diff options
Diffstat (limited to 'src/H5Distore.c')
| -rw-r--r-- | src/H5Distore.c | 882 |
1 files changed, 466 insertions, 416 deletions
diff --git a/src/H5Distore.c b/src/H5Distore.c index 25b81b2..c75a3b7 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -1,9 +1,9 @@ /* * Copyright (C) 1997 NCSA - * All rights reserved. + * All rights reserved. * * Programmer: Robb Matzke <matzke@llnl.gov> - * Wednesday, October 8, 1997 + * Wednesday, October 8, 1997 */ #include <H5private.h> #include <H5Dprivate.h> @@ -15,48 +15,48 @@ #include <H5Vprivate.h> typedef enum H5F_isop_t { - H5F_ISTORE_READ, /*read from file to memory */ - H5F_ISTORE_WRITE /*write from memory to file */ + H5F_ISTORE_READ, /*read from file to memory */ + H5F_ISTORE_WRITE /*write from memory to file */ } H5F_isop_t; /* Does the array domain include negative indices? */ #undef H5F_ISTORE_NEGATIVE_DOMAIN -#define PABLO_MASK H5F_istore_mask +#define PABLO_MASK H5F_istore_mask /* Interface initialization */ -static hbool_t interface_initialize_g = FALSE; +static hbool_t interface_initialize_g = FALSE; #define INTERFACE_INIT NULL /* PRIVATE PROTOTYPES */ -static size_t H5F_istore_sizeof_rkey(H5F_t *f, const void *_udata); -static herr_t H5F_istore_new_node(H5F_t *f, H5B_ins_t, void *_lt_key, - void *_udata, void *_rt_key, haddr_t *); -static intn H5F_istore_cmp2(H5F_t *f, void *_lt_key, void *_udata, - void *_rt_key); -static intn H5F_istore_cmp3(H5F_t *f, void *_lt_key, void *_udata, - void *_rt_key); -static herr_t H5F_istore_found(H5F_t *f, const haddr_t *addr, - const void *_lt_key, void *_udata, - const void *_rt_key); -static H5B_ins_t H5F_istore_insert(H5F_t *f, const haddr_t *addr, - void *_lt_key, hbool_t *lt_key_changed, - void *_md_key, void *_udata, - void *_rt_key, hbool_t *rt_key_changed, - haddr_t *); -static herr_t H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8 *raw, - void *_key); -static herr_t H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8 *raw, - void *_key); -static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, - H5F_isop_t op, - const size_t offset_f[], - const size_t size[], - const size_t offset_m[], - const size_t size_m[], const void *buf); +static size_t H5F_istore_sizeof_rkey(H5F_t *f, const void *_udata); +static herr_t H5F_istore_new_node(H5F_t *f, H5B_ins_t, void *_lt_key, + void *_udata, void *_rt_key, haddr_t *); +static intn H5F_istore_cmp2(H5F_t *f, void *_lt_key, void *_udata, + void *_rt_key); +static intn H5F_istore_cmp3(H5F_t *f, void *_lt_key, void *_udata, + void *_rt_key); +static herr_t H5F_istore_found(H5F_t *f, const haddr_t *addr, + const void *_lt_key, void *_udata, + const void *_rt_key); +static H5B_ins_t H5F_istore_insert(H5F_t *f, const haddr_t *addr, + void *_lt_key, hbool_t *lt_key_changed, + void *_md_key, void *_udata, + void *_rt_key, hbool_t *rt_key_changed, + haddr_t *new_node/*out*/); +static herr_t H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8 *raw, + void *_key); +static herr_t H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8 *raw, + void *_key); +static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, + H5F_isop_t op, const size_t offset_f[], + const size_t size[], + const size_t offset_m[], + const size_t size_m[], + void *buf); /* - * B-tree key. A key contains the minimum logical N-dimensional address and + * B-tree key. A key contains the minimum logical N-dimensional address and * the logical size of the chunk to which this key refers. The * fastest-varying dimension is assumed to reference individual bytes of the * array, so a 100-element 1-d array of 4-byte integers would really be a 2-d @@ -70,50 +70,49 @@ static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t * * The storage file address is part of the B-tree and not part of the key. */ typedef struct H5F_istore_key_t { - uintn file_number; /*external file number */ - size_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start */ - size_t size[H5O_LAYOUT_NDIMS]; /*logical chunk size */ + uintn file_number; /*external file number */ + size_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/ + size_t size[H5O_LAYOUT_NDIMS]; /*logical chunk size */ } H5F_istore_key_t; typedef struct H5F_istore_ud1_t { - H5F_istore_key_t key; /*key values */ - haddr_t addr; /*file address of chunk */ - H5O_layout_t mesg; /*layout message */ + H5F_istore_key_t key; /*key values */ + haddr_t addr; /*file address of chunk */ + H5O_layout_t mesg; /*layout message */ } H5F_istore_ud1_t; /* inherits B-tree like properties from H5B */ -H5B_class_t H5B_ISTORE[1] = -{ - { - H5B_ISTORE_ID, /*id */ - sizeof(H5F_istore_key_t), /*sizeof_nkey */ - H5F_istore_sizeof_rkey, /*get_sizeof_rkey */ - H5F_istore_new_node, /*new */ - H5F_istore_cmp2, /*cmp2 */ - H5F_istore_cmp3, /*cmp3 */ - H5F_istore_found, /*found */ - H5F_istore_insert, /*insert */ - FALSE, /*follow min branch? */ - FALSE, /*follow max branch? */ - NULL, /*list */ - H5F_istore_decode_key, /*decode */ - H5F_istore_encode_key, /*encode */ - }}; +H5B_class_t H5B_ISTORE[1] = {{ + H5B_ISTORE_ID, /*id */ + sizeof(H5F_istore_key_t), /*sizeof_nkey */ + H5F_istore_sizeof_rkey, /*get_sizeof_rkey */ + H5F_istore_new_node, /*new */ + H5F_istore_cmp2, /*cmp2 */ + H5F_istore_cmp3, /*cmp3 */ + H5F_istore_found, /*found */ + H5F_istore_insert, /*insert */ + FALSE, /*follow min branch? */ + FALSE, /*follow max branch? */ + NULL, /*list */ + H5F_istore_decode_key, /*decode */ + H5F_istore_encode_key, /*encode */ +}}; + /*------------------------------------------------------------------------- - * Function: H5F_istore_sizeof_rkey + * Function: H5F_istore_sizeof_rkey * - * Purpose: Returns the size of a raw key for the specified UDATA. The - * size of the key is dependent on the number of dimensions for - * the object to which this B-tree points. The dimensionality - * of the UDATA is the only portion that's referenced here. + * Purpose: Returns the size of a raw key for the specified UDATA. The + * size of the key is dependent on the number of dimensions for + * the object to which this B-tree points. The dimensionality + * of the UDATA is the only portion that's referenced here. * - * Return: Success: Size of raw key in bytes. + * Return: Success: Size of raw key in bytes. * - * Failure: abort() + * Failure: abort() * - * Programmer: Robb Matzke - * Wednesday, October 8, 1997 + * Programmer: Robb Matzke + * Wednesday, October 8, 1997 * * Modifications: * @@ -123,29 +122,30 @@ static size_t H5F_istore_sizeof_rkey(H5F_t *f, const void *_udata) { const H5F_istore_ud1_t *udata = (const H5F_istore_ud1_t *) _udata; - size_t nbytes; + size_t nbytes; assert(udata); assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); - nbytes = 4 + /*external file number */ - udata->mesg.ndims * 4 + /*dimension indices */ - udata->mesg.ndims * 4; /*dimension sizes */ + nbytes = 4 + /*external file number */ + udata->mesg.ndims * 4 + /*dimension indices */ + udata->mesg.ndims * 4; /*dimension sizes */ return nbytes; } + /*------------------------------------------------------------------------- - * Function: H5F_istore_decode_key + * Function: H5F_istore_decode_key * - * Purpose: Decodes a raw key into a native key for the B-tree + * Purpose: Decodes a raw key into a native key for the B-tree * - * Return: Success: SUCCEED + * Return: Success: SUCCEED * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke - * Friday, October 10, 1997 + * Programmer: Robb Matzke + * Friday, October 10, 1997 * * Modifications: * @@ -154,9 +154,9 @@ H5F_istore_sizeof_rkey(H5F_t *f, const void *_udata) static herr_t H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8 *raw, void *_key) { - H5F_istore_key_t *key = (H5F_istore_key_t *) _key; - intn i; - intn ndims = (intn)(bt->sizeof_rkey / 8); + H5F_istore_key_t *key = (H5F_istore_key_t *) _key; + intn i; + intn ndims = (intn)(bt->sizeof_rkey/8); FUNC_ENTER(H5F_istore_decode_key, FAIL); @@ -171,25 +171,25 @@ H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8 *raw, void *_key) UINT32DECODE(raw, key->file_number); assert(0 == key->file_number); for (i = 0; i < ndims; i++) { - UINT32DECODE(raw, key->offset[i]); - UINT32DECODE(raw, key->size[i]); + UINT32DECODE(raw, key->offset[i]); + UINT32DECODE(raw, key->size[i]); } FUNC_LEAVE(SUCCEED); - } + /*------------------------------------------------------------------------- - * Function: H5F_istore_encode_key + * Function: H5F_istore_encode_key * - * Purpose: Encode a key from native format to raw format. + * Purpose: Encode a key from native format to raw format. * - * Return: Success: SUCCEED + * Return: Success: SUCCEED * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke - * Friday, October 10, 1997 + * Programmer: Robb Matzke + * Friday, October 10, 1997 * * Modifications: * @@ -198,9 +198,9 @@ H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8 *raw, void *_key) static herr_t H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8 *raw, void *_key) { - H5F_istore_key_t *key = (H5F_istore_key_t *) _key; - intn ndims = (intn)(bt->sizeof_rkey / 8); - intn i; + H5F_istore_key_t *key = (H5F_istore_key_t *) _key; + intn ndims = (intn)(bt->sizeof_rkey / 8); + intn i; FUNC_ENTER(H5F_istore_encode_key, FAIL); @@ -215,29 +215,30 @@ H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8 *raw, void *_key) UINT32ENCODE(raw, key->file_number); assert(0 == key->file_number); for (i = 0; i < ndims; i++) { - UINT32ENCODE(raw, key->offset[i]); - UINT32ENCODE(raw, key->size[i]); + UINT32ENCODE(raw, key->offset[i]); + UINT32ENCODE(raw, key->size[i]); } FUNC_LEAVE(SUCCEED); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_cmp2 + * Function: H5F_istore_cmp2 * - * Purpose: Compares two keys sort of like strcmp(). The UDATA pointer - * is only to supply extra information not carried in the keys - * (in this case, the dimensionality) and is not compared - * against the keys. + * Purpose: Compares two keys sort of like strcmp(). The UDATA pointer + * is only to supply extra information not carried in the keys + * (in this case, the dimensionality) and is not compared + * against the keys. * - * Return: Success: -1 if LT_KEY is less than RT_KEY; - * 1 if LT_KEY is greater than RT_KEY; - * 0 if LT_KEY and RT_KEY are equal. + * Return: Success: -1 if LT_KEY is less than RT_KEY; + * 1 if LT_KEY is greater than RT_KEY; + * 0 if LT_KEY and RT_KEY are equal. * - * Failure: FAIL (same as LT_KEY<RT_KEY) + * Failure: FAIL (same as LT_KEY<RT_KEY) * - * Programmer: Robb Matzke - * Thursday, November 6, 1997 + * Programmer: Robb Matzke + * Thursday, November 6, 1997 * * Modifications: * @@ -246,10 +247,10 @@ H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8 *raw, void *_key) static intn H5F_istore_cmp2(H5F_t *f, void *_lt_key, void *_udata, void *_rt_key) { - H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; - H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; - H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; - intn cmp; + H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; + H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; + H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; + intn cmp; FUNC_ENTER(H5F_istore_cmp2, FAIL); @@ -263,31 +264,32 @@ H5F_istore_cmp2(H5F_t *f, void *_lt_key, void *_udata, void *_rt_key) FUNC_LEAVE(cmp); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_cmp3 + * Function: H5F_istore_cmp3 * - * Purpose: Compare the requested datum UDATA with the left and right - * keys of the B-tree. + * Purpose: Compare the requested datum UDATA with the left and right + * keys of the B-tree. * - * Return: Success: negative if the min_corner of UDATA is less - * than the min_corner of LT_KEY. + * Return: Success: negative if the min_corner of UDATA is less + * than the min_corner of LT_KEY. * - * positive if the min_corner of UDATA is - * greater than or equal the min_corner of - * RT_KEY. + * positive if the min_corner of UDATA is + * greater than or equal the min_corner of + * RT_KEY. * - * zero otherwise. The min_corner of UDATA is - * not necessarily contained within the address - * space represented by LT_KEY, but a key that - * would describe the UDATA min_corner address - * would fall lexicographically between LT_KEY - * and RT_KEY. - * - * Failure: FAIL (same as UDATA < LT_KEY) + * zero otherwise. The min_corner of UDATA is + * not necessarily contained within the address + * space represented by LT_KEY, but a key that + * would describe the UDATA min_corner address + * would fall lexicographically between LT_KEY + * and RT_KEY. + * + * Failure: FAIL (same as UDATA < LT_KEY) * - * Programmer: Robb Matzke - * Wednesday, October 8, 1997 + * Programmer: Robb Matzke + * Wednesday, October 8, 1997 * * Modifications: * @@ -296,10 +298,10 @@ H5F_istore_cmp2(H5F_t *f, void *_lt_key, void *_udata, void *_rt_key) static intn H5F_istore_cmp3(H5F_t *f, void *_lt_key, void *_udata, void *_rt_key) { - H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; - H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; - H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; - intn cmp = 0; + H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; + H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; + H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; + intn cmp = 0; FUNC_ENTER(H5F_istore_cmp3, FAIL); @@ -309,29 +311,30 @@ H5F_istore_cmp3(H5F_t *f, void *_lt_key, void *_udata, void *_rt_key) assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); if (H5V_vector_lt(udata->mesg.ndims, udata->key.offset, lt_key->offset)) { - cmp = -1; + cmp = -1; } else if (H5V_vector_ge(udata->mesg.ndims, udata->key.offset, - rt_key->offset)) { - cmp = 1; + rt_key->offset)) { + cmp = 1; } FUNC_LEAVE(cmp); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_new_node + * Function: H5F_istore_new_node * - * Purpose: Adds a new entry to an i-storage B-tree. We can assume that - * the domain represented by UDATA doesn't intersect the domain - * already represented by the B-tree. + * Purpose: Adds a new entry to an i-storage B-tree. We can assume that + * the domain represented by UDATA doesn't intersect the domain + * already represented by the B-tree. * - * Return: Success: SUCCEED. The address of leaf is returned - * through the ADDR argument. It is also added - * to the UDATA. + * Return: Success: SUCCEED. The address of leaf is returned + * through the ADDR argument. It is also added + * to the UDATA. * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke - * Tuesday, October 14, 1997 + * Programmer: Robb Matzke + * Tuesday, October 14, 1997 * * Modifications: * @@ -339,14 +342,14 @@ H5F_istore_cmp3(H5F_t *f, void *_lt_key, void *_udata, void *_rt_key) */ static herr_t H5F_istore_new_node(H5F_t *f, H5B_ins_t op, - void *_lt_key, void *_udata, void *_rt_key, - haddr_t *addr /*out */ ) + void *_lt_key, void *_udata, void *_rt_key, + haddr_t *addr/*out*/) { - H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; - H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; - H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; - size_t nbytes; - intn i; + H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; + H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; + H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; + size_t nbytes; + intn i; FUNC_ENTER(H5F_istore_new_node, FAIL); @@ -362,55 +365,56 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op, nbytes = H5V_vector_reduce_product(udata->mesg.ndims, udata->key.size); assert(nbytes > 0); if (H5MF_alloc(f, H5MF_RAW, nbytes, addr /*out */ ) < 0) { - HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL, - "couldn't allocate new file storage"); + HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL, + "couldn't allocate new file storage"); } udata->addr = *addr; udata->key.file_number = 0; lt_key->file_number = udata->key.file_number; if (H5B_INS_LEFT != op) - rt_key->file_number = 0; + rt_key->file_number = 0; /* Initialize the key(s) */ for (i = 0; i < udata->mesg.ndims; i++) { - /* - * The left key describes the storage of the UDATA chunk being inserted - * into the tree. - */ - assert(udata->key.size[i] > 0); - lt_key->offset[i] = udata->key.offset[i]; - lt_key->size[i] = udata->key.size[i]; - - /* - * The right key might already be present. If not, then add - * a zero-width chunk. - */ - if (H5B_INS_LEFT != op) { - rt_key->offset[i] = udata->key.offset[i] + udata->key.size[i]; - rt_key->size[i] = 0; - } + /* + * The left key describes the storage of the UDATA chunk being + * inserted into the tree. + */ + assert(udata->key.size[i] > 0); + lt_key->offset[i] = udata->key.offset[i]; + lt_key->size[i] = udata->key.size[i]; + + /* + * The right key might already be present. If not, then add + * a zero-width chunk. + */ + if (H5B_INS_LEFT != op) { + rt_key->offset[i] = udata->key.offset[i] + udata->key.size[i]; + rt_key->size[i] = 0; + } } FUNC_LEAVE(SUCCEED); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_found + * Function: H5F_istore_found * - * Purpose: This function is called when the B-tree search engine has - * found the leaf entry that points to a chunk of storage that - * contains the beginning of the logical address space - * represented by UDATA. The LT_KEY is the left key (the one - * that describes the chunk) and RT_KEY is the right key (the - * one that describes the next or last chunk). + * Purpose: This function is called when the B-tree search engine has + * found the leaf entry that points to a chunk of storage that + * contains the beginning of the logical address space + * represented by UDATA. The LT_KEY is the left key (the one + * that describes the chunk) and RT_KEY is the right key (the + * one that describes the next or last chunk). * - * Return: Success: SUCCEED with information about the chunk - * returned through the UDATA argument. + * Return: Success: SUCCEED with information about the chunk + * returned through the UDATA argument. * - * Failure: FAIL if not found. + * Failure: FAIL if not found. * - * Programmer: Robb Matzke - * Thursday, October 9, 1997 + * Programmer: Robb Matzke + * Thursday, October 9, 1997 * * Modifications: * @@ -418,11 +422,11 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op, */ static herr_t H5F_istore_found(H5F_t *f, const haddr_t *addr, const void *_lt_key, - void *_udata, const void *_rt_key) + void *_udata, const void *_rt_key) { - H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; + H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; const H5F_istore_key_t *lt_key = (const H5F_istore_key_t *) _lt_key; - int i; + int i; FUNC_ENTER(H5F_istore_found, FAIL); @@ -437,39 +441,40 @@ H5F_istore_found(H5F_t *f, const haddr_t *addr, const void *_lt_key, udata->key.file_number = lt_key->file_number; assert(0 == lt_key->file_number); for (i = 0; i < udata->mesg.ndims; i++) { - udata->key.offset[i] = lt_key->offset[i]; - udata->key.size[i] = lt_key->size[i]; - assert(lt_key->size[i] > 0); + udata->key.offset[i] = lt_key->offset[i]; + udata->key.size[i] = lt_key->size[i]; + assert(lt_key->size[i] > 0); } FUNC_LEAVE(SUCCEED); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_insert + * Function: H5F_istore_insert * - * Purpose: This function is called when the B-tree insert engine finds - * the node to use to insert new data. The UDATA argument - * points to a struct that describes the logical addresses being - * added to the file. This function allocates space for the - * data and returns information through UDATA describing a - * file chunk to receive (part of) the data. + * Purpose: This function is called when the B-tree insert engine finds + * the node to use to insert new data. The UDATA argument + * points to a struct that describes the logical addresses being + * added to the file. This function allocates space for the + * data and returns information through UDATA describing a + * file chunk to receive (part of) the data. * - * The LT_KEY is always the key describing the chunk of file - * memory at address ADDR. On entry, UDATA describes the logical - * addresses for which storage is being requested (through the - * `offset' and `size' fields). On return, UDATA describes the - * logical addresses contained in a chunk on disk. + * The LT_KEY is always the key describing the chunk of file + * memory at address ADDR. On entry, UDATA describes the logical + * addresses for which storage is being requested (through the + * `offset' and `size' fields). On return, UDATA describes the + * logical addresses contained in a chunk on disk. * - * Return: Success: An insertion command for the caller, one of - * the H5B_INS_* constants. The address of the - * new chunk is returned through the NEW_NODE - * argument. + * Return: Success: An insertion command for the caller, one of + * the H5B_INS_* constants. The address of the + * new chunk is returned through the NEW_NODE + * argument. * - * Failure: H5B_INS_ERROR + * Failure: H5B_INS_ERROR * - * Programmer: Robb Matzke - * Thursday, October 9, 1997 + * Programmer: Robb Matzke + * Thursday, October 9, 1997 * * Modifications: * @@ -477,18 +482,18 @@ H5F_istore_found(H5F_t *f, const haddr_t *addr, const void *_lt_key, */ static H5B_ins_t H5F_istore_insert(H5F_t *f, const haddr_t *addr, - void *_lt_key, hbool_t *lt_key_changed, - void *_md_key, void *_udata, - void *_rt_key, hbool_t *rt_key_changed, - haddr_t *new_node /*out */ ) + void *_lt_key, hbool_t *lt_key_changed, + void *_md_key, void *_udata, + void *_rt_key, hbool_t *rt_key_changed, + haddr_t *new_node/*out*/) { - H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; - H5F_istore_key_t *md_key = (H5F_istore_key_t *) _md_key; - H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; - H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; - intn i, cmp; - H5B_ins_t ret_value = H5B_INS_ERROR; - size_t nbytes; + H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key; + H5F_istore_key_t *md_key = (H5F_istore_key_t *) _md_key; + H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key; + H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata; + intn i, cmp; + H5B_ins_t ret_value = H5B_INS_ERROR; + size_t nbytes; FUNC_ENTER(H5F_istore_insert, H5B_INS_ERROR); @@ -507,86 +512,89 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, assert(cmp <= 0); if (cmp < 0) { - /* Negative indices not supported yet */ - assert("HDF5 INTERNAL ERROR -- see rpm" && 0); - HRETURN_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error"); + /* Negative indices not supported yet */ + assert("HDF5 INTERNAL ERROR -- see rpm" && 0); + HRETURN_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR, + "internal error"); } else if (H5V_hyper_eq(udata->mesg.ndims, - udata->key.offset, udata->key.size, - lt_key->offset, lt_key->size)) { - /* - * Already exists. Just return the info. - */ - udata->addr = *addr; - udata->key.file_number = lt_key->file_number; - ret_value = H5B_INS_NOOP; + udata->key.offset, udata->key.size, + lt_key->offset, lt_key->size)) { + /* + * Already exists. Just return the info. + */ + udata->addr = *addr; + udata->key.file_number = lt_key->file_number; + ret_value = H5B_INS_NOOP; } else if (H5V_hyper_disjointp(udata->mesg.ndims, - lt_key->offset, lt_key->size, - udata->key.offset, udata->key.size)) { - assert(H5V_hyper_disjointp(udata->mesg.ndims, - rt_key->offset, rt_key->size, - udata->key.offset, udata->key.size)); - - /* - * Split this node, inserting the new new node to the right of the - * current node. The MD_KEY is where the split occurs. - */ - md_key->file_number = udata->key.file_number; - for (i = 0, nbytes = 1; i < udata->mesg.ndims; i++) { - assert(0 == udata->key.offset[i] % udata->mesg.dim[i]); - assert(udata->key.size[i] == udata->mesg.dim[i]); - md_key->offset[i] = udata->key.offset[i]; - md_key->size[i] = udata->key.size[i]; - nbytes *= udata->key.size[i]; - } - - /* - * Allocate storage for the new chunk - */ - if (H5MF_alloc(f, H5MF_RAW, nbytes, new_node /*out */ ) < 0) { - HRETURN_ERROR(H5E_IO, H5E_CANTINIT, H5B_INS_ERROR, - "file allocation failed"); - } - udata->addr = *new_node; - udata->key.file_number = 0; - ret_value = H5B_INS_RIGHT; + lt_key->offset, lt_key->size, + udata->key.offset, udata->key.size)) { + assert(H5V_hyper_disjointp(udata->mesg.ndims, + rt_key->offset, rt_key->size, + udata->key.offset, udata->key.size)); + + /* + * Split this node, inserting the new new node to the right of the + * current node. The MD_KEY is where the split occurs. + */ + md_key->file_number = udata->key.file_number; + for (i = 0, nbytes = 1; i < udata->mesg.ndims; i++) { + assert(0 == udata->key.offset[i] % udata->mesg.dim[i]); + assert(udata->key.size[i] == udata->mesg.dim[i]); + md_key->offset[i] = udata->key.offset[i]; + md_key->size[i] = udata->key.size[i]; + nbytes *= udata->key.size[i]; + } + + /* + * Allocate storage for the new chunk + */ + if (H5MF_alloc(f, H5MF_RAW, nbytes, new_node /*out */ ) < 0) { + HRETURN_ERROR(H5E_IO, H5E_CANTINIT, H5B_INS_ERROR, + "file allocation failed"); + } + udata->addr = *new_node; + udata->key.file_number = 0; + ret_value = H5B_INS_RIGHT; } else { - assert("HDF5 INTERNAL ERROR -- see rpm" && 0); - HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error"); + assert("HDF5 INTERNAL ERROR -- see rpm" && 0); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, H5B_INS_ERROR, + "internal error"); } FUNC_LEAVE(ret_value); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_copy_hyperslab + * Function: H5F_istore_copy_hyperslab * - * Purpose: Reads or writes a hyperslab to disk depending on whether OP - * is H5F_ISTORE_READ or H5F_ISTORE_WRITE. The hyperslab - * storage is described with ISTORE and exists in file F. The - * file hyperslab begins at location OFFSET_F[] (an N-dimensional - * point in the domain in terms of elements) in the file and - * OFFSET_M[] in memory pointed to by BUF. Its size is SIZE[] - * elements. The dimensionality of memory is assumed to be the - * same as the file and the total size of the multi-dimensional - * memory buffer is SIZE_M[]. + * Purpose: Reads or writes a hyperslab to disk depending on whether OP + * is H5F_ISTORE_READ or H5F_ISTORE_WRITE. The hyperslab + * storage is described with ISTORE and exists in file F. The + * file hyperslab begins at location OFFSET_F[] (an N-dimensional + * point in the domain in terms of elements) in the file and + * OFFSET_M[] in memory pointed to by BUF. Its size is SIZE[] + * elements. The dimensionality of memory is assumed to be the + * same as the file and the total size of the multi-dimensional + * memory buffer is SIZE_M[]. * - * The slowest varying dimension is always listed first in the - * various offset and size arrays. + * The slowest varying dimension is always listed first in the + * various offset and size arrays. * - * A `chunk' is a hyperslab of the disk array which is stored - * contiguously. I/O occurs in units of chunks where the size of - * a chunk is determined by the alignment constraints specified - * in ISTORE. + * A `chunk' is a hyperslab of the disk array which is stored + * contiguously. I/O occurs in units of chunks where the size of + * a chunk is determined by the alignment constraints specified + * in ISTORE. * - * Return: Success: SUCCEED + * Return: Success: SUCCEED * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke - * Friday, October 17, 1997 + * Programmer: Robb Matzke + * Friday, October 17, 1997 * * Modifications: * @@ -594,22 +602,22 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, */ static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op, - const size_t offset_f[], const size_t size[], - const size_t offset_m[], const size_t size_m[], - const void *buf) + const size_t offset_f[], const size_t size[], + const size_t offset_m[], const size_t size_m[], + void *buf/*in or out*/) { - intn i, carry; - size_t idx_cur[H5O_LAYOUT_NDIMS]; - size_t idx_min[H5O_LAYOUT_NDIMS]; - size_t idx_max[H5O_LAYOUT_NDIMS]; - size_t sub_size[H5O_LAYOUT_NDIMS]; - size_t offset_wrt_chunk[H5O_LAYOUT_NDIMS]; - size_t sub_offset_m[H5O_LAYOUT_NDIMS]; - size_t chunk_size; - uint8 *chunk = NULL; - H5F_istore_ud1_t udata; - herr_t status; - herr_t ret_value = FAIL; + intn i, carry; + size_t idx_cur[H5O_LAYOUT_NDIMS]; + size_t idx_min[H5O_LAYOUT_NDIMS]; + size_t idx_max[H5O_LAYOUT_NDIMS]; + size_t sub_size[H5O_LAYOUT_NDIMS]; + size_t offset_wrt_chunk[H5O_LAYOUT_NDIMS]; + size_t sub_offset_m[H5O_LAYOUT_NDIMS]; + size_t chunk_size; + uint8 *chunk = NULL; + H5F_istore_ud1_t udata; + herr_t status; + herr_t ret_value = FAIL; FUNC_ENTER(H5F_istore_copy_hyperslab, FAIL); @@ -623,24 +631,64 @@ H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op, assert(size_m); assert(buf); #ifndef NDEBUG - for (i = 0; i < layout->ndims; i++) { - assert(size_m[i] > 0); /*destination must exist */ - /*hyperslab must fit in BUF */ - assert((offset_m ? offset_m[i] : 0) + size[i] <= size_m[i]); - assert(layout->dim[i] > 0); + for (i=0; i<layout->ndims; i++) { + assert(size_m[i] > 0); /*destination must exist */ + /*hyperslab must fit in BUF */ + assert((offset_m?offset_m[i]:0) + size[i] <= size_m[i]); + assert(layout->dim[i] > 0); } #endif - /* Initialize indices */ - for (i = 0; i < layout->ndims; i++) { - idx_min[i] = (offset_f ? offset_f[i] : 0) / layout->dim[i]; - idx_max[i] = ((offset_f ? offset_f[i] : 0) + size[i] - 1) / layout->dim[i] + 1; - idx_cur[i] = idx_min[i]; + /* + * As a special case of H5F_ISTORE_READ, if the source is aligned on + * a chunk boundary and is the same size as a chunk, and the destination + * is the same size as a chunk, then instead of reading into a temporary + * buffer and then into the destination, we read directly into the + * destination. + */ + if (H5F_ISTORE_READ==op) { + for (i=0, chunk_size=1; i<layout->ndims; i++) { + if (offset_f[i] % layout->dim[i]) break; /*src not aligned*/ + if (size[i]!=layout->dim[i]) break; /*src not a chunk*/ + if (size_m[i]!=layout->dim[i]) break; /*dst not a chunk*/ + udata.key.offset[i] = offset_f[i]; + udata.key.size[i] = layout->dim[i]; + chunk_size *= layout->dim[i]; + } + + if (i==layout->ndims) { + udata.mesg = *layout; + H5F_addr_undef (&(udata.addr)); + udata.key.file_number = 0; + status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata); + if (status>=0 && H5F_addr_defined (&(udata.addr))) { + assert (0==udata.key.file_number); + if (H5F_block_read (f, &(udata.addr), chunk_size, buf)<0) { + HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, + "unable to read raw storage chunk"); + } + } else { + HDmemset (buf, 0, chunk_size); + } + HRETURN (SUCCEED); + } + } + + /* + * This is the general case. We set up multi-dimensional counters + * (idx_min, idx_max, and idx_cur) and loop through the chunks copying + * each chunk into a temporary buffer, compressing or decompressing, and + * then copying it to it's destination. + */ + for (i=0; i<layout->ndims; i++) { + idx_min[i] = (offset_f?offset_f[i]:0) / layout->dim[i]; + idx_max[i] = ((offset_f?offset_f[i]:0) + size[i]-1) / layout->dim[i]+1; + idx_cur[i] = idx_min[i]; } /* Allocate buffers */ - for (i = 0, chunk_size = 1; i < layout->ndims; i++) { - chunk_size *= layout->dim[i]; + for (i=0, chunk_size=1; i<layout->ndims; i++) { + chunk_size *= layout->dim[i]; } chunk = H5MM_xmalloc(chunk_size); @@ -650,80 +698,77 @@ H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op, /* Loop over all chunks */ while (1) { - /* Read/Write chunk or create it if it doesn't exist */ - udata.mesg.ndims = layout->ndims; - H5F_addr_undef(&(udata.addr)); - udata.key.file_number = 0; - - for (i = 0; i < layout->ndims; i++) { - - /* The location and size of the chunk being accessed */ - udata.key.offset[i] = idx_cur[i] * layout->dim[i]; - udata.key.size[i] = layout->dim[i]; - - /* The offset and size wrt the chunk */ - offset_wrt_chunk[i] = MAX((offset_f ? offset_f[i] : 0), - udata.key.offset[i]) - - udata.key.offset[i]; - sub_size[i] = MIN((idx_cur[i] + 1) * layout->dim[i], - (offset_f ? offset_f[i] : 0) + size[i]) - - (udata.key.offset[i] + offset_wrt_chunk[i]); - - /* Offset into mem buffer */ - sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] + - (offset_m ? offset_m[i] : 0) - - (offset_f ? offset_f[i] : 0); - } - - if (H5F_ISTORE_WRITE == op) { - status = H5B_insert(f, H5B_ISTORE, &(layout->addr), &udata); - assert(status >= 0); - } else { - status = H5B_find(f, H5B_ISTORE, &(layout->addr), &udata); - } - - /* - * If the operation is reading from the disk or if we are writing a - * partial chunk then load the chunk from disk. - */ - if (H5F_ISTORE_READ == op || - !H5V_vector_zerop(layout->ndims, offset_wrt_chunk) || - !H5V_vector_eq(layout->ndims, sub_size, udata.key.size)) { - if (status >= 0 && H5F_addr_defined(&(udata.addr))) { - assert(0 == udata.key.file_number); - if (H5F_block_read(f, &(udata.addr), chunk_size, chunk) < 0) { - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, - "unable to read raw storage chunk"); - } - } else { - HDmemset(chunk, 0, chunk_size); - } - } - /* Transfer data to/from the chunk */ - if (H5F_ISTORE_WRITE == op) { - H5V_hyper_copy(layout->ndims, sub_size, - udata.key.size, offset_wrt_chunk, chunk, - size_m, sub_offset_m, buf); - assert(0 == udata.key.file_number); - if (H5F_block_write(f, &(udata.addr), chunk_size, chunk) < 0) { - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, - "unable to write raw storage chunk"); - } - } else { - H5V_hyper_copy(layout->ndims, sub_size, - size_m, sub_offset_m, (void *)buf, - udata.key.size, offset_wrt_chunk, chunk); - } - - /* Increment indices */ - for (i = layout->ndims - 1, carry = 1; i >= 0 && carry; --i) { - if (++idx_cur[i] >= idx_max[i]) - idx_cur[i] = idx_min[i]; - else - carry = 0; - } - if (carry) - break; + /* Read/Write chunk or create it if it doesn't exist */ + udata.mesg.ndims = layout->ndims; + H5F_addr_undef(&(udata.addr)); + udata.key.file_number = 0; + + for (i=0; i<layout->ndims; i++) { + + /* The location and size of the chunk being accessed */ + udata.key.offset[i] = idx_cur[i] * layout->dim[i]; + udata.key.size[i] = layout->dim[i]; + + /* The offset and size wrt the chunk */ + offset_wrt_chunk[i] = MAX((offset_f ? offset_f[i] : 0), + udata.key.offset[i]) - + udata.key.offset[i]; + sub_size[i] = MIN((idx_cur[i] + 1) * layout->dim[i], + (offset_f ? offset_f[i] : 0) + size[i]) - + (udata.key.offset[i] + offset_wrt_chunk[i]); + + /* Offset into mem buffer */ + sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] + + (offset_m ? offset_m[i] : 0) - + (offset_f ? offset_f[i] : 0); + } + + if (H5F_ISTORE_WRITE == op) { + status = H5B_insert(f, H5B_ISTORE, &(layout->addr), &udata); + assert(status >= 0); + } else { + status = H5B_find(f, H5B_ISTORE, &(layout->addr), &udata); + } + + /* + * If the operation is reading from the disk or if we are writing a + * partial chunk then load the chunk from disk. + */ + if (H5F_ISTORE_READ == op || + !H5V_vector_zerop(layout->ndims, offset_wrt_chunk) || + !H5V_vector_eq(layout->ndims, sub_size, udata.key.size)) { + if (status>=0 && H5F_addr_defined(&(udata.addr))) { + assert(0==udata.key.file_number); + if (H5F_block_read(f, &(udata.addr), chunk_size, chunk) < 0) { + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, + "unable to read raw storage chunk"); + } + } else { + HDmemset(chunk, 0, chunk_size); + } + } + /* Transfer data to/from the chunk */ + if (H5F_ISTORE_WRITE==op) { + H5V_hyper_copy(layout->ndims, sub_size, + udata.key.size, offset_wrt_chunk, chunk, + size_m, sub_offset_m, buf); + assert(0 == udata.key.file_number); + if (H5F_block_write(f, &(udata.addr), chunk_size, chunk) < 0) { + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "unable to write raw storage chunk"); + } + } else { + H5V_hyper_copy(layout->ndims, sub_size, + size_m, sub_offset_m, (void *)buf, + udata.key.size, offset_wrt_chunk, chunk); + } + + /* Increment indices */ + for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) { + if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i]; + else carry = 0; + } + if (carry) break; } ret_value = SUCCEED; @@ -731,19 +776,20 @@ H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op, chunk = H5MM_xfree(chunk); FUNC_LEAVE(ret_value); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_read + * Function: H5F_istore_read * - * Purpose: Reads a multi-dimensional buffer from (part of) an indexed raw - * storage array. + * Purpose: Reads a multi-dimensional buffer from (part of) an indexed raw + * storage array. * - * Return: Success: SUCCEED + * Return: Success: SUCCEED * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke - * Wednesday, October 15, 1997 + * Programmer: Robb Matzke + * Wednesday, October 15, 1997 * * Modifications: * @@ -751,7 +797,7 @@ H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op, */ herr_t H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, - const size_t offset[], const size_t size[], void *buf) + const size_t offset[], const size_t size[], void *buf) { FUNC_ENTER(H5F_istore_read, FAIL); @@ -763,25 +809,26 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, assert(buf); if (H5F_istore_copy_hyperslab(f, layout, H5F_ISTORE_READ, - offset, size, H5V_ZERO, size, buf) < 0) { - HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, - "hyperslab output failure"); + offset, size, H5V_ZERO, size, buf) < 0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "hyperslab output failure"); } FUNC_LEAVE(SUCCEED); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_write + * Function: H5F_istore_write * - * Purpose: Writes a multi-dimensional buffer to (part of) an indexed raw - * storage array. + * Purpose: Writes a multi-dimensional buffer to (part of) an indexed raw + * storage array. * - * Return: Success: SUCCEED + * Return: Success: SUCCEED * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke - * Wednesday, October 15, 1997 + * Programmer: Robb Matzke + * Wednesday, October 15, 1997 * * Modifications: * @@ -789,8 +836,8 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, - const size_t offset[], const size_t size[], - const void *buf) + const size_t offset[], const size_t size[], + const void *buf) { FUNC_ENTER(H5F_istore_write, FAIL); @@ -802,30 +849,32 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, assert(buf); if (H5F_istore_copy_hyperslab(f, layout, H5F_ISTORE_WRITE, - offset, size, H5V_ZERO, size, buf) < 0) { - HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, - "hyperslab output failure"); + offset, size, H5V_ZERO, size, + (void*)buf) < 0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "hyperslab output failure"); } FUNC_LEAVE(SUCCEED); } + /*------------------------------------------------------------------------- - * Function: H5F_istore_create + * Function: H5F_istore_create * - * Purpose: Creates a new indexed-storage B-tree and initializes the - * istore struct with information about the storage. The - * struct should be immediately written to the object header. + * Purpose: Creates a new indexed-storage B-tree and initializes the + * istore struct with information about the storage. The + * struct should be immediately written to the object header. * - * This function must be called before passing ISTORE to any of - * the other indexed storage functions! + * This function must be called before passing ISTORE to any of + * the other indexed storage functions! * - * Return: Success: SUCCEED with the ISTORE argument initialized - * and ready to write to an object header. + * Return: Success: SUCCEED with the ISTORE argument initialized + * and ready to write to an object header. * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke - * Tuesday, October 21, 1997 + * Programmer: Robb Matzke + * Tuesday, October 21, 1997 * * Modifications: * @@ -834,9 +883,9 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, herr_t H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ ) { - H5F_istore_ud1_t udata; + H5F_istore_ud1_t udata; #ifndef NDEBUG - int i; + int i; #endif FUNC_ENTER(H5F_istore_create, FAIL); @@ -847,13 +896,14 @@ H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ ) assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); #ifndef NDEBUG for (i = 0; i < layout->ndims; i++) { - assert(layout->dim[i] > 0); + assert(layout->dim[i] > 0); } #endif udata.mesg.ndims = layout->ndims; if (H5B_create(f, H5B_ISTORE, &udata, &(layout->addr) /*out */ ) < 0) { - HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't create B-tree"); + HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't create B-tree"); } + FUNC_LEAVE(SUCCEED); } |