,6 +896,11 @@ H5G_node_debug (hdf5_file_t *f, haddr_t addr, FILE *stream, intn indent, fwidth = MAX (0, fwidth-3); for (i=0; i<sn->nsyms; i++) { fprintf (stream, "%*sSymbol %d:\n", indent-3, "", i); + if (heap>0 && (s = H5H_peek (f, heap, sn->entry[i].name_off))) { + fprintf (stream, "%*s%-*s `%s'\n", indent, "", fwidth, + "Name:", + s); + } fprintf (stream, "%*s%-*s %lu\n", indent, "", fwidth, "Name offset into private heap:", (unsigned long)(sn->entry[i].name_off)); diff --git a/src/H5Gprivate.h b/src/H5Gprivate.h index fdfa10c..0e4057d 100644 --- a/src/H5Gprivate.h +++ b/src/H5Gprivate.h @@ -134,16 +134,16 @@ extern const H5B_class_t H5B_SNODE[1]; * Library prototypes... */ herr_t H5G_node_debug (hdf5_file_t *f, haddr_t addr, FILE *stream, intn indent, - intn fwidth); -haddr_t H5G_new (hdf5_file_t *f, size_t init); -haddr_t H5G_find (hdf5_file_t *f, haddr_t addr, const char *name, - H5G_entry_t *entry); -herr_t H5G_modify (hdf5_file_t *f, haddr_t addr, const char *name, - H5G_entry_t *entry); -herr_t H5G_insert (hdf5_file_t *f, haddr_t addr, const char *name, - H5G_entry_t *entry); -intn H5G_list (hdf5_file_t *f, haddr_t addr, int maxentries, - char *names[], H5G_entry_t entries[]); + intn fwidth, haddr_t heap); +haddr_t H5G_stab_new (hdf5_file_t *f, H5G_entry_t *self, size_t init); +haddr_t H5G_stab_find (hdf5_file_t *f, H5G_entry_t *self, const char *name, + H5G_entry_t *ent); +herr_t H5G_stab_modify (hdf5_file_t *f, H5G_entry_t *self, const char *name, + H5G_entry_t *ent); +herr_t H5G_stab_insert (hdf5_file_t *f, H5G_entry_t *self, const char *name, + H5G_entry_t *ent); +intn H5G_stab_list (hdf5_file_t *f, H5G_entry_t *self, intn maxentries, + char *names[], H5G_entry_t entries[]); herr_t H5G_decode (hdf5_file_t *f, uint8 **pp, H5G_entry_t *ent); herr_t H5G_decode_vec (hdf5_file_t *f, uint8 **pp, H5G_entry_t *ent, intn n); herr_t H5G_encode (hdf5_file_t *f, uint8 **pp, H5G_entry_t *ent); @@ -132,7 +132,7 @@ H5H_new (hdf5_file_t *f, H5H_type_t heap_type, size_t size_hint) heap->addr = addr + H5H_SIZEOF_HDR(f); heap->disk_alloc = size_hint; heap->mem_alloc = size_hint; - heap->chunk = H5MM_xmalloc (H5H_SIZEOF_HDR(f) + size_hint); + heap->chunk = H5MM_xcalloc (1, H5H_SIZEOF_HDR(f)+size_hint); /* free list */ if (size_hint) { @@ -179,7 +179,7 @@ H5H_load (hdf5_file_t *f, haddr_t addr, const void *udata) uint8 hdr[20], *p; H5H_t *heap=NULL; H5H_free_t *fl=NULL, *tail=NULL; - haddr_t free_block; + haddr_t free_block=H5H_FREE_NULL; FUNC_ENTER (H5H_load, NULL, NULL); @@ -211,7 +211,7 @@ H5H_load (hdf5_file_t *f, haddr_t addr, const void *udata) /* data */ H5F_decode_offset (f, p, heap->addr); - heap->chunk = H5MM_xmalloc (H5H_SIZEOF_HDR(f) + heap->mem_alloc); + heap->chunk = H5MM_xcalloc (1, H5H_SIZEOF_HDR(f) + heap->mem_alloc); if (heap->disk_alloc && H5F_block_read (f, heap->addr, heap->disk_alloc, heap->chunk + H5H_SIZEOF_HDR(f))<0) { @@ -517,12 +517,12 @@ H5H_remove_free (H5H_t *heap, H5H_free_t *fl) *------------------------------------------------------------------------- */ off_t -H5H_insert (hdf5_file_t *f, haddr_t addr, size_t size, const void *buf) +H5H_insert (hdf5_file_t *f, haddr_t addr, size_t buf_size, const void *buf) { H5H_t *heap=NULL; H5H_free_t *fl=NULL, *max_fl=NULL; off_t offset = -1; - size_t need_more; + size_t need, old_size, need_more; #ifndef NDEBUG static nmessages = 0; #endif @@ -533,9 +533,13 @@ H5H_insert (hdf5_file_t *f, haddr_t addr, size_t size, const void *buf) assert (f); if (H5H_GLOBAL==addr) addr = f->smallobj_off; assert (addr>0); - assert (size>0); + assert (buf_size>0); assert (buf); + /* allocate aligned file memory */ + need = buf_size; + H5H_ALIGN (need); + if (NULL==(heap=H5AC_find (f, H5AC_HEAP, addr, NULL))) { HRETURN_ERROR (H5E_HEAP, H5E_CANTLOAD, FAIL); } @@ -546,12 +550,12 @@ H5H_insert (hdf5_file_t *f, haddr_t addr, size_t size, const void *buf) * leave zero or at least H5G_SIZEOF_FREE bytes left over. */ for (fl=heap->freelist; fl; fl=fl->next) { - if (fl->size>size && fl->size-size>=H5H_SIZEOF_FREE(f)) { + if (fl->size>need && fl->size-need>=H5H_SIZEOF_FREE(f)) { offset = fl->offset; - fl->offset += size; - fl->size -= size; + fl->offset += need; + fl->size -= need; break; - } else if (fl->size==size) { + } else if (fl->size==need) { offset = fl->offset; H5H_remove_free (heap, fl); break; @@ -570,15 +574,15 @@ H5H_insert (hdf5_file_t *f, haddr_t addr, size_t size, const void *buf) if (offset<0) { need_more = MAX (2*heap->mem_alloc, H5H_SIZEOF_FREE(f)); - need_more = MAX (need_more, size); + need_more = MAX (need_more, need); if (max_fl && max_fl->offset+max_fl->size==heap->mem_alloc) { /* * Increase the size of the maximum free block. */ offset = max_fl->offset; - max_fl->offset += size; - max_fl->size += need_more - size; + max_fl->offset += need; + max_fl->size += need_more - need; if (max_fl->size < H5H_SIZEOF_FREE(f)) { #ifndef NDEBUG @@ -600,18 +604,18 @@ H5H_insert (hdf5_file_t *f, haddr_t addr, size_t size, const void *buf) * take some space out of it right away. */ offset = heap->mem_alloc; - if (need_more-size >= H5H_SIZEOF_FREE(f)) { + if (need_more-need >= H5H_SIZEOF_FREE(f)) { fl = H5MM_xmalloc (sizeof(H5H_free_t)); - fl->offset = heap->mem_alloc + size; - fl->size = need_more - size; + fl->offset = heap->mem_alloc + need; + fl->size = need_more - need; fl->prev = NULL; fl->next = heap->freelist; if (heap->freelist) heap->freelist->prev = fl; heap->freelist = fl; #ifndef NDEBUG - } else if (need_more>size) { + } else if (need_more>need) { fprintf (stderr, "H5H_insert: lost %d bytes at line %d\n", - need_more-size, __LINE__); + need_more-need, __LINE__); if (0==nmessages++) { fprintf (stderr, "Messages from H5H_insert() will go away " "when assertions are turned off.\n"); @@ -629,15 +633,19 @@ H5H_insert (hdf5_file_t *f, haddr_t addr, size_t size, const void *buf) "when assertions are turned off.\n"); } #endif + old_size = heap->mem_alloc; heap->mem_alloc += need_more; heap->chunk = H5MM_xrealloc (heap->chunk, H5H_SIZEOF_HDR(f)+heap->mem_alloc); + + /* clear new section so junk doesn't appear in the file */ + memset (heap->chunk+H5H_SIZEOF_HDR(f)+old_size, 0, need_more); } /* * Copy the data into the heap */ - HDmemcpy (heap->chunk + H5H_SIZEOF_HDR(f) + offset, buf, size); + HDmemcpy (heap->chunk + H5H_SIZEOF_HDR(f) + offset, buf, buf_size); FUNC_LEAVE (offset); } @@ -796,7 +804,7 @@ H5H_remove (hdf5_file_t *f, haddr_t addr, off_t offset, size_t size) * lost. */ if (size < H5H_SIZEOF_FREE(f)) { -#ifndef NDEUBG +#ifndef NDEBUG fprintf (stderr, "H5H_remove: lost %d bytes\n", size); if (0==nmessages++) { fprintf (stderr, "Messages from H5H_remove() will go away " diff --git a/src/H5Hprivate.h b/src/H5Hprivate.h index dc5318f..6a05049 100644 --- a/src/H5Hprivate.h +++ b/src/H5Hprivate.h @@ -22,6 +22,7 @@ #define H5H_MAGIC "HEAP" /*heap magic number */ #define H5H_SIZEOF_MAGIC 4 +#define H5H_ALIGN(X) ((X)=((X)+1) & ~0x01) typedef enum H5H_type_t { H5H_LOCAL =0, /*local symtab name heap */ diff --git a/src/H5Ocont.c b/src/H5Ocont.c index 068a768..7b184cb 100644 --- a/src/H5Ocont.c +++ b/src/H5Ocont.c @@ -23,6 +23,8 @@ #include "H5MMprivate.h" #include "H5Oprivate.h" +#define PABLO_MASK H5O_cont_mask + /* PRIVATE PROTOTYPES */ static void *H5O_cont_decode (hdf5_file_t *f, const uint8 *p); static herr_t H5O_cont_encode (hdf5_file_t *f, size_t size, uint8 *p, diff --git a/src/H5Onull.c b/src/H5Onull.c index 97e1ff7..965266d 100644 --- a/src/H5Onull.c +++ b/src/H5Onull.c @@ -18,6 +18,8 @@ #include "H5private.h" #include "H5Oprivate.h" +#define PABLO_MASK H5O_null_mask + /* This message derives from H5O */ const H5O_class_t H5O_NULL[1] = {{ H5O_NULL_ID, /*message id number */ diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index dfaa5b5..40d4a36 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -21,9 +21,9 @@ #include "H5Fprivate.h" #include "H5Gprivate.h" -#define H5O_MIN_SIZE 64 /*min obj header data size */ -#define H5O_NMESGS 64 /*initial number of messages */ -#define H5O_NCHUNKS 64 /*initial number of chunks */ +#define H5O_MIN_SIZE 16 /*min obj header data size */ +#define H5O_NMESGS 32 /*initial number of messages */ +#define H5O_NCHUNKS 8 /*initial number of chunks */ #define H5O_NEW_MESG (-1) /*new message */ #define H5O_NO_ADDR (-1) /*no disk address yet */ diff --git a/src/H5Ostab.c b/src/H5Ostab.c index ec6dd61..d2c1394 100644 --- a/src/H5Ostab.c +++ b/src/H5Ostab.c @@ -23,6 +23,8 @@ #include "H5MMprivate.h" #include "H5Oprivate.h" +#define PABLO_MASK H5O_stab_mask + /* PRIVATE PROTOTYPES */ static void *H5O_stab_decode (hdf5_file_t *f, const uint8 *p); static herr_t H5O_stab_encode (hdf5_file_t *f, size_t size, uint8 *p, @@ -200,20 +202,26 @@ H5O_stab_cache (H5G_entry_t *ent, const void *_mesg) assert (ent); assert (stab); - /* cache */ + /* + * We do this in two steps so Purify doesn't complain about + * uninitialized memory reads even though they don't bother + * anything. + */ if (H5G_CACHED_STAB != ent->type) { modified = TRUE; ent->type = H5G_CACHED_STAB; - } - - if (ent->cache.stab.btree != stab->btree) { - modified = TRUE; ent->cache.stab.btree = stab->btree; - } - - if (ent->cache.stab.heap != stab->heap) { - modified = TRUE; ent->cache.stab.heap = stab->heap; + } else { + if (ent->cache.stab.btree != stab->btree) { + modified = TRUE; + ent->cache.stab.btree = stab->btree; + } + + if (ent->cache.stab.heap != stab->heap) { + modified = TRUE; + ent->cache.stab.heap = stab->heap; + } } FUNC_LEAVE (modified); diff --git a/src/debug.c b/src/debug.c index d07b2cb..220b461 100644 --- a/src/debug.c +++ b/src/debug.c @@ -53,6 +53,7 @@ main (int argc, char *argv[]) uint8 sig[16]; intn i; herr_t status = SUCCEED; + haddr_t extra = 0; /* * Parse command arguments. @@ -61,6 +62,9 @@ main (int argc, char *argv[]) printf ("New address: %s\n", argv[2]); addr = strtol (argv[2], NULL, 0); } + if (argc>3) { + extra = strtol (argv[3], NULL, 0); + } /* * Open the file and get the file descriptor. @@ -99,7 +103,7 @@ main (int argc, char *argv[]) /* * Debug a symbol table node. */ - status = H5G_node_debug (f, addr, stdout, 0, VCOL); + status = H5G_node_debug (f, addr, stdout, 0, VCOL, extra); } else if (!memcmp (sig, H5B_MAGIC, H5B_SIZEOF_MAGIC)) { /* @@ -110,7 +114,7 @@ main (int argc, char *argv[]) H5B_subid_t subtype = sig[H5B_SIZEOF_MAGIC]; switch (subtype) { case H5B_SUBTYPE_SNODE: - status = H5G_node_debug (f, addr, stdout, 0, VCOL); + status = H5G_node_debug (f, addr, stdout, 0, VCOL, extra); break; default: @@ -33,6 +33,7 @@ #include "ProcIDs.h" #endif /* HAVE_PABLO */ + /* Determine the system and set up basic info. */ #include "hdf5plat.h" /* Platform/OS/CPU detection header file (should be first header included) */ diff --git a/src/hdf5pabl.h b/src/hdf5pabl.h index 008a265..6fa3922 100644 --- a/src/hdf5pabl.h +++ b/src/hdf5pabl.h @@ -20,7 +20,7 @@ #define HDF5PABL_H #ifdef HAVE_PABLO -#define PABLO_SAVE(func_id) int pablo_func_id = func_id +#define PABLO_SAVE(func_id) intn pablo_func_id = func_id #define PABLO_TRACE_ON(m, f) TRACE_ON(m,f) #define PABLO_TRACE_OFF(m, f) TRACE_OFF(m,f) #else /* no Pablo tracing enabled */ diff --git a/src/hdf5plat.h b/src/hdf5plat.h index 25d89cb..d73e7e6 100644 --- a/src/hdf5plat.h +++ b/src/hdf5plat.h @@ -332,6 +332,10 @@ typedef float float32; typedef double float64; typedef int intf; /* size of INTEGERs in Fortran compiler */ +#define HDF5_HAVE_NATIVE_INT64 +typedef __int64_t int64; +typedef __uint64_t uint64; + /* Fortran compatibility macros */ #define FNAME_POST_UNDERSCORE /* Fortran function names require trailing underscore */ #define _fcdtocp(desc) (desc) /* Macro to convert from Fortran character descriptor to C 'char *' */ |