/* * Copyright (C) 1997 NCSA * All rights reserved. * * Programmer: Robb Matzke * Wednesday, October 8, 1997 */ #include #include #include #include #include #include #include #include /* Interface initialization */ #define PABLO_MASK H5F_istore_mask 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 *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_debug_key (FILE *stream, intn indent, intn fwidth, const void *key, const void *udata); /* * B-tree key. A key contains the minimum logical N-dimensional address and * the logical size of the chunk to which this key refers. The * fastest-varying dimension is assumed to reference individual bytes of the * array, so a 100-element 1-d array of 4-byte integers would really be a 2-d * array with the slow varying dimension of size 100 and the fast varying * dimension of size 4 (the storage dimensionality has very little to do with * the real dimensionality). * * Only the first few values of the OFFSET and SIZE fields are actually * stored on disk, depending on the dimensionality. * * The chunk's file address is part of the B-tree and not part of the key. */ typedef struct H5F_istore_key_t { hsize_t nbytes; /*size of stored data */ hssize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/ } 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_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 */ H5F_istore_debug_key, /*debug */ }}; /*------------------------------------------------------------------------- * 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. * * Return: Success: Size of raw key in bytes. * * Failure: abort() * * Programmer: Robb Matzke * Wednesday, October 8, 1997 * * Modifications: * *------------------------------------------------------------------------- */ static size_t H5F_istore_sizeof_rkey(H5F_t __unused__ *f, const void *_udata) { const H5F_istore_ud1_t *udata = (const H5F_istore_ud1_t *) _udata; size_t nbytes; assert(udata); assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); nbytes = 4 + /*storage size */ udata->mesg.ndims * 4; /*dimension indices */ return nbytes; } /*------------------------------------------------------------------------- * Function: H5F_istore_decode_key * * Purpose: Decodes a raw key into a native key for the B-tree * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Friday, October 10, 1997 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5F_istore_decode_key(H5F_t __unused__ *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-4)/4); FUNC_ENTER(H5F_istore_decode_key, FAIL); /* check args */ assert(f); assert(bt); assert(raw); assert(key); assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS); /* decode */ UINT32DECODE (raw, key->nbytes); for (i = 0; i < ndims; i++) { UINT32DECODE(raw, key->offset[i]); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * Function: H5F_istore_encode_key * * Purpose: Encode a key from native format to raw format. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Friday, October 10, 1997 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5F_istore_encode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key) { H5F_istore_key_t *key = (H5F_istore_key_t *) _key; intn ndims = (intn)((bt->sizeof_rkey-4) / 4); intn i; FUNC_ENTER(H5F_istore_encode_key, FAIL); /* check args */ assert(f); assert(bt); assert(raw); assert(key); assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS); /* encode */ UINT32ENCODE (raw, key->nbytes); for (i = 0; i < ndims; i++) { UINT32ENCODE(raw, key->offset[i]); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * Function: H5F_istore_debug_key * * Purpose: Prints a key. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Thursday, April 16, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5F_istore_debug_key (FILE *stream, intn indent, intn fwidth, const void *_key, const void *_udata) { const H5F_istore_key_t *key = (const H5F_istore_key_t *)_key; const H5F_istore_ud1_t *udata = (const H5F_istore_ud1_t *)_udata; int i; FUNC_ENTER (H5F_istore_debug_key, FAIL); assert (key); HDfprintf (stream, "%*s%-*s %Hd bytes\n", indent, "", fwidth, "Chunk size:", key->nbytes); HDfprintf (stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:"); for (i=0; imesg.ndims; i++) { HDfprintf (stream, "%s%Hd", i?", ":"", key->offset[i]); } fputs ("}\n", stream); FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- * 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. * * 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_KEYmesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); /* Compare the offsets but ignore the other fields */ cmp = H5V_vector_cmp_s(udata->mesg.ndims, lt_key->offset, rt_key->offset); FUNC_LEAVE(cmp); } /*------------------------------------------------------------------------- * Function: H5F_istore_cmp3 * * 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. * * 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) * * Programmer: Robb Matzke * Wednesday, October 8, 1997 * * Modifications: * *------------------------------------------------------------------------- */ static intn H5F_istore_cmp3(H5F_t __unused__ *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; FUNC_ENTER(H5F_istore_cmp3, FAIL); assert(lt_key); assert(rt_key); assert(udata); assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); if (H5V_vector_lt_s(udata->mesg.ndims, udata->key.offset, lt_key->offset)) { cmp = -1; } else if (H5V_vector_ge_s(udata->mesg.ndims, udata->key.offset, rt_key->offset)) { cmp = 1; } FUNC_LEAVE(cmp); } /*------------------------------------------------------------------------- * 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. * * Return: Success: SUCCEED. The address of leaf is returned * through the ADDR argument. It is also added * to the UDATA. * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, October 14, 1997 * * Modifications: * *------------------------------------------------------------------------- */ 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*/) { 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 i; FUNC_ENTER(H5F_istore_new_node, FAIL); /* check args */ assert(f); assert(lt_key); assert(rt_key); assert(udata); assert(udata->mesg.ndims > 0 && udata->mesg.ndims < H5O_LAYOUT_NDIMS); assert(addr); /* Allocate new storage */ assert (udata->key.nbytes > 0); if (H5MF_alloc(f, H5MF_RAW, udata->key.nbytes, addr /*out */ ) < 0) { HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "couldn't allocate new file storage"); } udata->addr = *addr; /* * The left key describes the storage of the UDATA chunk being * inserted into the tree. */ lt_key->nbytes = udata->key.nbytes; for (i=0; imesg.ndims; i++) { lt_key->offset[i] = udata->key.offset[i]; } /* * The right key might already be present. If not, then add a zero-width * chunk. */ if (H5B_INS_LEFT != op) { rt_key->nbytes = 0; for (i=0; imesg.ndims; i++) { assert (udata->mesg.dim[i] < MAX_HSSIZET); assert (udata->key.offset[i]+(hssize_t)(udata->mesg.dim[i]) > udata->key.offset[i]); rt_key->offset[i] = udata->key.offset[i] + (hssize_t)(udata->mesg.dim[i]); } } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * 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). * * Return: Success: SUCCEED with information about the chunk * returned through the UDATA argument. * * Failure: FAIL if not found. * * Programmer: Robb Matzke * Thursday, October 9, 1997 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5F_istore_found(H5F_t __unused__ *f, const haddr_t *addr, const void *_lt_key, void *_udata, const void __unused__ *_rt_key) { 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; FUNC_ENTER(H5F_istore_found, FAIL); /* Check arguments */ assert(f); assert(addr && H5F_addr_defined(addr)); assert(udata); assert(lt_key); /* Initialize return values */ udata->addr = *addr; udata->key.nbytes = lt_key->nbytes; assert (lt_key->nbytes>0); for (i = 0; i < udata->mesg.ndims; i++) { udata->key.offset[i] = lt_key->offset[i]; } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * 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. * * 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. * * Failure: H5B_INS_ERROR * * Programmer: Robb Matzke * Thursday, October 9, 1997 * * Modifications: * *------------------------------------------------------------------------- */ static H5B_ins_t H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key, hbool_t __unused__ *lt_key_changed, void *_md_key, void *_udata, void *_rt_key, hbool_t __unused__ *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; FUNC_ENTER(H5F_istore_insert, H5B_INS_ERROR); /* check args */ assert(f); assert(addr && H5F_addr_defined(addr)); assert(lt_key); assert(lt_key_changed); assert(md_key); assert(udata); assert(rt_key); assert(rt_key_changed); assert(new_node); cmp = H5F_istore_cmp3(f, lt_key, udata, rt_key); 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"); } else if (H5V_vector_eq_s (udata->mesg.ndims, udata->key.offset, lt_key->offset) && lt_key->nbytes>0) { /* * Already exists. If the new size is not the same as the old size * then we should reallocate storage. */ #if 1 if (lt_key->nbytes != udata->key.nbytes) { if (H5MF_realloc (f, H5MF_RAW, lt_key->nbytes, addr, udata->key.nbytes, new_node/*out*/)<0) { HRETURN_ERROR (H5E_STORAGE, H5E_WRITEERROR, H5B_INS_ERROR, "unable to reallocate chunk storage"); } lt_key->nbytes = udata->key.nbytes; *lt_key_changed = TRUE; udata->addr = *new_node; ret_value = H5B_INS_CHANGE; } else { udata->addr = *addr; ret_value = H5B_INS_NOOP; } #else assert (lt_key->nbytes == udata->key.nbytes); assert (!H5F_addr_defined (&(udata->addr)) || H5F_addr_eq (&(udata->addr), addr)); udata->addr = *addr; ret_value = H5B_INS_NOOP; #endif } else if (H5V_hyper_disjointp(udata->mesg.ndims, lt_key->offset, udata->mesg.dim, udata->key.offset, udata->mesg.dim)) { assert(H5V_hyper_disjointp(udata->mesg.ndims, rt_key->offset, udata->mesg.dim, udata->key.offset, udata->mesg.dim)); /* * 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->nbytes = udata->key.nbytes; for (i=0; imesg.ndims; i++) { assert(0 == udata->key.offset[i] % udata->mesg.dim[i]); md_key->offset[i] = udata->key.offset[i]; } /* * Allocate storage for the new chunk */ if (H5MF_alloc(f, H5MF_RAW, udata->key.nbytes, new_node/*out*/)<0) { HRETURN_ERROR(H5E_IO, H5E_CANTINIT, H5B_INS_ERROR, "file allocation failed"); } udata->addr = *new_node; ret_value = H5B_INS_RIGHT; } else { 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_read * * Purpose: Reads a multi-dimensional buffer from (part of) an indexed raw * storage array. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Wednesday, October 15, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, const H5O_compress_t *comp, const hssize_t offset_f[], const hsize_t size[], void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; hsize_t size_m[H5O_LAYOUT_NDIMS]; intn i, carry; hsize_t idx_cur[H5O_LAYOUT_NDIMS]; hsize_t idx_min[H5O_LAYOUT_NDIMS]; hsize_t idx_max[H5O_LAYOUT_NDIMS]; hsize_t sub_size[H5O_LAYOUT_NDIMS]; hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS]; hssize_t sub_offset_m[H5O_LAYOUT_NDIMS]; size_t chunk_size; uint8 *chunk=NULL, *compressed=NULL; H5F_istore_ud1_t udata; herr_t status; herr_t ret_value = FAIL; FUNC_ENTER(H5F_istore_read, FAIL); /* Check args */ assert (f); assert (layout && H5D_CHUNKED==layout->type); assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert (H5F_addr_defined(&(layout->addr))); assert (offset_f); assert (size); assert (buf); /* * For now, a hyperslab of the file must be read into an array in * memory.We do not yet support reading into a hyperslab of memory. */ for (i=0; indims; i++) { offset_m[i] = 0; size_m[i] = size[i]; } #ifndef NDEBUG for (i=0; indims; i++) { assert (offset_f[i]>=0); /*negative offsets not supported*/ assert (offset_m[i]>=0); /*negative offsets not supported*/ assert (size[i]dim[i]>0); } #endif /* Determine the chunk size and allocate buffers */ for (i=0, chunk_size=1; indims; i++) { chunk_size *= layout->dim[i]; } chunk = H5MM_xmalloc(chunk_size); if (comp && H5Z_NONE!=comp->method) { compressed = H5MM_xmalloc (chunk_size); } /* * As a special case 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. */ for (i=0; indims; 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]; } if (i==layout->ndims) { udata.mesg = *layout; H5F_addr_undef (&(udata.addr)); status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata); if (status>=0 && H5F_addr_defined (&(udata.addr))) { if (compressed && udata.key.nbytesndims; i++) { idx_min[i] = offset_f[i] / layout->dim[i]; idx_max[i] = (offset_f[i]+size[i]-1) / layout->dim[i] + 1; idx_cur[i] = idx_min[i]; } /* Initialize non-changing part of udata */ udata.mesg = *layout; /* Loop over all chunks */ while (1) { for (i=0; indims; i++) { /* The location and size of the chunk being accessed */ assert (layout->dim[i] < MAX_HSSIZET); udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]); /* The offset and size wrt the chunk */ offset_wrt_chunk[i] = MAX(offset_f[i], udata.key.offset[i]) - udata.key.offset[i]; sub_size[i] = MIN((idx_cur[i]+1)*layout->dim[i], offset_f[i]+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[i] - offset_f[i]; } /* Read chunk */ H5F_addr_undef(&(udata.addr)); status = H5B_find(f, H5B_ISTORE, &(layout->addr), &udata); if (status>=0 && H5F_addr_defined(&(udata.addr))) { if (compressed && udata.key.nbytesndims, sub_size, size_m, sub_offset_m, (void *)buf, layout->dim, 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; done: H5MM_xfree(chunk); H5MM_xfree (compressed); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5F_istore_write * * Purpose: Writes a multi-dimensional buffer to (part of) an indexed raw * storage array. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Wednesday, October 15, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, const H5O_compress_t *comp, const hssize_t offset_f[], const hsize_t size[], const void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; hsize_t size_m[H5O_LAYOUT_NDIMS]; intn i, carry; hsize_t idx_cur[H5O_LAYOUT_NDIMS]; hsize_t idx_min[H5O_LAYOUT_NDIMS]; hsize_t idx_max[H5O_LAYOUT_NDIMS]; hsize_t sub_size[H5O_LAYOUT_NDIMS]; hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS]; hssize_t sub_offset_m[H5O_LAYOUT_NDIMS]; hsize_t chunk_size, nbytes; uint8 *chunk=NULL, *compressed=NULL, *outbuf; H5F_istore_ud1_t udata; herr_t ret_value = FAIL; FUNC_ENTER(H5F_istore_write, FAIL); /* Check args */ assert(f); assert(layout && H5D_CHUNKED==layout->type); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(&(layout->addr))); assert (offset_f); assert(size); assert(buf); /* * For now the source must not be a hyperslab. It must be an entire * memory buffer. */ for (i=0; indims; i++) { offset_m[i] = 0; size_m[i] = size[i]; } #ifndef NDEBUG for (i=0; indims; i++) { assert (offset_f[i]>=0); /*negative offsets not supported*/ assert (offset_m[i]>=0); /*negative offsets not supported*/ assert(size[i]dim[i]>0); } #endif /* * 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; indims; i++) { idx_min[i] = offset_f[i] / layout->dim[i]; idx_max[i] = (offset_f[i]+size[i]-1) / layout->dim[i] + 1; idx_cur[i] = idx_min[i]; } /* Allocate buffers */ for (i=0, chunk_size=1; indims; i++) { chunk_size *= layout->dim[i]; } chunk = H5MM_xmalloc(chunk_size); if (comp && H5Z_NONE!=comp->method) { compressed = H5MM_xmalloc (chunk_size); } /* Initialize non-changing part of udata */ udata.mesg = *layout; /* Loop over all chunks */ while (1) { for (i=0; indims; i++) { /* The location and size of the chunk being accessed */ assert (layout->dim[i] < MAX_HSSIZET); udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]); /* The offset and size wrt the chunk */ offset_wrt_chunk[i] = MAX(offset_f[i], udata.key.offset[i]) - udata.key.offset[i]; sub_size[i] = MIN((idx_cur[i]+1)*layout->dim[i], offset_f[i]+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[i] - offset_f[i]; } /* * If we are writing a partial chunk then load the chunk from disk * and uncompress it if it exists. */ if (!H5V_vector_zerop_s(layout->ndims, offset_wrt_chunk) || !H5V_vector_eq_u(layout->ndims, sub_size, layout->dim)) { if (H5B_find (f, H5B_ISTORE, &(layout->addr), &udata)>=0 && H5F_addr_defined (&(udata.addr))) { if (compressed && udata.key.nbytesndims, sub_size, layout->dim, offset_wrt_chunk, chunk, size_m, sub_offset_m, buf); /* Compress the chunk */ if (compressed && (nbytes=H5Z_compress (comp, chunk_size, chunk, compressed)) && nbytesaddr), &udata)<0) { HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk"); } if (H5F_block_write(f, &(udata.addr), nbytes, outbuf) < 0) { HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw storage 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; done: H5MM_xfree(chunk); H5MM_xfree (compressed); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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. * * 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. * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, October 21, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ ) { H5F_istore_ud1_t udata; #ifndef NDEBUG int i; #endif FUNC_ENTER(H5F_istore_create, FAIL); /* Check args */ assert(f); assert(layout && H5D_CHUNKED == layout->type); assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); #ifndef NDEBUG for (i = 0; i < layout->ndims; i++) { 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"); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * Function: H5F_istore_debug * * Purpose: Debugs a B-tree node for indexed raw data storage. * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Thursday, April 16, 1998 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent, intn fwidth, int ndims) { H5F_istore_ud1_t udata; FUNC_ENTER (H5F_istore_debug, FAIL); HDmemset (&udata, 0, sizeof udata); udata.mesg.ndims = ndims; H5B_debug (f, addr, stream, indent, fwidth, H5B_ISTORE, &udata); FUNC_LEAVE (SUCCEED); }