diff options
Diffstat (limited to 'src/H5D.c')
| -rw-r--r-- | src/H5D.c | 1096 |
1 files changed, 547 insertions, 549 deletions
@@ -19,6 +19,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ +#include "H5FOprivate.h" /* File objects */ #include "H5Gprivate.h" /* Group headers */ #include "H5HLprivate.h" /* Name heap */ #include "H5Iprivate.h" /* IDs */ @@ -64,12 +65,25 @@ static int interface_initialize_g = 0; /* Local functions */ static herr_t H5D_init_interface(void); -static herr_t H5D_alloc_storage (H5F_t *f, H5D_t *dset,H5D_time_alloc_t time_alloc); -static herr_t H5D_init_storage(H5D_t *dataset); -H5D_t * H5D_new(hid_t dcpl_id); +static herr_t H5D_alloc_storage (H5F_t *f, H5D_t *dset,H5D_time_alloc_t time_alloc, + hbool_t update_time, hbool_t full_overwrite); +static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite); +static H5D_t * H5D_new(hid_t dcpl_id, hbool_t creating); +static H5D_t * H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, + const H5S_t *space, hid_t dcpl_id); +static H5D_t * H5D_open_oid(H5G_entry_t *ent); +static herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, + const H5S_t *mem_space, const H5S_t *file_space, + hid_t dset_xfer_plist, void *buf/*out*/); +static herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, + const H5S_t *mem_space, const H5S_t *file_space, + hid_t dset_xfer_plist, const void *buf); static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space); static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation); +static hsize_t H5D_get_storage_size(H5D_t *dset); +static haddr_t H5D_get_offset(H5D_t *dset); +static herr_t H5D_set_extent(H5D_t *dataset, const hsize_t *size); /* Declare a free list to manage the H5D_t struct */ H5FL_DEFINE_STATIC(H5D_t); @@ -86,6 +100,9 @@ H5FL_BLK_DEFINE_STATIC(vlen_vl_buf); /* Declare a free list to manage other blocks of VL data */ H5FL_BLK_DEFINE_STATIC(vlen_fl_buf); +/* Define a static "default" dataset structure to use to initialize new datasets */ +static H5D_t H5D_def_dset; + /*------------------------------------------------------------------------- * Function: H5D_init @@ -188,6 +205,7 @@ H5D_init_interface(void) H5O_efl_t efl = H5D_CRT_EXT_FILE_LIST_DEF; H5O_pline_t pline = H5D_CRT_DATA_PIPELINE_DEF; + H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */ size_t nprops; /* Number of properties */ herr_t ret_value = SUCCEED; /* Return value */ @@ -202,7 +220,7 @@ H5D_init_interface(void) assert(H5P_CLS_DATASET_XFER_g!=(-1)); /* Get the pointer to the dataset transfer class */ - if (NULL == (xfer_pclass = H5I_object_verify(H5P_CLS_DATASET_XFER_g, H5I_GENPROP_CLS))) + if (NULL == (xfer_pclass = H5I_object(H5P_CLS_DATASET_XFER_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class"); /* Get the number of properties in the class */ @@ -282,7 +300,7 @@ H5D_init_interface(void) assert(H5P_CLS_DATASET_CREATE_g != -1); /* Get the pointer to the dataset creation class */ - if(NULL == (crt_pclass = H5I_object_verify(H5P_CLS_DATASET_CREATE_g, H5I_GENPROP_CLS))) + if(NULL == (crt_pclass = H5I_object(H5P_CLS_DATASET_CREATE_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class"); /* Get the number of properties in the class */ @@ -331,6 +349,37 @@ H5D_init_interface(void) HGOTO_ERROR (H5E_PLIST, H5E_CANTREGISTER, FAIL, "can't register default property list"); } /* end if */ + /* Reset the "default dataset" information */ + HDmemset(&H5D_def_dset,0,sizeof(H5D_t)); + + /* Get the default dataset cretion property list values and initialize the + * default dataset with them. + */ + if (NULL == (def_dcpl = H5I_object(H5P_LST_DATASET_CREATE_g))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, NULL, "can't get default dataset creation property list"); + + /* Set up the default allocation time information */ + if(H5P_get(def_dcpl, H5D_CRT_ALLOC_TIME_NAME, &H5D_def_dset.alloc_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); + if(H5D_def_dset.alloc_time==H5D_ALLOC_TIME_DEFAULT) + H5D_def_dset.alloc_time=H5D_ALLOC_TIME_LATE; + + /* Get the default external file list information */ + if(H5P_get(def_dcpl, H5D_CRT_EXT_FILE_LIST_NAME, &H5D_def_dset.efl) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list"); + + /* Get the default data storage method */ + if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout.type) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); + + /* Get the default fill value time */ + if (H5P_get(def_dcpl, H5D_CRT_FILL_TIME_NAME, &H5D_def_dset.fill_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time"); + + /* Get the default fill value */ + if (H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.fill) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value"); + done: FUNC_LEAVE(ret_value); } @@ -404,25 +453,21 @@ H5D_crt_copy(hid_t new_plist_id, hid_t old_plist_id, void UNUSED *copy_data) FUNC_ENTER_NOAPI(H5D_crt_copy, FAIL); /* Verify property list ID */ - if (NULL == (new_plist = H5P_object_verify(new_plist_id,H5P_DATASET_CREATE))) + if (NULL == (new_plist = H5I_object(new_plist_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); - if (NULL == (old_plist = H5P_object_verify(old_plist_id,H5P_DATASET_CREATE))) + if (NULL == (old_plist = H5I_object(old_plist_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the fill value, external file list, and data pipeline properties * from the old property list */ - HDmemset(&src_fill,0,sizeof(H5O_fill_t)); if(H5P_get(old_plist, H5D_CRT_FILL_VALUE_NAME, &src_fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value"); - HDmemset(&src_efl,0,sizeof(H5O_efl_t)); if(H5P_get(old_plist, H5D_CRT_EXT_FILE_LIST_NAME, &src_efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file list"); - HDmemset(&src_pline,0,sizeof(H5O_pline_t)); if(H5P_get(old_plist, H5D_CRT_DATA_PIPELINE_NAME, &src_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get pipeline"); /* Make copies of fill value, external file list, and data pipeline */ - HDmemset(&dst_fill,0,sizeof(H5O_fill_t)); if(src_fill.buf && (NULL==H5O_copy(H5O_FILL, &src_fill, &dst_fill))) { HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy fill value"); } @@ -433,7 +478,6 @@ H5D_crt_copy(hid_t new_plist_id, hid_t old_plist_id, void UNUSED *copy_data) HDmemset(&dst_efl,0,sizeof(H5O_efl_t)); if(NULL==H5O_copy(H5O_EFL, &src_efl, &dst_efl)) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy external file list"); - HDmemset(&dst_pline,0,sizeof(H5O_pline_t)); if(NULL==H5O_copy(H5O_PLINE, &src_pline, &dst_pline)) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy data pipeline"); @@ -481,18 +525,15 @@ H5D_crt_close(hid_t dcpl_id, void UNUSED *close_data) FUNC_ENTER_NOAPI(H5D_crt_close, FAIL); /* Check arguments */ - if (NULL == (plist = H5P_object_verify(dcpl_id,H5P_DATASET_CREATE))) + if (NULL == (plist = H5I_object(dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the fill value, external file list, and data pipeline properties * from the old property list */ - HDmemset(&fill,0,sizeof(H5O_fill_t)); if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value"); - HDmemset(&efl,0,sizeof(H5O_efl_t)); if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file list"); - HDmemset(&pline,0,sizeof(H5O_pline_t)); if(H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get pipeline"); @@ -540,7 +581,7 @@ H5D_xfer_create(hid_t dxpl_id, void UNUSED *create_data) FUNC_ENTER_NOAPI(H5D_xfer_create, FAIL); /* Check arguments */ - if (NULL == (plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) + if (NULL == (plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); /* Get the driver information */ @@ -634,7 +675,7 @@ H5D_xfer_close(hid_t dxpl_id, void UNUSED *close_data) FUNC_ENTER_NOAPI(H5D_xfer_close, FAIL); /* Check arguments */ - if (NULL == (plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) + if (NULL == (plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) @@ -717,8 +758,9 @@ H5Dcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); if(H5P_DEFAULT == plist_id) plist_id = H5P_DATASET_CREATE_DEFAULT; - if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_CREATE)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list"); + else + if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_CREATE)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list"); /* build and open the new dataset */ if (NULL == (new_dset = H5D_create(loc, name, type, space, plist_id))) @@ -728,6 +770,10 @@ H5Dcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, if ((ret_value = H5I_register(H5I_DATASET, new_dset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset"); + /* Add the dataset to the list of opened objects in the file */ + if(H5FO_insert(new_dset->ent.file,new_dset->ent.header,ret_value)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "can't insert dataset into list of open objects"); + done: if(ret_value<0) { if(new_dset!=NULL) @@ -762,7 +808,7 @@ hid_t H5Dopen(hid_t loc_id, const char *name) { H5G_entry_t *loc = NULL; /*location holding the dataset */ - H5D_t *dataset = NULL; /*the dataset */ + H5G_entry_t ent; /*dataset symbol table entry */ hid_t ret_value; FUNC_ENTER_API(H5Dopen, FAIL); @@ -774,20 +820,15 @@ H5Dopen(hid_t loc_id, const char *name) if (!name || !*name) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name"); - /* Find the dataset */ - if (NULL == (dataset = H5D_open(loc, name))) - HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "dataset not found"); - - /* Create an atom for the dataset */ - if ((ret_value = H5I_register(H5I_DATASET, dataset)) < 0) + /* Find the dataset object */ + if (H5G_find(loc, name, NULL, &ent) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found"); + + /* Open the dataset */ + if ((ret_value = H5D_open(&ent)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset"); done: - if(ret_value<0) { - if(dataset!=NULL) - H5D_close(dataset); - } /* end if */ - FUNC_LEAVE(ret_value); } @@ -874,7 +915,7 @@ H5Dget_space(hid_t dset_id) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); /* Read the data space message and return a data space object */ - if (NULL==(space=H5D_get_space (dset))) + if (NULL==(space=H5S_copy (dset->space))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get data space"); /* Create an atom */ @@ -892,42 +933,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_get_space - * - * Purpose: Returns the data space associated with the dataset. - * - * Return: Success: Ptr to a copy of the data space. - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -H5S_t * -H5D_get_space(H5D_t *dset) -{ - H5S_t *space; - H5S_t *ret_value; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_get_space, NULL); - assert(dset); - - if (NULL==(space=H5S_read(&(dset->ent)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load space info from dataset header"); - - /* Set return value */ - ret_value=space; - -done: - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- * Function: H5Dget_space_status * * Purpose: Returns the status of data space allocation. @@ -981,7 +986,7 @@ done: */ static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation) { - H5S_t *space=NULL; /* Dataset's dataspace */ + 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 */ @@ -990,9 +995,11 @@ static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation) FUNC_ENTER_NOINIT(H5D_get_space_status); + assert(dset); + /* Get the dataset's dataspace */ - if((space=H5D_get_space(dset))==NULL) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get dataspace"); + space=dset->space; + assert(space); /* Get the total number of elements in dataset's dataspace */ if((total_elem=H5S_get_simple_extent_npoints(space))<0) @@ -1022,8 +1029,6 @@ static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation) } /* end else */ done: - if(space) - H5S_close(space); FUNC_LEAVE(ret_value); } @@ -1247,9 +1252,9 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; - - if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); + else + if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); @@ -1338,9 +1343,9 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; - - if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); + else + if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); @@ -1416,8 +1421,8 @@ done: * *------------------------------------------------------------------------- */ -H5D_t * -H5D_new(hid_t dcpl_id) +static H5D_t * +H5D_new(hid_t dcpl_id, hbool_t creating) { H5P_genplist_t *plist; /* Property list created */ H5D_t *new_dset = NULL; /* New dataset object */ @@ -1425,16 +1430,31 @@ H5D_new(hid_t dcpl_id) FUNC_ENTER_NOAPI(H5D_new, NULL); - if (NULL==(new_dset = H5FL_ALLOC(H5D_t,1))) + if (NULL==(new_dset = H5FL_MALLOC(H5D_t))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); - if(H5P_DEFAULT == dcpl_id) - dcpl_id = H5P_DATASET_CREATE_DEFAULT; - /* Get the property list */ - if (NULL == (plist = H5P_object_verify(dcpl_id,H5P_DATASET_CREATE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list"); + /* If we are using the default dataset creation property list, during creation + * don't bother to copy it, just increment the reference count + */ + if(creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) { + /* Copy the default dataset information */ + HDmemcpy(new_dset,&H5D_def_dset,sizeof(H5D_t)); + + if(H5I_inc_ref(dcpl_id)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINC, NULL, "Can't increment default DCPL ID"); + new_dset->dcpl_id = dcpl_id; + } /* end if */ + else { + /* Reset the dataset information */ + HDmemset(new_dset,0,sizeof(H5D_t)); + + /* Get the property list */ + if (NULL == (plist = H5I_object(dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list"); + + new_dset->dcpl_id = H5P_copy_plist(plist); + } /* end else */ - new_dset->dcpl_id = H5P_copy_plist(plist); new_dset->ent.header = HADDR_UNDEF; /* Set return value */ @@ -1442,8 +1462,11 @@ H5D_new(hid_t dcpl_id) done: if(ret_value==NULL) { - if(new_dset!=NULL) + if(new_dset!=NULL) { + if(new_dset->dcpl_id!=0) + H5I_dec_ref(new_dset->dcpl_id); H5FL_FREE(H5D_t,new_dset); + } /* end if */ } /* end if */ FUNC_LEAVE(ret_value); @@ -1451,7 +1474,7 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_update_entry_cache + * Function: H5D_update_entry_info * * Purpose: Create and fill an H5G_entry_t object for insertion into * the group LOC. @@ -1471,72 +1494,86 @@ done: * *------------------------------------------------------------------------- */ -herr_t -H5D_update_entry_cache(H5F_t *file, H5G_entry_t *ent, H5G_entry_t *loc, - const char *name, const H5S_t *space, - H5P_genplist_t *plist, H5O_layout_t *layout, H5T_t *type, - hbool_t allocate_header, haddr_t header) +static herr_t +H5D_update_entry_info(H5F_t *file, H5D_t *dset, H5P_genplist_t *plist) { - H5O_pline_t dcpl_pline; - H5D_alloc_time_t alloc_time; size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ + H5G_entry_t *ent=NULL; /* Dataset's group entry */ + H5O_layout_t *layout; /* Dataset's layout information */ + H5T_t *type; /* Dataset's datatype */ + H5S_t *space; /* Dataset's dataspace */ + H5D_alloc_time_t alloc_time;/* Dataset's allocation time */ + H5O_efl_t *efl; /* Dataset's external file list */ /* fill value variables */ H5D_fill_time_t fill_time; - H5O_fill_t fill_prop = { NULL, 0, NULL }; + H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ H5O_fill_new_t fill = { NULL, 0, NULL, H5D_ALLOC_TIME_LATE, H5D_FILL_TIME_ALLOC, TRUE }; H5D_fill_value_t fill_status; + H5O_t *oh=NULL; /* Pointer to dataset's object header */ + /* return code */ herr_t ret_value = SUCCEED; - FUNC_ENTER_NOAPI(H5D_update_entry_cache, FAIL); + FUNC_ENTER_NOAPI(H5D_update_entry_info, FAIL); + + /* Sanity checking */ + assert(file); + assert(dset); + /* Pick up former parameters */ + ent=&dset->ent; + layout=&dset->layout; + type=dset->type; + space=dset->space; + alloc_time=dset->alloc_time; + efl=&dset->efl; + + /* 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->size; - /* If TRUE, then allocate the space in the file for the header */ - if (allocate_header) { - /* Create (open for write access) an object header */ - if (H5O_create(file, ohdr_size, ent) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to create dataset object header"); - } else { - /* - * Just initialize the header to the specified address and open - * it for us - */ - HDmemset(ent, 0, sizeof(H5G_entry_t)); + /* Create (open for write access) an object header */ + if (H5O_create(file, ohdr_size, ent) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header"); - if (H5O_init(file, ohdr_size, ent, header) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to initialize dataset object header"); - } + /* Get a pointer to the object header itself */ + if((oh=H5O_protect(ent))==NULL) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to protect dataset object header"); - /* - * Retrieve properties of fill value and others. Copy them into new fill - * value struct. Convert the fill value to the dataset type and write - * the message - */ - if (H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); + /* Point at dataset's copy, to cache it for later */ + fill_prop=&dset->fill; + fill_time=dset->fill_time; - if (H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time"); + /* Check if dataset has non-default creation property list */ + if(dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT) { + /* + * Retrieve properties of fill value and others. Copy them into new fill + * value struct. Convert the fill value to the dataset type and write + * the message + */ + if (H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time"); + dset->fill_time=fill_time; /* Cache this for later */ - if (H5P_fill_value_defined(plist, &fill_status) < 0) + if(fill_time==H5D_FILL_TIME_NEVER && H5T_detect_class(type, H5T_VLEN)) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined"); + + /* Get the fill value information from the property list */ + if (H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value"); + } /* end if */ + + if (H5P_is_fill_value_defined(fill_prop, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined"); if (fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { - if (H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value"); - - if (H5O_copy(H5O_FILL, &fill_prop, &fill) == NULL) + if (H5O_copy(H5O_FILL, fill_prop, &fill) == NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,FAIL, "unable to copy fill value"); - if (fill_prop.buf && fill_prop.size > 0 && H5O_fill_convert(&fill, type) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to convert fill value to dataset type"); + if (fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(&fill, type) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type"); fill.fill_defined = TRUE; } else if (fill_status == H5D_FILL_VALUE_UNDEFINED) { @@ -1544,8 +1581,7 @@ H5D_update_entry_cache(H5F_t *file, H5G_entry_t *ent, H5G_entry_t *loc, fill.type = fill.buf = NULL; fill.fill_defined = FALSE; } else { - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, - "unable to determine if fill value is defined"); + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine if fill value is defined"); } fill.alloc_time = alloc_time; @@ -1555,79 +1591,51 @@ H5D_update_entry_cache(H5F_t *file, H5G_entry_t *ent, H5G_entry_t *loc, HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,FAIL, "unable to create dataset"); /* Write new fill value message */ - if (H5O_modify(ent, H5O_FILL_NEW, 0, H5O_FLAG_CONSTANT, &fill) < 0) + if (H5O_append(file, oh, H5O_FILL_NEW, H5O_FLAG_CONSTANT, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update fill value header message"); - H5O_reset(H5O_FILL, &fill_prop); - if (fill.buf && H5O_copy(H5O_FILL, &fill, &fill_prop) == NULL) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,FAIL,"unable to copy fill value"); + /* If there is valid information for the old fill value struct, update it */ + if (fill.buf) { + /* Clear any previous values */ + H5O_reset(H5O_FILL, fill_prop); - H5O_reset(H5O_FILL_NEW, &fill); + /* Copy new fill value information to old fill value struct */ + if(H5O_copy(H5O_FILL, &fill, fill_prop) == NULL) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,FAIL,"unable to copy fill value"); - /* Write old fill value */ - if (fill_prop.buf && H5O_modify(ent, H5O_FILL, 0, H5O_FLAG_CONSTANT, &fill_prop) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to update fill value header message"); + /* Write old fill value */ + if (fill_prop->buf && H5O_append(file, oh, H5O_FILL, H5O_FLAG_CONSTANT, fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update fill value header message"); - if (H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value"); + /* Update dataset creation property */ + if (H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value"); + } /* end if */ /* Update the type and space header messages */ - if (H5O_modify(ent, H5O_DTYPE, 0, H5O_FLAG_CONSTANT | H5O_FLAG_SHARED, type) < 0 || - H5S_modify(ent, space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to update type or space header messages"); + if (H5O_append(file, oh, H5O_DTYPE, H5O_FLAG_CONSTANT | H5O_FLAG_SHARED, type) < 0 || + H5S_append(file, oh, space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update type or space header messages"); - /* Update the filters message */ - if (H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &dcpl_pline) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve pipeline filter"); - - if (dcpl_pline.nfilters > 0 && - H5O_modify(ent, H5O_PLINE, 0, H5O_FLAG_CONSTANT, &dcpl_pline) < 0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message"); - - /* Add a modification time message. */ - if (H5O_touch(ent, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to update modification time message"); - - /* Give the dataset a name */ - if (H5G_insert(loc, name, ent) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to name dataset"); + /* Update the filters message, if this is a chunked dataset */ + if(layout->type==H5D_CHUNKED) { + H5O_pline_t pline; /* Chunked data I/O pipeline info */ -done: - FUNC_LEAVE(ret_value); -} + if (H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve pipeline filter"); - -/*------------------------------------------------------------------------- - * Function: H5D_update_external_storage_cache - * - * Purpose: Update the external cache if the dataset uses external - * files. - * - * This code was originally found at the end of H5D_create() - * but was placed here for general use. - * - * Return: Success: SUCCEED - * Failure: FAIL - * - * Errors: - * - * Programmer: Bill Wendling - * Thursday, October 31, 2002 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_update_external_storage_cache(H5F_t *file, H5G_entry_t *ent, - H5O_efl_t *efl, H5O_layout_t *layout) -{ - herr_t ret_value = SUCCEED; + if (pline.nfilters > 0 && + H5O_append(file, oh, H5O_PLINE, H5O_FLAG_CONSTANT, &pline) < 0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message"); + } /* end if */ - FUNC_ENTER_NOAPI(H5D_update_external_storage_cache, FAIL); + /* + * Allocate storage if space allocate time is early; otherwise delay + * allocation until later. + */ + if (alloc_time == H5D_ALLOC_TIME_EARLY) + if (H5D_alloc_storage(file, dset, H5D_ALLOC_CREATE, FALSE, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); /* Update external storage message */ if (efl->nused > 0) { @@ -1639,13 +1647,11 @@ H5D_update_external_storage_cache(H5F_t *file, H5G_entry_t *ent, if (H5HL_create(file, heap_size, &efl->heap_addr/*out*/) < 0 || H5HL_insert(file, efl->heap_addr, 1, "") == (size_t)(-1)) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to create external file list name heap"); + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create external file list name heap"); for (i = 0; i < efl->nused; ++i) { size_t offset = H5HL_insert(file, efl->heap_addr, - HDstrlen(efl->slot[i].name) + 1, - efl->slot[i].name); + HDstrlen(efl->slot[i].name) + 1, efl->slot[i].name); assert(0 == efl->slot[i].name_offset); @@ -1655,16 +1661,26 @@ H5D_update_external_storage_cache(H5F_t *file, H5G_entry_t *ent, efl->slot[i].name_offset = offset; } - if (H5O_modify(ent, H5O_EFL, 0, H5O_FLAG_CONSTANT, efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to update external file list message"); + if (H5O_append(file, oh, H5O_EFL, H5O_FLAG_CONSTANT, efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message"); } /* Update layout message */ - if (H5D_COMPACT != layout->type && H5O_modify(ent, H5O_LAYOUT, 0, 0, layout) < 0) + /* (Don't make layout message constant yet, since space may not be allocated) */ + /* Note: this is relying on H5D_alloc_storage not calling H5O_modify during dataset creation */ + if (H5D_COMPACT != layout->type && H5O_append(file, oh, H5O_LAYOUT, 0, layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout"); + /* Add a modification time message. */ + if (H5O_touch_oh(file, oh, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message"); + done: + /* Release pointer to object header itself */ + if(ent!=NULL && oh!=NULL) + if(H5O_unprotect(ent,oh)<0) + HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to unprotect dataset object header"); + FUNC_LEAVE(ret_value); } @@ -1726,7 +1742,7 @@ done: * *------------------------------------------------------------------------- */ -H5D_t * +static H5D_t * H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, const H5S_t *space, hid_t dcpl_id) { @@ -1736,16 +1752,10 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, hsize_t comp_data_size; unsigned u; hsize_t max_dim[H5O_LAYOUT_NDIMS]={0}; - H5O_efl_t efl; - H5F_t *f = NULL; - H5O_pline_t dcpl_pline; - H5D_layout_t dcpl_layout; + H5F_t *file; int chunk_ndims = 0; hsize_t chunk_size[32]={0}; - H5D_alloc_time_t alloc_time; - H5D_fill_time_t fill_time; - H5P_genplist_t *plist; /* Property list */ - H5P_genplist_t *new_plist; /* New Property list */ + H5P_genplist_t *new_plist=NULL; /* New Property list */ FUNC_ENTER_NOAPI(H5D_create, NULL); @@ -1755,97 +1765,105 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, assert (type); assert (space); - /* Get property list object */ - if (NULL == (plist = H5P_object_verify(dcpl_id,H5P_DATASET_CREATE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); - - if(H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &dcpl_pline) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter"); - if(H5P_get(plist, H5D_CRT_LAYOUT_NAME, &dcpl_layout) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); - if(dcpl_pline.nfilters > 0 && H5D_CHUNKED != dcpl_layout) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout"); - if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); - - /* Check if the alloc_time is the default and set it accordingly */ - if(alloc_time==H5D_ALLOC_TIME_DEFAULT) { - switch(dcpl_layout) { - case H5D_COMPACT: - alloc_time=H5D_ALLOC_TIME_EARLY; - break; - - case H5D_CONTIGUOUS: - alloc_time=H5D_ALLOC_TIME_LATE; - break; - - case H5D_CHUNKED: - alloc_time=H5D_ALLOC_TIME_INCR; - break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); - } /* end switch */ - } /* end if */ - - /* Don't allow compact datasets to allocate space later */ - if(dcpl_layout==H5D_COMPACT && alloc_time!=H5D_ALLOC_TIME_EARLY) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset doesn't support late space allocation"); - - /* What file is the dataset being added to? */ - if (NULL==(f=H5G_insertion_file(loc, name))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to locate insertion point"); - - /* If MPIO or MPIPOSIX is used, no filter support yet. */ - if((IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) && dcpl_pline.nfilters > 0) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet"); - - /* Check if this dataset is going into a parallel file and set space allocation time */ - if(IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) - alloc_time=H5D_ALLOC_TIME_EARLY; - - if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill time"); - - if(fill_time==H5D_FILL_TIME_NEVER && H5T_detect_class(type, H5T_VLEN)) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Dataset doesn't support VL datatype when fill value is not defined"); - - /* Initialize the dataset object */ - if(NULL == (new_dset = H5D_new(dcpl_id))) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); - /* Check if the datatype is "sensible" for use in a dataset */ if(H5T_is_sensible(type)!=TRUE) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible"); + /* Initialize the dataset object */ + if(NULL == (new_dset = H5D_new(dcpl_id,TRUE))) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); + /* Copy datatype for dataset */ if((new_dset->type = H5T_copy(type, H5T_COPY_ALL))==NULL) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, NULL, "can't copy datatype"); + /* What file is the dataset being added to? */ + if (NULL==(file=H5G_insertion_file(loc, name))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to locate insertion point"); + /* Mark any VL datatypes as being on disk now */ - if (H5T_vlen_mark(new_dset->type, f, H5T_VLEN_DISK)<0) + if (H5T_vlen_mark(new_dset->type, file, H5T_VLEN_DISK)<0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid VL location"); - /* Get new dataset's property list object */ - if (NULL == (new_plist = H5I_object(new_dset->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); + /* Copy dataspace for dataset */ + if((new_dset->space = H5S_copy(space))==NULL) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, NULL, "can't copy dataspace"); + + /* Set the dataset's dataspace to 'all' selection */ + if(H5S_select_all(new_dset->space,1)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSET, NULL, "unable to set all selection"); + + /* Check if the dataset has a non-default DCPL & get important values, if so */ + if(new_dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT) { + H5D_layout_t dcpl_layout; /* Dataset's layout information */ + H5O_pline_t dcpl_pline; /* Dataset's I/O pipeline information */ + H5D_alloc_time_t alloc_time; /* Dataset's allocation time */ + + /* Get new dataset's property list object */ + if (NULL == (new_plist = H5I_object(new_dset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); + + if(H5P_get(new_plist, H5D_CRT_DATA_PIPELINE_NAME, &dcpl_pline) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter"); + if(H5P_get(new_plist, H5D_CRT_LAYOUT_NAME, &dcpl_layout) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); + if(dcpl_pline.nfilters > 0 && H5D_CHUNKED != dcpl_layout) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout"); + if(H5P_get(new_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); + + /* Check if the alloc_time is the default and set it accordingly */ + if(alloc_time==H5D_ALLOC_TIME_DEFAULT) { + switch(dcpl_layout) { + case H5D_COMPACT: + alloc_time=H5D_ALLOC_TIME_EARLY; + break; + + case H5D_CONTIGUOUS: + alloc_time=H5D_ALLOC_TIME_LATE; + break; + + case H5D_CHUNKED: + alloc_time=H5D_ALLOC_TIME_INCR; + break; + + default: + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); + } /* end switch */ + } /* end if */ - /* Set the alloc_time for the dataset, in case the default was used */ - if(H5P_set(new_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, NULL, "can't set allocation time"); + /* Don't allow compact datasets to allocate space later */ + if(dcpl_layout==H5D_COMPACT && alloc_time!=H5D_ALLOC_TIME_EARLY) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset doesn't support late space allocation"); - if(H5P_get(new_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); + /* Set the alloc_time for the dataset, in case the default was used */ + new_dset->alloc_time=alloc_time; + + /* If MPIO or MPIPOSIX is used, no filter support yet. */ + if((IS_H5FD_MPIO(file) || IS_H5FD_MPIPOSIX(file)) && dcpl_pline.nfilters > 0) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet"); + + /* Chunked datasets are non-default, so retrieve their info here */ + if(H5P_get(new_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); - if(H5P_get(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list"); + /* Get the dataset's external file list information */ + if(H5P_get(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->efl) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list"); - /* Total raw data size */ - if(H5P_get(new_plist, H5D_CRT_LAYOUT_NAME, &(new_dset->layout.type)) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); - new_dset->layout.ndims = H5S_get_simple_extent_ndims(space) + 1; + /* Get the dataset's data storage method */ + if(H5P_get(new_plist, H5D_CRT_LAYOUT_NAME, &(new_dset->layout.type)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); + } /* end if */ + + /* Check if this dataset is going into a parallel file and set space allocation time */ + if(IS_H5FD_MPIO(file) || IS_H5FD_MPIPOSIX(file)) + new_dset->alloc_time=H5D_ALLOC_TIME_EARLY; + + /* Set up layout information */ + new_dset->layout.ndims = H5S_get_simple_extent_ndims(new_dset->space) + 1; assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim)); - new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type); + new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type); new_dset->layout.addr = HADDR_UNDEF; /* Initialize to no address */ switch (new_dset->layout.type) { @@ -1855,15 +1873,15 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, * Also, only the slowest varying dimension of a simple data space * can be extendible. */ - if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim, max_dim))<0) + if ((ndims=H5S_get_simple_extent_dims(new_dset->space, new_dset->layout.dim, max_dim))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage"); for (i=1; i<ndims; i++) { if (max_dim[i]>new_dset->layout.dim[i]) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible"); } - if (efl.nused>0) { - hsize_t max_points = H5S_get_npoints_max (space); - hsize_t max_storage = H5O_efl_total_size (&efl); + if (new_dset->efl.nused>0) { + hsize_t max_points = H5S_get_npoints_max (new_dset->space); + hsize_t max_storage = H5O_efl_total_size (&new_dset->efl); if (H5S_UNLIMITED==max_points) { if (H5O_EFL_UNLIMITED!=max_storage) @@ -1883,9 +1901,9 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, * Chunked storage allows any type of data space extension, so we * don't even bother checking. */ - if(chunk_ndims != H5S_get_simple_extent_ndims(space)) + if(chunk_ndims != H5S_get_simple_extent_ndims(new_dset->space)) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space"); - if (efl.nused>0) + if (new_dset->efl.nused>0) HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout"); /* @@ -1895,7 +1913,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, if(H5P_get(new_plist, H5D_CRT_CHUNK_SIZE_NAME, chunk_size) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size"); - if (H5S_get_simple_extent_dims(space, NULL, max_dim)<0) + if (H5S_get_simple_extent_dims(new_dset->space, NULL, max_dim)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions"); for (u=0; u<new_dset->layout.ndims-1; u++) { if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < chunk_size[u]) @@ -1917,7 +1935,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, /* Verify data size is smaller than maximum header message size * (64KB) minus other layout message fields. */ - comp_data_size=H5O_MAX_SIZE-H5O_layout_meta_size(f, &(new_dset->layout)); + comp_data_size=H5O_MAX_SIZE-H5O_layout_meta_size(file, &(new_dset->layout)); if(new_dset->layout.size > comp_data_size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size"); if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim, max_dim))<0) @@ -1931,38 +1949,32 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, } /* end switch */ /* - * Update the entry cache. That is, create and add a new - * "H5G_entry_t" object to the group this dataset is being initially - * created in. + * Update the dataset's entry info. */ - if (H5D_update_entry_cache(f, &new_dset->ent, loc, name, space, new_plist, - &new_dset->layout, new_dset->type, TRUE, (haddr_t)0) != SUCCEED) + if (H5D_update_entry_info(file, new_dset, new_plist) != SUCCEED) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache"); - /* - * Allocate storage if space allocate time is early; otherwise delay - * allocation until later. + /* + * Give the dataset a name. That is, create and add a new + * "H5G_entry_t" object to the group this dataset is being initially + * created in. */ - if (H5P_get(new_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); - - if (alloc_time == H5D_ALLOC_TIME_EARLY) - if (H5D_alloc_storage(f, new_dset, H5D_ALLOC_CREATE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); - - /* Update the external storage cache if this is an external object */ - if (H5D_update_external_storage_cache(f, &new_dset->ent, &efl, &new_dset->layout) != SUCCEED) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the external metadata cache"); + if (H5G_insert(loc, name, &new_dset->ent) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset"); /* Success */ ret_value = new_dset; done: if (!ret_value && new_dset) { + if (new_dset->space) + H5S_close(new_dset->space); if (new_dset->type) H5T_close(new_dset->type); if (H5F_addr_defined(new_dset->ent.header)) H5O_close(&(new_dset->ent)); + if(new_dset->dcpl_id!=0) + H5I_dec_ref(new_dset->dcpl_id); new_dset->ent.file = NULL; H5FL_FREE(H5D_t,new_dset); } @@ -2024,53 +2036,59 @@ done: *------------------------------------------------------------------------- * Function: H5D_open * - * Purpose: Finds a dataset named NAME in file F and builds a descriptor - * for it, opening it for access. - * - * Return: Success: Pointer to a new dataset descriptor. + * Purpose: Checks if dataset is already open, or opens a dataset for + * access. * - * Failure: NULL + * Return: Success: Dataset ID + * Failure: FAIL * * Errors: * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 + * Programmer: Quincey Koziol + * Friday, December 20, 2002 * * Modifications: - * Robb Matzke, 9 Jun 1998 - * The data space message is no longer cached in the dataset struct. - * - * Quincey Koziol, 12 Oct 1998 - * Moved guts of function into H5D_open_oid - * - * Pedro Vicente, <pvn@ncsa.uiuc.edu> 18 Sep 2002 - * Added `id to name' support. * *------------------------------------------------------------------------- */ -H5D_t * -H5D_open(H5G_entry_t *loc, const char *name) +hid_t +H5D_open(H5G_entry_t *ent) { - H5D_t *dataset = NULL; /*the dataset which was found */ - H5D_t *ret_value = NULL; /*return value */ - H5G_entry_t ent; /*dataset symbol table entry */ + hid_t ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_open, NULL); /* check args */ - assert (loc); - assert (name && *name); + assert (ent); - /* Find the dataset object */ - if (H5G_find(loc, name, NULL, &ent) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found"); + /* Check if dataset was already open */ + if((ret_value=H5FO_opened(ent->file,ent->header))<0) { + H5D_t *dataset; /*the dataset which was found */ - /* Open the dataset object */ - if ((dataset=H5D_open_oid(&ent)) ==NULL) - HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found"); + H5E_clear(); - /* Success */ - ret_value = dataset; + /* Open the dataset object */ + if ((dataset=H5D_open_oid(ent)) ==NULL) + HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found"); + + /* Create an atom for the dataset */ + if ((ret_value = H5I_register(H5I_DATASET, dataset)) < 0) { + H5D_close(dataset); + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset"); + } /* end if */ + + /* Add the dataset to the list of opened objects in the file */ + if(H5FO_insert(ent->file,ent->header,ret_value)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "can't insert dataset into list of open objects"); + } /* end if */ + else { + /* Dataset is already open, increment the reference count on the ID */ + if(H5I_inc_ref(ret_value)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment dataset ID"); + + /* Release the dataset entry we located earlier */ + H5G_free_ent_name(ent); + } /* end else */ done: FUNC_LEAVE(ret_value); @@ -2104,15 +2122,14 @@ done: * *------------------------------------------------------------------------- */ -H5D_t * +static H5D_t * H5D_open_oid(H5G_entry_t *ent) { H5D_t *dataset = NULL; /*new dataset struct */ H5D_t *ret_value = NULL; /*return value */ H5O_fill_new_t fill = {NULL, 0, NULL, H5D_ALLOC_TIME_LATE, H5D_FILL_TIME_ALLOC, TRUE}; - H5O_fill_t fill_prop = {NULL, 0, NULL}; + H5O_fill_t *fill_prop; /* Pointer to dataset's fill value area */ H5O_pline_t pline; /* I/O pipeline information */ - H5O_efl_t efl; /* External file information */ H5D_layout_t layout; /* Dataset layout */ int chunk_ndims; H5P_genplist_t *plist; /* Property list */ @@ -2123,7 +2140,7 @@ H5D_open_oid(H5G_entry_t *ent) assert (ent); /* Allocate the dataset structure */ - if(NULL==(dataset = H5D_new(H5P_DEFAULT))) + if(NULL==(dataset = H5D_new(H5P_DATASET_CREATE_DEFAULT,FALSE))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); /* Shallow copy (take ownership) of the group entry object */ @@ -2137,12 +2154,14 @@ H5D_open_oid(H5G_entry_t *ent) if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load type info from dataset header"); + if (NULL==(dataset->space=H5S_read(&(dataset->ent)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load space info from dataset header"); + /* Get dataset creation property list object */ if (NULL == (plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); /* Get the optional filters message */ - HDmemset(&pline,0,sizeof(H5O_pline_t)); if(NULL == H5O_read(&(dataset->ent), H5O_PLINE, 0, &pline)) { H5E_clear(); HDmemset(&pline, 0, sizeof(pline)); @@ -2195,10 +2214,13 @@ H5D_open_oid(H5G_entry_t *ent) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ + /* Point at dataset's copy, to cache it for later */ + fill_prop=&dataset->fill; + /* Retrieve & release the previous fill-value settings */ - if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) + if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't get fill value"); - H5O_reset(H5O_FILL, &fill_prop); + H5O_reset(H5O_FILL, fill_prop); /* Get the new fill value message */ if(NULL == H5O_read(&(dataset->ent), H5O_FILL_NEW, 0, &fill)) { @@ -2224,35 +2246,37 @@ H5D_open_oid(H5G_entry_t *ent) } /* end switch */ } /* end if */ if(fill.fill_defined) { - if(NULL==H5O_copy(H5O_FILL, &fill, &fill_prop)) + if(NULL==H5O_copy(H5O_FILL, &fill, fill_prop)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy fill value"); } else { /* For compatibility with v1.4. Retrieve the old fill value message. * If size is 0, make it -1 for undefined. */ - if(NULL == H5O_read(&(dataset->ent), H5O_FILL, 0, &fill_prop)) { + if(NULL == H5O_read(&(dataset->ent), H5O_FILL, 0, fill_prop)) { H5E_clear(); - HDmemset(&fill_prop, 0, sizeof(fill_prop)); + HDmemset(fill_prop, 0, sizeof(H5O_fill_t)); } - if(fill_prop.size == 0) { - fill_prop.type = fill_prop.buf = NULL; - fill_prop.size = (size_t)-1; + if(fill_prop->size == 0) { + fill_prop->type = fill_prop->buf = NULL; + fill_prop->size = (size_t)-1; } } /* end else */ - /* Set fill value properties */ - if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) + /* Set revised fill value properties */ + if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); + dataset->alloc_time=fill.alloc_time; /* Cache this for later */ if(H5P_set(plist, H5D_CRT_ALLOC_TIME_NAME, &fill.alloc_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); + dataset->fill_time=fill.fill_time; /* Cache this for later */ if(H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill.fill_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); /* Get the external file list message, which might not exist. Space is * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */ if( !H5F_addr_defined(dataset->layout.addr)) { - HDmemset(&efl,0,sizeof(H5O_efl_t)); - if(NULL != H5O_read(&(dataset->ent), H5O_EFL, 0, &efl)) - if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) + HDmemset(&dataset->efl,0,sizeof(H5O_efl_t)); + if(NULL != H5O_read(&(dataset->ent), H5O_EFL, 0, &dataset->efl)) + if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set external file list"); } /* @@ -2263,7 +2287,7 @@ H5D_open_oid(H5G_entry_t *ent) if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) && (dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) && (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file))) { - if (H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_OPEN)<0) + if (H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_OPEN, TRUE, FALSE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize file storage"); } @@ -2274,6 +2298,8 @@ done: if (ret_value==NULL && dataset) { if (H5F_addr_defined(dataset->ent.header)) H5O_close(&(dataset->ent)); + if (dataset->space) + H5S_close(dataset->space); if (dataset->type) H5T_close(dataset->type); dataset->ent.file = NULL; @@ -2317,19 +2343,23 @@ H5D_close(H5D_t *dataset) assert(dataset && dataset->ent.file); /* - * Release data type and creation property list -- there isn't much we - * can do if one of these fails, so we just continue. + * 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 = (H5T_close(dataset->type) < 0 || + free_failed=(H5T_close(dataset->type)<0 || H5S_close(dataset->space)<0 || H5I_dec_ref(dataset->dcpl_id) < 0); /* Update header message of layout for compact dataset. */ if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) { - if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, &(dataset->layout))<0) + if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, 1, &(dataset->layout))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); dataset->layout.dirty = FALSE; } /* end if */ + /* Remove the dataset from the list of opened objects in the file */ + if(H5FO_delete(dataset->ent.file,dataset->ent.header)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects"); + /* Close the dataset object */ H5O_close(&(dataset->ent)); @@ -2400,7 +2430,7 @@ done: * *------------------------------------------------------------------------- */ -herr_t +static herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/) { @@ -2413,8 +2443,11 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ H5S_conv_t *sconv=NULL; /*space conversion funcs*/ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ + hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ + hbool_t bkg_iter_init=0; /*background iteration info has been initialized */ H5S_sel_iter_t file_iter; /*file selection iteration info*/ + hbool_t file_iter_init=0; /*file selection iteration info has been initialized */ herr_t ret_value = SUCCEED; /*return value */ herr_t status; /*function return status*/ size_t src_type_size; /*size of source type */ @@ -2422,7 +2455,6 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ H5T_bkg_t need_bkg; /*type of background buf*/ - H5S_t *free_this_space=NULL; /*data space to free */ #ifdef H5_HAVE_PARALLEL H5FD_mpio_dxpl_t *dx = NULL; H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ @@ -2432,10 +2464,6 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_t timer; #endif - H5O_efl_t efl; /* External File List info */ - H5O_fill_t fill; /* Fill value info */ - H5D_fill_time_t fill_time; /* When to write the fill values */ - H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ unsigned sconv_flags=0; /* Flags for the space conversion */ @@ -2447,24 +2475,16 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, assert(mem_type); assert(buf); - /* Initialize these before any errors can occur */ - HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t)); - HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t)); - HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t)); - /* Get the dataset's creation property list */ if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the dataset transfer property list */ - if (NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) + if (NULL == (dx_plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); - if (!file_space) { - if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); - file_space = free_this_space; - } /* end if */ + if (!file_space) + file_space = dataset->space; if (!mem_space) mem_space = file_space; nelmts = (*mem_space->select.get_npoints)(mem_space); @@ -2500,15 +2520,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); /* Retrieve dataset properties */ - if(H5P_fill_value_defined(dc_plist, &fill_status)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined"); - if((fill_status==H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED) - && H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill value"); - if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill time"); - if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); + /* <none needed in the general case> */ /* If space hasn't been allocated and not using external storage, * return fill value to buffer if fill time is upon allocation, or @@ -2516,8 +2528,20 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, * fill time is NEVER, there is no way to tell whether part of data * has been overwritten. So just proceed in reading. */ - if(nelmts > 0 && efl.nused==0 && dataset->layout.type!=H5D_COMPACT + if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { + H5O_fill_t fill; /* Fill value info */ + H5D_fill_time_t fill_time; /* When to write the fill values */ + H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ + + /* Retrieve dataset's fill-value properties */ + if(H5P_fill_value_defined(dc_plist, &fill_status)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined"); + if((fill_status==H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED) + && H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill value"); + if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill time"); /* Should be impossible, but check anyway... */ if(fill_status == H5D_FILL_VALUE_UNDEFINED && fill_time == H5D_FILL_TIME_ALLOC) @@ -2581,10 +2605,10 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ - assert(dataset->layout.addr!=HADDR_UNDEF || efl.nused>0 || dataset->layout.type==H5D_COMPACT); + assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); status = (sconv->read)(dataset->ent.file, &(dataset->layout), - dc_plist, H5T_get_size(dataset->type), - file_space, mem_space, dxpl_id, buf/*out*/); + dc_plist, &(dataset->efl), H5T_get_size(dataset->type), + file_space, mem_space, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].read_timer), &timer); sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type); @@ -2636,10 +2660,13 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* Figure out the strip mine size. */ if ((*file_space->select.iter_init)(file_space, src_type_size, &file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); + file_iter_init=1; /*file selection iteration info has been initialized */ if ((*mem_space->select.iter_init)(mem_space, dst_type_size, &mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); + mem_iter_init=1; /*file selection iteration info has been initialized */ if ((*mem_space->select.iter_init)(mem_space, dst_type_size, &bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); + bkg_iter_init=1; /*file selection iteration info has been initialized */ /* Sanity check elements in temporary buffer */ if (request_nelmts<=0) @@ -2662,13 +2689,13 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ - if((tconv_buf=H5FL_BLK_ALLOC(type_conv,target_size,0))==NULL) + if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); - if((bkg_buf=H5FL_BLK_ALLOC(type_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL) + if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ @@ -2687,9 +2714,9 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_timer_begin(&timer); #endif /* Sanity check that space is allocated, then read data from it */ - assert(dataset->layout.addr!=HADDR_UNDEF || efl.nused > 0); + assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused > 0); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), - dc_plist, src_type_size, file_space, + dc_plist, &(dataset->efl), src_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG @@ -2753,9 +2780,12 @@ done: } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Release selection iterators */ - (*file_space->select.iter_release)(&file_iter); - (*mem_space->select.iter_release)(&mem_iter); - (*mem_space->select.iter_release)(&bkg_iter); + if(file_iter_init) + (*file_space->select.iter_release)(&file_iter); + if(mem_iter_init) + (*mem_space->select.iter_release)(&mem_iter); + if(bkg_iter_init) + (*mem_space->select.iter_release)(&bkg_iter); if (src_id >= 0) H5I_dec_ref(src_id); @@ -2766,8 +2796,6 @@ done: H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); - if (free_this_space) - H5S_close(free_this_space); FUNC_LEAVE(ret_value); } /* end H5D_read() */ @@ -2816,7 +2844,7 @@ done: * *------------------------------------------------------------------------- */ -herr_t +static herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dxpl_id, const void *buf) { @@ -2829,8 +2857,11 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ H5S_conv_t *sconv=NULL; /*space conversion funcs*/ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ + hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ + hbool_t bkg_iter_init=0; /*background iteration info has been initialized */ H5S_sel_iter_t file_iter; /*file selection iteration info*/ + hbool_t file_iter_init=0; /*file selection iteration info has been initialized */ herr_t ret_value = SUCCEED; /*return value */ herr_t status; /*function return status*/ size_t src_type_size; /*size of source type */ @@ -2838,7 +2869,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ H5T_bkg_t need_bkg; /*type of background buf*/ - H5S_t *free_this_space=NULL; /*data space to free */ #ifdef H5_HAVE_PARALLEL H5FD_mpio_dxpl_t *dx = NULL; H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ @@ -2848,10 +2878,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_t timer; #endif - H5O_efl_t efl; /* External File List info */ - H5O_fill_t fill; /* Fill value info */ - H5D_fill_time_t fill_time; /* When to write the fill values */ - H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ unsigned sconv_flags=0; /* Flags for the space conversion */ @@ -2863,24 +2889,16 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, assert(mem_type); assert(buf); - /* Initialize these before any errors can occur */ - HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t)); - HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t)); - HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t)); - /* Get the dataset's creation property list */ if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the dataset transfer property list */ - if (NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) + if (NULL == (dx_plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); - if (!file_space) { - if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); - file_space = free_this_space; - } /* end if */ + if (!file_space) + file_space = dataset->space; if (!mem_space) mem_space = file_space; nelmts = (*mem_space->select.get_npoints)(mem_space); @@ -2941,20 +2959,19 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); /* Retrieve dataset properties */ - if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value"); - if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill time"); - if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); - if(H5P_get(dc_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); + /* <none needed currently> */ /* Allocate data space and initialize it if it hasn't been. */ if(nelmts > 0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { + hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ + + /* Get the number of elements in file dataset's dataspace */ + if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset"); + /* Allocate storage */ - if(H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_WRITE)<0) + if(H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_WRITE, TRUE, (hbool_t)((hsize_t)file_nelmts==nelmts ? TRUE : FALSE))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); } /* end if */ @@ -3005,8 +3022,8 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_timer_begin(&timer); #endif status = (sconv->write)(dataset->ent.file, &(dataset->layout), - dc_plist, H5T_get_size(dataset->type), - file_space, mem_space, dxpl_id, buf); + dc_plist, &(dataset->efl), H5T_get_size(dataset->type), + file_space, mem_space, dxpl_id, buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].write_timer), &timer); sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); @@ -3061,10 +3078,13 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* Figure out the strip mine size. */ if ((*file_space->select.iter_init)(file_space, dst_type_size, &file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); + file_iter_init=1; /*file selection iteration info has been initialized */ if ((*mem_space->select.iter_init)(mem_space, src_type_size, &mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); + mem_iter_init=1; /*file selection iteration info has been initialized */ if ((*file_space->select.iter_init)(file_space, dst_type_size, &bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); + bkg_iter_init=1; /*file selection iteration info has been initialized */ /* * Get a temporary buffer for type conversion unless the app has already @@ -3087,13 +3107,13 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ - if((tconv_buf=H5FL_BLK_ALLOC(type_conv,target_size,0))==NULL) + if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); - if((bkg_buf=H5FL_BLK_ALLOC(type_conv,(size_t)(request_nelmts*dst_type_size),1))==NULL) + if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ @@ -3126,9 +3146,8 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_timer_begin(&timer); #endif n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), - dc_plist, dst_type_size, file_space, - &bkg_iter, smine_nelmts, dxpl_id, - bkg_buf/*out*/); + dc_plist, &(dataset->efl), dst_type_size, file_space, + &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); @@ -3152,9 +3171,8 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_timer_begin(&timer); #endif status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), - dc_plist, dst_type_size, - file_space, &file_iter, smine_nelmts, - dxpl_id, tconv_buf); + dc_plist, &(dataset->efl), dst_type_size, file_space, &file_iter, + smine_nelmts, dxpl_id, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].scat_timer), &timer); @@ -3186,9 +3204,12 @@ done: } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Release selection iterators */ - (*file_space->select.iter_release)(&file_iter); - (*mem_space->select.iter_release)(&mem_iter); - (*file_space->select.iter_release)(&bkg_iter); + if(file_iter_init) + (*file_space->select.iter_release)(&file_iter); + if(mem_iter_init) + (*mem_space->select.iter_release)(&mem_iter); + if(bkg_iter_init) + (*file_space->select.iter_release)(&bkg_iter); if (src_id >= 0) H5I_dec_ref(src_id); @@ -3199,8 +3220,6 @@ done: H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); - if (free_this_space) - H5S_close(free_this_space); FUNC_LEAVE(ret_value); } /* end H5D_write() */ @@ -3230,8 +3249,6 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) { int changed; /* Flag to indicate that the dataspace was successfully extended */ H5S_t *space = NULL; /* Dataset's dataspace */ - H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ - H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_extend, FAIL); @@ -3240,12 +3257,6 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) assert (dataset); assert (size); - /* Get the dataset creation property list */ - if (NULL == (plist = H5I_object(dataset->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); - if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); - /* * NOTE: Restrictions on extensions were checked when the dataset was * created. All extensions are allowed here since none should be @@ -3253,24 +3264,22 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) */ /* Increase the size of the data space */ - if (NULL==(space=H5S_read (&(dataset->ent)))) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space info from dataset header"); + space=dataset->space; if ((changed=H5S_extend (space, size))<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to increase size of data space"); if (changed>0){ /* Save the new dataspace in the file if necessary */ - if (H5S_modify (&(dataset->ent), space)<0) + if (H5S_modify (&(dataset->ent), space, TRUE)<0) HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); /* Allocate space for the new parts of the dataset, if appropriate */ - if(alloc_time==H5D_ALLOC_TIME_EARLY) - if (H5D_alloc_storage(dataset->ent.file, dataset, H5D_ALLOC_EXTEND)<0) + if(dataset->alloc_time==H5D_ALLOC_TIME_EARLY) + if (H5D_alloc_storage(dataset->ent.file, dataset, H5D_ALLOC_EXTEND, TRUE, FALSE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); } /* end if */ done: - H5S_close(space); FUNC_LEAVE (ret_value); } @@ -3347,7 +3356,7 @@ H5D_typeof (H5D_t *dset) * *------------------------------------------------------------------------- */ -H5F_t * +static H5F_t * H5D_get_file (const H5D_t *dset) { /* Use FUNC_ENTER_NOINIT here to avoid performance issues */ @@ -3379,12 +3388,9 @@ H5D_get_file (const H5D_t *dset) *------------------------------------------------------------------------- */ static herr_t -H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc) +H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc, + hbool_t update_time, hbool_t full_overwrite) { - H5P_genplist_t *plist; /* Dataset's creation property list */ - H5O_efl_t efl; /* External File List info */ - H5D_fill_time_t fill_time; /* When to write fill values */ - H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ struct H5O_layout_t *layout; /* The dataset's layout information */ hsize_t nbytes; /* The number of bytes in the dataset */ unsigned space_allocated=0; /* Flag to indicate that space was allocated */ @@ -3397,23 +3403,11 @@ H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc) assert (f); assert (dset); - /* Get external file list properties */ - if (NULL == (plist = H5I_object(dset->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); - if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); - /* If the data is stored in external files, don't set an address for the layout * We assume that external storage is already * allocated by the caller, or at least will be before I/O is performed. */ - if(efl.nused==0) { - /* Get properties needed */ - if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time"); - if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); - + if(dset->efl.nused==0) { /* Get a pointer to the dataset's layout information */ layout=&(dset->layout); @@ -3441,6 +3435,11 @@ H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc) /* Indicate that we allocated space */ space_allocated=1; } /* end if */ + + /* If MPIO or MPIPOSIX is used, indicate that space was allocated, so the B-tree gets expanded */ + if(IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) + space_allocated=1; + break; case H5D_COMPACT: @@ -3462,19 +3461,22 @@ H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc) HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout"); } /* end switch */ - /* If we are filling the dataset on allocation, do that now */ - if(fill_time==H5D_FILL_TIME_ALLOC - && !(alloc_time==H5D_ALLOC_TIME_INCR && time_alloc==H5D_ALLOC_WRITE)) { - if(H5D_init_storage(dset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); - } /* end if */ + /* Check if we actually allocated space before performing other actions */ + if(space_allocated) { + /* If we are filling the dataset on allocation, do that now */ + if(dset->fill_time==H5D_FILL_TIME_ALLOC + && !(dset->alloc_time==H5D_ALLOC_TIME_INCR && time_alloc==H5D_ALLOC_WRITE)) { + if(H5D_init_storage(dset, full_overwrite) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); + } /* end if */ - /* Also update header message for layout with new address - * (this is only for forward compatibility). - */ - if(space_allocated && time_alloc!=H5D_ALLOC_CREATE) - if (H5O_modify (&(dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, &(dset->layout)) < 0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); + /* Also update header message for layout with new address + * (this is only for forward compatibility). + */ + if(time_alloc!=H5D_ALLOC_CREATE) + if (H5O_modify (&(dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, update_time, &(dset->layout)) < 0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); + } /* end if */ } /* end if */ done: @@ -3504,13 +3506,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_init_storage(H5D_t *dset) +H5D_init_storage(H5D_t *dset, hbool_t full_overwrite) { hssize_t snpoints; /* Number of points in space (for error checking) */ size_t npoints; /* Number of points in space */ - H5S_t *space = NULL; /* Dataset's dataspace */ - H5O_fill_t fill; /* Fill value information */ - H5O_efl_t efl; /* External File List info */ + H5S_t *space; /* Dataset's dataspace */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value = SUCCEED; /* Return value */ @@ -3518,17 +3518,8 @@ H5D_init_storage(H5D_t *dset) assert(dset); - /* Get fill value, external file list, and data pipeline properties */ - if (NULL == (plist = H5I_object(dset->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); - if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value"); - if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); - /* Get the dataset's dataspace */ - if (NULL==(space=H5S_read (&(dset->ent)))) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); + space=dset->space; /* Get the number of elements in the dataset's dataspace */ snpoints = H5S_get_simple_extent_npoints(space); @@ -3537,19 +3528,31 @@ H5D_init_storage(H5D_t *dset) switch (dset->layout.type) { case H5D_COMPACT: - /* If the fill value is defined, initialize the data buffer with it */ - if(fill.buf) - /* Initialize the cached data buffer with the fill value */ - H5V_array_fill(dset->layout.buf, fill.buf, fill.size, npoints); - else /* If the fill value is default, zero set data buf. */ - HDmemset(dset->layout.buf, 0, dset->layout.size); + /* If we will be immediately overwriting the values, don't bother to clear them */ + if(!full_overwrite) { + /* If the fill value is defined, initialize the data buffer with it */ + if(dset->fill.buf) + /* Initialize the cached data buffer with the fill value */ + H5V_array_fill(dset->layout.buf, dset->fill.buf, dset->fill.size, npoints); + else /* If the fill value is default, zero set data buf. */ + HDmemset(dset->layout.buf, 0, dset->layout.size); + } /* end if */ break; case H5D_CONTIGUOUS: - if (H5F_contig_fill(dset->ent.file, H5P_DATASET_XFER_DEFAULT, - &(dset->layout), plist, space, H5T_get_size(dset->type))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); - break; + /* Don't write default fill values to external files */ + /* If we will be immediately overwriting the values, don't bother to clear them */ + if((dset->efl.nused==0 || dset->fill.buf) && !full_overwrite) { + /* Get dataset's creation property list */ + if (NULL == (plist = H5I_object(dset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + + if (H5F_contig_fill(dset->ent.file, H5P_DATASET_XFER_DEFAULT, + &(dset->layout), plist, &(dset->efl), space, + &dset->fill, H5T_get_size(dset->type))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); + } /* end if */ + break; case H5D_CHUNKED: /* @@ -3561,21 +3564,22 @@ H5D_init_storage(H5D_t *dset) int ndims; hsize_t dim[H5O_LAYOUT_NDIMS]; + /* Get dataset's creation property list */ + if (NULL == (plist = H5I_object(dset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info"); dim[ndims] = dset->layout.dim[ndims]; if (H5F_istore_allocate(dset->ent.file, H5P_DATASET_XFER_DEFAULT, - &(dset->layout), dim, plist)<0) + &(dset->layout), dim, plist, full_overwrite)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); } /* end if */ break; } /* end switch */ done: - if (space) - H5S_close(space); - FUNC_LEAVE(ret_value); } @@ -3638,7 +3642,7 @@ done: * *------------------------------------------------------------------------- */ -hsize_t +static hsize_t H5D_get_storage_size(H5D_t *dset) { unsigned u; /* Index variable */ @@ -3732,7 +3736,7 @@ done: * *------------------------------------------------------------------------- */ -haddr_t +static haddr_t H5D_get_offset(H5D_t *dset) { haddr_t ret_value; @@ -3894,9 +3898,9 @@ H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf) /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; - - if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); + else + if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); /* Call H5Diterate with args, etc. */ ret_value=H5Diterate(buf,type_id,space_id,H5T_vlen_reclaim,&plist_id); @@ -3923,7 +3927,7 @@ done: * *------------------------------------------------------------------------- */ -void * +static void * H5D_vlen_get_buf_size_alloc(size_t size, void *info) { H5T_vlen_bufsize_t *vlen_bufsize=(H5T_vlen_bufsize_t *)info; @@ -3970,7 +3974,7 @@ done: * *------------------------------------------------------------------------- */ -herr_t +static herr_t H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, hsize_t UNUSED ndim, hssize_t *point, void *op_data) { H5T_vlen_bufsize_t *vlen_bufsize=(H5T_vlen_bufsize_t *)op_data; @@ -4060,9 +4064,9 @@ H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't create dataspace"); /* Grab the temporary buffers required */ - if((vlen_bufsize.fl_tbuf=H5FL_BLK_ALLOC(vlen_fl_buf,1,0))==NULL) + if((vlen_bufsize.fl_tbuf=H5FL_BLK_MALLOC(vlen_fl_buf,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available"); - if((vlen_bufsize.vl_tbuf=H5FL_BLK_ALLOC(vlen_vl_buf,1,0))==NULL) + if((vlen_bufsize.vl_tbuf=H5FL_BLK_MALLOC(vlen_vl_buf,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available"); /* Get the pointer to the dataset transfer class */ @@ -4160,7 +4164,7 @@ H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_t /* Get the maximum buffer size needed and allocate it */ buf_size=MAX(src_type_size,dst_type_size); - if (NULL==(tconv_buf = H5FL_BLK_ALLOC(type_elem,buf_size,0)) || NULL==(bkg_buf = H5FL_BLK_ALLOC(type_elem,buf_size,1))) + if (NULL==(tconv_buf = H5FL_BLK_MALLOC(type_elem,buf_size)) || NULL==(bkg_buf = H5FL_BLK_CALLOC(type_elem,buf_size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); /* Copy the user's data into the buffer for conversion */ @@ -4180,7 +4184,7 @@ H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_t } /* Perform data type conversion */ - if (H5T_convert(tpath, src_id, dst_id, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, H5P_DEFAULT)<0) + if (H5T_convert(tpath, src_id, dst_id, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, H5P_DATASET_XFER_DEFAULT)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed"); /* Fill the selection in the memory buffer */ @@ -4311,7 +4315,7 @@ done: * *------------------------------------------------------------------------- */ -herr_t +static herr_t H5D_set_extent(H5D_t *dset, const hsize_t *size) { hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */ @@ -4319,7 +4323,6 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size) herr_t ret_value = SUCCEED; /* Return value */ H5S_t *space = NULL; H5P_genplist_t *plist; - H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ int u; unsigned shrink = 0; /* Flag to indicate a dimension has shrank */ unsigned expand = 0; /* Flag to indicate a dimension has grown */ @@ -4335,8 +4338,7 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size) * Get the data space *------------------------------------------------------------------------- */ - if(NULL == (space = H5S_read(&(dset->ent)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space info from dset header"); + space = dset->space; /*------------------------------------------------------------------------- * Check if we are shrinking or expanding any of the dimensions @@ -4361,23 +4363,17 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size) /* Don't bother updating things, unless they've changed */ if(changed) { - /* Get the dataset creation property list */ - if(NULL == (plist = H5I_object(dset->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list"); - if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); - /*------------------------------------------------------------------------- * Modify the dataset storage *------------------------------------------------------------------------- */ /* Save the new dataspace in the file if necessary */ - if(H5S_modify(&(dset->ent), space) < 0) + if(H5S_modify(&(dset->ent), space, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); /* Allocate space for the new parts of the dataset, if appropriate */ - if(expand && alloc_time==H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(dset->ent.file, dset, H5D_ALLOC_EXTEND) < 0) + if(expand && dset->alloc_time==H5D_ALLOC_TIME_EARLY) + if(H5D_alloc_storage(dset->ent.file, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage"); @@ -4387,6 +4383,10 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size) *------------------------------------------------------------------------- */ if(shrink && H5D_CHUNKED == dset->layout.type) { + /* Get the dataset creation property list */ + if(NULL == (plist = H5I_object(dset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list"); + /* Remove excess chunks */ if(H5F_istore_prune_by_extent(dset->ent.file, &dset->layout, space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks "); @@ -4398,8 +4398,6 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size) } /* end if */ done: - if(space) - H5S_close(space); FUNC_LEAVE(ret_value); } @@ -4449,7 +4447,7 @@ H5D_flush(H5F_t *f) if(NULL==(dataset=H5I_object_verify(id_list[j], H5I_DATASET))) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset object"); if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) - if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, &(dataset->layout))<0) + if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, 1, &(dataset->layout))<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message"); dataset->layout.dirty = FALSE; } @@ -4459,7 +4457,7 @@ done: if(id_list!=NULL) H5MM_xfree(id_list); FUNC_LEAVE(ret_value); -} +} /* end H5D_flush() */ /*------------------------------------------------------------------------- |