/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /****************/ /* Module Setup */ /****************/ #define H5D_PACKAGE /*suppress error about including H5Dpkg */ /* Interface initialization */ #define H5_INTERFACE_INIT_FUNC H5D_init_interface /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #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 */ /****************/ /* Local Macros */ /****************/ /******************/ /* Local Typedefs */ /******************/ /* Struct for holding callback info during H5D_flush operation */ 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; /********************/ /* Local Prototypes */ /********************/ /* General stuff */ static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id); static H5D_shared_t *H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type); 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_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); /*********************/ /* Package Variables */ /*********************/ /* Define a "default" dataset transfer property list cache structure to use for default DXPLs */ H5D_dxpl_cache_t H5D_def_dxpl_cache; /* Declare a free list to manage blocks of VL data */ H5FL_BLK_DEFINE(vlen_vl_buf); /* Declare a free list to manage other blocks of VL data */ H5FL_BLK_DEFINE(vlen_fl_buf); /*****************************/ /* Library Private Variables */ /*****************************/ /*******************/ /* Local Variables */ /*******************/ /* Declare a free list to manage the H5D_t and H5D_shared_t structs */ H5FL_DEFINE_STATIC(H5D_t); H5FL_DEFINE_STATIC(H5D_shared_t); /* Declare the external PQ free list for the sieve buffer information */ H5FL_BLK_EXTERN(sieve_buf); /* Define a static "default" dataset structure to use to initialize new datasets */ static H5D_shared_t H5D_def_dset; /*------------------------------------------------------------------------- * Function: H5D_init * * Purpose: Initialize the interface from some other layer. * * Return: Success: non-negative * * Failure: negative * * Programmer: Quincey Koziol * Saturday, March 4, 2000 * *------------------------------------------------------------------------- */ herr_t H5D_init(void) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_init, FAIL) /* FUNC_ENTER() does all the work */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_init() */ /*-------------------------------------------------------------------------- NAME H5D_init_interface -- Initialize interface-specific information USAGE herr_t H5D_init_interface() RETURNS Non-negative on success/Negative on failure DESCRIPTION Initializes any interface-specific data or routines. NOTES Care must be taken when using the H5P functions, since they can cause a deadlock in the library when the library is attempting to terminate -QAK --------------------------------------------------------------------------*/ static herr_t H5D_init_interface(void) { H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_init_interface) /* Initialize the atom group for the dataset IDs */ if(H5I_register_type(H5I_DATASET, (size_t)H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (H5I_free_t)H5D_close)0) { /* The dataset API uses the "force" flag set to true because it * is using the "file objects" (H5FO) API functions to track open * objects in the file. Using the H5FO code means that dataset * IDs can have reference counts >1, when an existing dataset is * opened more than once. However, the H5I code does not attempt * to close objects with reference counts>1 unless the "force" flag * is set to true. * * At some point (probably after the group and datatypes use the * the H5FO code), the H5FO code might need to be switched around * to storing pointers to the objects being tracked (H5D_t, H5G_t, * etc) and reference count those itself instead of relying on the * reference counting in the H5I layer. Then, the "force" flag can * be put back to false. * * Setting the "force" flag to true for all the interfaces won't * work because the "file driver" (H5FD) APIs use the H5I reference * counting to avoid closing a file driver out from underneath an * open file... * * QAK - 5/13/03 */ H5I_clear_type(H5I_DATASET, TRUE); } else { H5I_dec_type_ref(H5I_DATASET); H5_interface_initialize_g = 0; n = 1; /*H5I*/ } } FUNC_LEAVE_NOAPI(n) } /* end H5D_term_interface() */ /*------------------------------------------------------------------------- * Function: H5D_create_named * * Purpose: Internal routine to create a new dataset. * * Return: Success: Non-NULL, pointer to new dataset object. * * Failure: NULL * * Programmer: Quincey Koziol * Thursday, April 5, 2007 * *------------------------------------------------------------------------- */ H5D_t * H5D_create_named(const H5G_loc_t *loc, const char *name, hid_t type_id, const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id, hid_t dxpl_id) { H5O_obj_create_t ocrt_info; /* Information for object creation */ H5D_obj_create_t dcrt_info; /* Information for dataset creation */ H5D_t *ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_create_named, NULL) /* Check arguments */ HDassert(loc); HDassert(name && *name); HDassert(type_id != H5P_DEFAULT); HDassert(space); HDassert(lcpl_id != H5P_DEFAULT); HDassert(dcpl_id != H5P_DEFAULT); HDassert(dapl_id != H5P_DEFAULT); HDassert(dxpl_id != H5P_DEFAULT); /* Set up dataset creation info */ dcrt_info.type_id = type_id; dcrt_info.space = space; dcrt_info.dcpl_id = dcpl_id; /* Set up object creation information */ ocrt_info.obj_type = H5O_TYPE_DATASET; ocrt_info.crt_info = &dcrt_info; ocrt_info.new_obj = NULL; /* Create the new dataset and link it to its parent group */ if(H5L_link_object(loc, name, &ocrt_info, lcpl_id, dapl_id, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create and link to dataset") HDassert(ocrt_info.new_obj); /* Set the return value */ ret_value = (H5D_t *)ocrt_info.new_obj; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_create_named() */ /*------------------------------------------------------------------------- * Function: H5D_get_space_status * * Purpose: Returns the status of data space allocation. * * Return: * Success: Non-negative * * Failture: Negative * * Programmer: Raymond Lu * *------------------------------------------------------------------------- */ herr_t 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 */ hsize_t full_size; /* The number of bytes in the dataset when fully populated */ herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT(H5D_get_space_status) HDassert(dset); /* Get the dataset's dataspace */ space = dset->shared->space; 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") /* 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") /* 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; /* 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); /* Decide on how much of the space is allocated */ if(space_allocated == 0) *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED; else if(space_allocated == full_size) *allocation = H5D_SPACE_STATUS_ALLOCATED; else { /* Should only happen for chunked datasets currently */ HDassert(dset->shared->layout.type == H5D_CHUNKED); *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_get_space_status() */ /*------------------------------------------------------------------------- * Function: H5D_new * * Purpose: Creates a new, empty dataset structure * * Return: Success: Pointer to a new dataset descriptor. * * Failure: NULL * * Programmer: Quincey Koziol * Monday, October 12, 1998 * *------------------------------------------------------------------------- */ static H5D_shared_t * H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) { H5P_genplist_t *plist; /* Property list created */ H5D_shared_t *new_dset = NULL; /* New dataset object */ H5D_shared_t *ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_new) /* Allocate new shared dataset structure */ if(NULL == (new_dset = H5FL_MALLOC(H5D_shared_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the default dataset information */ HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t)); /* If we are using the default dataset creation property list, during creation * 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) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "Can't increment default DCPL ID") new_dset->dcpl_id = dcpl_id; } /* end if */ else { /* Get the property list */ 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); } /* end else */ /* Set return value */ ret_value = new_dset; 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); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_new() */ /*------------------------------------------------------------------------- * Function: H5D_init_type * * Purpose: Copy a datatype for a dataset's use, performing all the * necessary adjustments, etc. * * Return: Success: SUCCEED * Failure: FAIL * * Programmer: Quincey Koziol * Thursday, June 24, 2004 * *------------------------------------------------------------------------- */ static herr_t H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type) { htri_t relocatable; /* Flag whether the type is relocatable */ htri_t immutable; /* Flag whether the type is immutable */ hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_init_type) /* Sanity checking */ HDassert(file); HDassert(dset); HDassert(type); /* Check whether the datatype is relocatable */ if((relocatable = H5T_is_relocatable(type)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?") /* Check whether the datatype is immutable */ if((immutable = H5T_is_immutable(type)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?") /* Get the file's 'use the latest version of the format' flag */ use_latest_format = H5F_USE_LATEST_FORMAT(file); /* Copy the datatype if it's a custom datatype or if it'll change when it's location is changed */ if(!immutable || relocatable || use_latest_format) { /* Copy datatype for dataset */ if((dset->shared->type = H5T_copy(type, H5T_COPY_ALL)) == NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy datatype") /* Mark any datatypes as being on disk now */ if(H5T_set_loc(dset->shared->type, file, H5T_LOC_DISK) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't set datatype location") /* Set the latest format, if requested */ if(use_latest_format) if(H5T_set_latest_version(dset->shared->type) < 0) 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) 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) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment datatype ID") /* Use existing datatype */ dset->shared->type_id = type_id; dset->shared->type = (H5T_t *)type; /* (Cast away const OK - QAK) */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_init_type() */ /*------------------------------------------------------------------------- * Function: H5D_init_space * * Purpose: Copy a dataspace for a dataset's use, performing all the * necessary adjustments, etc. * * Return: Success: SUCCEED * Failure: FAIL * * Programmer: Quincey Koziol * Tuesday, July 24, 2007 * *------------------------------------------------------------------------- */ static herr_t H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space) { hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_init_space) /* Sanity checking */ HDassert(file); HDassert(dset); HDassert(space); /* Get the file's 'use the latest version of the format' flag */ use_latest_format = H5F_USE_LATEST_FORMAT(file); /* Copy dataspace for dataset */ if(NULL == (dset->shared->space = H5S_copy(space, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataspace") /* Set the latest format, if requested */ if(use_latest_format) if(H5S_set_latest_version(dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype") /* Set the dataset's dataspace to 'all' selection */ if(H5S_select_all(dset->shared->space, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set all selection") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_init_space() */ /*------------------------------------------------------------------------- * Function: H5D_update_oh_info * * Purpose: Create and fill object header for dataset * * Return: Success: SUCCEED * Failure: FAIL * * Programmer: Bill Wendling * Thursday, October 31, 2002 * *------------------------------------------------------------------------- */ static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) { struct H5O_t *oh = NULL; /* Pointer to dataset's object header */ size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ H5O_loc_t *oloc = NULL; /* Dataset's object location */ H5O_layout_t *layout; /* Dataset's layout information */ H5T_t *type; /* Dataset's datatype */ hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ 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 */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_update_oh_info) /* Sanity checking */ HDassert(file); HDassert(dset); /* Set some local variables, for convenience */ oloc = &dset->oloc; layout = &dset->shared->layout; type = dset->shared->type; fill_prop = &dset->shared->dcpl_cache.fill; /* Get the file's 'use the latest version of the format' flag */ use_latest_format = H5F_USE_LATEST_FORMAT(file); /* Retrieve "defined" status of fill value */ 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") /* Special case handling for variable-length types */ if(H5T_detect_class(type, H5T_VLEN)) { /* 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 */ fill_prop->fill_time = H5D_FILL_TIME_ALLOC; /* Note that the fill value changed */ fill_changed = TRUE; } /* end if */ /* Don't allow never writing fill values with variable-length types */ if(fill_prop->fill_time == H5D_FILL_TIME_NEVER) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined") } /* end if */ /* Determine whether fill value is defined or not */ if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { /* Convert fill value buffer to dataset's datatype */ if(fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(fill_prop, type, &fill_changed, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type") fill_prop->fill_defined = TRUE; } else if(fill_status == H5D_FILL_VALUE_UNDEFINED) { fill_prop->fill_defined = FALSE; } else HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine if fill value is defined") /* Check for invalid fill & allocation time setting */ if(fill_prop->fill_defined == FALSE && fill_prop->fill_time == H5D_FILL_TIME_ALLOC) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "fill value writing on allocation set, but no fill value defined") /* Check if the fill value info changed */ if(fill_changed) { H5P_genplist_t *dc_plist; /* Dataset's creation property list */ /* Get dataset's property list object */ HDassert(dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT); if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") /* Update dataset creation property */ if(H5P_set(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value info") } /* end if */ /* 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; /* Create an object header for the dataset */ if(H5O_create(file, dxpl_id, ohdr_size, dset->shared->dcpl_id, oloc/*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header") /* Get a pointer to the object header itself */ if((oh = H5O_protect(oloc, dxpl_id)) == NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to protect dataset object header") /* Write new fill value message */ if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update new fill value header message") /* If there is valid information for the old fill value struct, add it */ /* (only if we aren't trying to write the latest version of the file format) */ if(fill_prop->buf && !use_latest_format) { H5O_fill_t old_fill_prop; /* Copy of fill value property, for writing as "old" fill value */ /* Shallow copy the fill value property */ /* (we only want to make certain that the shared component isnt' modified) */ HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); /* Reset shared component info */ H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop); /* Write old fill value */ if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message") } /* end if */ /* Update the datatype and dataspace header messages */ if(H5O_msg_append(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message") 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(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(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE, 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_PROTECT, 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_PROTECT, FAIL, "unable to unprotect EFL file name heap") heap = NULL; /* Insert EFL message into dataset object header */ if(H5O_msg_append(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 */ /* 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(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") #ifdef H5O_ENABLE_BOGUS { H5P_genplist_t *dc_plist; /* Dataset's creation property list */ /* Get dataset's property list object */ if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") /* Check whether to add a "bogus" message */ if(H5P_exist_plist(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME) > 0) { uint8_t bogus_flags = 0; /* Flags for creating "bogus" message */ /* Retrieve "bogus" message flags */ if(H5P_get(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME, &bogus_flags) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus message options") /* Add a "bogus" message (for error testing). */ if(H5O_bogus_oh(file, dxpl_id, oh, (unsigned)bogus_flags) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create 'bogus' message") } /* end if */ } #endif /* H5O_ENABLE_BOGUS */ /* Add a modification time message. */ if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") done: /* Release pointer to object header itself */ if(oloc != NULL && oh != NULL) if(H5O_unprotect(oloc, oh) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to unprotect dataset object header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_update_oh_info() */ /*------------------------------------------------------------------------- * Function: H5D_create * * Purpose: Creates a new dataset with name NAME in file F and associates * with it a datatype TYPE for each element as stored in the * file, dimensionality information or dataspace SPACE, and * other miscellaneous properties CREATE_PARMS. All arguments * are deep-copied before being associated with the new dataset, * so the caller is free to subsequently modify them without * affecting the dataset. * * Return: Success: Pointer to a new dataset * * Failure: NULL * * Programmer: Robb Matzke * Thursday, December 4, 1997 * *------------------------------------------------------------------------- */ H5D_t * H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, hid_t dxpl_id) { const H5T_t *type; /* Datatype for dataset */ H5D_t *new_dset = NULL; int i, ndims; unsigned chunk_ndims = 0; /* Dimensionality of chunk */ H5P_genplist_t *dc_plist = NULL; /* New Property list */ hbool_t has_vl_type = FALSE; /* Flag to indicate a VL-type for dataset */ hbool_t chunk_init = FALSE; /* Flag to indicate that chunk information was initialized */ H5G_loc_t dset_loc; /* Dataset location */ unsigned u; /* Local index variable */ H5D_t *ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_create, NULL) /* check args */ HDassert(file); 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)); /* Get the dataset's datatype */ if(NULL == (type = (const H5T_t *)H5I_object(type_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype") /* 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") /* Check if the datatype is/contains a VL-type */ if(H5T_detect_class(type, H5T_VLEN)) has_vl_type=TRUE; /* Check if the dataspace has an extent set (or is NULL) */ if(!(H5S_has_extent(space)) ) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "dataspace extent has not been set.") /* Initialize the dataset object */ if(NULL == (new_dset = H5FL_CALLOC(H5D_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Set up & reset dataset location */ dset_loc.oloc = &(new_dset->oloc); dset_loc.path = &(new_dset->path); H5G_loc_reset(&dset_loc); /* Initialize the shared dataset space */ if(NULL == (new_dset->shared = H5D_new(dcpl_id, TRUE, has_vl_type))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy & initialize datatype for dataset */ if(H5D_init_type(file, new_dset, type_id, type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy datatype") /* Copy & initialize dataspace for dataset */ if(H5D_init_space(file, new_dset, space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy dataspace") /* Set the dataset's checked_filters flag to enable writing */ new_dset->shared->checked_filters = TRUE; /* 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_pline_t *pline; /* Dataset's I/O pipeline information */ H5O_fill_t *fill; /* Dataset's fill value info */ /* Check if the filters in the DCPL can be applied to this dataset */ if(H5Z_can_apply(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset") /* Make the "set local" filter callbacks for this dataset */ if(H5Z_set_local(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters") /* Get new dataset's property list object */ if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(new_dset->shared->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list") /* Retrieve the properties we need */ pline = &new_dset->shared->dcpl_cache.pline; if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter") layout = &new_dset->shared->layout.type; 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) 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) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill value info") /* Check if the alloc_time is the default and error out */ if(fill->alloc_time == H5D_ALLOC_TIME_DEFAULT) 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) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation") /* If MPI VFD is used, no filter support yet. */ if(IS_H5FD_MPI(file) && pline->nused > 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(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk dimensions") /* Get the dataset's external file list information */ if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->shared->dcpl_cache.efl) < 0) 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 */ 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) 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 */ if(H5O_fill_set_latest_version(&new_dset->shared->dcpl_cache.fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of fill value") } /* end if */ /* Check if this dataset is going into a parallel file and set space allocation time */ if(IS_H5FD_MPI(file)) new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; switch(new_dset->shared->layout.type) { case H5D_CONTIGUOUS: { hssize_t tmp_size; /* Temporary holder for raw data size */ hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */ hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ /* * The maximum size of the dataset cannot exceed the storage size. * Also, only the slowest varying dimension of a simple data space * can be extendible (currently only for external data storage). */ new_dset->shared->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */ if((ndims = H5S_get_simple_extent_dims(new_dset->shared->space, 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] > dim[i]) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible") if(new_dset->shared->dcpl_cache.efl.nused > 0) { hsize_t max_points = H5S_get_npoints_max(new_dset->shared->space); hsize_t max_storage = H5O_efl_total_size(&new_dset->shared->dcpl_cache.efl); if(H5S_UNLIMITED == max_points) { if(H5O_EFL_UNLIMITED != max_storage) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage") } else if(max_points * H5T_get_size(type) < max_points) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed") } else if(max_points * H5T_get_size(type) > max_storage) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size") } /* Set the I/O functions for this layout type */ new_dset->shared->io_ops.readvv = H5D_efl_readvv; new_dset->shared->io_ops.writevv = H5D_efl_writevv; } /* end if */ else { if(ndims > 0 && max_dim[0] > dim[0]) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset") /* Set the I/O functions for this layout type */ new_dset->shared->io_ops.readvv = H5D_contig_readvv; new_dset->shared->io_ops.writevv = H5D_contig_writevv; } /* end else */ /* Compute the total size of a chunk */ tmp_size = H5S_GET_EXTENT_NPOINTS(new_dset->shared->space) * H5T_get_size(new_dset->shared->type); H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t); /* Get the sieve buffer size for this dataset */ new_dset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(file); } /* end case */ break; case H5D_CHUNKED: { hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ /* Set up layout information */ if((ndims = H5S_GET_EXTENT_NDIMS(new_dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank") new_dset->shared->layout.u.chunk.ndims = (unsigned)ndims + 1; HDassert((unsigned)(new_dset->shared->layout.u.chunk.ndims) <= NELMTS(new_dset->shared->layout.u.chunk.dim)); /* Initialize to no address */ new_dset->shared->layout.u.chunk.addr = HADDR_UNDEF; /* * Chunked storage allows any type of data space extension, so we * don't even bother checking. */ if(chunk_ndims != (unsigned)ndims) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space") if(new_dset->shared->dcpl_cache.efl.nused > 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout") /* * The chunk size of a dimension with a fixed size cannot exceed * the maximum dimension size */ if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, new_dset->shared->layout.u.chunk.dim) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size") new_dset->shared->layout.u.chunk.dim[new_dset->shared->layout.u.chunk.ndims-1] = H5T_get_size(new_dset->shared->type); if(H5S_get_simple_extent_dims(new_dset->shared->space, NULL, max_dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions") for(u = 0; u < new_dset->shared->layout.u.chunk.ndims - 1; u++) if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < new_dset->shared->layout.u.chunk.dim[u]) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions") /* Compute the total size of a chunk */ for(u = 1, new_dset->shared->layout.u.chunk.size = new_dset->shared->layout.u.chunk.dim[0]; u < new_dset->shared->layout.u.chunk.ndims; u++) new_dset->shared->layout.u.chunk.size *= new_dset->shared->layout.u.chunk.dim[u]; /* Set the I/O functions for this layout type */ new_dset->shared->io_ops.readvv = H5D_istore_readvv; new_dset->shared->io_ops.writevv = H5D_istore_writevv; /* Initialize the chunk cache for the dataset */ if(H5D_istore_init(file, new_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize chunk cache") /* Indicate that the chunk information was initialized */ chunk_init = TRUE; } /* end case */ break; case H5D_COMPACT: { hssize_t tmp_size; /* Temporary holder for raw data size */ hsize_t comp_data_size; /* * Compact dataset is stored in dataset object header message of * layout. */ tmp_size = H5S_GET_EXTENT_NPOINTS(space) * H5T_get_size(new_dset->shared->type); H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.compact.size, tmp_size, hssize_t, size_t); /* Verify data size is smaller than maximum header message size * (64KB) minus other layout message fields. */ comp_data_size = H5O_MESG_MAX_SIZE - H5O_layout_meta_size(file, &(new_dset->shared->layout)); if(new_dset->shared->layout.u.compact.size > comp_data_size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size") /* Set the I/O functions for this layout type */ new_dset->shared->io_ops.readvv = H5D_compact_readvv; new_dset->shared->io_ops.writevv = H5D_compact_writevv; } /* end case */ break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") } /* end switch */ /*lint !e788 All appropriate cases are covered */ /* Update the dataset's object header info. */ if(H5D_update_oh_info(file, dxpl_id, new_dset) != SUCCEED) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache") /* 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") new_dset->shared->fo_count = 1; /* Success */ ret_value = new_dset; done: if(!ret_value && new_dset && new_dset->shared) { if(new_dset->shared) { if(new_dset->shared->layout.type == H5D_CHUNKED && chunk_init) { if(H5D_istore_dest(new_dset,H5AC_dxpl_id) < 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->type) { if(H5I_dec_ref(new_dset->shared->type_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") } /* end if */ if(H5F_addr_defined(new_dset->oloc.addr)) { if(H5O_close(&(new_dset->oloc)) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header") if(file) { if(H5O_delete(file, dxpl_id, new_dset->oloc.addr) < 0) 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); } /* end if */ new_dset->oloc.file = NULL; H5FL_FREE(H5D_t, new_dset); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_create() */ /* *------------------------------------------------------------------------- * Function: H5D_open * * Purpose: Checks if dataset is already open, or opens a dataset for * access. * * Return: Success: Dataset ID * Failure: FAIL * * Programmer: Quincey Koziol * Friday, December 20, 2002 * *------------------------------------------------------------------------- */ H5D_t * H5D_open(const H5G_loc_t *loc, hid_t dxpl_id) { H5D_shared_t *shared_fo = NULL; H5D_t *dataset = NULL; H5D_t *ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_open, NULL) /* check args */ HDassert(loc); /* Allocate the dataset structure */ if(NULL == (dataset = H5FL_CALLOC(H5D_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Shallow copy (take ownership) of the object location object */ if(H5O_loc_copy(&(dataset->oloc), loc->oloc, H5_COPY_SHALLOW) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy object location") /* Shallow copy (take ownership) of the group hier. path */ if(H5G_name_copy(&(dataset->path), loc->path, H5_COPY_SHALLOW) < 0) 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) { /* Clear any errors from H5FO_opened() */ H5E_clear_stack(NULL); /* Open the dataset object */ if(H5D_open_oid(dataset, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") /* Add the dataset to the list of opened objects in the file */ if(H5FO_insert(dataset->oloc.file, dataset->oloc.addr, dataset->shared, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") /* Increment object count for the object in the top file */ if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count") /* We're the first dataset to use the the shared info */ dataset->shared->fo_count = 1; } /* end if */ else { /* Point to shared info */ dataset->shared = shared_fo; /* Increment # of datasets using shared information */ shared_fo->fo_count++; /* Check if the object has been opened through the top file yet */ if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) { /* Open the object through this top file */ if(H5O_open(&(dataset->oloc)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open object header") } /* end if */ /* Increment object count for the object in the top file */ if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count") } /* end else */ ret_value = dataset; done: if(ret_value == NULL) { /* Free the location--casting away const*/ if(dataset) { if(shared_fo == NULL) /* Need to free shared fo */ H5FL_FREE(H5D_shared_t, dataset->shared); H5O_loc_free(&(dataset->oloc)); H5G_name_free(&(dataset->path)); H5FL_FREE(H5D_t, dataset); } if(shared_fo) shared_fo->fo_count--; } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_open() */ /*------------------------------------------------------------------------- * Function: H5D_open_oid * * Purpose: Opens a dataset for access. * * Return: Dataset pointer on success, NULL on failure * * Programmer: Quincey Koziol * Monday, October 12, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) { H5P_genplist_t *plist; /* Property list */ H5O_pline_t *pline; /* I/O pipeline information */ H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */ unsigned alloc_time_state; /* Allocation time state */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_open_oid) /* check args */ HDassert(dataset); /* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */ if(NULL == (dataset->shared = H5D_new(H5P_DATASET_CREATE_DEFAULT, FALSE, FALSE))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") /* Open the dataset object */ if(H5O_open(&(dataset->oloc)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open") /* 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(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") /* Get a datatype ID for the dataset's datatype */ if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type)) < 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 */ pline = &dataset->shared->dcpl_cache.pline; if(NULL != H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, pline, dxpl_id)) { if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline") } /* end if */ else H5E_clear_stack(NULL); /* * 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") 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 */ /* Set the I/O functions for this layout type */ dataset->shared->io_ops.readvv = H5D_contig_readvv; dataset->shared->io_ops.writevv = H5D_contig_writevv; /* 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_istore_init(dataset->oloc.file, dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache") } /* Set the I/O functions for this layout type */ dataset->shared->io_ops.readvv = H5D_istore_readvv; dataset->shared->io_ops.writevv = H5D_istore_writevv; break; case H5D_COMPACT: /* Set the I/O functions for this layout type */ dataset->shared->io_ops.readvv = H5D_compact_readvv; dataset->shared->io_ops.writevv = H5D_compact_writevv; break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") } /* end switch */ /*lint !e788 All appropriate cases are covered */ /* Point at dataset's copy, to cache it for later */ fill_prop = &dataset->shared->dcpl_cache.fill; /* Try to get the new fill value message from the object header */ if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop, dxpl_id)) { H5E_clear_stack(NULL); /* For backward compatibility, try to retrieve the old fill value message */ if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop, dxpl_id)) { H5E_clear_stack(NULL); /* Set the space allocation time appropriately, based on the type of dataset storage */ switch(dataset->shared->layout.type) { case H5D_COMPACT: fill_prop->alloc_time = H5D_ALLOC_TIME_EARLY; break; case H5D_CONTIGUOUS: fill_prop->alloc_time = H5D_ALLOC_TIME_LATE; break; case H5D_CHUNKED: fill_prop->alloc_time = H5D_ALLOC_TIME_INCR; break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") } /* end switch */ /*lint !e788 All appropriate cases are covered */ } /* end if */ /* If "old" fill value size is 0 (undefined), map it to -1 */ if(fill_prop->size == 0) fill_prop->size = (size_t)-1; } /* end if */ alloc_time_state = 0; if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) || (dataset->shared->layout.type == H5D_CONTIGUOUS && fill_prop->alloc_time == H5D_ALLOC_TIME_LATE) || (dataset->shared->layout.type == H5D_CHUNKED && fill_prop->alloc_time == H5D_ALLOC_TIME_INCR)) alloc_time_state = 1; /* Set revised fill value properties, if they are different from the defaults */ if(H5P_fill_value_cmp(&H5D_def_dset.dcpl_cache.fill, fill_prop, sizeof(H5O_fill_t))) { if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set fill value") if(H5P_set(plist, H5D_CRT_ALLOC_TIME_STATE_NAME, &alloc_time_state) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set allocation time state") } /* end if */ /* 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(NULL != H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id)) { 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") /* Override the I/O functions for this layout type */ dataset->shared->io_ops.readvv = H5D_efl_readvv; dataset->shared->io_ops.writevv = H5D_efl_writevv; } /* end if */ else H5E_clear_stack(NULL); } /* end if */ /* * Make sure all storage is properly initialized. * 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))) && IS_H5FD_MPI(dataset->oloc.file)) { if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_OPEN, TRUE, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage") } /* end if */ 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(dataset->shared->type) { if(dataset->shared->type_id > 0) { if(H5I_dec_ref(dataset->shared->type_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") } /* end if */ else { if(H5T_close(dataset->shared->type) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") } /* end else */ } /* end if */ } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_open_oid() */ /*------------------------------------------------------------------------- * Function: H5D_close * * Purpose: Insures that all data has been saved to the file, closes the * dataset object header, and frees all resources used by the * descriptor. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, December 4, 1997 * *------------------------------------------------------------------------- */ herr_t H5D_close(H5D_t *dataset) { unsigned free_failed = FALSE; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_close, FAIL) /* check args */ HDassert(dataset && dataset->oloc.file && dataset->shared); HDassert(dataset->shared->fo_count >0); /* Dump debugging info */ #ifdef H5D_ISTORE_DEBUG H5D_istore_stats(dataset, FALSE); #endif /* H5F_ISTORE_DEBUG */ dataset->shared->fo_count--; if(dataset->shared->fo_count == 0) { /* Update the dataspace on disk, if it's been changed */ if(dataset->shared->space_dirty) { if(H5S_write(&(dataset->oloc), dataset->shared->space, TRUE, H5AC_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") dataset->shared->space_dirty = FALSE; } /* end if */ /* Free the data sieve buffer, if it's been allocated */ if(dataset->shared->cache.contig.sieve_buf) { HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ /* Flush the raw data buffer, if its dirty */ if(dataset->shared->cache.contig.sieve_dirty) { /* 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, H5AC_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 */ dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); } /* end if */ /* Free cached information for each kind of dataset */ switch(dataset->shared->layout.type) { case H5D_CONTIGUOUS: break; case H5D_CHUNKED: /* Flush and destroy chunks in the cache */ if(H5D_istore_dest(dataset,H5AC_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache") break; case H5D_COMPACT: /* Update header message of layout for compact dataset. */ if(dataset->shared->layout.u.compact.dirty) { if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), H5AC_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to update layout message") dataset->shared->layout.u.compact.dirty = FALSE; } /* end if */ /* Free the buffer for the raw data for compact datasets */ dataset->shared->layout.u.compact.buf = H5MM_xfree(dataset->shared->layout.u.compact.buf); 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 */ /* * 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); /* Remove the dataset from the list of opened objects in the file */ if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") if(H5FO_delete(dataset->oloc.file, H5AC_dxpl_id, dataset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects") /* Close the dataset object */ /* (This closes the file, if this is the last object open) */ if(H5O_close(&(dataset->oloc)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") /* * Free memory. Before freeing the memory set the file pointer to NULL. * We always check for a null file pointer in other H5D functions to be * sure we're not accessing an already freed dataset (see the HDassert() * above). */ dataset->oloc.file = NULL; H5FL_FREE(H5D_shared_t, dataset->shared); } /* end if */ else { /* Decrement the ref. count for this object in the top file */ if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") /* Check reference count for this object in the top file */ if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) if(H5O_close(&(dataset->oloc)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close") } /* end else */ /* Release the dataset's path info */ if(H5G_name_free(&(dataset->path)) < 0) free_failed = TRUE; /* Free the dataset's memory structure */ H5FL_FREE(H5D_t, dataset); /* Check if anything failed in the middle... */ if(free_failed) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free a component of the dataset, but the dataset was freed anyway.") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_close() */ /*------------------------------------------------------------------------- * Function: H5D_oloc * * Purpose: Returns a pointer to the object location for a dataset. * * Return: Success: Ptr to location * Failure: NULL * * Programmer: Robb Matzke * Friday, April 24, 1998 * *------------------------------------------------------------------------- */ H5O_loc_t * H5D_oloc(H5D_t *dataset) { /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_oloc) FUNC_LEAVE_NOAPI(dataset ? &(dataset->oloc) : (H5O_loc_t *)NULL) } /* end H5D_oloc() */ /*------------------------------------------------------------------------- * Function: H5D_nameof * * Purpose: Returns a pointer to the group hier. path for a dataset. * * Return: Success: Ptr to entry * Failure: NULL * * Programmer: Quincey Koziol * Monday, September 12, 2005 * *------------------------------------------------------------------------- */ H5G_name_t * H5D_nameof(H5D_t *dataset) { /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_nameof) FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : (H5G_name_t *)NULL) } /* end H5D_nameof() */ /*------------------------------------------------------------------------- * Function: H5D_typeof * * Purpose: Returns a pointer to the dataset's datatype. The datatype * is not copied. * * Return: Success: Ptr to the dataset's datatype, uncopied. * * Failure: NULL * * Programmer: Robb Matzke * Thursday, June 4, 1998 * *------------------------------------------------------------------------- */ H5T_t * H5D_typeof(const H5D_t *dset) { /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_typeof) HDassert(dset); HDassert(dset->shared->type); FUNC_LEAVE_NOAPI(dset->shared->type) } /* end H5D_typeof() */ /*------------------------------------------------------------------------- * 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. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, January 16, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc, hbool_t update_time, hbool_t full_overwrite) { struct H5O_layout_t *layout; /* The dataset's layout information */ hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */ hbool_t addr_set = FALSE; /* Flag to indicate that the dataset's storage address was set */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_alloc_storage) /* check args */ HDassert(f); HDassert(dset); /* 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(!(H5S_NULL == H5S_GET_EXTENT_TYPE(dset->shared->space) || dset->shared->dcpl_cache.efl.nused > 0)) { /* Get a pointer to the dataset's layout information */ layout = &(dset->shared->layout); switch(layout->type) { case H5D_CONTIGUOUS: if(!H5F_addr_defined(layout->u.contig.addr)) { /* Reserve space in the file for the entire array */ if(H5D_contig_create(f, dxpl_id, layout/*out*/) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") /* Indicate that we set the storage addr */ addr_set = TRUE; /* Indicate that we should initialize storage space */ must_init_space = TRUE; } /* end if */ break; case H5D_CHUNKED: if(!H5F_addr_defined(layout->u.chunk.addr)) { /* Create the root of the B-tree that describes chunked storage */ if(H5D_istore_create(f, dxpl_id, layout/*out*/) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") /* Indicate that we set the storage addr */ addr_set = TRUE; /* Indicate that we should initialize storage space */ must_init_space = TRUE; } /* end if */ /* If space allocation is set to 'early' and we are extending * the dataset, indicate that space should be allocated, so the * B-tree gets expanded. -QAK */ if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY && time_alloc == H5D_ALLOC_EXTEND) must_init_space = TRUE; break; case H5D_COMPACT: /* Check if space is already allocated */ if(layout->u.compact.buf==NULL) { /* 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))) 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; /* Indicate that we should initialize storage space */ must_init_space = TRUE; } /* 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 */ /* Check if we need to initialize the space */ if(must_init_space) { if(layout->type == H5D_CHUNKED) { /* If we are doing incremental allocation and the B-tree got * created during a H5Dwrite call, don't initialize the storage * now, wait for the actual writes to each block and let the * low-level chunking routines handle initialize the fill-values. * Otherwise, pass along the space initialization call and let * the low-level chunking routines sort out whether to write * fill values to the chunks they allocate space for. Yes, * this is icky. -QAK */ if(!(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR && time_alloc == H5D_ALLOC_WRITE)) if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end if */ else { H5D_fill_value_t fill_status; /* The fill value status */ /* Check the dataset's fill-value status */ if(H5P_is_fill_value_defined(&dset->shared->dcpl_cache.fill, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* If we are filling the dataset on allocation or "if set" and * the fill value _is_ set, do that now */ if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end if */ } /* end else */ } /* end if */ /* Also update header message for layout with new address, if we * set the address. (this is improves forward compatibility). */ if(time_alloc != H5D_ALLOC_CREATE && addr_set) if(H5O_msg_write(&dset->oloc, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_time, &dset->shared->layout, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_alloc_storage() */ /*------------------------------------------------------------------------- * Function: H5D_init_storage * * Purpose: Initialize the data for a new dataset. If a selection is * defined for SPACE then initialize only that part of the * dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Monday, October 5, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_init_storage) HDassert(dset); switch (dset->shared->layout.type) { case H5D_COMPACT: /* If we will be immediately overwriting the values, don't bother to clear them */ if(!full_overwrite) { /* Fill the compact dataset storage */ if(H5D_compact_fill(dset, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize compact dataset storage") } /* end if */ break; case H5D_CONTIGUOUS: /* 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->shared->dcpl_cache.efl.nused == 0 || dset->shared->dcpl_cache.fill.buf) && !full_overwrite) if(H5D_contig_fill(dset, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") break; case H5D_CHUNKED: /* * Allocate file space * for all chunks now and initialize each chunk with the fill value. */ if(H5D_istore_allocate(dset, dxpl_id, full_overwrite) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") 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 */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_init_storage() */ /*------------------------------------------------------------------------- * Function: H5D_get_storage_size * * Purpose: Determines how much space has been reserved to store the raw * data of a dataset. * * Return: Success: Number of bytes reserved to hold raw data. * * Failure: 0 * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * *------------------------------------------------------------------------- */ hsize_t H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id) { hsize_t ret_value; FUNC_ENTER_NOAPI_NOINIT(H5D_get_storage_size) switch(dset->shared->layout.type) { case H5D_CHUNKED: if(dset->shared->layout.u.chunk.addr == HADDR_UNDEF) ret_value = 0; else ret_value = H5D_istore_allocated(dset, dxpl_id); 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; else ret_value = dset->shared->layout.u.contig.size; break; case H5D_COMPACT: ret_value = dset->shared->layout.u.compact.size; break; default: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type") } /*lint !e788 All appropriate cases are covered */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_get_storage_size() */ /*------------------------------------------------------------------------- * Function: H5D_get_offset * * Purpose: Private function for H5D_get_offset. Returns the address * of dataset in file. * * Return: Success: the address of dataset * * Failure: HADDR_UNDEF * * Programmer: Raymond Lu * November 6, 2002 * *------------------------------------------------------------------------- */ 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) HDassert(dset); switch(dset->shared->layout.type) { case H5D_CHUNKED: case H5D_COMPACT: break; 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; break; default: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type") } /*lint !e788 All appropriate cases are covered */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_get_offset() */ /*------------------------------------------------------------------------- * Function: H5D_iterate * * Purpose: Internal version of H5Diterate() * * Return: Returns the return value of the last operator if it was non-zero, * or zero if all elements were processed. Otherwise returns a * negative value. * * Programmer: Quincey Koziol * Tuesday, November 22, 2005 * *------------------------------------------------------------------------- */ herr_t H5D_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t op, void *operator_data) { herr_t ret_value; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_iterate) /* Check args */ HDassert(buf); HDassert(H5I_DATATYPE == H5I_get_type(type_id)); HDassert(space); HDassert(H5S_has_extent(space)); HDassert(op); ret_value = H5S_select_iterate(buf, type_id, space, op, operator_data); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_iterate() */ /*------------------------------------------------------------------------- * Function: H5D_vlen_reclaim * * Purpose: Frees the buffers allocated for storing variable-length data * in memory. Only frees the VL data in the selection defined in the * dataspace. The dataset transfer property list is required to find the * correct allocation/free methods for the VL data in the buffer. * * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, November 22, 2005 * *------------------------------------------------------------------------- */ herr_t H5D_vlen_reclaim(hid_t type_id, H5S_t *space, hid_t plist_id, void *buf) { H5T_vlen_alloc_info_t _vl_alloc_info; /* VL allocation info buffer */ H5T_vlen_alloc_info_t *vl_alloc_info = &_vl_alloc_info; /* VL allocation info */ herr_t ret_value; FUNC_ENTER_NOAPI(H5D_vlen_reclaim, FAIL) /* Check args */ HDassert(H5I_DATATYPE == H5I_get_type(type_id)); HDassert(space); HDassert(H5P_isa_class(plist_id, H5P_DATASET_XFER)); HDassert(buf); /* Get the allocation info */ if(H5T_vlen_get_alloc_info(plist_id,&vl_alloc_info) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to retrieve VL allocation info") /* Call H5D_iterate with args, etc. */ ret_value = H5D_iterate(buf, type_id, space ,H5T_vlen_reclaim, vl_alloc_info); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_vlen_reclaim() */ /*------------------------------------------------------------------------- * Function: H5D_vlen_get_buf_size_alloc * * Purpose: This routine makes certain there is enough space in the temporary * buffer for the new data to read in. All the VL data read in is actually * placed in this buffer, overwriting the previous data. Needless to say, * this data is not actually usable. * * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, August 17, 1999 * *------------------------------------------------------------------------- */ void * H5D_vlen_get_buf_size_alloc(size_t size, void *info) { H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)info; void *ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_vlen_get_buf_size_alloc) /* Get a temporary pointer to space for the VL data */ if((vlen_bufsize->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize->vl_tbuf, size)) != NULL) vlen_bufsize->size += size; /* Set return value */ ret_value = vlen_bufsize->vl_tbuf; FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_vlen_get_buf_size_alloc() */ /*------------------------------------------------------------------------- * Function: H5D_vlen_get_buf_size * * Purpose: This routine checks the number of bytes required to store a single * element from a dataset in memory, creating a selection with just the * single element selected to read in the element and using a custom memory * allocator for any VL data encountered. * The *size value is modified according to how many bytes are * required to store the element in memory. * * Implementation: This routine actually performs the read with a custom * memory manager which basically just counts the bytes requested and * uses a temporary memory buffer (through the H5FL API) to make certain * enough space is available to perform the read. Then the temporary * buffer is released and the number of bytes allocated is returned. * Kinda kludgy, but easier than the other method of trying to figure out * the sizes without actually reading the data in... - QAK * * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, August 17, 1999 * *------------------------------------------------------------------------- */ /* ARGSUSED */ herr_t H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t *point, void *op_data) { H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data; H5T_t *dt; /* Datatype for operation */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_vlen_get_buf_size) HDassert(op_data); HDassert(H5I_DATATYPE == H5I_get_type(type_id)); /* Check args */ if(NULL == (dt = (H5T_t *)H5I_object(type_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") /* Make certain there is enough fixed-length buffer available */ if(NULL == (vlen_bufsize->fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->fl_tbuf, H5T_get_size(dt)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't resize tbuf") /* Select point to read in */ if(H5Sselect_elements(vlen_bufsize->fspace_id, H5S_SELECT_SET, (size_t)1, (const hsize_t **)point) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't select point") /* Read in the point (with the custom VL memory allocator) */ if(H5Dread(vlen_bufsize->dataset_id, type_id, vlen_bufsize->mspace_id, vlen_bufsize->fspace_id, vlen_bufsize->xfer_pid, vlen_bufsize->fl_tbuf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_vlen_get_buf_size() */ /*------------------------------------------------------------------------- * Function: H5D_check_filters * * Purpose: Check if the filters have be initialized for the dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, October 11, 2007 * *------------------------------------------------------------------------- */ herr_t H5D_check_filters(H5D_t *dataset) { H5O_fill_t *fill; /* Dataset's fill value */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_check_filters) /* Check args */ HDassert(dataset); /* Check if the filters in the DCPL will need to encode, and if so, can they? * * Filters need encoding if fill value is defined and a fill policy is set * that requires writing on an extend. */ fill = &dataset->shared->dcpl_cache.fill; if(!dataset->shared->checked_filters) { H5D_fill_value_t fill_status; /* Whether the fill value is defined */ /* Retrieve the "defined" status of the fill value */ if(H5P_is_fill_value_defined(fill, &fill_status) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Couldn't retrieve fill value from dataset.") /* See if we can check the filter status */ if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { if(fill->fill_time == H5D_FILL_TIME_ALLOC || (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { /* Filters must have encoding enabled. Ensure that all filters can be applied */ if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") dataset->shared->checked_filters = TRUE; } /* end if */ } /* end if */ } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_check_filters() */ /*------------------------------------------------------------------------- * Function: H5D_set_extent * * Purpose: Based on H5D_extend, allows change to a lower dimension, * calls H5S_set_extent and H5D_istore_prune_by_extent instead * * Return: Non-negative on success, negative on failure * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * April 9, 2002 * *------------------------------------------------------------------------- */ 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 */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_set_extent) /* Check args */ HDassert(dset); 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") /* 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") /* Get the data space */ space = dset->shared->space; /* 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") /* 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") /* Don't bother updating things, unless they've changed */ if(changed) { hbool_t shrink = FALSE; /* Flag to indicate a dimension has shrank */ hbool_t expand = FALSE; /* Flag to indicate a dimension has grown */ unsigned u; /* Local index variable */ /* Determine if we are shrinking and/or expanding any dimensions */ for(u = 0; u < (unsigned)rank; u++) { if(size[u] < curr_dims[u]) shrink = TRUE; if(size[u] > curr_dims[u]) expand = TRUE; } /* end for */ /*------------------------------------------------------------------------- * Modify the dataset storage *------------------------------------------------------------------------- */ /* Update the index values for the cached chunks for this dataset */ if(H5D_CHUNKED == dset->shared->layout.type) if(H5D_istore_update_cache(dset, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") /* 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->oloc.file, dxpl_id, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage") /*------------------------------------------------------------------------- * Remove chunk information in the case of chunked datasets * This removal takes place only in case we are shrinking the dateset *------------------------------------------------------------------------- */ if(shrink && H5D_CHUNKED == dset->shared->layout.type) { H5D_io_info_t io_info; /* Dataset I/O info */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Construct dataset I/O info */ H5D_BUILD_IO_INFO(&io_info, dset, dxpl_cache, dxpl_id, NULL); /* Remove excess chunks */ if(H5D_istore_prune_by_extent(&io_info, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ") /* Reset the elements outsize the new dimensions, but in existing chunks */ if(H5D_istore_initialize_by_extent(&io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ") } /* end if */ /* Mark the dataspace as dirty, for later writing to the file */ dset->shared->space_dirty = TRUE; } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_set_extent() */ /*------------------------------------------------------------------------- * Function: H5D_flush_cb * * Purpose: Flush any dataset information cached in memory * * Return: Success: Non-negative * Failure: Negative * * Programmer: Quincey Koziol * November 8, 2007 * *------------------------------------------------------------------------- */ static int H5D_flush_cb(void *_dataset, hid_t UNUSED id, void *_udata) { H5D_t *dataset = (H5D_t *)_dataset; /* Dataset pointer */ H5D_flush_ud_t *udata = (H5D_flush_ud_t *)_udata; /* User data for callback */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_flush_cb) /* Check args */ HDassert(dataset); /* Check for dataset in same file */ if(udata->f == dataset->oloc.file) { /* Update the dataspace on disk, if it's been changed */ if(dataset->shared->space_dirty) { if(H5S_write(&(dataset->oloc), dataset->shared->space, TRUE, udata->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") dataset->shared->space_dirty = FALSE; } /* 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(udata->f, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, dataset->shared->cache.contig.sieve_size, udata->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_istore_flush(dataset, udata->dxpl_id, udata->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), udata->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 */ } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_flush_cb() */ /*------------------------------------------------------------------------- * Function: H5D_flush * * Purpose: Flush any dataset information cached in memory * * Return: Success: Non-negative * Failure: Negative * * Programmer: Ray Lu * August 14, 2002 * *------------------------------------------------------------------------- */ herr_t H5D_flush(const H5F_t *f, hid_t dxpl_id, unsigned flags) { H5D_flush_ud_t udata; /* User data for callback */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_flush, FAIL) /* Check args */ HDassert(f); /* 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); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_flush() */