tcl.git - Tcl is a high-level, general-purpose, interpreted, dynamic programming language. It was designed with the goal of being very simple but powerful.

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Diffstat (limited to 'unix/tclLoadDyld.c')

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 COPYING file, which can be found at the root of the source code * * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /****************/ /* Module Setup */ /****************/ #include "H5Dmodule.h" /* This source code file is part of the H5D module */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Datasets */ #include "H5CXprivate.h" /* API Contexts */ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5FOprivate.h" /* File objects */ #include "H5Iprivate.h" /* IDs */ #include "H5Lprivate.h" /* Links */ #include "H5MMprivate.h" /* Memory management */ /****************/ /* Local Macros */ /****************/ /******************/ /* Local Typedefs */ /******************/ /********************/ /* Local Prototypes */ /********************/ /* General stuff */ 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__cache_dataspace_info(const H5D_t *dset); 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, H5D_t *dset, hid_t dapl_id); static herr_t H5D__build_file_prefix(const H5D_t *dset, hid_t dapl_id, const char *prefix_type, char **file_prefix); static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id); static herr_t H5D__init_storage(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_t old_dim[]); static herr_t H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id); static herr_t H5D__close_cb(H5D_t *dataset); /*********************/ /* Package Variables */ /*********************/ /* 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); /* Declare the external free list to manage the H5D_chunk_info_t struct */ H5FL_EXTERN(H5D_chunk_info_t); /* Declare extern the free list to manage blocks of type conversion data */ H5FL_BLK_EXTERN(type_conv); /* Define a static "default" dataset structure to use to initialize new datasets */ static H5D_shared_t H5D_def_dset; /* Dataset ID class */ static const H5I_class_t H5I_DATASET_CLS[1] = {{ H5I_DATASET, /* ID class value */ 0, /* Class flags */ 0, /* # of reserved IDs for class */ (H5I_free_t)H5D__close_cb /* Callback routine for closing objects of this class */ }}; /* Flag indicating "top" of interface has been initialized */ static hbool_t H5D_top_package_initialize_s = FALSE; /*------------------------------------------------------------------------- * Function: H5D_init * * Purpose: Initialize the interface from some other layer. * * Return: Success: non-negative * * Failure: negative *------------------------------------------------------------------------- */ herr_t H5D_init(void) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* FUNC_ENTER() does all the work */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_init() */ /*-------------------------------------------------------------------------- NAME H5D__init_package -- Initialize interface-specific information USAGE herr_t H5D__init_package() 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 --------------------------------------------------------------------------*/ herr_t H5D__init_package(void) { H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Initialize the atom group for the dataset IDs */ if(H5I_register_type(H5I_DATASET_CLS) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize interface") /* Reset the "default dataset" information */ HDmemset(&H5D_def_dset, 0, sizeof(H5D_shared_t)); /* Get the default dataset creation property list values and initialize the * default dataset with them. */ if(NULL == (def_dcpl = (H5P_genplist_t *)H5I_object(H5P_LST_DATASET_CREATE_ID_g))) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list") /* Get the default data storage layout */ if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve layout") /* Get the default dataset creation properties */ if(H5P_get(def_dcpl, H5D_CRT_EXT_FILE_LIST_NAME, &H5D_def_dset.dcpl_cache.efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve external file list") if(H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.dcpl_cache.fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value") if(H5P_get(def_dcpl, H5O_CRT_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve pipeline filter") /* Mark "top" of interface as initialized, too */ H5D_top_package_initialize_s = TRUE; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__init_package() */ /*------------------------------------------------------------------------- * Function: H5D_top_term_package * * Purpose: Close the "top" of the interface, releasing IDs, etc. * * Return: Success: Positive if anything was done that might * affect other interfaces; zero otherwise. * Failure: Negative. *------------------------------------------------------------------------- */ int H5D_top_term_package(void) { int n = 0; FUNC_ENTER_NOAPI_NOINIT_NOERR if(H5D_top_package_initialize_s) { if(H5I_nmembers(H5I_DATASET) > 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 */ (void)H5I_clear_type(H5I_DATASET, TRUE, FALSE); n++; /*H5I*/ } /* end if */ /* Mark closed */ if(0 == n) H5D_top_package_initialize_s = FALSE; } /* end if */ FUNC_LEAVE_NOAPI(n) } /* end H5D_top_term_package() */ /*------------------------------------------------------------------------- * Function: H5D_term_package * * Purpose: Terminate this interface. * * Note: Finishes shutting down the interface, after * H5D_top_term_package() is called * * Return: Success: Positive if anything was done that might * affect other interfaces; zero otherwise. * Failure: Negative. *------------------------------------------------------------------------- */ int H5D_term_package(void) { int n = 0; FUNC_ENTER_NOAPI_NOINIT_NOERR if(H5_PKG_INIT_VAR) { /* Sanity checks */ HDassert(0 == H5I_nmembers(H5I_DATASET)); HDassert(FALSE == H5D_top_package_initialize_s); /* Destroy the dataset object id group */ n += (H5I_dec_type_ref(H5I_DATASET) > 0); /* Mark closed */ if(0 == n) H5_PKG_INIT_VAR = FALSE; } /* end if */ FUNC_LEAVE_NOAPI(n) } /* end H5D_term_package() */ /*------------------------------------------------------------------------- * Function: H5D__create_named * * Purpose: Internal routine to create a new dataset. * * Return: Success: Non-NULL, pointer to new dataset object. * * Failure: NULL *------------------------------------------------------------------------- */ 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) { H5O_obj_create_t ocrt_info; /* Information for object creation */ H5D_obj_create_t dcrt_info; /* Information for dataset creation */ H5D_t *ret_value = NULL; /* Return value */ FUNC_ENTER_PACKAGE /* 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); /* Set up dataset creation info */ dcrt_info.type_id = type_id; dcrt_info.space = space; dcrt_info.dcpl_id = dcpl_id; dcrt_info.dapl_id = dapl_id; /* Set up object creation information */ ocrt_info.obj_type = H5O_TYPE_DATASET; 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) < 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 dataspace allocation. * * Return: * Success: Non-negative * Failture: Negative *------------------------------------------------------------------------- */ herr_t H5D__get_space_status(const H5D_t *dset, H5D_space_status_t *allocation) { herr_t ret_value = SUCCEED; FUNC_ENTER_PACKAGE HDassert(dset); /* Check for chunked layout */ if(dset->shared->layout.type == H5D_CHUNKED) { hsize_t space_allocated; /* The number of bytes allocated for chunks */ hssize_t snelmts; /* Temporary holder for number of elements in dataspace */ hsize_t nelmts; /* Number of elements in dataspace */ size_t dt_size; /* Size of datatype */ hsize_t full_size; /* The number of bytes in the dataset when fully populated */ /* For chunked layout set the space status by the storage size */ /* Get the dataset's dataspace */ HDassert(dset->shared->space); /* Get the total number of elements in dataset's dataspace */ if((snelmts = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace") nelmts = (hsize_t)snelmts; /* Get the size of the dataset's datatype */ if(0 == (dt_size = H5T_GET_SIZE(dset->shared->type))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype") /* Compute the maximum size of the dataset in bytes */ full_size = nelmts * dt_size; /* Check for overflow during multiplication */ if(nelmts != (full_size / dt_size)) HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed") /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */ if(H5D__get_storage_size(dset, &space_allocated) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of dataset's storage") /* 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 *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; } /* end if */ else { /* For non-chunked layouts set space status by result of is_space_alloc * function */ if(dset->shared->layout.ops->is_space_alloc(&dset->shared->layout.storage)) *allocation = H5D_SPACE_STATUS_ALLOCATED; else *allocation = H5D_SPACE_STATUS_NOT_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 *------------------------------------------------------------------------- */ static H5D_shared_t * H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) { H5D_shared_t *new_dset = NULL; /* New dataset object */ H5P_genplist_t *plist; /* Property list created */ H5D_shared_t *ret_value = NULL; /* Return value */ FUNC_ENTER_STATIC /* 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, FALSE) < 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, FALSE); } /* end else */ /* Set return value */ ret_value = new_dset; done: if(ret_value == NULL) if(new_dset != NULL) { if(new_dset->dcpl_id != 0 && H5I_dec_ref(new_dset->dcpl_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "can't decrement temporary datatype ID") new_dset = 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 *------------------------------------------------------------------------- */ 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_at_least_v18; /* Flag indicating to use at least v18 format versions */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* 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?") /* To use at least v18 format versions or not */ use_at_least_v18 = (H5F_LOW_BOUND(file) >= H5F_LIBVER_V18); /* Copy the datatype if it's a custom datatype or if it'll change when it's location is changed */ if(!immutable || relocatable || use_at_least_v18) { /* 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") /* Convert a datatype (if committed) to a transient type if the committed datatype's file location is different from the file location where the dataset will be created */ if(H5T_convert_committed_datatype(dset->shared->type, file) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get shared datatype info") /* 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 version for datatype */ if(H5T_set_version(file, dset->shared->type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set version of datatype") /* Get a datatype ID for the dataset's datatype */ if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type, FALSE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") } /* end if */ /* Not a custom datatype, just use it directly */ else { if(H5I_inc_ref(type_id, FALSE) < 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__cache_dataspace_info * * Purpose: Cache dataspace info for a dataset * * Return: Success: SUCCEED * Failure: FAIL *------------------------------------------------------------------------- */ static herr_t H5D__cache_dataspace_info(const H5D_t *dset) { int sndims; /* Signed number of dimensions of dataspace rank */ unsigned u; /* Local index value */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity checking */ HDassert(dset); /* Cache info for dataset's dataspace */ if((sndims = H5S_get_simple_extent_dims(dset->shared->space, dset->shared->curr_dims, dset->shared->max_dims)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't cache dataspace dimensions") dset->shared->ndims = (unsigned)sndims; /* Compute the initial 'power2up' values */ for(u = 0; u < dset->shared->ndims; u++) { hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */ if( !(scaled_power2up = H5VM_power2up(dset->shared->curr_dims[u])) ) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get the next power of 2") dset->shared->curr_power2up[u] = scaled_power2up; } /* end for */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__cache_dataspace_info() */ /*------------------------------------------------------------------------- * Function: H5D__init_space * * Purpose: Copy a dataspace for a dataset's use, performing all the * necessary adjustments, etc. * * Return: Success: SUCCEED * Failure: FAIL *------------------------------------------------------------------------- */ static herr_t H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity checking */ HDassert(file); HDassert(dset); HDassert(space); /* 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") /* Cache the dataset's dataspace info */ if(H5D__cache_dataspace_info(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't cache dataspace info") /* Set the version for dataspace */ if(H5S_set_version(file, 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 *------------------------------------------------------------------------- */ static herr_t H5D__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id) { H5O_t *oh = NULL; /* Pointer to dataset's object header */ size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ H5O_loc_t *oloc = NULL; /* Dataset's object location */ H5O_layout_t *layout; /* Dataset's layout information */ H5T_t *type; /* Dataset's datatype */ H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ H5D_fill_value_t fill_status; /* Fill value status */ hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */ hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ hbool_t use_at_least_v18; /* Flag indicating to use at least v18 format versions */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* 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; /* To use at least v18 format versions or not */ use_at_least_v18 = (H5F_LOW_BOUND(file) >= H5F_LIBVER_V18); /* 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, FALSE)) { /* If the default fill value is chosen for variable-length types, always write it */ if(fill_prop->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_DEFAULT) { /* Update dataset creation property */ 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) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type") fill_prop->fill_defined = TRUE; } /* end if */ 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->storage.u.compact.size; /* Create an object header for the dataset */ if(H5O_create(file, ohdr_size, (size_t)1, dset->shared->dcpl_id, oloc/*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header") HDassert(file == dset->oloc.file); /* Pin the object header */ if(NULL == (oh = H5O_pin(oloc))) HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Write the dataspace header message */ if(H5S_append(file, oh, dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message") /* Write the datatype header message */ if(H5O_msg_append_oh(file, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message") /* Write new fill value message */ if(H5O_msg_append_oh(file, 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 using v18 format versions and above */ if(fill_prop->buf && !use_at_least_v18) { 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 isn't 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_oh(file, 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/create the layout (and I/O pipeline & EFL) messages */ if(H5D__layout_oh_create(file, oh, dset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout/pline/efl header message") /* Indicate that the layout information was initialized */ layout_init = TRUE; #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) && (H5P_exist_plist(dc_plist, H5O_BOGUS_MSG_ID_NAME) > 0) ) { uint8_t bogus_flags = 0; /* Flags for creating "bogus" message */ unsigned bogus_id; /* "bogus" ID */ /* Retrieve "bogus" message ID */ if(H5P_get(dc_plist, H5O_BOGUS_MSG_ID_NAME, &bogus_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus ID options") /* 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, oh, bogus_id, (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 using older format. */ /* (If using v18 format versions and above, the the modification time is part of the object * header and doesn't use a separate message -QAK) */ if(!use_at_least_v18) 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(oh != NULL) if(H5O_unpin(oh) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header") /* Error cleanup */ if(ret_value < 0) if(layout_init) /* Destroy the layout information for the dataset */ if(dset->shared->layout.ops->dest && (dset->shared->layout.ops->dest)(dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__update_oh_info() */ /*-------------------------------------------------------------------------- * Function: H5D__build_file_prefix * * Purpose: Determine the file prefix to be used and store * it in file_prefix. Stores an empty string if no prefix * should be used. * * Return: SUCCEED/FAIL *-------------------------------------------------------------------------- */ static herr_t H5D__build_file_prefix(const H5D_t *dset, hid_t dapl_id, const char *prefix_type, char **file_prefix /*out*/) { char *prefix = NULL; /* prefix used to look for the file */ char *filepath = NULL; /* absolute path of directory the HDF5 file is in */ size_t filepath_len; /* length of file path */ size_t prefix_len; /* length of prefix */ size_t file_prefix_len; /* length of expanded prefix */ H5P_genplist_t *plist = NULL; /* Property list pointer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity checks */ HDassert(dset); HDassert(dset->oloc.file); filepath = H5F_EXTPATH(dset->oloc.file); HDassert(filepath); /* XXX: Future thread-safety note - getenv is not required * to be reentrant. */ if(HDstrcmp(prefix_type, H5D_ACS_VDS_PREFIX_NAME) == 0) prefix = HDgetenv("HDF5_VDS_PREFIX"); else if (HDstrcmp(prefix_type, H5D_ACS_EFILE_PREFIX_NAME) == 0) prefix = HDgetenv("HDF5_EXTFILE_PREFIX"); else HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "prefix name is not sensible") if(prefix == NULL || *prefix == '\0') { /* Set prefix to value of prefix_type property */ if(NULL == (plist = H5P_object_verify(dapl_id, H5P_DATASET_ACCESS))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID") if(H5P_peek(plist, prefix_type, &prefix) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get file prefix") } /* end if */ /* Prefix has to be checked for NULL / empty string again because the * code above might have updated it. */ if(prefix == NULL || *prefix == '\0' || HDstrcmp(prefix, ".") == 0) { /* filename is interpreted as relative to the current directory, * does not need to be expanded */ if(NULL == (*file_prefix = (char *)H5MM_strdup(""))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") } /* end if */ else { if (HDstrncmp(prefix, "${ORIGIN}", HDstrlen("${ORIGIN}")) == 0) { /* Replace ${ORIGIN} at beginning of prefix by directory of HDF5 file */ filepath_len = HDstrlen(filepath); prefix_len = HDstrlen(prefix); file_prefix_len = filepath_len + prefix_len - HDstrlen("${ORIGIN}") + 1; if(NULL == (*file_prefix = (char *)H5MM_malloc(file_prefix_len))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate buffer") HDsnprintf(*file_prefix, file_prefix_len, "%s%s", filepath, prefix + HDstrlen("${ORIGIN}")); } /* end if */ else { if(NULL == (*file_prefix = (char *)H5MM_strdup(prefix))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") } /* end else */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__build_file_prefix() */ /*------------------------------------------------------------------------- * 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 *------------------------------------------------------------------------- */ H5D_t * H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, hid_t dapl_id) { const H5T_t *type; /* Datatype for dataset */ H5D_t *new_dset = NULL; 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 layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ hbool_t layout_copied = FALSE; /* Flag to indicate that layout message was copied */ hbool_t fill_copied = FALSE; /* Flag to indicate that fill-value message was copied */ hbool_t pline_copied = FALSE; /* Flag to indicate that pipeline message was copied */ hbool_t efl_copied = FALSE; /* Flag to indicate that external file list message was copied */ H5G_loc_t dset_loc; /* Dataset location */ H5D_t *ret_value = NULL; /* Return value */ FUNC_ENTER_PACKAGE /* check args */ HDassert(file); HDassert(H5I_DATATYPE == H5I_get_type(type_id)); HDassert(space); HDassert(H5I_GENPROP_LST == H5I_get_type(dcpl_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, FALSE)) 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) { H5O_layout_t *layout; /* Dataset's layout information */ H5O_pline_t *pline; /* Dataset's I/O pipeline information */ H5O_fill_t *fill; /* Dataset's fill value info */ H5O_efl_t *efl; /* Dataset's external file list 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, H5O_CRT_PIPELINE_NAME, pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve pipeline filter") pline_copied = TRUE; layout = &new_dset->shared->layout; if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve layout") layout_copied = TRUE; fill = &new_dset->shared->dcpl_cache.fill; if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve fill value info") fill_copied = TRUE; efl = &new_dset->shared->dcpl_cache.efl; if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve external file list") efl_copied = TRUE; /* Check that chunked layout is used if filters are enabled */ if(pline->nused > 0 && H5D_CHUNKED != layout->type) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout") /* 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->type == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation") } /* end if */ /* Set the version for the I/O pipeline message */ if(H5O_pline_set_version(file, &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 version for the fill message */ if(H5O_fill_set_version(file, &new_dset->shared->dcpl_cache.fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of fill value") /* Set the latest version for the layout message */ if(H5D__layout_set_version(file, &new_dset->shared->layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of layout") if(new_dset->shared->layout.version >= H5O_LAYOUT_VERSION_4) { /* Use latest indexing type for layout message version >= 4 */ if(H5D__layout_set_latest_indexing(&new_dset->shared->layout, new_dset->shared->space, &new_dset->shared->dcpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest indexing") } /* end if */ /* Check if this dataset is going into a parallel file and set space allocation time */ if(H5F_HAS_FEATURE(file, H5FD_FEAT_ALLOCATE_EARLY)) new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; /* Set the dataset's I/O operations */ if(H5D__layout_set_io_ops(new_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize I/O operations") /* Create the layout information for the new dataset */ if(new_dset->shared->layout.ops->construct && (new_dset->shared->layout.ops->construct)(file, new_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to construct layout information") /* Update the dataset's object header info. */ if(H5D__update_oh_info(file, new_dset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache") /* Indicate that the layout information was initialized */ layout_init = TRUE; /* Set up append flush parameters for the dataset */ if(H5D__append_flush_setup(new_dset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set up flush append property") /* Set the external file prefix */ if(H5D__build_file_prefix(new_dset, dapl_id, H5D_ACS_EFILE_PREFIX_NAME, &new_dset->shared->extfile_prefix) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix") /* Set the VDS file prefix */ if(H5D__build_file_prefix(new_dset, dapl_id, H5D_ACS_VDS_PREFIX_NAME, &new_dset->shared->vds_prefix) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize VDS prefix") /* 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(layout_init) if(new_dset->shared->layout.ops->dest && (new_dset->shared->layout.ops->dest)(new_dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy layout info") if(pline_copied) if(H5O_msg_reset(H5O_PLINE_ID, &new_dset->shared->dcpl_cache.pline) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset I/O pipeline info") if(layout_copied) if(H5O_msg_reset(H5O_LAYOUT_ID, &new_dset->shared->layout) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset layout info") if(fill_copied) if(H5O_msg_reset(H5O_FILL_ID, &new_dset->shared->dcpl_cache.fill) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset fill-value info") if(efl_copied) if(H5O_msg_reset(H5O_EFL_ID, &new_dset->shared->dcpl_cache.efl) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset external file list info") if(new_dset->shared->space && H5S_close(new_dset->shared->space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace") if(new_dset->shared->type && H5I_dec_ref(new_dset->shared->type_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") if(H5F_addr_defined(new_dset->oloc.addr)) { if(H5O_dec_rc_by_loc(&(new_dset->oloc)) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement refcount on newly created object") if(H5O_close(&(new_dset->oloc), NULL) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header") if(file) { if(H5O_delete(file, 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 && H5I_dec_ref(new_dset->shared->dcpl_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list") new_dset->shared->extfile_prefix = (char *)H5MM_xfree(new_dset->shared->extfile_prefix); new_dset->shared->vds_prefix = (char *)H5MM_xfree(new_dset->shared->vds_prefix); new_dset->shared = H5FL_FREE(H5D_shared_t, new_dset->shared); } /* end if */ new_dset->oloc.file = NULL; new_dset = H5FL_FREE(H5D_t, new_dset); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__create() */ /*------------------------------------------------------------------------- * Function: H5D__open_name * * Purpose: Opens an existing dataset by name. * * Return: Success: Ptr to a new dataset. * Failure: NULL *------------------------------------------------------------------------- */ H5D_t * H5D__open_name(const H5G_loc_t *loc, const char *name, hid_t dapl_id) { H5D_t *dset = NULL; H5G_loc_t dset_loc; /* Object location of dataset */ H5G_name_t path; /* Dataset group hier. path */ H5O_loc_t oloc; /* Dataset object location */ H5O_type_t obj_type; /* Type of object at location */ hbool_t loc_found = FALSE; /* Location at 'name' found */ H5D_t *ret_value = NULL; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(loc); HDassert(name); /* Set up dataset location to fill in */ dset_loc.oloc = &oloc; dset_loc.path = &path; H5G_loc_reset(&dset_loc); /* Find the dataset object */ if(H5G_loc_find(loc, name, &dset_loc) < 0) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") loc_found = TRUE; /* Check that the object found is the correct type */ if(H5O_obj_type(&oloc, &obj_type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get object type") if(obj_type != H5O_TYPE_DATASET) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, NULL, "not a dataset") /* Open the dataset */ if(NULL == (dset = H5D_open(&dset_loc, dapl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't open dataset") /* Set return value */ ret_value = dset; done: if(!ret_value) if(loc_found && H5G_loc_free(&dset_loc) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "can't free location") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__open_name() */ /* *------------------------------------------------------------------------- * Function: H5D_open * * Purpose: Checks if dataset is already open, or opens a dataset for * access. * * Return: Success: Dataset ID * Failure: FAIL *------------------------------------------------------------------------- */ H5D_t * H5D_open(const H5G_loc_t *loc, hid_t dapl_id) { H5D_shared_t *shared_fo = NULL; H5D_t *dataset = NULL; char *extfile_prefix = NULL; /* Expanded external file prefix */ char *vds_prefix = NULL; /* Expanded vds prefix */ H5D_t *ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI(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") /* Get the external file prefix */ if(H5D__build_file_prefix(dataset, dapl_id, H5D_ACS_EFILE_PREFIX_NAME, &extfile_prefix) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix") /* Get the VDS prefix */ if(H5D__build_file_prefix(dataset, dapl_id, H5D_ACS_VDS_PREFIX_NAME, &vds_prefix) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize VDS prefix") /* Check if dataset was already open */ if(NULL == (shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr))) { /* Clear any errors from H5FO_opened() */ H5E_clear_stack(NULL); /* Open the dataset object */ if(H5D__open_oid(dataset, dapl_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; /* Set the external file prefix */ dataset->shared->extfile_prefix = extfile_prefix; /* Prevent string from being freed during done: */ extfile_prefix = NULL; /* Set the vds file prefix */ dataset->shared->vds_prefix = vds_prefix; /* Prevent string from being freed during done: */ vds_prefix = NULL; } /* end if */ else { /* Point to shared info */ dataset->shared = shared_fo; /* Increment # of datasets using shared information */ shared_fo->fo_count++; /* Check whether the external file prefix of the already open dataset * matches the new external file prefix */ if(HDstrcmp(extfile_prefix, dataset->shared->extfile_prefix) != 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "new external file prefix does not match external file prefix of already open dataset") /* 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 */ /* Set the dataset to return */ ret_value = dataset; done: extfile_prefix = (char *)H5MM_xfree(extfile_prefix); vds_prefix = (char *)H5MM_xfree(vds_prefix); if(ret_value == NULL) { /* Free the location--casting away const*/ if(dataset) { if(shared_fo == NULL && dataset->shared) { /* Need to free shared fo */ dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix); dataset->shared->vds_prefix = (char *)H5MM_xfree(dataset->shared->vds_prefix); dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared); } /* end if */ H5O_loc_free(&(dataset->oloc)); H5G_name_free(&(dataset->path)); dataset = H5FL_FREE(H5D_t, dataset); } /* end if */ if(shared_fo) shared_fo->fo_count--; } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_open() */ /* *------------------------------------------------------------------------- * Function: H5D__flush_append_setup * * Purpose: Set the append flush parameters for a dataset * * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ static herr_t H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id) { herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_STATIC /* Check args */ HDassert(dset); HDassert(dset->shared); /* Set default append flush values */ HDmemset(&dset->shared->append_flush, 0, sizeof(dset->shared->append_flush)); /* If the dataset is chunked and there is a non-default DAPL */ if(dapl_id != H5P_DATASET_ACCESS_DEFAULT && dset->shared->layout.type == H5D_CHUNKED) { H5P_genplist_t *dapl; /* data access property list object pointer */ /* Get dataset access property list */ if(NULL == (dapl = (H5P_genplist_t *)H5I_object(dapl_id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for dapl ID"); /* Check if append flush property exists */ if(H5P_exist_plist(dapl, H5D_ACS_APPEND_FLUSH_NAME) > 0) { H5D_append_flush_t info; /* Get append flush property */ if(H5P_get(dapl, H5D_ACS_APPEND_FLUSH_NAME, &info) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get append flush info") if(info.ndims > 0) { hsize_t curr_dims[H5S_MAX_RANK]; /* current dimension sizes */ hsize_t max_dims[H5S_MAX_RANK]; /* current dimension sizes */ int rank; /* dataspace # of dimensions */ unsigned u; /* local index variable */ /* Get dataset rank */ if((rank = H5S_get_simple_extent_dims(dset->shared->space, curr_dims, max_dims)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") if(info.ndims != (unsigned)rank) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "boundary dimension rank does not match dataset rank") /* Validate boundary sizes */ for(u = 0; u < info.ndims; u++) if(info.boundary[u] != 0) /* when a non-zero boundary is set */ /* the dimension is extendible? */ if(max_dims[u] != H5S_UNLIMITED && max_dims[u] == curr_dims[u]) break; /* At least one boundary dimension is not extendible */ if(u != info.ndims) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "boundary dimension is not valid") /* Copy append flush settings */ dset->shared->append_flush.ndims = info.ndims; dset->shared->append_flush.func = info.func; dset->shared->append_flush.udata = info.udata; HDmemcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary)); } /* end if */ } /* end if */ } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__append_flush_setup() */ /*------------------------------------------------------------------------- * Function: H5D__open_oid * * Purpose: Opens a dataset for access. * * Return: Dataset pointer on success, NULL on failure *------------------------------------------------------------------------- */ static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id) { H5P_genplist_t *plist; /* Property list */ H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */ unsigned alloc_time_state; /* Allocation time state */ htri_t msg_exists; /* Whether a particular type of message exists */ hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC_TAG(dataset->oloc.addr) /* 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))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load type info from dataset header") if(H5T_set_loc(dataset->shared->type, dataset->oloc.file, H5T_LOC_DISK) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid datatype location") if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") /* Cache the dataset's dataspace info */ if(H5D__cache_dataspace_info(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't cache dataspace info") /* Get a datatype ID for the dataset's datatype */ if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type, FALSE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") /* Get dataset creation property list object */ if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") /* Get the layout/pline/efl message information */ if(H5D__layout_oh_read(dataset, dapl_id, plist) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout/pline/efl info") /* Indicate that the layout information was initialized */ layout_init = TRUE; /* Set up flush append property */ if(H5D__append_flush_setup(dataset, dapl_id)) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set up flush append property") /* 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((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_NEW_ID)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") if(msg_exists) { if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") } /* end if */ else { /* For backward compatibility, try to retrieve the old fill value message */ if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_ID)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") if(msg_exists) { if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") } /* end if */ else { /* 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; case H5D_VIRTUAL: fill_prop->alloc_time = H5D_ALLOC_TIME_INCR; break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") } /* end switch */ /*lint !e788 All appropriate cases are covered */ } /* end else */ /* If "old" fill value size is 0 (undefined), map it to -1 */ if(fill_prop->size == 0) fill_prop->size = (ssize_t)-1; } /* end if */ alloc_time_state = 0; if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) || (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) || (dataset->shared->layout.type == H5D_VIRTUAL && 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 */ /* * 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_INTENT(dataset->oloc.file) & H5F_ACC_RDWR) && !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) && H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_ALLOCATE_EARLY)) { H5D_io_info_t io_info; io_info.dset = dataset; if(H5D__alloc_storage(&io_info, H5D_ALLOC_OPEN, FALSE, NULL) < 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) && H5O_close(&(dataset->oloc), NULL) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") if(dataset->shared) { if(layout_init) if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") if(dataset->shared->space && H5S_close(dataset->shared->space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") if(dataset->shared->type) { if(dataset->shared->type_id > 0) { if(H5I_dec_ref(dataset->shared->type_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") } /* end if */ else { if(H5T_close_real(dataset->shared->type) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") } /* end else */ } /* end if */ } /* end if */ } /* end if */ FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__open_oid() */ /*------------------------------------------------------------------------- * Function: H5D__close_cb * * Purpose: Callback routine for closing a dataset ID. Closes the dataset * object that was attached to the ID. * * Return: Non-negative on success/Negative on failure * *------------------------------------------------------------------------- */ static herr_t H5D__close_cb(H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* check args */ HDassert(dataset && dataset->oloc.file && dataset->shared); HDassert(dataset->shared->fo_count > 0); /* Call actual dataset close routine */ if(H5D_close(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "can't close dataset"); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__close_cb() */ /*------------------------------------------------------------------------- * 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 *------------------------------------------------------------------------- */ herr_t H5D_close(H5D_t *dataset) { hbool_t free_failed = FALSE; /* Set if freeing sub-components failed */ hbool_t corked; /* Whether the dataset is corked or not */ hbool_t file_closed = TRUE; /* H5O_close also closed the file? */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* check args */ HDassert(dataset && dataset->oloc.file && dataset->shared); HDassert(dataset->shared->fo_count > 0); /* Dump debugging info */ #ifdef H5D_CHUNK_DEBUG H5D__chunk_stats(dataset, FALSE); #endif /* H5D_CHUNK_DEBUG */ dataset->shared->fo_count--; if(dataset->shared->fo_count == 0) { /* Flush the dataset's information. Continue to close even if it fails. */ if(H5D__flush_real(dataset) < 0) HDONE_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info") /* Set a flag to indicate the dataset is closing, before we start freeing things */ /* (Avoids problems with flushing datasets twice, when one is holding * the file open and it iterates through dataset to flush them -QAK) */ dataset->shared->closing = TRUE; /* Free cached information for each kind of dataset */ switch(dataset->shared->layout.type) { case H5D_CONTIGUOUS: /* Free the data sieve buffer, if it's been allocated */ if(dataset->shared->cache.contig.sieve_buf) dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); break; case H5D_CHUNKED: /* Check for skip list for iterating over chunks during I/O to close */ if(dataset->shared->cache.chunk.sel_chunks) { HDassert(H5SL_count(dataset->shared->cache.chunk.sel_chunks) == 0); H5SL_close(dataset->shared->cache.chunk.sel_chunks); dataset->shared->cache.chunk.sel_chunks = NULL; } /* end if */ /* Check for cached single chunk dataspace */ if(dataset->shared->cache.chunk.single_space) { (void)H5S_close(dataset->shared->cache.chunk.single_space); dataset->shared->cache.chunk.single_space = NULL; } /* end if */ /* Check for cached single element chunk info */ if(dataset->shared->cache.chunk.single_chunk_info) { dataset->shared->cache.chunk.single_chunk_info = H5FL_FREE(H5D_chunk_info_t, dataset->shared->cache.chunk.single_chunk_info); dataset->shared->cache.chunk.single_chunk_info = NULL; } /* end if */ break; case H5D_COMPACT: /* Nothing special to do (info freed in the layout destroy) */ break; case H5D_VIRTUAL: { size_t i, j; HDassert(dataset->shared->layout.storage.u.virt.list || (dataset->shared->layout.storage.u.virt.list_nused == 0)); /* Close source datasets */ for(i = 0; i < dataset->shared->layout.storage.u.virt.list_nused; i++) { /* Close source dataset */ if(dataset->shared->layout.storage.u.virt.list[i].source_dset.dset) { HDassert(dataset->shared->layout.storage.u.virt.list[i].source_dset.dset != dataset); if(H5D_close(dataset->shared->layout.storage.u.virt.list[i].source_dset.dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to close source dataset") dataset->shared->layout.storage.u.virt.list[i].source_dset.dset = NULL; } /* end if */ /* Close sub datasets */ for(j = 0; j < dataset->shared->layout.storage.u.virt.list[i].sub_dset_nused; j++) if(dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset) { HDassert(dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset != dataset); if(H5D_close(dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to close source dataset") dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset = NULL; } /* end if */ } /* end for */ } /* end block */ break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: 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 */ /* Destroy any cached layout information for the dataset */ if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") /* Free the external file prefix */ dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix); /* Free the vds file prefix */ dataset->shared->vds_prefix = (char *)H5MM_xfree(dataset->shared->vds_prefix); /* Release layout, fill-value, efl & pipeline messages */ if(dataset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) free_failed |= (H5O_msg_reset(H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline) < 0) || (H5O_msg_reset(H5O_LAYOUT_ID, &dataset->shared->layout) < 0) || (H5O_msg_reset(H5O_FILL_ID, &dataset->shared->dcpl_cache.fill) < 0) || (H5O_msg_reset(H5O_EFL_ID, &dataset->shared->dcpl_cache.efl) < 0); /* Uncork cache entries with object address tag */ if(H5AC_cork(dataset->oloc.file, dataset->oloc.addr, H5AC__GET_CORKED, &corked) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve an object's cork status") if(corked) if(H5AC_cork(dataset->oloc.file, dataset->oloc.addr, H5AC__UNCORK, NULL) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTUNCORK, FAIL, "unable to uncork an object") /* * 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) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") if(H5FO_delete(dataset->oloc.file, dataset->oloc.addr) < 0) HDONE_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), &file_closed) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") /* Evict dataset metadata if evicting on close */ if(!file_closed && H5F_SHARED(dataset->oloc.file) && H5F_EVICT_ON_CLOSE(dataset->oloc.file)) { if(H5AC_flush_tagged_metadata(dataset->oloc.file, dataset->oloc.addr) < 0) HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata") if(H5AC_evict_tagged_metadata(dataset->oloc.file, dataset->oloc.addr, FALSE) < 0) HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to evict tagged metadata") } /* end if */ /* * 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; dataset->shared = 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), NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close") } /* end if */ else /* Free object location (i.e. "unhold" the file if appropriate) */ if(H5O_loc_free(&(dataset->oloc)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "problem attempting to free location") } /* end else */ /* Release the dataset's path info */ if(H5G_name_free(&(dataset->path)) < 0) free_failed = TRUE; /* Free the dataset's memory structure */ dataset = 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_mult_refresh_close * * Purpose: Closing down the needed information when the dataset has * multiple opens. (From H5O_refresh_metadata_close()) * * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ herr_t H5D_mult_refresh_close(hid_t dset_id) { H5D_t *dataset; /* Dataset to refresh */ herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_NOAPI(FAIL) if(NULL == (dataset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") /* check args */ HDassert(dataset && dataset->oloc.file && dataset->shared); HDassert(dataset->shared->fo_count > 0); if(dataset->shared->fo_count > 1) { /* Free cached information for each kind of dataset */ switch(dataset->shared->layout.type) { case H5D_CONTIGUOUS: /* Free the data sieve buffer, if it's been allocated */ if(dataset->shared->cache.contig.sieve_buf) dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); break; case H5D_CHUNKED: /* Check for skip list for iterating over chunks during I/O to close */ if(dataset->shared->cache.chunk.sel_chunks) { HDassert(H5SL_count(dataset->shared->cache.chunk.sel_chunks) == 0); H5SL_close(dataset->shared->cache.chunk.sel_chunks); dataset->shared->cache.chunk.sel_chunks = NULL; } /* end if */ /* Check for cached single chunk dataspace */ if(dataset->shared->cache.chunk.single_space) { (void)H5S_close(dataset->shared->cache.chunk.single_space); dataset->shared->cache.chunk.single_space = NULL; } /* end if */ /* Check for cached single element chunk info */ if(dataset->shared->cache.chunk.single_chunk_info) { dataset->shared->cache.chunk.single_chunk_info = H5FL_FREE(H5D_chunk_info_t, dataset->shared->cache.chunk.single_chunk_info); dataset->shared->cache.chunk.single_chunk_info = NULL; } /* end if */ break; case H5D_COMPACT: case H5D_VIRTUAL: /* Nothing special to do (info freed in the layout destroy) */ break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: 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 */ /* Destroy any cached layout information for the dataset */ if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_mult_refresh_close() */ /*------------------------------------------------------------------------- * Function: H5D_mult_refresh_reopen * * Purpose: Re-initialize the needed info when the dataset has multiple * opens. * * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ herr_t H5D_mult_refresh_reopen(H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* check args */ HDassert(dataset && dataset->oloc.file && dataset->shared); HDassert(dataset->shared->fo_count > 0); if(dataset->shared->fo_count > 1) { /* Release dataspace info */ if(H5S_close(dataset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release dataspace") /* Re-load dataspace info */ if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") /* Cache the dataset's dataspace info */ if(H5D__cache_dataspace_info(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't cache dataspace info") /* Release layout info */ if(H5O_msg_reset(H5O_LAYOUT_ID, &dataset->shared->layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset layout info") /* Re-load layout message info */ if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_mult_refresh_reopen() */ /*------------------------------------------------------------------------- * Function: H5D_oloc * * Purpose: Returns a pointer to the object location for a dataset. * * Return: Success: Ptr to location * Failure: NULL *------------------------------------------------------------------------- */ H5O_loc_t * H5D_oloc(H5D_t *dataset) { /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOERR 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 *------------------------------------------------------------------------- */ H5G_name_t * H5D_nameof(H5D_t *dataset) { /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOERR 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 *------------------------------------------------------------------------- */ H5T_t * H5D_typeof(const H5D_t *dset) { /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOERR HDassert(dset); HDassert(dset->shared); HDassert(dset->shared->type); FUNC_LEAVE_NOAPI(dset->shared->type) } /* end H5D_typeof() */ /*------------------------------------------------------------------------- * Function: H5D__alloc_storage * * Purpose: Allocate storage for the raw data of a dataset. * * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ herr_t H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, hbool_t full_overwrite, hsize_t old_dim[]) { const H5D_t *dset = io_info->dset; /* The dataset object */ H5F_t *f = dset->oloc.file; /* The dataset's file pointer */ 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_PACKAGE /* check args */ HDassert(dset); HDassert(f); /* 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(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { /* Check if we have a zero-sized dataset */ if(layout->storage.u.contig.size > 0) { /* Reserve space in the file for the entire array */ if(H5D__contig_alloc(f, &layout->storage.u.contig/*out*/) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") /* Indicate that we should initialize storage space */ must_init_space = TRUE; } /* end if */ else layout->storage.u.contig.addr = HADDR_UNDEF; /* Indicate that we set the storage addr */ addr_set = TRUE; } /* end if */ break; case H5D_CHUNKED: if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { /* Create the root of the index that manages chunked storage */ if(H5D__chunk_create(dset /*in,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 * index 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(NULL == layout->storage.u.compact.buf) { /* Reserve space in layout header message for the entire array. * Starting from the 1.8.7 release, we allow dataspace to have * zero dimension size. So the storage size can be zero. * SLU 2011/4/4 */ if(layout->storage.u.compact.size > 0) { if(NULL == (layout->storage.u.compact.buf = H5MM_malloc(layout->storage.u.compact.size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset") if(!full_overwrite) HDmemset(layout->storage.u.compact.buf, 0, layout->storage.u.compact.size); layout->storage.u.compact.dirty = TRUE; /* Indicate that we should initialize storage space */ must_init_space = TRUE; } else { layout->storage.u.compact.dirty = FALSE; must_init_space = FALSE; } } /* end if */ break; case H5D_VIRTUAL: /* No-op, as the raw data is stored elsewhere and the global * heap object containing the mapping information is created * when the layout message is encoded. We may wish to move the * creation of the global heap object here at some point, but we * will have to make sure is it always created before the * dataset is closed. */ break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: 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 index 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(io_info, full_overwrite, old_dim) < 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(io_info, full_overwrite, old_dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") } /* end else */ } /* end if */ /* If we set the address (and aren't in the middle of creating the * dataset), mark the layout header message for later writing to * the file. (this improves forward compatibility). */ /* (The layout message is already in the dataset's object header, this * operation just sets the address and makes it constant) */ if(time_alloc != H5D_ALLOC_CREATE && addr_set) /* Mark the layout as dirty, for later writing to the file */ if(H5D__mark(dset, H5D_MARK_LAYOUT) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark dataspace as dirty") } /* 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 *------------------------------------------------------------------------- */ static herr_t H5D__init_storage(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_t old_dim[]) { const H5D_t *dset = io_info->dset; /* dataset pointer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC 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) < 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(io_info) < 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. */ { hsize_t zero_dim[H5O_LAYOUT_NDIMS] = {0}; /* Use zeros for old dimensions if not specified */ if(old_dim == NULL) old_dim = zero_dim; if(H5D__chunk_allocate(io_info, full_overwrite, old_dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") break; } /* end block */ case H5D_VIRTUAL: /* No-op, as the raw data is stored elsewhere */ case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: 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: Non-negative on success, negative on failure *------------------------------------------------------------------------- */ herr_t H5D__get_storage_size(const H5D_t *dset, hsize_t *storage_size) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) switch(dset->shared->layout.type) { case H5D_CHUNKED: if((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { if(H5D__chunk_allocated(dset, storage_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve chunked dataset allocated size") } /* end if */ else *storage_size = 0; break; case H5D_CONTIGUOUS: /* Datasets which are not allocated yet are using no space on disk */ if((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) *storage_size = dset->shared->layout.storage.u.contig.size; else *storage_size = 0; break; case H5D_COMPACT: *storage_size = dset->shared->layout.storage.u.compact.size; break; case H5D_VIRTUAL: /* Just set to 0, as virtual datasets do not actually store raw data */ *storage_size = 0; break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: default: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset type") } /*lint !e788 All appropriate cases are covered */ done: FUNC_LEAVE_NOAPI_TAG(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 *------------------------------------------------------------------------- */ haddr_t H5D__get_offset(const H5D_t *dset) { haddr_t ret_value = HADDR_UNDEF; FUNC_ENTER_PACKAGE HDassert(dset); switch(dset->shared->layout.type) { case H5D_VIRTUAL: 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. */ if(dset->shared->dcpl_cache.efl.nused == 0 || H5F_addr_defined(dset->shared->layout.storage.u.contig.addr)) /* Return the absolute dataset offset from the beginning of file. */ ret_value = dset->shared->layout.storage.u.contig.addr + H5F_BASE_ADDR(dset->oloc.file); break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: 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_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. * * Return: Non-negative on success, negative on failure *------------------------------------------------------------------------- */ herr_t H5D_vlen_reclaim(hid_t type_id, H5S_t *space, void *buf) { H5T_t *type; /* Datatype */ H5S_sel_iter_op_t dset_op; /* Operator for iteration */ H5T_vlen_alloc_info_t vl_alloc_info; /* VL allocation info */ herr_t ret_value = FAIL; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* Check args */ HDassert(H5I_DATATYPE == H5I_get_type(type_id)); HDassert(space); HDassert(buf); if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype") /* Get the allocation info */ if(H5CX_get_vlen_alloc_info(&vl_alloc_info) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to retrieve VL allocation info") /* Call H5S_select_iterate with args, etc. */ dset_op.op_type = H5S_SEL_ITER_OP_APP; dset_op.u.app_op.op = H5T_vlen_reclaim; dset_op.u.app_op.type_id = type_id; ret_value = H5S_select_iterate(buf, type, space, &dset_op, &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 *------------------------------------------------------------------------- */ 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 = NULL; /* Return value */ FUNC_ENTER_PACKAGE_NOERR /* 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 *------------------------------------------------------------------------- */ herr_t H5D__vlen_get_buf_size(void H5_ATTR_UNUSED *elem, hid_t type_id, unsigned H5_ATTR_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_PACKAGE 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_DATASET, 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_DATASET, H5E_NOSPACE, FAIL, "can't resize tbuf") /* Select point to read in */ if(H5S_select_elements(vlen_bufsize->fspace, H5S_SELECT_SET, (size_t)1, point) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't select point") /* Read in the point (with the custom VL memory allocator) */ if(H5D__read(vlen_bufsize->dset, type_id, vlen_bufsize->mspace, vlen_bufsize->fspace, 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 *------------------------------------------------------------------------- */ 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_PACKAGE /* 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__chunk_prune_by_extent instead * * Return: Non-negative on success, negative on failure *------------------------------------------------------------------------- */ herr_t H5D__set_extent(H5D_t *dset, const hsize_t *size) { hsize_t curr_dims[H5S_MAX_RANK]; /* Current dimension sizes */ htri_t changed; /* Whether the dataspace changed size */ size_t u, v; /* Local index variable */ unsigned dim_idx; /* Dimension index */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) /* Check args */ HDassert(dset); HDassert(size); /* Check if we are allowed to modify this file */ if(0 == (H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file") /* Check if we are allowed to modify the space; only datasets with chunked and external storage are allowed to be modified */ if(H5D_COMPACT == dset->shared->layout.type) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "dataset has compact storage") if(H5D_CONTIGUOUS == dset->shared->layout.type && 0 == dset->shared->dcpl_cache.efl.nused) HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "dataset has contiguous storage") /* Check if the filters in the DCPL will need to encode, and if so, can they? */ if(H5D__check_filters(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't apply filters") /* Keep the current dataspace dimensions for later */ HDcompile_assert(sizeof(curr_dims) == sizeof(dset->shared->curr_dims)); HDmemcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0])); /* Modify the size of the dataspace */ if((changed = H5S_set_extent(dset->shared->space, size)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") /* 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 */ hbool_t update_chunks = FALSE; /* Flag to indicate chunk cache update is needed */ /* Determine if we are shrinking and/or expanding any dimensions */ for(dim_idx = 0; dim_idx < dset->shared->ndims; dim_idx++) { /* Check for various status changes */ if(size[dim_idx] < curr_dims[dim_idx]) shrink = TRUE; if(size[dim_idx] > curr_dims[dim_idx]) expand = TRUE; /* Chunked storage specific checks */ if(H5D_CHUNKED == dset->shared->layout.type && dset->shared->ndims > 1) { hsize_t scaled; /* Scaled value */ /* Compute the scaled dimension size value */ if(dset->shared->layout.u.chunk.dim[dim_idx] == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", dim_idx) scaled = size[dim_idx] / dset->shared->layout.u.chunk.dim[dim_idx]; /* Check if scaled dimension size changed */ if(scaled != dset->shared->cache.chunk.scaled_dims[dim_idx]) { hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */ /* Update the scaled dimension size value for the current dimension */ dset->shared->cache.chunk.scaled_dims[dim_idx] = scaled; /* Check if algorithm for computing hash values will change */ if((scaled > dset->shared->cache.chunk.nslots && dset->shared->cache.chunk.scaled_dims[dim_idx] <= dset->shared->cache.chunk.nslots) || (scaled <= dset->shared->cache.chunk.nslots && dset->shared->cache.chunk.scaled_dims[dim_idx] > dset->shared->cache.chunk.nslots)) update_chunks = TRUE; if(!(scaled_power2up = H5VM_power2up(scaled))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get the next power of 2") /* Check if the number of bits required to encode the scaled size value changed */ if(dset->shared->cache.chunk.scaled_power2up[dim_idx] != scaled_power2up) { /* Update the 'power2up' & 'encode_bits' values for the current dimension */ dset->shared->cache.chunk.scaled_power2up[dim_idx] = scaled_power2up; dset->shared->cache.chunk.scaled_encode_bits[dim_idx] = H5VM_log2_gen(scaled_power2up); /* Indicate that the cached chunk indices need to be updated */ update_chunks = TRUE; } /* end if */ } /* end if */ } /* end if */ /* Update the cached copy of the dataset's dimensions */ dset->shared->curr_dims[dim_idx] = size[dim_idx]; } /* end for */ /*------------------------------------------------------------------------- * Modify the dataset storage *------------------------------------------------------------------------- */ /* Update the index values for the cached chunks for this dataset */ if(H5D_CHUNKED == dset->shared->layout.type) { /* Set the cached chunk info */ if(H5D__chunk_set_info(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to update # of chunks") /* Check if updating the chunk cache indices is necessary */ if(update_chunks) /* Update the chunk cache indices */ if(H5D__chunk_update_cache(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") } /* end if */ /* Operations for virtual datasets */ if(H5D_VIRTUAL == dset->shared->layout.type) { /* Check that the dimensions of the VDS are large enough */ if(H5D_virtual_check_min_dims(dset) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "virtual dataset dimensions not large enough to contain all limited dimensions in all selections") /* Patch the virtual selection dataspaces */ for(u = 0; u < dset->shared->layout.storage.u.virt.list_nused; u++) { /* Patch extent */ if(H5S_set_extent(dset->shared->layout.storage.u.virt.list[u].source_dset.virtual_select, size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") dset->shared->layout.storage.u.virt.list[u].virtual_space_status = H5O_VIRTUAL_STATUS_CORRECT; /* Patch sub-source datasets */ for(v = 0; v < dset->shared->layout.storage.u.virt.list[u].sub_dset_nalloc; v++) if(H5S_set_extent(dset->shared->layout.storage.u.virt.list[u].sub_dset[v].virtual_select, size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") } /* end for */ /* Mark virtual datasets as not fully initialized so internal * selections are recalculated (at next I/O operation) */ dset->shared->layout.storage.u.virt.init = FALSE; } /* end if */ /* Allocate space for the new parts of the dataset, if appropriate */ if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY) { H5D_io_info_t io_info; io_info.dset = dset; if(H5D__alloc_storage(&io_info, H5D_ALLOC_EXTEND, FALSE, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset storage") } /* end if */ /*------------------------------------------------------------------------- * Remove chunk information in the case of chunked datasets * This removal takes place only in case we are shrinking the dateset * and if the chunks are written *------------------------------------------------------------------------- */ if(H5D_CHUNKED == dset->shared->layout.type) { if(shrink && (*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) /* Remove excess chunks */ if(H5D__chunk_prune_by_extent(dset, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks") /* Update chunks that are no longer edge chunks as a result of * expansion */ if(expand && (dset->shared->layout.u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) && (dset->shared->dcpl_cache.pline.nused > 0)) if(H5D__chunk_update_old_edge_chunks(dset, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to do update old edge chunks") } /* end if */ /* Mark the dataspace as dirty, for later writing to the file */ if(H5D__mark(dset, H5D_MARK_SPACE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark dataspace as dirty") } /* end if */ done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__set_extent() */ /*------------------------------------------------------------------------- * Function: H5D__flush_sieve_buf * * Purpose: Flush any dataset sieve buffer info cached in memory * * Return: Success: Non-negative * Failure: Negative *------------------------------------------------------------------------- */ herr_t H5D__flush_sieve_buf(H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dataset); /* Flush the raw data buffer, if we have a dirty one */ if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) { HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ /* Write dirty data sieve buffer to file */ if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, dataset->shared->cache.contig.sieve_size, dataset->shared->cache.contig.sieve_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") /* Reset sieve buffer dirty flag */ dataset->shared->cache.contig.sieve_dirty = FALSE; } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__flush_sieve_buf() */ /*------------------------------------------------------------------------- * Function: H5D__flush_real * * Purpose: Flush any dataset information cached in memory * * Return: Success: Non-negative * Failure: Negative *------------------------------------------------------------------------- */ herr_t H5D__flush_real(H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) /* Check args */ HDassert(dataset); HDassert(dataset->shared); /* Avoid flushing the dataset (again) if it's closing */ if(!dataset->shared->closing) /* Flush cached raw data for each kind of dataset layout */ if(dataset->shared->layout.ops->flush && (dataset->shared->layout.ops->flush)(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush raw data") done: FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__flush_real() */ /*------------------------------------------------------------------------- * Function: H5D__flush * * Purpose: Flush dataset information cached in memory * * Return: Success: Non-negative * Failure: Negative *------------------------------------------------------------------------- */ herr_t H5D__flush(H5D_t *dset, hid_t dset_id) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dset); HDassert(dset->shared); /* Flush any dataset information still cached in memory */ if(H5D__flush_real(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush cached dataset info") /* Flush object's metadata to file */ if(H5O_flush_common(&dset->oloc, dset_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush dataset and object flush callback") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__flush() */ /*------------------------------------------------------------------------- * Function: H5D__format_convert * * Purpose: For chunked: downgrade the chunk indexing type to version 1 B-tree * For compact/contiguous: downgrade layout version to 3 * * Return: Success: Non-negative * Failure: Negative *------------------------------------------------------------------------- */ herr_t H5D__format_convert(H5D_t *dataset) { H5D_chk_idx_info_t new_idx_info; /* Index info for the new layout */ H5D_chk_idx_info_t idx_info; /* Index info for the current layout */ H5O_layout_t *newlayout = NULL; /* The new layout */ hbool_t init_new_index = FALSE; /* Indicate that the new chunk index is initialized */ hbool_t delete_old_layout = FALSE; /* Indicate that the old layout message is deleted */ hbool_t add_new_layout = FALSE; /* Indicate that the new layout message is added */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) /* Check args */ HDassert(dataset); switch(dataset->shared->layout.type) { case H5D_CHUNKED: HDassert(dataset->shared->layout.u.chunk.idx_type != H5D_CHUNK_IDX_BTREE); if(NULL == (newlayout = (H5O_layout_t *)H5MM_calloc(sizeof(H5O_layout_t)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate buffer") /* Set up the current index info */ idx_info.f = dataset->oloc.file; idx_info.pline = &dataset->shared->dcpl_cache.pline; idx_info.layout = &dataset->shared->layout.u.chunk; idx_info.storage = &dataset->shared->layout.storage.u.chunk; /* Copy the current layout info to the new layout */ HDmemcpy(newlayout, &dataset->shared->layout, sizeof(H5O_layout_t)); /* Set up info for version 1 B-tree in the new layout */ newlayout->version = H5O_LAYOUT_VERSION_3; newlayout->storage.u.chunk.idx_type = H5D_CHUNK_IDX_BTREE; newlayout->storage.u.chunk.idx_addr = HADDR_UNDEF; newlayout->storage.u.chunk.ops = H5D_COPS_BTREE; newlayout->storage.u.chunk.u.btree.shared = NULL; /* Set up the index info to version 1 B-tree */ new_idx_info.f = dataset->oloc.file; new_idx_info.pline = &dataset->shared->dcpl_cache.pline; new_idx_info.layout = &(newlayout->u).chunk; new_idx_info.storage = &(newlayout->storage).u.chunk; /* Initialize version 1 B-tree */ if(new_idx_info.storage->ops->init && (new_idx_info.storage->ops->init)(&new_idx_info, dataset->shared->space, dataset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information") init_new_index = TRUE; /* If the current chunk index exists */ if(H5F_addr_defined(idx_info.storage->idx_addr)) { /* Create v1 B-tree chunk index */ if((new_idx_info.storage->ops->create)(&new_idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index") /* Iterate over the chunks in the current index and insert the chunk addresses * into the version 1 B-tree chunk index */ if(H5D__chunk_format_convert(dataset, &idx_info, &new_idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate/convert chunk index") } /* end if */ /* Delete the old "current" layout message */ if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE) < 0) HGOTO_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message") delete_old_layout = TRUE; /* Append the new layout message to the object header */ if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, newlayout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout header message") add_new_layout = TRUE; /* Release the old (current) chunk index */ if(idx_info.storage->ops->dest && (idx_info.storage->ops->dest)(&idx_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") /* Copy the new layout to the dataset's layout */ HDmemcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t)); break; case H5D_CONTIGUOUS: case H5D_COMPACT: HDassert(dataset->shared->layout.version > H5O_LAYOUT_VERSION_DEFAULT); dataset->shared->layout.version = H5O_LAYOUT_VERSION_DEFAULT; if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout)) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") break; case H5D_VIRTUAL: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "virtual dataset layout not supported") case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type") default: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unknown dataset layout type") } /* end switch */ done: if(ret_value < 0 && dataset->shared->layout.type == H5D_CHUNKED) { /* Remove new layout message */ if(add_new_layout) if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE) < 0) HDONE_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message") /* Add back old layout message */ if(delete_old_layout) if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &dataset->shared->layout) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to add layout header message") /* Clean up v1 b-tree chunk index */ if(init_new_index) { if(H5F_addr_defined(new_idx_info.storage->idx_addr)) { /* Check for valid address i.e. tag */ if(!H5F_addr_defined(dataset->oloc.addr)) HDONE_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "address undefined") /* Expunge from cache all v1 B-tree type entries associated with tag */ if(H5AC_expunge_tag_type_metadata(dataset->oloc.file, dataset->oloc.addr, H5AC_BT_ID, H5AC__NO_FLAGS_SET)) HDONE_ERROR(H5E_DATASET, H5E_CANTEXPUNGE, FAIL, "unable to expunge index metadata") } /* end if */ /* Delete v1 B-tree chunk index */ if(new_idx_info.storage->ops->dest && (new_idx_info.storage->ops->dest)(&new_idx_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") } /* end if */ } /* end if */ if(newlayout != NULL) newlayout = (H5O_layout_t *)H5MM_xfree(newlayout); FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__format_convert() */ /*------------------------------------------------------------------------- * Function: H5D__mark * * Purpose: Mark some aspect of a dataset as dirty * * Return: Success: Non-negative * Failure: Negative *------------------------------------------------------------------------- */ herr_t H5D__mark(const H5D_t *dataset, unsigned flags) { H5O_t *oh = NULL; /* Pointer to dataset's object header */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dataset); HDassert(!(flags & (unsigned)~(H5D_MARK_SPACE | H5D_MARK_LAYOUT))); /* Mark aspects of the dataset as dirty */ if(flags) { unsigned update_flags = H5O_UPDATE_TIME; /* Modification time flag */ /* Pin the object header */ if(NULL == (oh = H5O_pin(&dataset->oloc))) HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Update the layout on disk, if it's been changed */ if(flags & H5D_MARK_LAYOUT) { if(H5D__layout_oh_write(dataset, oh, update_flags) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout info") /* Reset the "update the modification time" flag, so we only do it once */ update_flags = 0; } /* end if */ /* Update the dataspace on disk, if it's been changed */ if(flags & H5D_MARK_SPACE) { if(H5S_write(dataset->oloc.file, oh, update_flags, dataset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") /* Reset the "update the modification time" flag, so we only do it once */ update_flags = 0; } /* end if */ /* _Somebody_ should have update the modification time! */ HDassert(update_flags == 0); } /* end if */ done: /* Release pointer to object header */ if(oh != NULL) if(H5O_unpin(oh) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__mark() */ /*------------------------------------------------------------------------- * Function: H5D__flush_all_cb * * Purpose: Flush any dataset information cached in memory * * Return: Success: Non-negative * Failure: Negative *------------------------------------------------------------------------- */ static int H5D__flush_all_cb(void *_dataset, hid_t H5_ATTR_UNUSED id, void *_udata) { H5D_t *dataset = (H5D_t *)_dataset; /* Dataset pointer */ H5F_t *f = (H5F_t *)_udata; /* User data for callback */ int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_STATIC /* Check args */ HDassert(dataset); HDassert(f); /* Check for dataset in same file */ if(f == dataset->oloc.file) /* Flush the dataset's information */ if(H5D__flush_real(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to flush cached dataset info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__flush_all_cb() */ /*------------------------------------------------------------------------- * Function: H5D_flush_all * * Purpose: Flush any dataset information cached in memory * * Return: Success: Non-negative * Failure: Negative *------------------------------------------------------------------------- */ herr_t H5D_flush_all(const H5F_t *f) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* Check args */ HDassert(f); /* Iterate over all the open datasets */ if(H5I_iterate(H5I_DATASET, H5D__flush_all_cb, (void *)f, FALSE) < 0) /* Casting away const OK -QAK */ HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to flush cached dataset info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_flush_all() */ /*------------------------------------------------------------------------- * Function: H5D_get_create_plist * * Purpose: Private function for H5Dget_create_plist * * Return: Success: ID for a copy of the dataset creation * property list. The template should be * released by calling H5P_close(). * Failure: FAIL *------------------------------------------------------------------------- */ hid_t H5D_get_create_plist(const H5D_t *dset) { H5P_genplist_t *dcpl_plist; /* Dataset's DCPL */ H5P_genplist_t *new_plist; /* Copy of dataset's DCPL */ H5O_layout_t copied_layout; /* Layout to tweak */ H5O_fill_t copied_fill; /* Fill value to tweak */ H5O_efl_t copied_efl; /* External file list to tweak */ hid_t new_dcpl_id = FAIL; hid_t ret_value = H5I_INVALID_HID; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* Check args */ if(NULL == (dcpl_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get property list") /* Copy the creation property list */ if((new_dcpl_id = H5P_copy_plist(dcpl_plist, TRUE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to copy the creation property list") if(NULL == (new_plist = (H5P_genplist_t *)H5I_object(new_dcpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get property list") /* Retrieve any object creation properties */ if(H5O_get_create_plist(&dset->oloc, new_plist) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get object creation info") /* Get the layout property */ if(H5P_peek(new_plist, H5D_CRT_LAYOUT_NAME, &copied_layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout") /* Reset layout values set when dataset is created */ copied_layout.ops = NULL; switch(copied_layout.type) { case H5D_COMPACT: copied_layout.storage.u.compact.buf = H5MM_xfree(copied_layout.storage.u.compact.buf); HDmemset(&copied_layout.storage.u.compact, 0, sizeof(copied_layout.storage.u.compact)); break; case H5D_CONTIGUOUS: copied_layout.storage.u.contig.addr = HADDR_UNDEF; copied_layout.storage.u.contig.size = 0; break; case H5D_CHUNKED: /* Reset chunk size */ copied_layout.u.chunk.size = 0; /* Reset index info, if the chunk ops are set */ if(copied_layout.storage.u.chunk.ops) /* Reset address and pointer of the array struct for the chunked storage index */ if(H5D_chunk_idx_reset(&copied_layout.storage.u.chunk, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to reset chunked storage index in dest") /* Reset chunk index ops */ copied_layout.storage.u.chunk.ops = NULL; break; case H5D_VIRTUAL: copied_layout.storage.u.virt.serial_list_hobjid.addr = HADDR_UNDEF; copied_layout.storage.u.virt.serial_list_hobjid.idx = 0; break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: default: HDassert(0 && "Unknown layout type!"); } /* end switch */ /* Set back the (possibly modified) layout property to property list */ if(H5P_poke(new_plist, H5D_CRT_LAYOUT_NAME, &copied_layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set layout") /* Get the fill value property */ if(H5P_peek(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value") /* Check if there is a fill value, but no type yet */ if(copied_fill.buf != NULL && copied_fill.type == NULL) { H5T_path_t *tpath; /* Conversion information*/ /* Copy the dataset type into the fill value message */ if(NULL == (copied_fill.type = H5T_copy(dset->shared->type, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy dataset datatype for fill value") /* Set up type conversion function */ if(NULL == (tpath = H5T_path_find(dset->shared->type, copied_fill.type))) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types") /* Convert disk form of fill value into memory form */ if(!H5T_path_noop(tpath)) { hid_t dst_id, src_id; /* Source & destination datatypes for type conversion */ uint8_t *bkg_buf = NULL; /* Background conversion buffer */ size_t bkg_size; /* Size of background buffer */ /* Wrap copies of types to convert */ dst_id = H5I_register(H5I_DATATYPE, H5T_copy(copied_fill.type, H5T_COPY_TRANSIENT), FALSE); if(dst_id < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy/register datatype") src_id = H5I_register(H5I_DATATYPE, H5T_copy(dset->shared->type, H5T_COPY_ALL), FALSE); if(src_id < 0) { H5I_dec_ref(dst_id); HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy/register datatype") } /* end if */ /* Allocate a background buffer */ bkg_size = MAX(H5T_GET_SIZE(copied_fill.type), H5T_GET_SIZE(dset->shared->type)); if(H5T_path_bkg(tpath) && NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, bkg_size))) { H5I_dec_ref(src_id); H5I_dec_ref(dst_id); HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed") } /* end if */ /* Convert fill value */ if(H5T_convert(tpath, src_id, dst_id, (size_t)1, (size_t)0, (size_t)0, copied_fill.buf, bkg_buf) < 0) { H5I_dec_ref(src_id); H5I_dec_ref(dst_id); if(bkg_buf) bkg_buf = H5FL_BLK_FREE(type_conv, bkg_buf); HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "datatype conversion failed") } /* end if */ /* Release local resources */ if(H5I_dec_ref(src_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to close temporary object") if(H5I_dec_ref(dst_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to close temporary object") if(bkg_buf) bkg_buf = H5FL_BLK_FREE(type_conv, bkg_buf); } /* end if */ } /* end if */ /* Set back the (possibly modified) fill value property to property list */ if(H5P_poke(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set fill value") /* Get the fill value property */ if(H5P_peek(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &copied_efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list") /* Reset efl name_offset and heap_addr, these are the values when the dataset is created */ if(copied_efl.slot) { unsigned u; copied_efl.heap_addr = HADDR_UNDEF; for(u = 0; u < copied_efl.nused; u++) copied_efl.slot[u].name_offset = 0; } /* end if */ /* Set back the (possibly modified) external file list property to property list */ if(H5P_poke(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &copied_efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set external file list") /* Set the return value */ ret_value = new_dcpl_id; done: if(ret_value < 0) if(new_dcpl_id > 0) if(H5I_dec_app_ref(new_dcpl_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to close temporary object") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_get_create_plist() */ /*------------------------------------------------------------------------- * Function: H5D_get_access_plist * * Purpose: Returns a copy of the dataset access property list. * * Return: Success: ID for a copy of the dataset access * property list. * Failure: FAIL *------------------------------------------------------------------------- */ hid_t H5D_get_access_plist(const H5D_t *dset) { H5P_genplist_t *old_plist; /* Default DAPL */ H5P_genplist_t *new_plist; /* New DAPL */ hid_t new_dapl_id = FAIL; hid_t ret_value = FAIL; FUNC_ENTER_NOAPI_NOINIT /* Make a copy of the default dataset access property list */ if(NULL == (old_plist = (H5P_genplist_t *)H5I_object(H5P_LST_DATASET_ACCESS_ID_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list") if((new_dapl_id = H5P_copy_plist(old_plist, TRUE)) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_CANTINIT, FAIL, "can't copy dataset access property list") if(NULL == (new_plist = (H5P_genplist_t *)H5I_object(new_dapl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list") /* If the dataset is chunked then copy the rdcc & append flush parameters */ if(dset->shared->layout.type == H5D_CHUNKED) { if(H5P_set(new_plist, H5D_ACS_DATA_CACHE_NUM_SLOTS_NAME, &(dset->shared->cache.chunk.nslots)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set data cache number of slots") if(H5P_set(new_plist, H5D_ACS_DATA_CACHE_BYTE_SIZE_NAME, &(dset->shared->cache.chunk.nbytes_max)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set data cache byte size") if(H5P_set(new_plist, H5D_ACS_PREEMPT_READ_CHUNKS_NAME, &(dset->shared->cache.chunk.w0)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set preempt read chunks") if(H5P_set(new_plist, H5D_ACS_APPEND_FLUSH_NAME, &dset->shared->append_flush) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set append flush property") } /* end if */ /* Set the VDS view & printf gap options */ if(H5P_set(new_plist, H5D_ACS_VDS_VIEW_NAME, &(dset->shared->layout.storage.u.virt.view)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set VDS view") if(H5P_set(new_plist, H5D_ACS_VDS_PRINTF_GAP_NAME, &(dset->shared->layout.storage.u.virt.printf_gap)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set VDS printf gap") /* Set the vds prefix option */ if(H5P_set(new_plist, H5D_ACS_VDS_PREFIX_NAME, &(dset->shared->vds_prefix)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set vds prefix") /* Set the external file prefix option */ if(H5P_set(new_plist, H5D_ACS_EFILE_PREFIX_NAME, &(dset->shared->extfile_prefix)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set external file prefix") /* Set the return value */ ret_value = new_dapl_id; done: if(ret_value < 0) if(new_dapl_id > 0) if(H5I_dec_app_ref(new_dapl_id) < 0) HDONE_ERROR(H5E_SYM, H5E_CANTDEC, FAIL, "can't free") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_get_access_plist() */ /*------------------------------------------------------------------------- * Function: H5D__get_space * * Purpose: Returns and ID for the dataspace of the dataset. * * Return: Success: ID for dataspace * Failure: FAIL *------------------------------------------------------------------------- */ hid_t H5D__get_space(const H5D_t *dset) { H5S_t *space = NULL; hid_t ret_value = H5I_INVALID_HID; FUNC_ENTER_PACKAGE /* If the layout is virtual, update the extent */ if(dset->shared->layout.type == H5D_VIRTUAL) if(H5D__virtual_set_extent_unlim(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update virtual dataset extent") /* Read the dataspace message and return a dataspace object */ if(NULL == (space = H5S_copy(dset->shared->space, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get dataspace") /* Create an atom */ if((ret_value = H5I_register(H5I_DATASPACE, space, TRUE)) < 0) HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace") done: if(ret_value < 0) if(space != NULL) if(H5S_close(space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__get_space() */ /*------------------------------------------------------------------------- * Function: H5D__get_type * * Purpose: Returns and ID for the datatype of the dataset. * * Return: Success: ID for datatype * Failure: FAIL * *------------------------------------------------------------------------- */ hid_t H5D__get_type(const H5D_t *dset) { H5T_t *dt = NULL; hid_t ret_value = FAIL; FUNC_ENTER_PACKAGE /* Patch the datatype's "top level" file pointer */ if(H5T_patch_file(dset->shared->type, dset->oloc.file) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to patch datatype's file pointer") /* Copy the dataset's datatype */ if(NULL == (dt = H5T_copy(dset->shared->type, H5T_COPY_REOPEN))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy datatype") /* Mark any datatypes as being in memory now */ if(H5T_set_loc(dt, NULL, H5T_LOC_MEMORY) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid datatype location") /* Lock copied type */ if(H5T_lock(dt, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to lock transient datatype") if((ret_value = H5I_register(H5I_DATATYPE, dt, TRUE)) < 0) HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register datatype") done: if(ret_value < 0) if(dt && H5T_close(dt) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__get_type() */ /*------------------------------------------------------------------------- * Function: H5D__refresh * * Purpose: Refreshes all buffers associated with a dataset. * * Return: SUCCEED/FAIL *------------------------------------------------------------------------- */ herr_t H5D__refresh(hid_t dset_id, H5D_t *dset) { H5D_virtual_held_file_t *head = NULL; /* Pointer to list of files held open */ hbool_t virt_dsets_held = FALSE; /* Whether virtual datasets' files are held open */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(dset); HDassert(dset->shared); /* If the layout is virtual... */ if(dset->shared->layout.type == H5D_VIRTUAL) { /* Hold open the source datasets' files */ if(H5D__virtual_hold_source_dset_files(dset, &head) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "unable to hold VDS source files open") virt_dsets_held = TRUE; /* Refresh source datasets for virtual dataset */ if(H5D__virtual_refresh_source_dsets(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh VDS source datasets") } /* end if */ /* Refresh dataset object */ if((H5O_refresh_metadata(dset_id, dset->oloc)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh dataset") done: /* Release hold on (source) virtual datasets' files */ if(virt_dsets_held) if(H5D__virtual_release_source_dset_files(head) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't release VDS source files held open") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__refresh() */


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