diff options
Diffstat (limited to 'src/H5Dint.c')
| -rw-r--r-- | src/H5Dint.c | 640 |
1 files changed, 212 insertions, 428 deletions
diff --git a/src/H5Dint.c b/src/H5Dint.c index 3b2faf2..85f093d 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -30,7 +30,6 @@ #include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #include "H5FOprivate.h" /* File objects */ -#include "H5HLprivate.h" /* Local heaps */ #include "H5Iprivate.h" /* IDs */ #include "H5Lprivate.h" /* Links */ #include "H5MMprivate.h" /* Memory management */ @@ -49,7 +48,6 @@ typedef struct { const H5F_t *f; /* Pointer to file being flushed */ hid_t dxpl_id; /* DXPL for I/O operations */ - unsigned flags; /* Flags for flush operation */ } H5D_flush_ud_t; @@ -65,10 +63,10 @@ static H5D_shared_t *H5D_new(hid_t dcpl_id, hbool_t creating, static herr_t H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type); static herr_t H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space); -static herr_t H5D_set_io_ops(H5D_t *dataset); -static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset); -static herr_t H5D_open_oid(H5D_t *dataset, hid_t dxpl_id); -static herr_t H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags); +static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, + hid_t dapl_id); +static herr_t H5D_open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id); +static herr_t H5D_flush_real(H5D_t *dataset, hid_t dxpl_id); /*********************/ @@ -172,8 +170,8 @@ H5D_init_interface(void) if(NULL == (def_dcpl = (H5P_genplist_t *)H5I_object(H5P_LST_DATASET_CREATE_g))) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list") - /* Get the default data storage method */ - if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout.type) < 0) + /* Get the default data storage layout */ + if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve layout") /* Get the default dataset creation properties */ @@ -181,7 +179,7 @@ H5D_init_interface(void) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve external file list") if(H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.dcpl_cache.fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value") - if(H5P_get(def_dcpl, H5D_CRT_DATA_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0) + if(H5P_get(def_dcpl, H5O_CRT_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve pipeline filter") /* Reset the "default DXPL cache" information */ @@ -242,7 +240,7 @@ H5D_term_interface(void) * * QAK - 5/13/03 */ - H5I_clear_type(H5I_DATASET, TRUE); + H5I_clear_type(H5I_DATASET, TRUE, FALSE); } else { H5I_dec_type_ref(H5I_DATASET); H5_interface_initialize_g = 0; @@ -419,6 +417,7 @@ H5D_create_named(const H5G_loc_t *loc, const char *name, hid_t type_id, dcrt_info.type_id = type_id; dcrt_info.space = space; dcrt_info.dcpl_id = dcpl_id; + dcrt_info.dapl_id = dapl_id; /* Set up object creation information */ ocrt_info.obj_type = H5O_TYPE_DATASET; @@ -457,8 +456,9 @@ H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id) { H5S_t *space; /* Dataset's dataspace */ hsize_t space_allocated; /* The number of bytes allocated for chunks */ - hssize_t total_elem; /* The total number of elements in dataspace */ - size_t type_size; /* The size of the datatype for the dataset */ + hssize_t snelmts; /* Temporary holder for number of elements in dataspace */ + hsize_t nelmts; /* Number of elements in dataspace */ + size_t dt_size; /* Size of datatype */ hsize_t full_size; /* The number of bytes in the dataset when fully populated */ herr_t ret_value = SUCCEED; @@ -471,16 +471,20 @@ H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id) HDassert(space); /* Get the total number of elements in dataset's dataspace */ - if((total_elem=H5S_GET_EXTENT_NPOINTS(space)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get # of dataspace elements") + if((snelmts = H5S_GET_EXTENT_NPOINTS(space)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace") + nelmts = (hsize_t)snelmts; /* Get the size of the dataset's datatype */ - if((type_size = H5T_get_size(dset->shared->type)) == 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get size of datatype") + if(0 == (dt_size = H5T_GET_SIZE(dset->shared->type))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype") /* Compute the maximum size of the dataset in bytes */ - H5_CHECK_OVERFLOW(total_elem,hssize_t,hsize_t); - full_size=((hsize_t)total_elem)*type_size; + full_size = nelmts * dt_size; + + /* Check for overflow during multiplication */ + if(nelmts != (full_size / dt_size)) + HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed") /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */ space_allocated = H5D_get_storage_size(dset, dxpl_id); @@ -536,7 +540,7 @@ H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) * don't bother to copy it, just increment the reference count */ if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) { - if(H5I_inc_ref(dcpl_id) < 0) + if(H5I_inc_ref(dcpl_id, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment default DCPL ID") new_dset->dcpl_id = dcpl_id; } /* end if */ @@ -545,7 +549,7 @@ H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) if(NULL == (plist = (H5P_genplist_t *)H5I_object(dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list") - new_dset->dcpl_id = H5P_copy_plist(plist); + new_dset->dcpl_id = H5P_copy_plist(plist, FALSE); } /* end else */ /* Set return value */ @@ -555,8 +559,8 @@ done: if(ret_value == NULL) if(new_dset != NULL) { if(new_dset->dcpl_id != 0) - (void)H5I_dec_ref(new_dset->dcpl_id); - H5FL_FREE(H5D_shared_t, new_dset); + (void)H5I_dec_ref(new_dset->dcpl_id, FALSE); + (void)H5FL_FREE(H5D_shared_t, new_dset); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) @@ -619,12 +623,12 @@ H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype") /* Get a datatype ID for the dataset's datatype */ - if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type)) < 0) + if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type, FALSE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") } /* end if */ /* Not a custom datatype, just use it directly */ else { - if(H5I_inc_ref(type_id) < 0) + if(H5I_inc_ref(type_id, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment datatype ID") /* Use existing datatype */ @@ -686,58 +690,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_set_io_ops - * - * Purpose: Set the I/O operation function pointers for a dataset - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Thursday, March 20, 2008 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_set_io_ops(H5D_t *dataset) -{ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_set_io_ops) - - /* check args */ - HDassert(dataset); - - /* Set the I/O functions for each layout type */ - switch(dataset->shared->layout.type) { - case H5D_CONTIGUOUS: - if(dataset->shared->dcpl_cache.efl.nused > 0) - dataset->shared->layout.ops = H5D_LOPS_EFL; - else - dataset->shared->layout.ops = H5D_LOPS_CONTIG; - break; - - case H5D_CHUNKED: - dataset->shared->layout.ops = H5D_LOPS_CHUNK; - - /* Set the chunk operations */ - /* (Only "istore" indexing type currently supported */ - dataset->shared->layout.u.chunk.ops = H5D_COPS_ISTORE; - break; - - case H5D_COMPACT: - dataset->shared->layout.ops = H5D_LOPS_COMPACT; - break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method") - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_set_io_ops() */ - - -/*------------------------------------------------------------------------- * Function: H5D_update_oh_info * * Purpose: Create and fill object header for dataset @@ -751,7 +703,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) +H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id) { H5O_t *oh = NULL; /* Pointer to dataset's object header */ size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ @@ -762,6 +714,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ H5D_fill_value_t fill_status; /* Fill value status */ hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */ + hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_update_oh_info) @@ -784,7 +737,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* Special case handling for variable-length types */ - if(H5T_detect_class(type, H5T_VLEN)) { + if(H5T_detect_class(type, H5T_VLEN, FALSE)) { /* If the default fill value is chosen for variable-length types, always write it */ if(fill_prop->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_DEFAULT) { /* Update dataset creation property */ @@ -831,7 +784,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) /* Add the dataset's raw data size to the size of the header, if the raw data will be stored as compact */ if(layout->type == H5D_COMPACT) - ohdr_size += layout->u.compact.size; + ohdr_size += layout->storage.u.compact.size; /* Create an object header for the dataset */ if(H5O_create(file, dxpl_id, ohdr_size, dset->shared->dcpl_id, oloc/*out*/) < 0) @@ -839,8 +792,8 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) HDassert(file == dset->oloc.file); /* Get a pointer to the object header itself */ - if(NULL == (oh = H5O_protect(oloc, dxpl_id))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect dataset object header") + if(NULL == (oh = H5O_pin(oloc, dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Write new fill value message */ if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) @@ -869,78 +822,12 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message") - /* Update the filters message, if this is a chunked dataset */ - if(layout->type == H5D_CHUNKED) { - H5O_pline_t *pline; /* Dataset's I/O pipeline information */ - - pline = &dset->shared->dcpl_cache.pline; - if(pline->nused > 0 && H5O_msg_append_oh(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message") - } /* end if */ - - /* - * Allocate storage if space allocate time is early; otherwise delay - * allocation until later. - */ - if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") - - /* Update external storage message, if it's used */ - if(dset->shared->dcpl_cache.efl.nused > 0) { - H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */ - H5HL_t *heap; /* Pointer to local heap for EFL file names */ - size_t heap_size = H5HL_ALIGN(1); - size_t u; - - /* Determine size of heap needed to stored the file names */ - for(u = 0; u < efl->nused; ++u) - heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1); - - /* Create the heap for the EFL file names */ - if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap") - - /* Pin the heap down in memory */ - if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect EFL file name heap") - - /* Insert "empty" name first */ - if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) { - H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr); - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") - } /* end if */ - - for(u = 0; u < efl->nused; ++u) { - size_t offset; /* Offset of file name in heap */ - - /* Insert file name into heap */ - if((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap, - HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) { - H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr); - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") - } /* end if */ - - /* Store EFL file name offset */ - HDassert(0 == efl->slot[u].name_offset); - efl->slot[u].name_offset = offset; - } /* end for */ - - /* Release the heap */ - if(H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect EFL file name heap") - heap = NULL; - - /* Insert EFL message into dataset object header */ - if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message") - } /* end if */ + /* Update/create the layout (and I/O pipeline & EFL) messages */ + if(H5D_layout_oh_create(file, dxpl_id, oh, dset, dapl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout/pline/efl header message") - /* Create layout message */ - /* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */ - /* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */ - if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout") + /* Indicate that the layout information was initialized */ + layout_init = TRUE; #ifdef H5O_ENABLE_BOGUS { @@ -966,6 +853,9 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) #endif /* H5O_ENABLE_BOGUS */ /* Add a modification time message, if using older format. */ + /* (If using the latest format, the modification time is part of the object + * header and doesn't use a separate message -QAK) + */ if(!use_latest_format) if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") @@ -973,8 +863,16 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) done: /* Release pointer to object header itself */ if(oloc != NULL && oh != NULL) - if(H5O_unprotect(oloc, oh) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect dataset object header") + if(H5O_unpin(oloc, oh) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header") + + /* Error cleanup */ + if(ret_value < 0) { + if(dset->shared->layout.type == H5D_CHUNKED && layout_init) { + if(H5D_chunk_dest(file, dxpl_id, dset) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache") + } /* end if */ + } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_update_oh_info() */ @@ -1002,7 +900,7 @@ done: */ H5D_t * H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, - hid_t dxpl_id) + hid_t dapl_id, hid_t dxpl_id) { const H5T_t *type; /* Datatype for dataset */ H5D_t *new_dset = NULL; @@ -1016,10 +914,10 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, /* check args */ HDassert(file); - HDassert(H5I_DATATYPE==H5I_get_type(type_id)); + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); HDassert(space); - HDassert(H5I_GENPROP_LST==H5I_get_type(dcpl_id)); - HDassert(H5I_GENPROP_LST==H5I_get_type(dxpl_id)); + HDassert(H5I_GENPROP_LST == H5I_get_type(dcpl_id)); + HDassert(H5I_GENPROP_LST == H5I_get_type(dxpl_id)); /* Get the dataset's datatype */ if(NULL == (type = (const H5T_t *)H5I_object(type_id))) @@ -1030,11 +928,11 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible") /* Check if the datatype is/contains a VL-type */ - if(H5T_detect_class(type, H5T_VLEN)) - has_vl_type=TRUE; + if(H5T_detect_class(type, H5T_VLEN, FALSE)) + has_vl_type = TRUE; /* Check if the dataspace has an extent set (or is NULL) */ - if(!(H5S_has_extent(space)) ) + if(!H5S_has_extent(space)) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "dataspace extent has not been set.") /* Initialize the dataset object */ @@ -1063,7 +961,7 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, /* Check if the dataset has a non-default DCPL & get important values, if so */ if(new_dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) { - H5D_layout_t *layout; /* Dataset's layout information */ + H5O_layout_t *layout; /* Dataset's layout information */ H5O_pline_t *pline; /* Dataset's I/O pipeline information */ H5O_fill_t *fill; /* Dataset's fill value info */ @@ -1081,12 +979,12 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, /* Retrieve the properties we need */ pline = &new_dset->shared->dcpl_cache.pline; - if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0) + if(H5P_get(dc_plist, H5O_CRT_PIPELINE_NAME, pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter") - layout = &new_dset->shared->layout.type; + layout = &new_dset->shared->layout; if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout") - if(pline->nused > 0 && H5D_CHUNKED != *layout) + if(pline->nused > 0 && H5D_CHUNKED != layout->type) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout") fill = &new_dset->shared->dcpl_cache.fill; if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0) @@ -1097,7 +995,7 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "invalid space allocation state") /* Don't allow compact datasets to allocate space later */ - if(*layout == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY) + if(layout->type == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation") /* If MPI VFD is used, no filter support yet. */ @@ -1109,10 +1007,10 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list") } /* end if */ - /* Set the latest version of the pline & fill messages, if requested */ + /* Set the latest version of the layout, pline & fill messages, if requested */ if(H5F_USE_LATEST_FORMAT(file)) { /* Set the latest version for the I/O pipeline message */ - if(H5Z_set_latest_version(&new_dset->shared->dcpl_cache.pline) < 0) + if(H5O_pline_set_latest_version(&new_dset->shared->dcpl_cache.pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of I/O filter pipeline") /* Set the latest version for the fill value message */ @@ -1125,25 +1023,25 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; /* Set the dataset's I/O operations */ - if(H5D_set_io_ops(new_dset) < 0) + if(H5D_layout_set_io_ops(new_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize I/O operations") /* Create the layout information for the new dataset */ - if((new_dset->shared->layout.ops->new)(file, dxpl_id, new_dset, dc_plist) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize layout information") - - /* Indicate that the layout information was initialized */ - layout_init = TRUE; + if((new_dset->shared->layout.ops->construct)(file, new_dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to construct layout information") /* Update the dataset's object header info. */ - if(H5D_update_oh_info(file, dxpl_id, new_dset) != SUCCEED) + if(H5D_update_oh_info(file, dxpl_id, new_dset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache") + /* Indicate that the layout information was initialized */ + layout_init = TRUE; + /* Add the dataset to the list of opened objects in the file */ if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count") if(H5FO_insert(new_dset->oloc.file, new_dset->oloc.addr, new_dset->shared, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") new_dset->shared->fo_count = 1; @@ -1157,12 +1055,10 @@ done: if(H5D_chunk_dest(file, dxpl_id, new_dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy chunk cache") } /* end if */ - if(new_dset->shared->space) { - if(H5S_close(new_dset->shared->space) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace") - } /* end if */ + if(new_dset->shared->space && H5S_close(new_dset->shared->space) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace") if(new_dset->shared->type) { - if(H5I_dec_ref(new_dset->shared->type_id) < 0) + if(H5I_dec_ref(new_dset->shared->type_id, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") } /* end if */ if(H5F_addr_defined(new_dset->oloc.addr)) { @@ -1173,14 +1069,12 @@ done: HDONE_ERROR(H5E_DATASET, H5E_CANTDELETE, NULL, "unable to delete object header") } /* end if */ } /* end if */ - if(new_dset->shared->dcpl_id != 0) { - if(H5I_dec_ref(new_dset->shared->dcpl_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list") - } /* end if */ - H5FL_FREE(H5D_shared_t, new_dset->shared); + if(new_dset->shared->dcpl_id != 0 && H5I_dec_ref(new_dset->shared->dcpl_id, FALSE) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list") + (void)H5FL_FREE(H5D_shared_t, new_dset->shared); } /* end if */ new_dset->oloc.file = NULL; - H5FL_FREE(H5D_t, new_dset); + (void)H5FL_FREE(H5D_t, new_dset); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) @@ -1203,7 +1097,7 @@ done: *------------------------------------------------------------------------- */ H5D_t * -H5D_open(const H5G_loc_t *loc, hid_t dxpl_id) +H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id) { H5D_shared_t *shared_fo = NULL; H5D_t *dataset = NULL; @@ -1227,12 +1121,12 @@ H5D_open(const H5G_loc_t *loc, hid_t dxpl_id) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path") /* Check if dataset was already open */ - if((shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr)) == NULL) { + if(NULL == (shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr))) { /* Clear any errors from H5FO_opened() */ H5E_clear_stack(NULL); /* Open the dataset object */ - if(H5D_open_oid(dataset, dxpl_id) < 0) + if(H5D_open_oid(dataset, dapl_id, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") /* Add the dataset to the list of opened objects in the file */ @@ -1272,13 +1166,13 @@ done: /* Free the location--casting away const*/ if(dataset) { if(shared_fo == NULL) /* Need to free shared fo */ - H5FL_FREE(H5D_shared_t, dataset->shared); + (void)H5FL_FREE(H5D_shared_t, dataset->shared); H5O_loc_free(&(dataset->oloc)); H5G_name_free(&(dataset->path)); - H5FL_FREE(H5D_t, dataset); - } + (void)H5FL_FREE(H5D_t, dataset); + } /* end if */ if(shared_fo) shared_fo->fo_count--; } /* end if */ @@ -1300,7 +1194,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) +H5D_open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id) { H5P_genplist_t *plist; /* Property list */ H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */ @@ -1324,109 +1218,24 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) /* Get the type and space */ if(NULL == (dataset->shared->type = (H5T_t *)H5O_msg_read(&(dataset->oloc), H5O_DTYPE_ID, NULL, dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load type info from dataset header") + + if(H5T_set_loc(dataset->shared->type, dataset->oloc.file, H5T_LOC_DISK) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid datatype location") + if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc), dxpl_id))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load space info from dataset header") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") /* Get a datatype ID for the dataset's datatype */ - if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type)) < 0) + if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type, FALSE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") /* Get dataset creation property list object */ if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") - /* Get the optional filters message */ - if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_PLINE_ID, dxpl_id)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") - if(msg_exists) { - /* Retrieve the I/O pipeline message */ - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline, dxpl_id)) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") - - /* Set the I/O pipeline info in the property list */ - if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, &dataset->shared->dcpl_cache.pline) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline") - } /* end if */ - - /* - * Get the raw data layout info. It's actually stored in two locations: - * the storage message of the dataset (dataset->storage) and certain - * values are copied to the dataset create plist so the user can query - * them. - */ - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id)) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message") - if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout.type) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout") - - /* Get the external file list message, which might not exist. Space is - * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */ - if((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) - || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) { - if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") - if(msg_exists) { - /* Retrieve the EFL message */ - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id)) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") - - /* Set the EFL info in the property list */ - if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list") - - /* Set the dataset's I/O operations */ - dataset->shared->layout.ops = H5D_LOPS_EFL; - } /* end if */ - } /* end if */ - - /* Sanity check that the layout operations are set up */ - HDassert(dataset->shared->layout.ops); - - switch(dataset->shared->layout.type) { - case H5D_CONTIGUOUS: - /* Compute the size of the contiguous storage for versions of the - * layout message less than version 3 because versions 1 & 2 would - * truncate the dimension sizes to 32-bits of information. - QAK 5/26/04 - */ - if(dataset->shared->layout.version < 3) { - hssize_t tmp_size; /* Temporary holder for raw data size */ - - tmp_size = H5S_GET_EXTENT_NPOINTS(dataset->shared->space) * H5T_get_size(dataset->shared->type); - H5_ASSIGN_OVERFLOW(dataset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t); - } /* end if */ - - /* Get the sieve buffer size for this dataset */ - dataset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->oloc.file); - break; - - case H5D_CHUNKED: - /* - * Chunked storage. The creation plist's dimension is one less than - * the chunk dimension because the chunk includes a dimension for the - * individual bytes of the datatype. - */ - { - unsigned chunk_ndims; /* Dimensionality of chunk */ - - chunk_ndims = dataset->shared->layout.u.chunk.ndims - 1; - - if(H5P_set(plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk dimensions") - if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->shared->layout.u.chunk.dim) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk size") - - /* Initialize the chunk cache for the dataset */ - if(H5D_chunk_init(dataset->oloc.file, dxpl_id, dataset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache") - } - break; - - case H5D_COMPACT: - break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method") - } /* end switch */ /*lint !e788 All appropriate cases are covered */ + /* Get the layout/pline/efl message information */ + if(H5D_layout_oh_read(dataset, dxpl_id, dapl_id, plist) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout/pline/efl info") /* Point at dataset's copy, to cache it for later */ fill_prop = &dataset->shared->dcpl_cache.fill; @@ -1468,7 +1277,7 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) /* If "old" fill value size is 0 (undefined), map it to -1 */ if(fill_prop->size == 0) - fill_prop->size = (size_t)-1; + fill_prop->size = (ssize_t)-1; } /* end if */ alloc_time_state = 0; if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) @@ -1489,9 +1298,8 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) * This is important only for parallel I/O where the space must * be fully allocated before I/O can happen. */ - if((H5F_get_intent(dataset->oloc.file) & H5F_ACC_RDWR) - && ((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) - || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) + if((H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR) + && !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) && IS_H5FD_MPI(dataset->oloc.file)) { if(H5D_alloc_storage(dataset, dxpl_id, H5D_ALLOC_OPEN, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage") @@ -1499,17 +1307,13 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) done: if(ret_value < 0) { - if(H5F_addr_defined(dataset->oloc.addr)) { - if(H5O_close(&(dataset->oloc)) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") - } /* end if */ - if(dataset->shared->space) { - if(H5S_close(dataset->shared->space) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") - } /* end if */ + if(H5F_addr_defined(dataset->oloc.addr) && H5O_close(&(dataset->oloc)) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") + if(dataset->shared->space && H5S_close(dataset->shared->space) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") if(dataset->shared->type) { if(dataset->shared->type_id > 0) { - if(H5I_dec_ref(dataset->shared->type_id) < 0) + if(H5I_dec_ref(dataset->shared->type_id, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") } /* end if */ else { @@ -1557,7 +1361,7 @@ H5D_close(H5D_t *dataset) dataset->shared->fo_count--; if(dataset->shared->fo_count == 0) { /* Flush the dataset's information */ - if(H5D_flush_real(dataset, H5AC_dxpl_id, H5F_FLUSH_NONE) < 0) + if(H5D_flush_real(dataset, H5AC_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info") /* Free the data sieve buffer, if it's been allocated */ @@ -1599,7 +1403,7 @@ H5D_close(H5D_t *dataset) case H5D_COMPACT: /* Free the buffer for the raw data for compact datasets */ - dataset->shared->layout.u.compact.buf = H5MM_xfree(dataset->shared->layout.u.compact.buf); + dataset->shared->layout.storage.u.compact.buf = H5MM_xfree(dataset->shared->layout.storage.u.compact.buf); break; default: @@ -1613,8 +1417,8 @@ H5D_close(H5D_t *dataset) * Release datatype, dataspace and creation property list -- there isn't * much we can do if one of these fails, so we just continue. */ - free_failed = (H5I_dec_ref(dataset->shared->type_id) < 0 || H5S_close(dataset->shared->space) < 0 || - H5I_dec_ref(dataset->shared->dcpl_id) < 0); + free_failed = (unsigned)(H5I_dec_ref(dataset->shared->type_id, FALSE) < 0 || H5S_close(dataset->shared->space) < 0 || + H5I_dec_ref(dataset->shared->dcpl_id, FALSE) < 0); /* Remove the dataset from the list of opened objects in the file */ if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) @@ -1635,7 +1439,7 @@ H5D_close(H5D_t *dataset) */ dataset->oloc.file = NULL; - H5FL_FREE(H5D_shared_t, dataset->shared); + (void)H5FL_FREE(H5D_shared_t, dataset->shared); } /* end if */ else { /* Decrement the ref. count for this object in the top file */ @@ -1653,7 +1457,7 @@ H5D_close(H5D_t *dataset) free_failed = TRUE; /* Free the dataset's memory structure */ - H5FL_FREE(H5D_t, dataset); + (void)H5FL_FREE(H5D_t, dataset); /* Check if anything failed in the middle... */ if(free_failed) @@ -1717,7 +1521,6 @@ H5D_nameof(H5D_t *dataset) * is not copied. * * Return: Success: Ptr to the dataset's datatype, uncopied. - * * Failure: NULL * * Programmer: Robb Matzke @@ -1732,6 +1535,7 @@ H5D_typeof(const H5D_t *dset) FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_typeof) HDassert(dset); + HDassert(dset->shared); HDassert(dset->shared->type); FUNC_LEAVE_NOAPI(dset->shared->type) @@ -1739,33 +1543,6 @@ H5D_typeof(const H5D_t *dset) /*------------------------------------------------------------------------- - * Function: H5D_get_file - * - * Purpose: Returns the dataset's file pointer. - * - * Return: Success: Ptr to the dataset's file pointer. - * - * Failure: NULL - * - * Programmer: Quincey Koziol - * Thursday, October 22, 1998 - * - *------------------------------------------------------------------------- - */ -static H5F_t * -H5D_get_file(const H5D_t *dset) -{ - /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_get_file) - - HDassert(dset); - HDassert(dset->oloc.file); - - FUNC_LEAVE_NOAPI(dset->oloc.file) -} /* end H5D_get_file() */ - - -/*------------------------------------------------------------------------- * Function: H5D_alloc_storage * * Purpose: Allocate storage for the raw data of a dataset. @@ -1803,9 +1580,9 @@ H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_al switch(layout->type) { case H5D_CONTIGUOUS: - if(!H5F_addr_defined(layout->u.contig.addr)) { + if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { /* Reserve space in the file for the entire array */ - if(H5D_contig_alloc(f, dxpl_id, layout/*out*/) < 0) + if(H5D_contig_alloc(f, dxpl_id, &layout->storage.u.contig/*out*/) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") /* Indicate that we set the storage addr */ @@ -1817,7 +1594,7 @@ H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_al break; case H5D_CHUNKED: - if(!H5F_addr_defined(layout->u.chunk.addr)) { + if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { /* Create the root of the B-tree that describes chunked storage */ if(H5D_chunk_create(dset /*in,out*/, dxpl_id) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") @@ -1840,17 +1617,14 @@ H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_al case H5D_COMPACT: /* Check if space is already allocated */ - if(layout->u.compact.buf==NULL) { + if(NULL == layout->storage.u.compact.buf) { /* Reserve space in layout header message for the entire array. */ - HDassert(layout->u.compact.size > 0); - if(NULL == (layout->u.compact.buf = H5MM_malloc(layout->u.compact.size))) + HDassert(layout->storage.u.compact.size > 0); + if(NULL == (layout->storage.u.compact.buf = H5MM_malloc(layout->storage.u.compact.size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset") if(!full_overwrite) - HDmemset(layout->u.compact.buf, 0, layout->u.compact.size); - layout->u.compact.dirty = TRUE; - - /* Indicate that we set the storage addr */ - addr_set = TRUE; + HDmemset(layout->storage.u.compact.buf, 0, layout->storage.u.compact.size); + layout->storage.u.compact.dirty = TRUE; /* Indicate that we should initialize storage space */ must_init_space = TRUE; @@ -1999,23 +1773,24 @@ H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id) switch(dset->shared->layout.type) { case H5D_CHUNKED: - if(dset->shared->layout.u.chunk.addr == HADDR_UNDEF) - ret_value = 0; - else + if((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { if(H5D_chunk_allocated(dset, dxpl_id, &ret_value) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't retrieve chunked dataset allocated size") + } /* end if */ + else + ret_value = 0; break; case H5D_CONTIGUOUS: /* Datasets which are not allocated yet are using no space on disk */ - if(dset->shared->layout.u.contig.addr == HADDR_UNDEF) - ret_value = 0; + if((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) + ret_value = dset->shared->layout.storage.u.contig.size; else - ret_value = dset->shared->layout.u.contig.size; + ret_value = 0; break; case H5D_COMPACT: - ret_value = dset->shared->layout.u.compact.size; + ret_value = dset->shared->layout.storage.u.compact.size; break; default: @@ -2045,8 +1820,6 @@ done: haddr_t H5D_get_offset(const H5D_t *dset) { - haddr_t base_addr; - H5F_t *f; haddr_t ret_value = HADDR_UNDEF; FUNC_ENTER_NOAPI_NOINIT(H5D_get_offset) @@ -2061,15 +1834,9 @@ H5D_get_offset(const H5D_t *dset) case H5D_CONTIGUOUS: /* If dataspace hasn't been allocated or dataset is stored in * an external file, the value will be HADDR_UNDEF. */ - f = H5D_get_file(dset); - base_addr = H5F_get_base_addr(f); - - /* If there's user block in file, returns the absolute dataset offset - * from the beginning of file. */ - if(base_addr != HADDR_UNDEF) - ret_value = dset->shared->layout.u.contig.addr + base_addr; - else - ret_value = dset->shared->layout.u.contig.addr; + if(dset->shared->dcpl_cache.efl.nused == 0 || H5F_addr_defined(dset->shared->layout.storage.u.contig.addr)) + /* Return the absolute dataset offset from the beginning of file. */ + ret_value = dset->shared->layout.storage.u.contig.addr + H5F_BASE_ADDR(dset->oloc.file); break; default: @@ -2322,9 +2089,9 @@ herr_t H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) { H5S_t *space; /* Dataset's dataspace */ - int rank; /* Dataspace # of dimensions */ - hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */ - htri_t changed; /* Whether the dataspace changed size */ + int rank; /* Dataspace # of dimensions */ + hsize_t curr_dims[H5O_LAYOUT_NDIMS];/* Current dimension sizes */ + htri_t changed; /* Whether the dataspace changed size */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_set_extent) @@ -2334,9 +2101,15 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) HDassert(size); /* Check if we are allowed to modify this file */ - if(0 == (H5F_get_intent(dset->oloc.file) & H5F_ACC_RDWR)) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file") - + if(0 == (H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR)) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file") + + /* Check if we are allowed to modify the space; only datasets with chunked and external storage are allowed to be modified */ + if(H5D_COMPACT == dset->shared->layout.type) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "dataset has compact storage") + if(H5D_CONTIGUOUS == dset->shared->layout.type && 0 == dset->shared->dcpl_cache.efl.nused) + HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "dataset has contiguous storage") + /* Check if the filters in the DCPL will need to encode, and if so, can they? */ if(H5D_check_filters(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't apply filters") @@ -2346,11 +2119,11 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) /* Check if we are shrinking or expanding any of the dimensions */ if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") /* Modify the size of the data space */ if((changed = H5S_set_extent(space, size)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") /* Don't bother updating things, unless they've changed */ if(changed) { @@ -2371,11 +2144,14 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) *------------------------------------------------------------------------- */ /* Update the index values for the cached chunks for this dataset */ - if(H5D_CHUNKED == dset->shared->layout.type) + if(H5D_CHUNKED == dset->shared->layout.type) { + if(H5D_chunk_set_info(dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to update # of chunks") if(H5D_chunk_update_cache(dset, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") + } /* end if */ - /* Allocate space for the new parts of the dataset, if appropriate */ + /* Allocate space for the new parts of the dataset, if appropriate */ if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY) if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_EXTEND, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage") @@ -2384,13 +2160,15 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) /*------------------------------------------------------------------------- * Remove chunk information in the case of chunked datasets * This removal takes place only in case we are shrinking the dateset + * and if the chunks are written *------------------------------------------------------------------------- */ - if(shrink && H5D_CHUNKED == dset->shared->layout.type) { - /* Remove excess chunks */ - if(H5D_chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ") - } /* end if */ + if(shrink && H5D_CHUNKED == dset->shared->layout.type && + (*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { + /* Remove excess chunks */ + if(H5D_chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ") + } /* end if */ /* Mark the dataspace as dirty, for later writing to the file */ dset->shared->space_dirty = TRUE; @@ -2402,6 +2180,47 @@ done: /*------------------------------------------------------------------------- + * Function: H5D_flush_sieve_buf + * + * Purpose: Flush any dataset sieve buffer info cached in memory + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Quincey Koziol + * July 27, 2009 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_flush_sieve_buf) + + /* Check args */ + HDassert(dataset); + + /* Flush the raw data buffer, if we have a dirty one */ + if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) { + HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ + + /* Write dirty data sieve buffer to file */ + if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, + dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") + + /* Reset sieve buffer dirty flag */ + dataset->shared->cache.contig.sieve_dirty = FALSE; + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_flush_sieve_buf() */ + + +/*------------------------------------------------------------------------- * Function: H5D_flush_real * * Purpose: Flush any dataset information cached in memory @@ -2415,7 +2234,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags) +H5D_flush_real(H5D_t *dataset, hid_t dxpl_id) { H5O_t *oh = NULL; /* Pointer to dataset's object header */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2430,13 +2249,13 @@ H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags) unsigned update_flags = H5O_UPDATE_TIME; /* Modification time flag */ /* Get a pointer to the dataset's object header */ - if((oh = H5O_protect(&dataset->oloc, dxpl_id)) == NULL) - HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect dataset object header") + if(NULL == (oh = H5O_pin(&dataset->oloc, dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Update the layout on disk, if it's been changed */ if(dataset->shared->layout_dirty) { - if(H5O_msg_write_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_flags, &dataset->shared->layout) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout message") + if(H5D_layout_oh_write(dataset, dxpl_id, oh, update_flags) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout/pline/efl info") dataset->shared->layout_dirty = FALSE; /* Reset the "update the modification time" flag, so we only do it once */ @@ -2457,50 +2276,16 @@ H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags) HDassert(update_flags == 0); } /* end if */ - /* Flush the raw data buffer, if we have a dirty one */ - if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) { - HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ - - /* Write dirty data sieve buffer to file */ - if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, - dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") - - /* Reset sieve buffer dirty flag */ - dataset->shared->cache.contig.sieve_dirty = FALSE; - } /* end if */ - - /* Flush cached information for each kind of dataset */ - switch(dataset->shared->layout.type) { - case H5D_CONTIGUOUS: - break; - - case H5D_CHUNKED: - /* Flush the raw data cache */ - if(H5D_chunk_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache") - break; - - case H5D_COMPACT: - if(dataset->shared->layout.u.compact.dirty) { - if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0) - HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") - dataset->shared->layout.u.compact.dirty = FALSE; - } /* end if */ - break; - - default: - HDassert("not implemented yet" && 0); -#ifdef NDEBUG - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") -#endif /* NDEBUG */ - } /* end switch */ /*lint !e788 All appropriate cases are covered */ + /* Flush cached raw data for each kind of dataset layout */ + if(dataset->shared->layout.ops->flush && + (dataset->shared->layout.ops->flush)(dataset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush raw data") done: /* Release pointer to object header */ if(oh != NULL) - if(H5O_unprotect(&(dataset->oloc), oh) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect dataset object header") + if(H5O_unpin(&(dataset->oloc), oh) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_flush_real() */ @@ -2534,7 +2319,7 @@ H5D_flush_cb(void *_dataset, hid_t UNUSED id, void *_udata) /* Check for dataset in same file */ if(udata->f == dataset->oloc.file) { /* Flush the dataset's information */ - if(H5D_flush_real(dataset, udata->dxpl_id, udata->flags) < 0) + if(H5D_flush_real(dataset, udata->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to flush cached dataset info") } /* end if */ @@ -2557,7 +2342,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D_flush(const H5F_t *f, hid_t dxpl_id, unsigned flags) +H5D_flush(const H5F_t *f, hid_t dxpl_id) { H5D_flush_ud_t udata; /* User data for callback */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2570,10 +2355,9 @@ H5D_flush(const H5F_t *f, hid_t dxpl_id, unsigned flags) /* Set user data for callback */ udata.f = f; udata.dxpl_id = dxpl_id; - udata.flags = flags; /* Iterate over all the open datasets */ - H5I_search(H5I_DATASET, H5D_flush_cb, &udata); + H5I_search(H5I_DATASET, H5D_flush_cb, &udata, FALSE); done: FUNC_LEAVE_NOAPI(ret_value) |