diff options
Diffstat (limited to 'src/H5Olayout.c')
| -rw-r--r-- | src/H5Olayout.c | 223 |
1 files changed, 82 insertions, 141 deletions
diff --git a/src/H5Olayout.c b/src/H5Olayout.c index 838a80f..8e6e204 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -33,25 +33,23 @@ /* Local macros */ -/* Version # of encoded virtual dataset global heap blocks */ -#define H5O_LAYOUT_VDS_GH_ENC_VERS 0 - /* PRIVATE PROTOTYPES */ -static void *H5O__layout_decode(H5F_t *f, hid_t dxpl_id, H5O_t *open_oh, - unsigned mesg_flags, unsigned *ioflags, const uint8_t *p); +static void *H5O__layout_decode(H5F_t *f, H5O_t *open_oh, unsigned mesg_flags, + unsigned *ioflags, size_t p_size, const uint8_t *p); static herr_t H5O__layout_encode(H5F_t *f, hbool_t disable_shared, uint8_t *p, const void *_mesg); static void *H5O__layout_copy(const void *_mesg, void *_dest); static size_t H5O__layout_size(const H5F_t *f, hbool_t disable_shared, const void *_mesg); static herr_t H5O__layout_reset(void *_mesg); static herr_t H5O__layout_free(void *_mesg); -static herr_t H5O__layout_delete(H5F_t *f, hid_t dxpl_id, H5O_t *open_oh, - void *_mesg); +static herr_t H5O__layout_delete(H5F_t *f, H5O_t *open_oh, void *_mesg); +static herr_t H5O__layout_pre_copy_file(H5F_t *file_src, const void *mesg_src, + hbool_t *deleted, const H5O_copy_t *cpy_info, void *udata); static void *H5O__layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, hbool_t *recompute_size, unsigned *mesg_flags, - H5O_copy_t *cpy_info, void *udata, hid_t dxpl_id); -static herr_t H5O__layout_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, - FILE * stream, int indent, int fwidth); + H5O_copy_t *cpy_info, void *udata); +static herr_t H5O__layout_debug(H5F_t *f, const void *_mesg, FILE *stream, + int indent, int fwidth); /* This message derives from H5O message class */ const H5O_msg_class_t H5O_MSG_LAYOUT[1] = {{ @@ -69,7 +67,7 @@ const H5O_msg_class_t H5O_MSG_LAYOUT[1] = {{ NULL, /* link method */ NULL, /* set share method */ NULL, /* can share method */ - NULL, /* pre copy native value to file */ + H5O__layout_pre_copy_file, /* pre copy native value to file */ H5O__layout_copy_file, /* copy native value to file */ NULL, /* post copy native value to file */ NULL, /* get creation index */ @@ -98,8 +96,9 @@ H5FL_DEFINE(H5O_layout_t); *------------------------------------------------------------------------- */ static void * -H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED *open_oh, - unsigned H5_ATTR_UNUSED mesg_flags, unsigned H5_ATTR_UNUSED *ioflags, const uint8_t *p) +H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, + unsigned H5_ATTR_UNUSED mesg_flags, unsigned H5_ATTR_UNUSED *ioflags, + size_t H5_ATTR_UNUSED p_size, const uint8_t *p) { H5O_layout_t *mesg = NULL; uint8_t *heap_block = NULL; @@ -126,8 +125,8 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED /* Dimensionality */ ndims = *p++; - if(ndims > H5O_LAYOUT_NDIMS) - HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large") + if(!ndims || ndims > H5O_LAYOUT_NDIMS) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is out of range") /* Layout class */ mesg->type = (H5D_layout_t)*p++; @@ -190,7 +189,7 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED if(mesg->storage.u.compact.size > 0) { if(NULL == (mesg->storage.u.compact.buf = H5MM_malloc(mesg->storage.u.compact.size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for compact data buffer") - HDmemcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); + H5MM_memcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); p += mesg->storage.u.compact.size; } /* end if */ } /* end if */ @@ -211,7 +210,7 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED HGOTO_ERROR(H5E_OHDR, H5E_CANTALLOC, NULL, "memory allocation failed for compact data buffer") /* Compact data */ - HDmemcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); + H5MM_memcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); p += mesg->storage.u.compact.size; } /* end if */ @@ -244,9 +243,15 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED H5F_addr_decode(f, &p, &(mesg->storage.u.chunk.idx_addr)); /* Chunk dimensions */ - for(u = 0; u < mesg->u.chunk.ndims; u++) + for(u = 0; u < mesg->u.chunk.ndims; u++) { UINT32DECODE(p, mesg->u.chunk.dim[u]); + /* Just in case that something goes very wrong, such as file corruption. */ + if(mesg->u.chunk.dim[u] == 0) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "chunk dimension must be positive: mesg->u.chunk.dim[%u] = %u", + u, mesg->u.chunk.dim[u]) + } /* end for */ + /* Compute chunk size */ for(u = 1, mesg->u.chunk.size = mesg->u.chunk.dim[0]; u < mesg->u.chunk.ndims; u++) mesg->u.chunk.size *= mesg->u.chunk.dim[u]; @@ -368,7 +373,7 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED /* Check version */ if(mesg->version < H5O_LAYOUT_VERSION_4) HGOTO_ERROR(H5E_OHDR, H5E_VERSION, NULL, "invalid layout version with virtual layout") - + /* Heap information */ H5F_addr_decode(f, &p, &(mesg->storage.u.virt.serial_list_hobjid.addr)); UINT32DECODE(p, mesg->storage.u.virt.serial_list_hobjid.idx); @@ -395,7 +400,7 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED size_t i; /* Read heap */ - if(NULL == (heap_block = (uint8_t *)H5HG_read(f, dxpl_id, &(mesg->storage.u.virt.serial_list_hobjid), NULL, &block_size))) + if(NULL == (heap_block = (uint8_t *)H5HG_read(f, &(mesg->storage.u.virt.serial_list_hobjid), NULL, &block_size))) HGOTO_ERROR(H5E_OHDR, H5E_READERROR, NULL, "Unable to read global heap block") heap_block_p = (const uint8_t *)heap_block; @@ -420,14 +425,14 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED tmp_size = HDstrlen((const char *)heap_block_p) + 1; if(NULL == (mesg->storage.u.virt.list[i].source_file_name = (char *)H5MM_malloc(tmp_size))) HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, NULL, "unable to allocate memory for source file name") - (void)HDmemcpy(mesg->storage.u.virt.list[i].source_file_name, heap_block_p, tmp_size); + (void)H5MM_memcpy(mesg->storage.u.virt.list[i].source_file_name, heap_block_p, tmp_size); heap_block_p += tmp_size; /* Source dataset name */ tmp_size = HDstrlen((const char *)heap_block_p) + 1; if(NULL == (mesg->storage.u.virt.list[i].source_dset_name = (char *)H5MM_malloc(tmp_size))) HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, NULL, "unable to allocate memory for source dataset name") - (void)HDmemcpy(mesg->storage.u.virt.list[i].source_dset_name, heap_block_p, tmp_size); + (void)H5MM_memcpy(mesg->storage.u.virt.list[i].source_dset_name, heap_block_p, tmp_size); heap_block_p += tmp_size; /* Source selection */ @@ -550,8 +555,6 @@ static herr_t H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, const void *_mesg) { const H5O_layout_t *mesg = (const H5O_layout_t *) _mesg; - uint8_t *heap_block = NULL; - size_t *str_size = NULL; unsigned u; herr_t ret_value = SUCCEED; /* Return value */ @@ -567,7 +570,7 @@ H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, H5O_LAYOUT_VERSION_3 : mesg->version); /* Layout class */ - *p++ = mesg->type; + *p++ = (uint8_t)mesg->type; /* Write out layout class specific information */ switch(mesg->type) { @@ -578,7 +581,7 @@ H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, /* Raw data */ if(mesg->storage.u.compact.size > 0) { if(mesg->storage.u.compact.buf) - HDmemcpy(p, mesg->storage.u.compact.buf, mesg->storage.u.compact.size); + H5MM_memcpy(p, mesg->storage.u.compact.buf, mesg->storage.u.compact.size); else HDmemset(p, 0, mesg->storage.u.compact.size); p += mesg->storage.u.compact.size; @@ -676,106 +679,9 @@ H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, break; case H5D_VIRTUAL: - /* Create heap block if it has not been created yet */ - /* Note that we assume here that the contents of the heap block - * cannot change! If this ever stops being the case we must change - * this code to allow overwrites of the heap block. -NAF */ - if((mesg->storage.u.virt.serial_list_hobjid.addr == HADDR_UNDEF) - && (mesg->storage.u.virt.list_nused > 0)) { - uint8_t *heap_block_p; - size_t block_size; - hssize_t select_serial_size; - hsize_t tmp_hsize; - uint32_t chksum; - size_t i; - - /* Allocate array for caching results of strlen */ - if(NULL == (str_size = (size_t *)H5MM_malloc(2 * mesg->storage.u.virt.list_nused *sizeof(size_t)))) - HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, FAIL, "unable to allocate string length array") - - /* - * Calculate heap block size - */ - /* Version and number of entries */ - block_size = (size_t)1 + H5F_SIZEOF_SIZE(f); - - /* Calculate size of each entry */ - for(i = 0; i < mesg->storage.u.virt.list_nused; i++) { - HDassert(mesg->storage.u.virt.list[i].source_file_name); - HDassert(mesg->storage.u.virt.list[i].source_dset_name); - HDassert(mesg->storage.u.virt.list[i].source_select); - HDassert(mesg->storage.u.virt.list[i].source_dset.virtual_select); - - /* Source file name */ - str_size[2 * i] = HDstrlen(mesg->storage.u.virt.list[i].source_file_name) + (size_t)1; - block_size += str_size[2 * i]; - - /* Source dset name */ - str_size[(2 * i) + 1] = HDstrlen(mesg->storage.u.virt.list[i].source_dset_name) + (size_t)1; - block_size += str_size[(2 * i) + 1]; - - /* Source selection */ - if((select_serial_size = H5S_SELECT_SERIAL_SIZE(mesg->storage.u.virt.list[i].source_select)) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to check dataspace selection size") - block_size += (size_t)select_serial_size; - - /* Virtual dataset selection */ - if((select_serial_size = H5S_SELECT_SERIAL_SIZE(mesg->storage.u.virt.list[i].source_dset.virtual_select)) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to check dataspace selection size") - block_size += (size_t)select_serial_size; - } /* end for */ - - /* Checksum */ - block_size += 4; - - /* Allocate heap block */ - if(NULL == (heap_block = (uint8_t *)H5MM_malloc(block_size))) - HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, FAIL, "unable to allocate heap block") - - /* - * Encode heap block - */ - heap_block_p = heap_block; - - /* Encode heap block encoding version */ - *heap_block_p++ = (uint8_t)H5O_LAYOUT_VDS_GH_ENC_VERS; - - /* Number of entries */ - tmp_hsize = (hsize_t)mesg->storage.u.virt.list_nused; - H5F_ENCODE_LENGTH(f, heap_block_p, tmp_hsize) - - /* Encode each entry */ - for(i = 0; i < mesg->storage.u.virt.list_nused; i++) { - /* Source file name */ - (void)HDmemcpy((char *)heap_block_p, mesg->storage.u.virt.list[i].source_file_name, str_size[2 * i]); - heap_block_p += str_size[2 * i]; - - /* Source dataset name */ - (void)HDmemcpy((char *)heap_block_p, mesg->storage.u.virt.list[i].source_dset_name, str_size[(2 * i) + 1]); - heap_block_p += str_size[(2 * i) + 1]; - - /* Source selection */ - if(H5S_SELECT_SERIALIZE(mesg->storage.u.virt.list[i].source_select, &heap_block_p) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to serialize source selection") - - /* Virtual selection */ - if(H5S_SELECT_SERIALIZE(mesg->storage.u.virt.list[i].source_dset.virtual_select, &heap_block_p) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to serialize virtual selection") - } /* end for */ - - /* Checksum */ - chksum = H5_checksum_metadata(heap_block, block_size - (size_t)4, 0); - UINT32ENCODE(heap_block_p, chksum) - - /* Insert block into global heap */ - if(H5HG_insert(f, H5AC_ind_read_dxpl_id, block_size, heap_block, &((H5O_layout_t *)mesg)->storage.u.virt.serial_list_hobjid) < 0) /* Casting away const OK --NAF */ - HGOTO_ERROR(H5E_OHDR, H5E_CANTINSERT, FAIL, "unable to insert virtual dataset heap block") - } /* end if */ - - /* Heap information */ + /* Encode heap ID for VDS info */ H5F_addr_encode(f, &p, mesg->storage.u.virt.serial_list_hobjid.addr); UINT32ENCODE(p, mesg->storage.u.virt.serial_list_hobjid.idx); - break; case H5D_LAYOUT_ERROR: @@ -785,9 +691,6 @@ H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, } /* end switch */ done: - heap_block = (uint8_t *)H5MM_xfree(heap_block); - str_size = (size_t *)H5MM_xfree(str_size); - FUNC_LEAVE_NOAPI(ret_value) } /* end H5O__layout_encode() */ @@ -839,7 +742,7 @@ H5O__layout_copy(const void *_mesg, void *_dest) HGOTO_ERROR(H5E_OHDR, H5E_NOSPACE, NULL, "unable to allocate memory for compact dataset") /* Copy over the raw data */ - HDmemcpy(dest->storage.u.compact.buf, mesg->storage.u.compact.buf, dest->storage.u.compact.size); + H5MM_memcpy(dest->storage.u.compact.buf, mesg->storage.u.compact.buf, dest->storage.u.compact.size); } /* end if */ else HDassert(dest->storage.u.compact.buf == NULL); @@ -997,7 +900,7 @@ H5O__layout_free(void *_mesg) *------------------------------------------------------------------------- */ static herr_t -H5O__layout_delete(H5F_t *f, hid_t dxpl_id, H5O_t *open_oh, void *_mesg) +H5O__layout_delete(H5F_t *f, H5O_t *open_oh, void *_mesg) { H5O_layout_t *mesg = (H5O_layout_t *) _mesg; herr_t ret_value = SUCCEED; /* Return value */ @@ -1017,19 +920,19 @@ H5O__layout_delete(H5F_t *f, hid_t dxpl_id, H5O_t *open_oh, void *_mesg) case H5D_CONTIGUOUS: /* Contiguous block on disk */ /* Free the file space for the raw data */ - if(H5D__contig_delete(f, dxpl_id, &mesg->storage) < 0) + if(H5D__contig_delete(f, &mesg->storage) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free raw data") break; case H5D_CHUNKED: /* Chunked blocks on disk */ /* Free the file space for the index & chunk raw data */ - if(H5D__chunk_delete(f, dxpl_id, open_oh, &mesg->storage) < 0) + if(H5D__chunk_delete(f, open_oh, &mesg->storage) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free raw data") break; case H5D_VIRTUAL: /* Virtual dataset */ /* Free the file space virtual dataset */ - if(H5D__virtual_delete(f, dxpl_id, &mesg->storage) < 0) + if(H5D__virtual_delete(f, &mesg->storage) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free raw data") break; @@ -1045,6 +948,42 @@ done: /*------------------------------------------------------------------------- + * Function: H5O__layout_pre_copy_file + * + * Purpose: Perform any necessary actions before copying message between + * files. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Vailin Choi; Dec 2017 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5O__layout_pre_copy_file(H5F_t H5_ATTR_UNUSED *file_src, const void *mesg_src, + hbool_t H5_ATTR_UNUSED *deleted, const H5O_copy_t *cpy_info, void H5_ATTR_UNUSED *udata) +{ + const H5O_layout_t *layout_src = (const H5O_layout_t *)mesg_src; /* Source layout */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* check args */ + HDassert(cpy_info); + HDassert(cpy_info->file_dst); + + /* Check to ensure that the version of the message to be copied does not exceed + the message version allowed by the destination file's high bound */ + if(layout_src->version > H5O_layout_ver_bounds[H5F_HIGH_BOUND(cpy_info->file_dst)]) + HGOTO_ERROR(H5E_OHDR, H5E_BADRANGE, FAIL, "layout message version out of bounds") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5O__layout_pre_copy_file() */ + + +/*------------------------------------------------------------------------- * Function: H5O__layout_copy_file * * Purpose: Copies a message from _MESG to _DEST in file @@ -1061,7 +1000,7 @@ done: static void * H5O__layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, hbool_t H5_ATTR_UNUSED *recompute_size, unsigned H5_ATTR_UNUSED *mesg_flags, - H5O_copy_t *cpy_info, void *_udata, hid_t dxpl_id) + H5O_copy_t *cpy_info, void *_udata) { H5D_copy_file_ud_t *udata = (H5D_copy_file_ud_t *)_udata; /* Dataset copying user data */ H5O_layout_t *layout_src = (H5O_layout_t *) mesg_src; @@ -1085,7 +1024,7 @@ H5O__layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, case H5D_COMPACT: if(layout_src->storage.u.compact.buf) { /* copy compact raw data */ - if(H5D__compact_copy(file_src, &layout_src->storage.u.compact, file_dst, &layout_dst->storage.u.compact, udata->src_dtype, cpy_info, dxpl_id) < 0) + if(H5D__compact_copy(file_src, &layout_src->storage.u.compact, file_dst, &layout_dst->storage.u.compact, udata->src_dtype, cpy_info) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy chunked storage") copied = TRUE; } /* end if */ @@ -1100,18 +1039,20 @@ H5O__layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, layout_dst->storage.u.contig.size = H5S_extent_nelem(udata->src_space_extent) * H5T_get_size(udata->src_dtype); - if(H5D__contig_is_space_alloc(&layout_src->storage)) { + if(H5D__contig_is_space_alloc(&layout_src->storage) + || (cpy_info->shared_fo && H5D__contig_is_data_cached((const H5D_shared_t *)cpy_info->shared_fo))) { /* copy contiguous raw data */ - if(H5D__contig_copy(file_src, &layout_src->storage.u.contig, file_dst, &layout_dst->storage.u.contig, udata->src_dtype, cpy_info, dxpl_id) < 0) + if(H5D__contig_copy(file_src, &layout_src->storage.u.contig, file_dst, &layout_dst->storage.u.contig, udata->src_dtype, cpy_info) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy contiguous storage") copied = TRUE; } /* end if */ break; case H5D_CHUNKED: - if(H5D__chunk_is_space_alloc(&layout_src->storage)) { + if(H5D__chunk_is_space_alloc(&layout_src->storage) + || (cpy_info->shared_fo && H5D__chunk_is_data_cached((const H5D_shared_t *)cpy_info->shared_fo))) { /* Create chunked layout */ - if(H5D__chunk_copy(file_src, &layout_src->storage.u.chunk, &layout_src->u.chunk, file_dst, &layout_dst->storage.u.chunk, udata->src_space_extent, udata->src_dtype, udata->common.src_pline, cpy_info, dxpl_id) < 0) + if(H5D__chunk_copy(file_src, &layout_src->storage.u.chunk, &layout_src->u.chunk, file_dst, &layout_dst->storage.u.chunk, udata->src_space_extent, udata->src_dtype, udata->common.src_pline, cpy_info) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy chunked storage") copied = TRUE; } /* end if */ @@ -1120,7 +1061,7 @@ H5O__layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, case H5D_VIRTUAL: /* Copy virtual layout. Always copy so the memory fields get copied * properly. */ - if(H5D__virtual_copy(file_dst, layout_dst, dxpl_id) < 0) + if(H5D__virtual_copy(file_dst, layout_dst) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy virtual storage") break; @@ -1159,8 +1100,8 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5O__layout_debug(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, const void *_mesg, - FILE * stream, int indent, int fwidth) +H5O__layout_debug(H5F_t H5_ATTR_UNUSED *f, const void *_mesg, FILE *stream, + int indent, int fwidth) { const H5O_layout_t *mesg = (const H5O_layout_t *) _mesg; size_t u; |